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The dataset generation failed
Error code: DatasetGenerationError
Exception: TypeError
Message: Couldn't cast array of type string to null
Traceback: Traceback (most recent call last):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2011, in _prepare_split_single
writer.write_table(table)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 585, in write_table
pa_table = table_cast(pa_table, self._schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2302, in table_cast
return cast_table_to_schema(table, schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2261, in cast_table_to_schema
arrays = [cast_array_to_feature(table[name], feature) for name, feature in features.items()]
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2261, in <listcomp>
arrays = [cast_array_to_feature(table[name], feature) for name, feature in features.items()]
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1802, in wrapper
return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1802, in <listcomp>
return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2075, in cast_array_to_feature
casted_array_values = _c(array.values, feature.feature)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1804, in wrapper
return func(array, *args, **kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2116, in cast_array_to_feature
return array_cast(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1804, in wrapper
return func(array, *args, **kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1962, in array_cast
raise TypeError(f"Couldn't cast array of type {_short_str(array.type)} to {_short_str(pa_type)}")
TypeError: Couldn't cast array of type string to null
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1524, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1099, in stream_convert_to_parquet
builder._prepare_split(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1882, in _prepare_split
for job_id, done, content in self._prepare_split_single(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2038, in _prepare_split_single
raise DatasetGenerationError("An error occurred while generating the dataset") from e
datasets.exceptions.DatasetGenerationError: An error occurred while generating the datasetNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
doi
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sequence | license
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|---|---|---|---|
10.1186/1472-6920-5-10 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": "A qualitative study of the perceptions and experiences of Pre-Registration House Officers on teamwork and support",
"authors": "Lempp, Heidi, 1, 2, [email protected], Cochrane, Mac, 1, [email protected], Rees, John, 1, [email protected]",
"abstract": "Background Following the implementation of a new final Year 5 curriculum in one medical school we carried out a study to explore the experience of the transition from final student year to Pre-Registration House Officer (PRHO). This study looks at the experiences of two successive cohorts of PRHOs in relation to team work, support and shared responsibility in their transition from final year students to qualified doctors. The involvement of PRHOs in teams is likely to change in the development of Foundation programmes. Methods A qualitative study with semi-structured interviews with 33 PRHOs, stratified by gender, ethnicity and maturity, from two study cohorts, qualifying in 2001 and 2002, from one medical school in the UK, in their first three months following medical graduation. Results Most PRHOs reported positive experiences for their inclusion as a full member of their first ward teams. This contributed to their increasing confidence and competence in this early period of career transition. However, a number of organisational barriers were identified, e.g. incomplete teams, shift work, which produced problems in their integration for one third of newly qualified doctors. Conclusion Recently introduced policies, intended to improve the working lives of newly qualified doctors have produced both benefits and unintended adverse impacts on PRHOs. The changes of the new PRHO Foundation programme will have further impact. Foundation doctors may need to relate to wider teams with more interaction and less protection. Such changes will need to be managed carefully to protect the PRHO at a vulnerable time.",
"body_text": "Background There is increasing emphasis on multi-disciplinary teams in modern clinical care [ 1 3 1 4 6 7 9 Concern has been expressed about whether such teamwork skills can be effectively practised by junior doctors during the PRHO year while they cope with multiple professional, personal, physical and emotional demands [ 10 12 The New Doctor 13 14 17 18 19 20 21 We wanted to explore how well our undergraduate curriculum, particularly the final year with 16 weeks shadowing in a student house officer role, prepared PRHOs for their new posts. In this study issues emerged about the stability of ward teams and the full integration of PRHOs in to teams. These findings may have relevance to the development of Foundation programmes. Methods Two study cohorts of 33 PRHOs were selected by convenience (16 participants from year 2000/2001) and quota sampling (17 participants from year 2001/2002), stratified by gender, ethnicity and maturity, using the respective final year student population of the Medical School as the sampling frame (see Tables 1 2 Additional file 1 The New Doctor 13 12 22 22 22 24 Table 1 Socio-demographic data from 16 PRHO cohort 2000/2001 Table 2 Socio-demographic data from 17 PRHO cohort 2001/2002 Results The 33 PRHOs worked in four acute hospital trusts and seven District General Hospitals (DGHs) in England, 16 in surgical and 17 in medical wards. They commented frequently on the importance of their clinical teams. Findings from PRHOs' accounts are reported around 3 key themes: supportive environment, educational environment and organisational changes. Overall the transition from being an 'outsider' to a professional 'insider' was a welcome change for all PRHOs, including involvement in the team. Comments on finding a role were common: 'When I was a medical students in the 5 th 'In the previous years we haven't been actually part of a team. We've been assigned a team but you're not working with a team....... you're not part of that patient's everyday care'. 'It's so different being a house officer than being a medical student – you're a team, like, straightaway. The first day, that's it! That's a very big difference.' 1) Supportive environment Most PRHOs (27/33) described their clinical teams in positive terms (see Table 3 Table 3 Descriptions by 27/33 PRHOs about their medical and surgical ward teams Constructive feedback from senior colleagues PRHOs reporting support by senior medical staff (24/33) felt that they integrated with their clinical teams early and well, especially in emergency situations. Acute or life threatening events affected them emotionally, usually with little time for debriefing. Without senior support PRHOs often felt out of their depth. When they had dealt independently with a complex clinical situation, constructive feedback from senior staff added to their positive experiences. Conversely PRHOs who received no or little supervision or response from senior staff recorded these events as a negative impact on their confidence. The latter situations were more common in surgery, where PRHOs reported that senior staff was less accessible. 'I would have quite liked an SHO [Senior House Officer] or somebody to tell me what I should be doing in that situation, or whether I should be phoning the GP or writing or speaking to him, or who actually should be talking to her [patient] and what actually telling them [the couple] ...ahm...so I basically did it all myself.' '...getting called to see a man that had collapsed on his way back from the loo, and had no blood pressure and was basically dying. And I thought: Ahhh! But I just called the SHO and said: \"Can you come and help me?\" And I couldn't get access in him [patient] at all, and it was just a bit scary. When the SHO arrived we sorted him out and he was then fine after that, although he died a few days later'. Sharing responsibilities and tasks A sense of collective responsibility with other team members was positively expressed by most PRHOs (26/33). The predominant ethos was one of sharing the workload between medical and nursing colleagues in the team (see Table 4 Table 4 Phrases used by 26/33 PRHOs about sharing work load and responsibilities *some used more than one phrase PRHOs reported that sharing jobs was not always straightforward, particularly if individual team members did not work well together (7/33), or if teams were incomplete due to staff shortage and/or locum cover (8/33). 'I mean it's [work] so erratic and our team is so disjointed! I don't really know half the patients and I don't...I don't even know if half the jobs are getting done. I mean mine all get done but I don't know whether the other half's, the other House Officers are thinking I'm doing theirs or they're doing mine, or the SHO's doing whatever'. Interprofessional working 28/33 PRHOs reported that the relationship with nursing staff changed with qualification. Former inter-professional tensions seemed due to the perceived inconvenience that medical students caused to nurses. Prior to qualification students had relied on nurses in hospital and community for help with 'log book' skills, such as catheterisation and injections, and they appreciated their patience and enthusiasm. 'Before as a medical student you were a piece of furniture according to nurses....but now, obviously you are the first-line if they want anything doing, I think in that respect there's a lot more regard....and appreciation for what you do'. However, a number of inter-professional conflicts were identified such as adjustment to professional roles (x 15), discordant communication (x9), unclear what nurses are willing or (un)able to do (x10) and others. Relationship with PRHOs in the same team 8/33 commented positively on working with other PRHOs from their final year group in the same team, making sharing the workload and responsibility easier due to closer personal relationships. However, 2/33 identified this as impacting on their teamwork and patient care when PRHOs did not get on well together and 4/33 found competition to learn additional clinical skills. 'There always has been camaraderie with other PRHOs, but at least I get to spend time around now as well, so ahm...you know it is great, when you literally you say, will you do this, I will do that, and we meet up at the end [of the day]....that is always really nice'. 'There's a mutual understanding there (amongst the PRHOs in the team], and we...amazingly, we are ever so professional on the job. I mean on the team, we're very good friends – we go out for dinner, all sorts – but when we're on the job, it's ever so professional'. 2) Educational environment PRHOs sought out educational opportunities to achieve a sense of progression after qualification within their clinical teams. Learning consisted of performing new practical skills, as well as observation, to acquire inter-personal and professional competencies. Continuity in their relationship with patients was perceived as important as team members, rather than temporary bystanders as students. Observing delicate situations Most PRHOs (23/33) had witnessed delicate clinical or ethical situations, which required advanced communication skills between team members, patients and their families, e.g. breaking bad news, communicating with uncooperative patients. The interviewees had a variety of opportunities to observe how senior medical and nursing staff within their teams managed such situations sensitively and professionally. '....it is quite interesting, watching your seniors how they deal with difficult patients: patients who are too demanding, or patients who, you know, are rude or angry, or breaking bad news, I try to sort of sit in on all that, so I can see how they [seniors] do it....' ' ... when family gets involved, it gets awfully sad [resuscitation status]. I had a patient who died; I got to know the family relatively well – two sons – and they divulged that their mother had died, and...all sorts of complex family dynamics going on there. They were quite clearly worried about their father. And then there's only so much input the house officer can do – essentially, the seniors make the decisions...' PRHOs were acutely aware that consultants were ultimately in charge of final decisions in ethical dilemmas. 6/33 PRHOs reported that they were given tasks which they felt were inappropriate, such as asking patients for consent to undergo an operation or investigation which they had never seen themselves. Learning new clinical skills from seniors 7/33 PRHOs were able to extend their practical skills, such as lumbar punctures or insertion of chest drains during their first house jobs. However, these opportunities were reduced where ward teams were incomplete and depended on the willingness and clinical competence of senior staff in their teams. Such limitations sometimes caused frustration. The message around unstable teams was often close to: 'Our team's so disjointed at the moment. The SHO that we've got is constant. But, she does 'on-calls' for other teams as well so we don't see her that often. Our Registrars change every day because they're all locums. So on some days we don't have one and some days we do ...I don't feel....I'm not learning the things I thought I'd learn.' 'There's only one regular member of the team and that's the staff grade, and so the consultant is a locum. He's been here a couple of months, or just before we started, basically he was here. The SHO is a locum SHO, who has now finished her rotation, and I've just started so there was not much stability in the team to begin with.' 3) Organisational changes Organisational changes, such as new work patterns, and inadequate staffing levels caused frustration and anxiety affecting the PRHOs emotionally and their team work. Continuity of relationships with patients Most PRHOs (25/33) described continuity of patient care in positive terms. They welcomed the fact that they could approach patients without apologies because they had a defined role and responsibility. 11/33 PRHOs reported fragmentation in their relationships with patients which they related to shift work and/or staff shortages. '...the continuity is great, you know, walking on the ward, and sort of saying \"hi\" to people and you know they know you, and getting on with them and kind of trying to do your best for them.' '....there's no continuity of care: we start in the morning, we finish, and then someone else comes on – and they [consultant] don't know the person. And then the next day that patient either moved to somewhere else or they've gone home. So we're not following them [patients].' New work patterns One third of PRHOs in study cohort 2001/2002 confirmed that their hospital complied with new working hours while two thirds encountered difficulties. The 2001/2002 group had a range of concerns: continuous long working hours, despite the implementation of new working patterns (12/17), loss of emergency experience at night (4/17), confusion from non-compliance or experimentation with new working hours (12/17), and unhappiness and ridicule by senior colleagues (5/17). These caused resentment and dissatisfaction amongst the majority of the cohort (12/17) more than the 2000/2001 group (5/16). Staffing levels In addition to the new working arrangements, there was a change from 2000/01 to 2001/02 in the availability and continuity of permanent staff members, doctors and nurses. This was reported only by the second PRHO cohort. One third of this group commented that team work was disrupted and undermined by incomplete teams. 'It's just working in a big hospital, and having an incomplete team was...it was just unfortunate that that was the situation when I joined...I didn't enjoy that and it upset me because, you know, it's taken me a long time to get through Medicine and I felt that that was bad.' Discussion In a few areas such as changes in rotas and hours the interviewees commented on the views of more senior doctors. These views may have influenced their responses. In order to encourage open responses interviewees were guaranteed anonymity. Interviews were conducted mainly by one interviewer, who was not part of the medical school hierarchy or trusts and had established a good rapport with the PRHOs cohorts. The interviews in this study ranged over a number of areas. They explored the preparation of PRHOs through their undergraduate curriculum and the sources of stress in the transition to the PRHO role. PRHOs discussed their experience of the working environment and their relationships with colleagues in a number of areas and team work was addressed specifically in a direct question. The themes explored in this study were identified clearly by the three authors and the independent researcher on analysis of the transcripts. The PRHOs were enthusiastic about the way their assumption of their professional role allowed integration into multi-disciplinary working with a clear change in the working relationships with nursing colleagues. This was an area that changed from their medical school experience despite efforts to give them clearly defined patient management roles during 16 weeks of experience as student house officers in hospital. It is possible that interprofessional education and even clearer integration of student house officers may help to minimise the changes on transition in future. Clear evidence about the efficacy of interprofessional education, however, has not yet been established. The supportive and educational environments facilitated by ward teams received a welcome positive reaction from the majority of newly qualified PRHOs in both study cohorts. The importance of adequate senior supervision in the early stages of the PRHO experience has been emphasised in previous studies [ 25 The New Deal [ 20 13 21 26 The problems were exacerbated by instability of the working teams which meant that supervision was not always adequate at these times when it needed to be most effective. Shortage of permanent staff in the ward teams was stressful and unsettling for one third of the PRHOs. These organisational difficulties affected five key areas of work: continuity of patient care, sharing responsibilities within the team, delayed integration in to the new teams, ad hoc learning opportunities to acquire new skills and ongoing lack of support from senior staff. These areas emerged without prompting from interviewers. It may be that PRHOs early in their post and low in confidence are worried by the possibility of inadequate support which might come from the unstable teams. However, the reports suggested that it was causing real concern for the interviewees who responded in this way. It is important that these areas are addressed for the introduction of the Foundation programmes. It is possible that changes in working patterns may mean that those in F1 posts in the future will have to relate to larger teams with a broader range of skills with clear responsibilities but less opportunity for continuity of care. Instability in these larger teams could be even more of a problem. Both PRHOs and more senior doctors will have to learn such new ways of working. The loss of traditional clinical \"firms\" also needs to be addressed in undergraduate training. Many medical schools retain periods of apprenticeship, teaching traditionally and linking a small number of students to a small clinical team. This allows the students to relate to the staff and build their confidence. The combination and interaction of these teams and the increase in day and outpatient care means that new patterns have already been developed to optimise the students' experience in the hospital environment. Changes in the student experience need to be developed in line with Foundation programmes to be sure that junior doctors are prepared for their roles on graduation. The greatest satisfaction for PRHOs in this study came from involvement with a clear role and feeling part of the team, and this will be one of the core competencies assessed in Foundation programmes. Mechanisms of working within these teams and handover arrangements need to be clear. While the increased attention on evaluation should lead to clarity of roles with appropriate supervision, the greater emphasis on evaluation could also change the nature of the relationships. Conclusion Overall this study emphasises the enthusiasm of PRHOs for well organised structures with adequate supervision in a supportive multidisciplinary environment. Over the period studied rotas and unstable staffing patterns affected this environment significantly. Competing interests Dr. Mac Cochrane received funding from the Oak Foundation for both studies. Authors' contributions HL developed study design, carried out most interviews, conducted the analyses and wrote the paper. MC supervised study, commented on study design, carried out few interviews, assisted in the data analysis. JR supervised the study, commented on study design, data analysis and contributed in the writing of paper. Pre-publication history The pre-publication history for this paper can be accessed here: Supplementary Material Additional File 1 Microsoft word file (teamwork additional.doc) containing details of the semi-structured interview. Click here for file Acknowledgements We are grateful to all the students who participated in the study for their time and contributions during their first few weeks in post; Dr. Mary Seabrook, Dr. Sue Clarke and Dr. Paul Booton for their support and advice and Ms. Floss Chittenden for her unfailing support with the transcriptions of the interviews. Formal permission to carry out both studies was obtained from the Education Committee of the Medical School where the study was undertaken. All relevant ethical conduct research procedures were adhered to and all interviewees gave written, informed consent.",
"bibliography": "General Medical Council, Tomorrow's Doctors, Recommendations on undergraduate medical education, 2002, General Medical Council, London\nGeorge, C, Teamworking in Medicine, 2000, General Medical Council, London\nBoaden, N, Leaviss, J, Putting teamwork in context, Medical Education, 2000, 34, 921, 27, 11107017, 10.1046/j.1365-2923.2000.00794.x\nGeneral Medical Council, Tomorrow's Doctors, Recommendations on undergraduate medical education, 1993, General Medical Council, London\nCalman, K, The profession of medicine, British Medical Journal, 1994, 309, 1140, 43, 7987111\nDepartment of Health, Working Together – Learning Together, 2001, DoH, London\nStephenson, A, Higgs, R, Sugarman, J, Teaching professional development in medical schools, The Lancet, 2001, 357, 867, 70, 11265967, 10.1016/S0140-6736(00)04201-X\nHowe, A, Twelve tips for community-based medical education, Medical Teacher, 2002, 24, 9, 12, 12098450\nPope, C, Coldicott, Y, No-one forgets a bad teacher, Medical Education, 2002, 36, 5, 6, 11849517, 10.1046/j.1365-2923.2002.01083.x\nFirth-Cozens, J, Emotional distress in junior house officers, British Medical Journal, 1987, 295, 533, 5, 3117213\nDepartment of Health, The European Working Time Directive, 1998, Department of Health, London\nHesketh, EA, Allan, MS, Harden, RM, Macpherson, SG, New doctors' perceptions of their educational development during their first year of postgraduate training, Medical Teacher, 2003, 25, 67, 76, 14741862, 10.1080/0142159021000067011\nGeneral Medical Council, The New Doctor, 1997, General Medical Council, London\nDawe, V, Medical training flunks its test, Hospital Doctor, 1992, C12, 34\nMoss, F, The pre-registration year, Medical Education, 1997, 31, 10, 11, 10664731\nGoldacre, M, Stear, S, Lambert, T, The pre-registration year. The trainees' experiences, Medical Education, 1997, 31, 57, 60, 10664742\nMcManus, IC, Winder, B, Paice, E, How consultants, hospitals trusts and deaneries affect pre-registration house officer posts: a multi-level model, Medical Education, 2002, 36, 5, 44, 11849517, 10.1046/j.1365-2923.2002.01123.x\nClack, GB, Medical graduates evaluate the effectiveness of their education, Medical Education, 1994, 28, 418, 31, 7845261\nWhitehouse, CR, O'Neill, P, Dornan, T, Building confidence for work as house officers: student experience in the final year of a new problem-based curriculum, Medical Education, 2002, 36, 718, 27, 12191054, 10.1046/j.1365-2923.2002.01287.x\nDepartment of Health, The European Working Time Directive, 1999, Department of Health, London\nKapur, N, House, A, Job satisfaction and psychological morbidity in medical house officers, Journal of the Royal College of Physicians, London, 1997, 31, 162, 7\nSeale, C, The Quality of Qualitative Research, Introducing qualitative methods, 1999, Sage Publications, London, 119, 139\nSilverman, D, Interpreting Qualitative Data: Methods for Analysing Talk, Text and Interaction, 1993, Sage Publications: London\nBryman, A, Quantity and Quality in Social Research, 1988, Unwin Hyman: London\nPaice, E, Rutter, H, Wetherell, M, Winder, B, McManus, IC, A well supervised working environment may offset reduction in hours or a high work intensity, Medical Education, 2002, 36, 56, 65, 11849525, 10.1046/j.1365-2923.2002.01101.x\nSalter, R, The US residency programme – lessons for pre-registration house officer education in the UK?, Postgraduate Medical Journal, 1995, 71, 273, 7, 7596930"
} |
10.1186/1475-925X-4-20 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": "Review of \"Contemporary IMRT: Developing Physics and Clinical Implementation\"\nby Steve Webb",
"authors": "Panagiotopoulos, Vasos-Peter John, II, 1, [email protected]",
"abstract": "",
"body_text": "IMRT is Intensity Modulated Radiation Therapy: Irradiating from several directions repeatedly targets a tumor, but less its surroundings, due to differing projections; yet minimising such collateral damage may be cost-controversial. Beams are modulated 1 2 3 4 5 In the second chapter on rotation IMRT and tomotherapy, pseudo structures flagged for dose minimisation are especially interesting. The third chapter discusses multileaf collimators (MLC) and sequencers (leaf moving algorithms, aka, curiously shamanistically, not Accuray.com 3-dimensional planning spans book's last half, discussing margin definition, distortion correction, contrast agents, fluence smoothing, patient motion (esp respiration, modelled as cosine to power of assymetry) and surface marker gating, and movement correction. Tracking patient motion is preferrable over immobilisation techniques resembling medieval torture. Image importing planning softwares include Nomos Corvus Plato Helax Pinnacle CadPlan Helios Focus Since Cyberknife robot \"chases the moving patient\" (p. 164), one hopes for more engineering, integrating \"planning\" with therapy, instead of \"batch\" methods, which the author prefers, like older automobiles, in his 2001 text, because they do \"not remove the human from decision making\". Engineers would prototype in MathWorks.Com MatLab production 6 7 Nirx.Net Competing interests Reviewer holds restricted securities in a developer of a through-the-sputtered-target, minimal-Bremsstrahlung, relativistically-collimated miniaturised X-Ray tube.",
"bibliography": "Cember, H, Introduction to Health Physics, 1996, NY:McGraw-Hill\nKhan, FM, Potish, RA, (eds), Treatment Planning in Radiation Oncology, 1998, Philadelphia: Lippincott\nKak, AC, Slaney, M, Principles of Computerized Tomographic Imaging (Classics in Applied Mathematics, 33), 2001, Philadelphia: SIAM\nPham, DT, Dimov, SS, Rapid Manufacturing, 2001, Springer-Verlag,. Secaucus & Heidelberg: SPringer-Verlag\nWells, DA, Schaum's Outline of Lagrangian Dynamics, 1967, NY: McGraw-Hill\nEighth International Conference on the Use of Computers in Radiation Therapy (July 9–12, 1984, Toronto), 1984, Silver Spring, MD: IEEE\nWright, AE, Boyer, AL, (eds), Advances in radiation therapy treatment planning, 1983, Medical physics monograph, no. 9, NY: Amer Asn of Physicists in Medicine\nFelix Wachsmann, Gunther Barth, Tr. Elisabeth Farber Lanzl, Adapted and expanded by Lawrence H Lanzl & James WJ Carpender, Moving field radiation therapy, 1962, Chicago: Univ of Chicago Press, (orig: Bewegungsbestrahlung, Stuttgart: Thieme; 1959.)"
} |
10.1186/1475-2875-4-17 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": "Data mining of the transcriptome of ",
"authors": "Bozdech, Zbynek, 1, [email protected], Ginsburg, Hagai, 2, [email protected]",
"abstract": "The general paradigm that emerges from the analysis of the transcriptome of the malaria parasite Plasmodium falciparum + + + + P. falciparum +",
"body_text": "Introduction The analysis of the transcriptome of Plasmodium falciparum 1 3 4 During the erythrocytic stage the malaria parasite is engaged in intensive synthesis of nucleotides and is subjected to endogenously produced oxidative radicals that must be detoxified. Like other cells, in order to perform its anabolism, the parasite needs not only energy (ATP): it also needs reducing power, under the form of NADPH. Enzymes that function primarily in the reductive direction utilize NADP + + 1 Figure 1 Pentose phosphate pathway P. falciparum The reactions of the PPP operate exclusively in the cytoplasm. PPP has both an oxidative and a non-oxidative arm. The oxidation steps, utilizing glucose-6-phosphate (G6P) as the substrate, occur at the beginning of the pathway and are the reactions that generate NADPH. Thus, the first carbon of glucose-6-phosphate is first oxidized to a lactone (catalyzed by glucose-6-phosphate dehydrogenase) concomitantly releasing two electrons that reduce one molecule of NADP + + The non-oxidative reactions of the PPP are primarily designed to generate R5P. Equally important reactions of the PPP are to convert dietary 5 carbon sugars or D-ribose-1-phosphate generated in the salvage of purines (that can be slowly converted to R5P by phosphoglucomutase; EC: 5.4.2.2) into both 6 (fructose-6-phosphate) and 3 (glyceraldehyde-3-phosphate) carbon sugars which can then be utilized by the pathways of glycolysis. In the first reaction, R5P will accept two carbon atoms from xylulose-5-phosphate (obtained by epimerization of ribulose-5-P), yielding sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate (catalyzed by transketolase). Sedoheptulose-7-phosphate transfers three carbons to glyceraldehyde-3-phosphate (catalyzed by transaldolase), yielding fructose-6-phosphate (F6P) and erythrose-4-phosphate. Erythrose-4-phosphate then accepts two carbon atoms from a second molecule of xylulose-5-phosphate (catalyzed again by transketolase), yielding a second molecule of F6P and a glyceraldehyde-3-P (GAP) molecule. F6P and a GAP can then enter glycolysis and eventually produce ATP. The intermediate erythrose-4-phosphate is a substrate for the shikimate pathway The non-oxidative part of PPP can also work in the reverse direction utilizing fructose-6-phosphate glyceraldehyde-3-phosphate generated by glycolysis to produce ribose-5-phosphate. In essence, the PPP can operate in different modes (Figure 2 2 2 2 Figure 2 Different modes of PPP action. not The genes that code for enzymes participating in ancillary processes that produce NADP + PPP activity in P. falciparum- 5 7 14 6 8 et al 9 The gene coding for G6PD has been cloned [ 10 11 12 13 14 Plasmodium- 15 17 P. falciparum P. falciparum- 8 18 The parasite contains substantial levels of the pyridine nucleotides NAD + + 19 P. falciparum + + 1 20 21 + Table 1 NADP utilizing enzymes Enzymes are arranged by their sequential functional order. They are given by their name, their EC numbers, the gene identification (PfID) in the Plasmodium In this in silico Materials and methods The expression data used in this study was obtained from the transcriptome database P. falciparum 2 22 2 2 Table 2 Enzymes of the pentose phosphate pathway and pyridine nucleotide metabolism. Enzymes are grouped into pathways. They are given by their name, their EC numbers, the gene identification (PfID) in the Plasmodium Results and Discussion At the onset of the present analysis, it should be underscored that time-dependent transcription does not always overlaps translation. Hence, transcript levels cannot be directly extrapolated to levels of their translated product. Moreover, transient transcription does not divulge on the stability of the translated products. Indeed, a recent analysis has shown for several genes that while the transcript peaks at the trophozoite stage and declines thereafter, the translated protein continues to accumulate [ 23 P. falciparum et al 24 In this analysis, the transcription of genes coding for enzymes that constitute the PPP will be discussed first followed by those that are involved in the synthesis of NAD(P) + The pentose phosphate pathway The pathway is shown in Figure 1 3 2 2 25 2 9 + Figure 3 Time dependent transcription of genes coding for enzymes involved in the pentose phosphate pathway The situation of the non-oxidative arm genes is different. The gene that codes for ribose phosphate isomerase (EC: 5.1.3.1) peaks at 21 HPI and this seems to restrict the expression of the non-oxidative arm, since transketolase (EC: 2.2.1.1) is transcribed maximally immediately following invasion. Most importantly, the gene that codes for transaldolase (EC: 2.2.1.2) could not be found in the genome of P. falciparum Plasmodium 2 + 2 1 3 24 NAD(P) biosynthesis The pathway is shown in Figure 4 5 + + 3 1 + of P. falciparum 26 + + 27 et al 26 + + P. falciparum + + + + P. falciparum Plasmodium Giardia lamblia Figure 4 Nicotine nucleotide metabolism P. falciparum Figure 5 Time dependent transcription of genes coding for enzymes involved in the biosynthesis of NAD(P) + + Table 3 NAD + Plasmodium Inspection of the time-dependent transcription of genes coding enzymes that are involved in NAD(P) + + + + + 2 + 28 + 3 + 23 + + + 19 + 1 Transhydrogenase operates at an important interface between NAD(H) and NADP(H) and between the mitochondrial proton electrochemical gradient ??; [ 29 NADH + NADP + + out_ + + in The energy of the gradient can drive the [NADPH][NAD + + + 30 31 Thiamine biosynthesis The essential product of this pathway, thiamine diphosphate, is a cofactor of many enzymes (Table 4 6 7 1 P. berghei 32 in vivo 33 34 35 Table 4 Thiamine diphosphate utilizing enzymes. Enzymes are arranged by their sequential functional order. They are given by their name, their EC numbers, the gene identification (PfID) in the Plasmodium Figure 6 Biosynthesis of thiamine diphosphate P. falciparum Figure 7 Time dependent transcription of genes coding for enzymes involved in the biosynthesis of thiamine diphosphate The transcription of all genes coding for enzymes involved in thiamine pyrophosphate seems to be coordinated, single phased and peaking between 20 and 30 HPI. If thiamine is obtained from the host and thiamine pyrophosphate is synthesized by the single step mediated by thiamine diphosphokinase, the peak transcription of this gene at 28 HPI lags by several hours after that of transketolase (17 HPI), but since transketoalse is not the expression time-setter of PPP, this lag does not seem to limit the full activity of PPP. However, if most of the thiamine is generated endogenously by the parasite, the supply of this precursor will peak only at 33 HPI, thus limiting full PPP activity. It is not unlikely that both processes occur in tandem or that at advanced stage of parasite development, the need for thiamine cannot be met anymore by exogenous supply and the endogenous synthesis joins the game. Conclusion The analysis of time-dependence transcription of parasite genes concluded that the parasite has evolved a highly specialized mode of transcriptional regulation that produces a continuous cascade of gene expression, beginning with genes corresponding to general cellular processes, such as protein synthesis, and ending with Plasmodium 2 Authors' contributions Each author contributed equally to this investigation. Acknowledgements We thank Professor I. Ohad for critical reading of the manuscript.",
"bibliography": "Ben Mamoun, C, Gluzman, IY, Hott, C, MacMillan, SK, Amarakone, AS, Anderson, DL, Co-ordinated programme of gene expression during asexual intraerythrocytic development of the human malaria parasite, Plasmodium falciparum, Mol Microbiol, 2001, 39, 26, 36, 11123685, 10.1046/j.1365-2958.2001.02222.x\nBozdech, Z, Llinas, M, Pulliam, BL, Wong, ED, Zhu, J, DeRisi, JL, The transcriptome of the intraerythrocytic developmental cycle of, Plasmodium falciparum, PLoS Biol, 2003, 1, E5, 12929205, 10.1371/journal.pbio.0000005\nLe Roch, KG, Zhou, Y, Blair, PL, Grainger, M, Moch, JK, Haynes, JD, De La Vega, P, Holder, AA, Batalov, S, Carucci, DJ, Winzeler, EA, Discovery of gene function by expression profiling of the malaria parasite life cycle, Science, 2003, 301, 1503, 1508, 12893887, 10.1126/science.1087025\nBozdech, Z, Ginsburg, H, Antioxidant defense in, Plasmodium falciparum, Malar J, 2004, 3, 23, 15245577, 10.1186/1475-2875-3-23\nRoth, EF, Raventos-Suarez, C, Perkins, M, Nagel, RL, Glutathione stability and oxidative stress in, P. falciparum, Biochem Biophys Res Commun, 1982, 109, 355, 362, 6758788, 10.1016/0006-291X(82)91728-4\nAtamna, H, Pescarmona, G, Ginsburg, H, Hexose-monophosphate shunt activity in intact, Plasmodium falciparum, Mol Biochem Parasitol, 1994, 67, 79, 89, 7838186, 10.1016/0166-6851(94)90098-1\nCappadoro, M, Giribaldi, G, Obrien, E, Turrini, F, Mannu, F, Ulliers, D, Simula, G, Luzzatto, L, Arese, P, Early phagocytosis of glucose-6-phosphate dehydrogenase (G6PD)- deficient erythrocytes parasitized by, Plasmodium falciparum, Blood, 1998, 92, 2527, 2534, 9746794\nRoth, E, Ruprecht, R, Schulman, S, Vanderberg, J, Olson, J, Ribose metabolism and nucleic acid synthesis in normal and glucose-6-phosphate dehydrogenase-deficient human erythrocytes infected with, Plasmodium falciparum, J Clin Invest, 1986, 77, 1129, 1135, 2420826\nAtamna, H, Ginsburg, H, Origin of reactive oxygen species in erythrocytes infected with, Plasmodium falciparum, Mol Biochem Parasitol, 1993, 61, 231, 241, 8264727, 10.1016/0166-6851(93)90069-A\nO'Brien, E, Kurdi-Haidar, B, Wanachiwanawin, W, Carvajal, JL, Vulliamy, TJ, Cappadoro, M, Mason, PJ, Luzzatto, L, Cloning of the glucose 6-phosphate dehydrogenase gene from, Plasmodium falciparum, Mol Biochem Parasitol, 1994, 64, 313, 326, 7935609, 10.1016/0166-6851(94)00028-X\nYoshida, A, Roth, E, Glucose-6-phosphate dehydrogenase of malaria parasite, Plasmodium falciparum, Blood, 1987, 69, 1528, 1530, 3552078\nKurdi-Haidar, B, Luzzatto, L, Expression and characterization of glucose-6-phosphate dehydrogenase of, Plasmodium falciparum, Mol Biochem Parasitol, 1990, 41, 83, 92, 2200964, 10.1016/0166-6851(90)90099-8\nSodeinde, O, Clarke, JL, Vulliamy, TJ, Luzzatto, L, Mason, PJ, Expression of, Plasmodium falciparum, Br J Haematol, 2003, 122, 662, 668, 12899722, 10.1046/j.1365-2141.2003.04397.x\nClarke, JL, Scopes, DA, Sodeinde, O, Mason, PJ, Glucose-6-phosphate dehydrogenase-6-phosphogluconolactonase – A novel bifunctional enzyme in malaria parasites, Eur J Biochem, 2001, 268, 2013, 2019, 11277923, 10.1046/j.1432-1327.2001.02078.x\nTheakston, R, Ali, S, Moore, G, Electron microscope autoradiographic studies on the effect of chloroquine on the uptake of tritiated nucleosides and methionine by, Plasmodium berghei, Ann Trop Med Parasitol, 1972, 66, 295, 302, 4564246\nTheakston, R, Fletcher, K, An electron cytochemical study of 6-phosphogluconate dehydrogenase activity in infected erythrocytes during malaria, Life Sci, 1973, 13, 405, 410, 4201713, 10.1016/0024-3205(73)90233-6\nFletcher, KA, Canning, MV, Theakston, RD, Electrophoresis of glucose-6-phosphate and 6-phosphogluconate dehydrogenases in erythrocytes from malaria-infected animals, Ann Trop Med Parasitol, 1977, 71, 125, 130, 405935\nReyes, P, Rathod, PK, Sanchez, DJ, Mrema, JE, Rieckmann, KH, Heidrich, HG, Enzymes of purine and pyrimidine metabolism from the human malaria parasite,, Plasmodium falciparum, Mol Biochem Parasitol, 1982, 5, 275, 290, 6285190, 10.1016/0166-6851(82)90035-4\nSherman, IW, Biochemistry of plasmodium (malarial parasites), Microbiol Rev, 1979, 43, 453, 495, 94424\nKanzok, SM, Schirmer, RH, Turbachova, I, Iozef, R, Becker, K, The thioredoxin system of the malaria parasite, Plasmodium falciparum, J Biol Chem, 2000, 275, 40180, 40186, 11013257, 10.1074/jbc.M007633200\nBecker, K, Rahlfs, S, Nickel, C, Schirmer, RH, Glutathione – functions and metabolism in the malarial parasite, Plasmodium falciparum, Biol Chem, 2003, 384, 551, 566, 12751785, 10.1515/BC.2003.063\nBozdech, Z, Zhu, J, Joachimiak, MP, Cohen, FE, Pulliam, B, DeRisi, JL, Expression profiling of the schizont and trophozoite stages of, Plasmodium falciparum, Genome Biol, 2003, 4, R9, 12620119, 10.1186/gb-2003-4-2-r9\nNirmalan, N, Sims, PF, Hyde, JE, Quantitative proteomics of the human malaria parasite, Plasmodium falciparum, Mol Microbiol, 2004, 52, 1187, 1199, 15130134, 10.1111/j.1365-2958.2004.04049.x\nLe Roch, KG, Johnson, JR, Florens, L, Zhou, Y, Santrosyan, A, Grainger, M, Yan, SF, Williamson, KC, Holder, AA, Carucci, DJ, Yates, JR, 3rd, Winzeler, EA, Global analysis of transcript and protein levels across the, Plasmodium falciparum, Genome Res, 2004, 14, 2308, 2318, 15520293, 10.1101/gr.2523904\nScott, H, Gero, AM, O'Sullivan, WJ, In vitro inhibition of, Plasmodium falciparum, de novo, Mol Biochem Parasitol, 1986, 18, 3, 15, 3515174, 10.1016/0166-6851(86)90045-9\nZerez, C, Roth, E, Schulman, S, Tanaka, K, Increased nicotinamide adenine dinucleotide content and synthesis in, Plasmodium falciparum-, Blood, 1990, 75, 1705, 1710, 2183889\nMicheli, V, Simmonds, HA, Sestini, S, Ricci, C, Importance of nicotinamide as an NAD precursor in the human erythrocyte, Arch Biochem Biophys, 1990, 283, 40, 45, 2146924, 10.1016/0003-9861(90)90609-3\nPfaller, M, Krogstad, D, Parquette, A, Nguyen-Dinh, P, Plasmodium falciparum, Exp Parasitol, 1982, 54, 391, 396, 6759150, 10.1016/0014-4894(82)90048-0\nHatefi, Y, Yamaguchi, M, Nicotinamide nucleotide transhydrogenase: a model for utilization of substrate binding energy for proton translocation, FASEB J, 1996, 10, 444, 452, 8647343\nKrugkrai, J, The multiple roles of the mitochondrion of the malarial parasite, Parasitology, 2004, 129, 511, 524, 15552397, 10.1017/S0031182004005888\nDivo, AA, Geary, TG, Jensen, JB, Ginsburg, H, The mitochondrion of, Plasmodium falciparum, J Protozool, 1985, 32, 442, 446, 3900366\nSinger, I, Tissue thiamine changes in rats with experimental trypanosomiasis or malaria, Exp Parasitol, 1961, 11, 391, 401, 13913283, 10.1016/0014-4894(61)90043-1\nSinger, I, Coenzyme A changes in liver, spleen and kidneys of rats with infections of, Plasmodium berghei, Proc Soc Exp Biol Med, 1956, 91, 315, 318, 13297787\nKrishna, S, Taylor, AM, Supanaranond, W, Pukrittayakamee, S, ter Kuile, F, Tawfiq, KM, Holloway, PA, White, NJ, Thiamine deficiency and malaria in adults from southeast Asia, Lancet, 1999, 353, 546, 549, 10028983, 10.1016/S0140-6736(98)06316-8\nHohmann, S, Meacock, PA, Thiamin metabolism and thiamin diphosphate-dependent enzymes in the yeast, Saccharomyces cerevisiae, Biochim Biophys Acta, 1998, 1385, 201, 219, 9655908"
} |
10.1186/1471-2334-5-60 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": null,
"authors": "Ma, Edmond SK, 1, [email protected], Wong, Chris LP, 1, [email protected], Lai, Kristi TW, 1, [email protected], Chan, Edmond CH, 2, [email protected], Yam, WC, 3, [email protected], Chan, Angus CW, 4, [email protected]",
"abstract": "Background Kocuria Micrococcus K. rosea K. kristinae Case presentation We describe the first case of K. kristinae Conclusion Our report of K. kristinae Kocuria spp. Kocuria spp.",
"body_text": "Background Kocuria Micrococcaceae Micrococcus Micrococcus 1 Kocuria spp. K. rosea 2 K. kristinae Micrococcus kristinae 3 K. rosea K. kristinae 4 K. kristinae Case presentation A 56-year old Chinese man, who had a known history of asymptomatic gallstones, presented with right upper quadrant abdominal pain for five days associated with fever. Laboratory investigations showed neutrophilia, but the liver function test was normal. Ultrasound examination of the abdomen revealed distended gallbladder associated with multiple gallstones, prominent intrahepatic ducts and enlarged lymph nodes at the porta hepatitis region. Laparoscopic cholecystectomy performed for a diagnosis of acute cholecystitis showed distended and gross thickened gallbladder and omental adhesions. The bile was turbid and two stones were found impacted at the Hartmann's pouch. The cystic duct was normal. The patient developed post-operative fever and intravenous levofloxacin at a dosage of 500 mg daily was started as empirical treatment. Bile culture subsequently yielded a pure growth of K. kristinae Microbiological diagnosis Culture of bile from gall bladder was performed with sheep blood agar, MacConkey agar and chocolate agar. The plates were incubated at 35°C for 48 hours. Anaerobic culture was performed using Schaedler blood agar and incubated at 35°C for 48 hours. Gram-positive cocci arranged in tetrads were isolated from pale cream colonies after two days incubation. The organism was non-hemolytic, catalase positive, coagulase negative and non-motile. Identification was performed using Biomerieux ID32 Staph ATB system and BD Phoenix PMC/ID-13 system. The isolate was identified as Kocuria kristinae Kocuria 5 K. kristinae Staphylococcus Discussion Members of the genus Micrococcus Micrococcus spp. M. luteus 6 7 8 9 10 11 Micrococcus 12 13 14 Micrococcus spp. 15 16 Kocuria Micrococcus K. rosea K. kristinae 2 4 Kocuria 5 K. kristinae Kocuria Micrococcus 17 Bile cultures are sterile in 25 – 50% of acutely inflamed gallbladders. Bacterial infection in acute cholecystitis is usually a secondary event, and is most commonly due to enteric bacteria. A recent study from the Netherlands on microbes isolated from bile after cholecystectomy [ 18 Escherichia coli Klebsiella spp. Streptococcus spp. 18 19 20 We describe the first case of K. kristinae Staphylococcus aureus 21 S. aureus 21 Conclusion Although previously regarded as an innocuous microorganism, there have been a number of recent reports describing the association between Kocuria spp. K. kristinae Competing interests The author(s) declare that they have no competing interests. Authors' contributions ESKM, CLPW and KTWL carried out the laboratory studies of the patient. WCY performed the 16s rRNA sequencing. ACWC performed the operation and provided clinical details. ECHC followed up the patient and obtained consent from the patient to publish this case report. ESKM and CLPW drafted the manuscript. All authors read and approved the final manuscript. Pre-publication history The pre-publication history for this paper can be accessed here: Acknowledgements Written consent was obtained from the patient for publication of this case report.",
"bibliography": "Stackebrandt, E, Koch, C, Gvozdiak, O, Schumann, P, Taxonomic dissection of the genus, Micrococcus, Kocuria, Nesterenkonia, Kytococcus, Dermacoccus, Micrococcus, Int J Syst Bacteriol, 1995, 45, 682, 692, 7547287\nAltuntas, F, Yildiz, O, Eser, B, Gundogan, K, Sumerkan, B, Cetin, M, Catheter-related bacteremia due to, Kocuria rosea, BMC Infect Dis, 2004, 4, 62, 15615593, 10.1186/1471-2334-4-62\nKloos, WE, Tornabene, TG, Schleifer, KH, Isolation and characterization of micrococci from human skin, including two new species:, Micrococcus lylae, Micrococcus kristinae, Int J Syst Bacteriol, 1974, 24, 79, 101\nBasaglia, G, Carretto, E, Barbarini, D, Moras, L, Scalone, S, Marone, P, De Paoli, P, Catheter-related bacteremia due to, Kocuria kristinae, J Clin Microbiol, 2002, 40, 311, 313, 11773142, 10.1128/JCM.40.1.311-313.2002\nBen-Ami, R, Navon-Venezia, S, Schwartz, D, Schlezinger, Y, Mekuzas, Y, Carmeli, Y, Erroneous reporting of coagulase-negative staphylococci as, Kocuria spp., J Clin Microbiol, 2005, 43, 1448, 1450, 15750130, 10.1128/JCM.43.3.1448-1450.2005\nFosse, T, Peloux, Y, Granthil, C, Toga, B, Bertrando, J, Sethian, M, Meningitis due to, Micrococcus luteus, Infection, 1985, 13, 280, 281, 4077270, 10.1007/BF01645439\nSelladurai, B, Sivakumaran, S, Subramanian, A, Mohamad, AR, Intracranial suppuration caused by, Micrococcus luteus, Br J Neurosurg, 1993, 7, 205, 208, 8098607\nWharton, M, Rice, JR, McCallum, R, Gallis, HA, Septic arthritis due to, Micrococcus luteus, J Rheumatol, 1986, 13, 659, 660, 3735296\nSouhami, L, Feld, R, TuVnell, PG, Fellner, T, Micrococcus luteus, Med Pediatr Oncol, 1979, 7, 309, 314, 296784\nPeces, R, Gago, E, Tejada, F, Laures, AS, Alvarez-Grande, J, Relapsing bacteraemia due to, Micrococcus luteus, Nephrol Dial Transplant, 1997, 12, 2428, 2429, 9394339, 10.1093/ndt/12.11.2428\nShanks, D, Goldwater, P, Pena, A, Saxon, B, Fatal, Micrococcus, Med Pediatr Oncol, 2001, 37, 553, 554, 11745898, 10.1002/mpo.1253\nSpencer, RC, Infections in continuous ambulatory peritoneal dialysis, J Clin Microbiol, 1988, 27, 1, 9, 3050104\nRichardson, JF, Marples, RR, de Saze, MJ, Characteristics of coagulase-negative staphylococci and micrococci from cases of endocarditis, J Hosp Infect, 1984, 5, 164, 171, 6205056, 10.1016/0195-6701(84)90120-8\nShapiro, S, Boaz, J, Kleiman, M, Kalsbeek, J, Mealy, J, Origin of organisms infecting ventricular shunts, Neurosurgery, 1988, 22, 868, 872, 3380276\nYap, RL, Mermel, LA, Micrococcus, Eur J Clin Microbiol Infect Dis, 2003, 22, 704, 705, 14576986, 10.1007/s10096-003-1024-1\nOudiz, RJ, Widlitz, A, Beckmann, XJ, Camanga, D, Alfie, J, Brundage, BH, Barst, RJ, Micrococcus-associated central venous catheter infection in patients with pulmonary arterial hypertension, Chest, 2004, 126, 90, 94, 15249447, 10.1378/chest.126.1.90\nSzczerba, I, Susceptibility to antibiotics of bacteria from genera Micrococcus, Kocuria, Nesternkonia, Kytococcus and Dermacoccus, Med Dosw Mikrobiol, 2003, 55, 75, 80, 12908418\nden Hoed, PT, Boelhouwer, RU, Veen, HF, Hop, WC, Bruining, HA, Infections and bacteriological data after laparoscopic and open gallbladder surgery, J Hosp Infect, 1998, 39, 27, 37, 9617682, 10.1016/S0195-6701(98)90240-7\nAl-Abassi, AA, Farghaly, MM, Ahmed, HL, Mobasher, LL, Al-Manee, MS, Infection after laparoscopic cholecystectomy: effect of infected bile and infected gallbladder wall, Eur J Surg, 2001, 167, 268, 73, 11354318, 10.1080/110241501300091426\nSwoboda, S, Oberdorfer, K, Klee, F, Hoppe-Tichy, T, von Baum, H, Geiss, HK, Tissue and serum concentrations of levofloxacin 500 mg administered intravenously or orally for antibiotic prophylaxis in biliary surgery, J Antimicrob Chemother, 2003, 51, 459, 462, 12562723, 10.1093/jac/dgk056\nMerchant, SS, Falsey, AR, Staphylococcus aureus cholecystitis: a report of three cases with review of the literature, Yale J Biol Med, 2002, 75, 285, 291, 14580109"
} |
10.1186/1471-2172-6-15 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": "Cloning and functional characterization of the rabbit C-C chemokine receptor 2",
"authors": "Lu, Deshun, 1, [email protected], Yuan, Xiu-juan, 1, [email protected], Evans, Robert J, Jr, 1, [email protected], Pappas, Amy T, 1, [email protected], Wang, He, 1, [email protected], Su, Eric W, 1, [email protected], Hamdouchi, Chafiq, 1, [email protected], Venkataraman, Chandrasekar, 1, [email protected]",
"abstract": "Background CC-family chemokine receptor 2 (CCR2) is implicated in the trafficking of blood-borne monocytes to sites of inflammation and is implicated in the pathogenesis of several inflammatory diseases such as rheumatoid arthritis, multiple sclerosis and atherosclerosis. The major challenge in the development of small molecule chemokine receptor antagonists is the lack of cross-species activity to the receptor in the preclinical species. Rabbit models have been widely used to study the role of various inflammatory molecules in the development of inflammatory processes. Therefore, in this study, we report the cloning and characterization of rabbit CCR2. Data regarding the activity of the CCR2 antagonist will provide valuable tools to perform toxicology and efficacy studies in the rabbit model. Results Sequence alignment indicated that rabbit CCR2 shares 80 % identity to human CCR2b. Tissue distribution indicated that rabbit CCR2 is abundantly expressed in spleen and lung. Recombinant rabbit CCR2 expressed as stable transfectants in U-937 cells binds radiolabeled 125 K d 125 IC 50 Conclusion In this study, we report the cloning of rabbit CCR2 and demonstrate that this receptor is a functional chemotactic receptor for MCP-1.",
"body_text": "Background Chemokine receptors are seven-transmembrane G-protein coupled receptors that direct the migration of various immune cells to the sites of inflammation in addition to their pivotal role in maintaining immune cell homeostasis in various lymphoid compartments [ 1 2 3 3 αi 4 The CC family chemokine receptor 2 (CCR2) is primarily expressed in almost all circulating monocytes. CCR2 is believed to mediate extravasation of blood monocytes to the sites of inflammation [ 5 7 8 9 7 10 11 The major challenge in the development of small molecule chemokine receptor antagonists is the lack of cross-species activity to the receptor in the preclinical species. For example, BX-471, a small molecule antagonist for CCR1, exhibits low nano-molar affinity to the human receptor but has sub-micromolar to high micromolar affinity to the rat and mouse CCR1 receptors, respectively [ 12 13 In recent years, rabbits have been used to study the pathogenesis of inflammatory disease model. It has been recently shown that the therapeutic potential of thiazolidinediones in rabbit model of balloon injury and re-endothelialization is associated with a decrease in MCP-1 expression [ 14 15 13 Results and Discussion Cloning and expression analysis of rabbit CCR2 Full-length cDNA sequence of rabbit CCR2 was cloned from total spleen RNA of New Zealand white rabbits using a PCR based method. The deduced amino acid sequence of rabbit CCR2 encoded a protein of 369 amino acids (Fig. 1 2 2 16 3 Radioligand binding studies in rabbit CCR2 expressing cells Stable cell lines expressing rabbit CCR2 in U-937 cells were generated to characterize the binding properties of radiolabeled human MCP-1 or mouse JE to rabbit CCR2. The binding affinity of radiolabeled human MCP-1 or mouse JE was measured using a competition binding assay of the respective cold ligands. As shown in Figs. 4 125 K d B max 125 125 Receptor pharmacology of rabbit CCR2 was studied using a variety of ligands that belonged to the MCP subfamily and irrelevant ligands such as RANTES, MIP-1α and MIP-1β. As expected, human MCP-1, -2, and -4 differentially competed the binding of radiolabeled mouse JE with K i 5A Ki 5B 17 5C IC 50 Functional characterization of Rabbit CCR2 stable cell line In order to confirm whether rabbit CCR2 expressed in U-937 cells is functionally coupled to G αi 6A 6B 6C IC 50 6D 6E IC 50 6F Conclusion In summary, we have cloned the full-length rabbit CCR2 cDNA and proved that the receptor is functional by expressing rabbit CCR2 in U-937 cells. The sequence of rabbit CCR2 will provide additional insight into the molecular evolution of chemokine receptors in different species. More importantly, the data obtained on cross-species activity of the CCR2 antagonist will provide valuable tools to perform toxicology and efficacy studies in the rabbit model. Methods Materials Recombinant human chemokines (MCP-1, -2, -3, -4, RANTES, MIP-1α, MIP-1β) were purchased from Pepro Tech (Rocky Hill, NJ). Mouse JE and human SDF-1α were obtained from R&D Systems (Minneapolis, MN). Radiolabeled ligands ( 125 125 14 Rabbit cDNA cloning Total RNA was prepared from the spleen of New Zealand white rabbits by the Trizol method and the cDNA was transcribed by using SuperScript™ First-Strand Synthesis System for RT-PCR (Invitrogen, Carlson, CA). Then the cDNA was amplified by PCR by using conserved primers (primer 1: 5'-GTATTCATCTTTGGTTTTGTGGGCAACATG-3' and primer 2: 5'-CAAAGGTAACTGTCCTGGCTTTTAAAGCAA-3'). The resultant PCR fragment was sequenced and this information was used to design the rabbit CCR2 gene specific primers. Rabbit CCR2 gene specific primers were used to amplify two fragments of rabbit cDNA by 5'- and 3'- rapid amplification of cDNA ends (RACE) using SMART RACE cDNA Amplification Kit (Clonetech, Palo Alto, CA). The sequence information from 5'- and 3'- RACE products was further used to design two primers (5'-GGTTGCTGAGAAGCCTGACACGC-3', and 5'-CAGGTCTGTATTCTTCAACAAGCCCTCG-3') out of start and stop codons, and full-length rabbit CCR2 cDNA was cloned using PCR amplification. The final PCR product with corresponding size was cloned to PCRII-TAPO (Invitrogen) and sequenced. Tissue distribution Rabbit cDNA from brain, heart, liver, lung, spleen and testis were quantitated for expression levels of CCR2 and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) by Taqman method. TaqMan primers and probes were designed using the Primer Express Computer Program (Applied Biosystems, Foster City, CA). The forward and reverse primers and probe selected for rabbit CCR2 are: 5'-catgacacactgctgcatcaac-3', 5'-gagaggtagctccggaacttctc-3' and 5'-[6-FAM]-ccgtggtctacgccttcgtcgg-[TAMRA-6-FAM]-3'. The forward, reverse primers and probe selected for rabbit GAPDH are: 5'-ggatttggccgcattgg-3', 5'-caacatccactttgccagagttaa-3' and 5'-[6-FAM]-cgcctggtcaccagggctgct-[TAMRA-6-FAM]-3'. Amplification mixture contained a total volume of 10 μl with 6 μl of TaqMan universal PCR master mixture (300 nM forward primer, 300 nM reverse primer, and 900 nM probe) and 4 μl of diluted samples. Taqman amplification was conducted on a ABI PRISM 7900HT Sequence Detector System (Applied Biosystems, Foster City, CA) with the following thermal profile: 1 cycle each of 50°C for 2 minutes and 95°C for 10 minutes followed by 40 cycles each of 95°C for 15 seconds and 60°C for 1 minute. Data was analyzed using a built-in standard curve method. Generation of retrovirus infected rabbit CCR2 stable cell line Rabbit cDNA described above was amplified by PCR with primer 11: 5'-ggaggc agatct gaattc Bgl EcoR Bgl EcoR puro puro Equilibrium binding assays Equilibrium binding assay was conducted in RPMI 1640 medium with 10 mM HEPES and 0.2% BSA in room temperature with constant shaking for 2 hours. Reaction mixture contained a total volume of 100 μl with various concentrations of 125 125 125 5 125 4 125 K d B max Competition binding assays The assay was conducted under the identical conditions as saturation binding assay described above with the radiolabeled ligand concentration fixed (0.11 nM 125 IC 50 Chemotaxis assays Chemotaxis assay was performed as described elsewhere [ 18 6 max Abbreviations CCR2, CC chemokine receptor 2; MCP, monocyte chemoattactant protein; RANTES, regulated on activation-regulated chemokine; MIP, macrophage inflammatory protein; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; RACE, rapid amplification of cDNA ends, HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid; BSA, bovine serum albumin; PCR, polymerase chain reaction. Authors' contributions DL designed experiments, oversaw research and wrote the paper. X-JY conducted the experiments. RJE conducted the experiments. ATP conducted the experiments. HW and EWS participated in sequence alignments. CH synthesized the compound. CV conceived the study, designed experiments, oversaw research and wrote the paper.",
"bibliography": "Rollins, BJ, Chemokines, Blood, 1997, 90, 909, 928, 9242519\nFernandez, EJ, Lolis, E, Structure, function, and inhibition of chemokines, Annu Rev of Pharmacol Toxicol, 2002, 42, 469, 499, 11807180, 10.1146/annurev.pharmtox.42.091901.115838\nRossi, D, Zlotnik, A, The biology of chemokines and their receptors, Annual Review of Immunology, 2000, 18, 217, 242, 10837058, 10.1146/annurev.immunol.18.1.217\nStievano, LPE, Amadori, A, C and CX3C chemokines: cell sources and physiopathological implications, Crit Rev Immunol, 2004, 24, 205, 228, 15482255, 10.1615/CritRevImmunol.v24.i3.40\nWong, L-M, Myers, SJ, Tsou, C-L, Gosling, J, Arai, H, Charo, IF, Organization and differential expression of the human monocyte chemoattractant protein 1 receptor gene. Evidence for the role of the carboxyl-terminal tail in receptor trafficking, J Biol Chem, 1997, 272, 1038, 1045, 8995400, 10.1074/jbc.272.2.1038\nYamagami, S, Tokuda, Y, Ishii, K, Tanaka, H, Endo, N, CDNA cloning and functional expression of a human monocyte chemoattractant protein 1 receptor, Biochem and Biophys Res Commun, 1994, 202, 1156, 1162, 8048929, 10.1006/bbrc.1994.2049\nCharo, I, Myers, S, Herman, A, Franci, C, Connolly, A, Coughlin, S, Molecular cloning and functional expression of two monocyte chemoattractant protein 1 receptors reveals alternative splicing of the carboxyl-terminal tails, PNAS, 1994, 91, 2752, 2756, 8146186\nGerard, C, Rollins, BJ, Chemokines and disease, Nat Immunol, 2001, 2, 108, 115, 11175802, 10.1038/84209\nCharo, IF, Taubman, MB, Chemokines in the pathogenesis of vascular disease, Circ Res, 2004, 95, 858, 866, 15514167, 10.1161/01.RES.0000146672.10582.17\nFranci, C, Wong, L, Van Damme, J, Proost, P, Charo, I, Monocyte chemoattractant protein-3, but not monocyte chemoattractant protein-2, is a functional ligand of the human monocyte chemoattractant protein-1 receptor, J Immunol, 1995, 154, 6511, 6517, 7759884\nGong, X, Gong, W, Kuhns, DB, Ben-Baruch, A, Howard, OMZ, Wang, JM, Monocyte chemotactic protein-2 (MCP-2) uses CCR1 and CCR2b as its functional receptors, J Biol Chem, 1997, 272, 11682, 11685, 9115216, 10.1074/jbc.272.18.11682\nLiang, M, Mallari, C, Rosser, M, Ng, HP, May, K, Monahan, S, Bauman, JG, Islam, I, Ghannam, A, Buckman, B, Shaw, K, Wei, G-P, Xu, W, Zhao, Z, Ho, E, Shen, J, Oanh, H, Subramanyam, B, Vergona, R, Taub, D, Dunning, L, Harvey, S, Snider, RM, Hesselgesser, J, Morrissey, MM, Perez, HD, Horuk, R, Identification and characterization of a potent, selective, and orally active antagonist of the CC chemokine receptor-1, J Biol Chem, 2000, 275, 19000, 19008, 10748002, 10.1074/jbc.M001222200\nHoruk, R, Shurey, S, Ng, HP, May, K, Bauman, JG, Islam, I, Ghannam, A, Buckman, B, Wei, GP, Xu, W, CCR1-specific non-peptide antagonist: efficacy in a rabbit allograft rejection model, Immunology Letters, 2001, 76, 193, 201, 11306147, 10.1016/S0165-2478(01)00172-9\nTanaka, T, Fukunaga, Y, Itoh, H, Doi, K, Yamashita, J, Chun, T-H, Inuoe, M, Masatsugu, K, Saito, T, Sawada, N, Sakaguchi, S, Arai, H, Nakao, K, Therapeutic potential of thiazolidinediones in activation of peroxisome proliferator-activated receptor γ for monocyte recruitment and endothelial regeneration, Eur J Pharmacol, 2005, 508, 255, 265, 15680279, 10.1016/j.ejphar.2004.10.056\nPodolin, P, Bolognese, BJ, Foley, JJ, Schmidt, DB, Buckley, PT, Widdowson, KL, Jin, Q, White, JR, Lee, JM, Goodman, RB, Hagen, TR, Kajikawa, O, Marshall, LA, Hay, DWP, Sarau, HM, A potent and selective nonpeptide anatagonist of CXCR2 inhibits acute and chronic models of arthritis in the rabbit, J Immunol, 2002, 169, 6435, 6444, 12444152\nShi, X, Liu, S, Xiangyu, J, Zhang, J, Liu, S, Liu, C, Structural analysis of human CCR2b and primate CCR2b by modeling and molecular dynamics simulation, J Mol Model (online), 2002, 8, 217, 222, 12192431, 10.1007/s00894-002-0089-6\nBaba, M, Nishimura, O, Kanzaki, N, Okamoto, M, Sawada, H, Iizawa, Y, Shiraishi, M, Aramaki, Y, Okonogi, K, Ogawa, Y, Meguro, K, Fujino, M, A small-molecule, nonpeptide CCR5 antagonist with highly potent and selective anti-HIV-1 activity, PNAS, 1999, 96, 5698, 5703, 10318947, 10.1073/pnas.96.10.5698\nChung, CD, Kuo, F, Kumer, J, Motani, AS, Lawrence, CE, Henderson, WR, Jr, Venkataraman, C, CCR8 Is not essential for the development of inflammation in a mouse model of allergic airway disease, J Immunol, 2003, 170, 581, 587, 12496446"
} |
10.1186/1743-422X-2-77 | [
"acute retinal necrosis",
"acyclovir",
"contusion",
"corticosteroids",
"varicella zoster virus"
] | http://creativecommons.org/licenses/by/2.0 | {
"title": "Varicella zoster virus acute retinal necrosis following eye contusion: case report",
"authors": "Svozílková, Petra, 1, [email protected], Říhová, Eva, 1, [email protected], Diblík, Pavel, 1, [email protected], Kuthan, Pavel, 1, [email protected], Kovařík, Zdeněk, 1, [email protected], Kalvodová, Bohdana, 1, [email protected]",
"abstract": "Background Acute retinal necrosis is a sight-threatening disease caused by the group of herpesviruses. The aim of this paper is to report a case of acute retinal necrosis following ocular trauma in a patient initially treated with vaso-active drugs and corticosteroids for presumed ocular ischemic syndrome. Case presentation A 51-years-old otherwise healthy man, who suffered from sudden visual loss in the left eye following contusion, was commenced on vaso-active drugs and systemic corticosteroids for suspected ocular ischemic syndrome with extensive swelling of the optic disc and macular edema. Subsequently, vision in the initially uninvolved right eye decreased. Polymerase chain reaction of vitreous samples and retinal biopsy confirmed varicella zoster virus. Despite intensive treatment with intravenous antiviral medication, the patient became completely blind in both eyes. Conclusion Initial treatment of acute, unexplained visual decrease with systemic corticosteroids may lead to visual loss in patients with developing acute retinal necrosis. Ocular trauma could have induced and corticosteroid treatment promoted reactivation of a latent viral infection in our patient.",
"body_text": "Acute retinal necrosis (ARN) is a sight-threatening clinical syndrome caused by the group of herpesviruses (herpes simplex virus; HSV-1 and HSV-2, varicella zoster virus; VZV, cytomegalovirus; CMV or Epstein-Barr virus; EBV). Rapidly progressing retinal inflammation leads to severe impairment of vision. Case presentation We present a case of a 51-year-old otherwise healthy man, who suffered from rapid visual loss in the left eye following contusion. Ocular trauma was caused during a football match by a ball, which hit an index finger located just in front of the bulbus. The patient attended our department on April 27, 2004, one week after the injury, when the vision in the left eye decreased to light perception with inaccurate light projection and hand movements in a lower part of visual field. The best-corrected visual acuity in the right eye was 1.0. Intraocular pressures were 18 mmHg in the right eye and 45 mmHg in the left eye. Examination of the anterior segment and fundus of the right eye revealed no pathology. The left eye showed discrete injection of the conjunctiva and keratic precipitates with mild anterior chamber flare and cells. There was iridodonesis, cleft syndrome and a relative afferent pupillary defect in the left eye. The fundus examination of the left eye revealed swelling of the optic disc, large ischemic macular edema, superficial retinal hemorrhages, narrowing of the arterioles and dilatation of the venules (Figure 1A 1B Figure 1 Red free fundus photographs and late phases of fluorescein angiography. (A, B) On initial examination, red free photograph and late phase of fluorescein angiography of the left eye demonstrated swelling of the optic disc, ischemic macular edema, narrowing of the arterioles, dilatation of the venules and superficial retinal hemorrhages. (C, D) Four weeks later, fundus examination of the initially uninvolved right eye revealed swelling of the optic disc with hemorrhages and ischemic macular edema. Based on the clinical findings, the presumed diagnosis of ocular ischemic syndrome was made. The patient was initially treated with vaso-active drugs in addition to corticosteroids. Intravenous methylprednisolone (500 mg daily for 5 days) followed by 60 mg of oral prednisone daily was indicated due to swelling of the optic disc and macular edema. Despite intensive therapy, the fundus examination showed progression of ischemic lesions. Visual acuity in the left eye was light perception with inaccurate light projection. The finding on the right eye was without changes. The patient was discharged on oral prednisone 50 mg daily. On May 24, 2004, four weeks after pulse intravenous corticosteroid treatment, vision in the initially uninvolved right eye decreased to 0.25. Fundus examination of the right eye disclosed swelling of the optic disc with hemorrhages, blurring of the optic disk margins and ischemic macular edema (Figure 1C, D A differential diagnosis of antiphospholipide syndrome, masquerading syndrome, viral retinitis or specific inflammation was considered. No neurological or other abnormalities were found on systemic examination. The findings from magnetic resonance imaging and magnetic resonance angiography of brain and orbits were within normal limits. The cerebrospinal fluid was negative for VZV DNA and enteroviruses RNA. Chest X ray and abdominal ultrasonography were normal. Leukocyte count, hematocrit and activated partial tromboplastin time (APTT) were normal, liver tests showed elevated levels of alaninaminotranspherase (ALT; 2.63 ukat/l). Anti-cardiolipin antibodies were negative. Serologic tests for syphilis and human immunodeficiency virus (HIV-1/-2) were negative. Serum was evaluated regarding evidence for herpesviruses by means of polymerase chain reaction (PCR). Low levels of VZV and EBV EBNA-1 IgG antibodies were detected in serum, whereas IgM antibodies were absent; as well antibodies of respiratory infections or neuroinfections were negative. Blood cultures were also negative. Immunofenotypization showed lower count of lymphocytes in peripheral blood, without plasma cell neoplasia. On May 27, 2004, an aqueous tap of the left eye was performed and samples were submitted for cytological and virological analysis. PCR of aqueous humour was negative for herpesviruses family and cytology confirmed non-purulent intraocular inflammation. The patient was treated with corticosteroids. The best-corrected visual acuity in the right eye decreased to 0.02. Due to progressive impairment of the clinical status, the corticosteroid therapy was stopped. Fundus examination demonstrated several enlarging foci of necrotizing retinitis with extensive posterior pole involvement (Figure 2 Figure 2 Red free fundus photograph of the right eye after intravenous corticosteroid treatment. Fundus examination disclosed several enlarging foci of necrotizing retinitis. On June 4, 2004, a diagnostic pars plana vitrectomy and retinal biopsy were carried out in the left eye. The vitreous cavity was filled with 16% perfluoropropane (C 3 8 PCR of retina of the left eye and undiluted vitreous of both eyes were positive for VZV. Undiluted vitreous was negative for HSV-1 and -2, CMV, EBV. PCR of diluted vitreous was negative for herpesviruses family. Mycobacterium tuberculosis was not detected using PCR in vitreous of both eyes. Cultivation of vitreous for bacteria and fungi was negative; Toxoplasma gondii In two weeks, intravenous acyclovir was followed by oral acyclovir (5 × 400 mg daily). In the right eye, large foci of retinal atrophy with reduced inflammatory reaction were present. Owing the cataract induced by gas, fundus of the left eye was not visible. The patient was discharged on acyclovir 4 × 400 mg daily. However, an exudative retinal detachment was seen in the right eye and vision decreased to 0. Vision in the left eye was light perception with inaccurate light projection. On examination 4 weeks later, B-scan ultrasonography of the left eye confirmed the exudative retinal detachment. Nevertheless, despite intensive treatment with intravenous antiviral medication, the patient became completely blind in both eyes. Discussion ARN is a serious ophthalmic manifestation of infection caused by the herpesviruses family. A rapid and accurate diagnosis of herpetic infection is crucial for prompt administration of specific antiviral therapy. Although the precise pathogenesis of ARN is not completely understood, Kezuka and coworkers [ 1 We present a case of a 51-year-old otherwise healthy man with rapid visual loss initially treated with vaso-active drugs and systemic corticosteroids for presumed ocular ischemic syndrome with swelling of the optic disc and macular edema. The causative agent was diagnosed as VZV based on PCR analysis of vitreous and retinal samples. Possible mechanisms of VZV necrotizing retinopathy include reinfection by an exogenous virus or reactivation of a latent infection. In our opinion, ocular trauma probably induced reactivation of a latent virus in the presented patient. Absence of high VZV titers in the serum makes systemic reinfection unlikely. Thompson and coworkers [ 2 A unique case of acute HSV encephalitis associated with bilateral ARN syndrome after craniotomy for resection of a suprasellar craniopharyngioma has been reported. The authors hypothesized reactivation of previously latent HSV in the area of the inferior frontal lobe and optic chiasm. Reactivated virus may have migrated to the retina by axonal transport, through the optic nerves, to induce the ARN syndrome [ 3 4 Ocular trauma could have induced, and systemic corticosteroid treatment probably promoted, reactivation of a latent virus in our patient. Initial treatment of acute, unexplained decrease of vision with systemic corticosteroids may lead to visual loss in patients with developing necrotizing herpetic retinopathy [ 5 Competing interests The author(s) declare that they have no competing interests. Acknowledgements Written consent was obtained from the patient for publication of case including clinical photographs.",
"bibliography": "Kezuka, T, Sakai, J, Usui, N, Streilein, JW, Usui, M, Evidence for antigen-specific immune deviation in patients with acute retinal necrosis, Arch Ophthalmol, 2001, 119, 1044, 1049, 11448326\nThompson, WS, Culbertson, WW, Smiddy, WE, Robertson, JE, Rosenbaum, JT, Acute retinal necrosis caused by reactivation of herpes simplex virus type 2, Am J Ophthalmol, 1994, 118, 205, 211, 8053466\nPerry, JD, Girkin, CA, Miller, NR, Kerr, DA, Herpes simplex encephalitis and bilateral acute retinal necrosis syndrome after craniotomy, Am J Ophthalmol, 1998, 126, 456, 460, 9744385, 10.1016/S0002-9394(98)00108-1\nVerma, L, Venkatesh, P, Satpal, G, Rathore, K, Tewari, HK, Bilateral necrotizing herpetic retinopathy three years after herpes simplex encephalitis following pulse corticosteroid treatment, Retina, 1999, 19, 464, 467, 10546950\nBenz, MS, Glaser, JS, Davis, JL, Progressive outer retinal necrosis in immunocompetent patients treated initially for optic neuropathy with systemic corticosteroids, Am J Ophthalmol, 2003, 135, 551, 553, 12654381, 10.1016/S0002-9394(02)01978-5"
} |
10.1186/1472-6963-5-61 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": "The use of end-quintile comparisons to identify under-servicing of the poor and over-servicing of the rich: A longitudinal study describing the effect of socioeconomic status on healthcare",
"authors": "Brameld, Kate J, 1, [email protected], Holman, C D'Arcy J, 1, [email protected]",
"abstract": "Background To demonstrate the use of end-quintile comparisons in assessing the effect of socio-economic status on hospital utilisation and outcomes in Western Australia. Methods Hospital morbidity records were extracted from the WA Data Linkage System for the period 1994–99, with follow-up to the end of 2000. Multivariate modelling was used to estimate the effect of socio-economic status on hospital admission rates, average and total length of stay (LOS), cumulative incidence of readmission at 30 days and one year, and case fatality at one year. Results The study demonstrated higher rate ratios of hospital admission in the more disadvantaged quintiles: rate ratios were 1.31 (95% CI 1.25–1.37) and 1.32 (1.26–1.38) in the first quintile (most disadvantaged) and the second quintile respectively, compared with the fifth quintile (most advantaged). There was a longer total LOS in the most disadvantaged quintile compared with quintile 5 (LOS ratio 1.24; 1.23–1.26). The risk of readmission at 30 days and one year and the risk of death at one year were also greater in those with greater disadvantage: the hazard ratios for quintiles 1:quintile 5 were 1.07 (1.05–1.09), 1.17 (1.16–1.18) and 1.10 (1.07–1.13) respectively. In contradiction to the trends towards higher hospital utilisation and poorer outcomes with increasing social disadvantage, in some MDC's the rate ratio of quintile 1:quintile 2 was less than 1, and quintile 4:quintile 5 was greater than 1. For all surgical admissions the most disadvantaged had a significantly lower admission rate than the second quintile. Conclusion This study has shown that the disadvantaged within Western Australia are more intensive users of hospital services but their outcomes following hospitalisation are worse, consistent with their health status. Instances of overuse in the least disadvantaged and under use in the most disadvantaged have also been identified.",
"body_text": "Background A recent review of the Australian literature unequivocally showed that the \"disadvantaged\" had higher mortality rates from most major causes of death, experienced more ill-health and were less likely to act to prevent disease or detect it at an asymptomatic stage [ 1 2 3 4 This study utilises the unique facility of the Western Australian Linked Data System to provide an overview of the effects of socio-economic status on hospital utilisation and outcomes throughout the State of Western Australia for each major diagnostic category, while adjusting for the effects of age, sex, Aboriginality, comorbidity, geography and possession of health insurance. In addition to providing this general overview of inequalities in hospital utilisation and outcomes in WA, the study also attempts to identify possible examples of under- and over-servicing. Examples of over/under servicing may be indicated, particularly where the procedure is discretionary and where other factors such as disease prevalence, demographic characteristics, medical resources and differing physician practice patterns have been accounted for. [ 5 A particular asset of the study is the assignment of socioeconomic status at the level of the Census Collectors' District (CD), which consists of approximately 250 households in urban areas and fewer dwellings in a rural area. This is thus a far more accurate measure than has previously been possible at the postcode level. The data linkage system also enables us to present a greater range of hospital utilisation and outcomes measures and these are given for the complete range of diagnostic categories. In addition we have also been able to adjust for age, sex, aboriginality, accessibility, comorbidity and possession of private health insurance at the individual level. The study allows areas of inequity to be identified, thus facilitating the development of policies and targeting of resources to address these inequalities. Method All linked hospital morbidity and death records were selected from the WA Data Linkage System where a patient had any diagnosis in a specified major diagnostic category (MDC) during the period 1994–1999. For the study of hospital admissions and length of stay (LOS) only records with a diagnosis in the specified MDC between 1994 and 1999 were selected. For the study of cumulative risk of readmission within 30 days and 1 year and case fatality within one year, the patient's first record with a diagnosis of the specified MDC in the period 1994–1999 was selected (the index admission) along with the next admission record with any diagnosis that occurred within a 30 day or 1 year timeframe, as well as any linked death record. The effect of socio-economic status on hospital admission rates was modelled using Poisson regression. All models were corrected for overdispersion of the data. Multiple linear regression was used to model average LOS of all admissions during the 12 months following index admission and cumulative LOS in the 12 months following index admission. LOS analyses were based on logarithm-transformed data because of skewness in the distribution. Age was squared to improve the model fit. The effects of the study variables on the cumulative risk of readmission within 30 days and 1 year and case fatality within one year were measured using Cox regression. Here the confounding effect of age was modelled using fractional polynomial regression[ 6 7 8 Socio-economic status was measured using the Australian Bureau of Statistics socio-economic indices for areas (SEIFA), specifically the index of relative disadvantage at the level of the census Collector's District (CD). The index of relative socioeconomic disadvantage was one of five SEIFA indices [ 9 9 Locational disadvantage was measured using the accessibility/remoteness index of Australia (ARIA),[ 10 The measures of locational and social disadvantage were matched to the hospital morbidity records using the CD of residence of the patient as a linkage key. CD's were derived from a geographical point defined by a specific longitude and latitude (a geocode). All patient addresses in the hospital morbidity database were geocoded commencing from records collected in 1993, prior to which the records contained insufficient address information. Even so, approximately 20% of records from 1993 onwards were unable to be geocoded due to incomplete address information. In some sparsely populated areas, CDs for records with missing geocodes could be allocated from the postcodes. In other cases it was possible to allocate a CD from the patient's other linked records, provided that the patient had maintained the same residential postcode and a period of less than five years had elapsed between the admissions. In most of the remaining 16% of records, where a CD was still missing at this stage, the SEIFA and ARIA codes were allocated on the basis of postcode. This left a small proportion of records (1.5%) still without SEIFA and ARIA codes, because not all postcodes were assigned a SEIFA code during the 1996 census. These records were excluded from the analysis. Possession of private health insurance was allocated on the basis of the payment classification variable having the value of 'private insured'. A patient only required one record with this payment classification to be recorded as privately insured for all analyses in the study. This is based on the assumption that some patients did not always declare or utilise their private health cover, depending on the circumstances of the admission, such as whether emergency or elective treatment was needed; anticipated levels of copayment as a private patient; and whether a privately insured classification was really necessary to secure the patient's choice of doctor. This enabled us to gain an overview of how insurance status affected the patient's entire treatment history, as distinct from the times when they elected to use their private insurance. Population denominators for the Poisson regression were based on data from the ABS CDATA96 [ 11 12 The study involved a total of 1,061101 patients admitted over the five year period. Descriptive information about these patients is given in table 1 Table 1 Descriptive statistics for Patients in the Study Results The overall admission rates showed a clear difference between the most and least disadvantaged groups, but there was little difference between the two most disadvantaged quintiles and between the two least advantaged quintiles (table 2 Table 2 The effect of socio-economic status on hospital utilisation and outcomes Socioeconomic status had little effect on average length of stay, but total length of stay decreased with increasing advantage. The risk of readmission within 30 days and 1 year and case fatality within 1 year decreased with increasing social advantage (table 2 Examination of medical admission rate ratios at the MDC level (table 3 Table 3 The effect of socio-economic status on hospital admission rates for medical DRGs Bold text denotes over or underservicing * questionable convergence of poisson model † restricted subgroups to allow model convergence MDC 7 age ≥ 20 years MDC 10 age ≥ 25 years and 0–2 comorbid conditions MDC11 age ≥ 30 MDC12 age range 30–64 years and sex male MDC13 age range 30–64 years and sex female Analysis of surgical admission rate ratios (table 4 Table 4 The effect of socio-economic status on hospital admission rates for surgical DRGs Bold text denotes over or underservicing * questionable convergence of poisson model † restricted subgroups to allow model convergence End-quintile comparisons of medical and surgical admission rates was used to highlight possible instances of under- and overservicing, whereby the admission rate in the first quintile was at least 10% less than that in the second quintile (ie, rate ratio ≤ 0.90) or the admission rate in the fifth quintile was more than 10% greater than in the fourth quintile (ie. rate ratio ≥ 1.10). Examples of where this occurred are highlighted in tables 3 4 5 6 Table 5 Most common procedures in the MDCs for which underservicing of the socially disadvantaged occurred Table 6 Most common procedures in the MDCs for which overservicing of the socially advantaged occurred Discussion Medicare, Australia's universal health insurance scheme was designed to ensure that all Australians had equal access to health care [ 13 14 15 2 Our study demonstrated higher hospital admission rates in the disadvantaged. A number of studies have shown that those of low socio-economic status, as measured by various indicators, most commonly income, have a greater risk of hospitalisation than those of high socio-economic status [ 16 18 1 16 1 2 In some cases, for example chemotherapy, apparent over- or underservicing may have occurred as a result of some patients being treated as day patients (and thus were not included in our hospital morbidity data). Nevertheless, this would still represent a differential pattern of treatment according to socioeconomic group. The cost of surgical extraction of teeth is not covered by Medicare and this is clearly resulting in differential treatment according to socioeconomic status. In other cases, it is likely that those in higher socio-economic groups are better able to negotiate their way through the health system to achieve their desired outcome [ 19 20 The study showed that hospital admission rates in the most disadvantaged were up to 35% higher than in the most advantaged. In contrast, age-standardised mortality rates for those aged under 65 in Australia during 1998–2000 were 50–90% higher for the most disadvantaged, dependant on age-group and sex [ 21 22 The study also demonstrated that the most disadvantaged had a significantly longer total LOS. Canadian data examining all hospitalisations in residents of Winnipeg from 1989–1996, have shown a strong association between length of stay for admissions of 59 days or less and socio-economic status, poorer patients staying in hospital for up to 2.4 times longer than the most affluent patients [ 18 23 Socio-economic status was also shown to have a significant effect on the outcome measures, risk being greatest in those with greatest disadvantage. However, the effect on the risk of readmission was greater at 1 year than 30 days. This is important because early readmission rates are indicative of possible deficiencies in the process of inpatient care, whereas readmission rates in general may be more an effect of disease progression or the onset of new disease [ 24 25 The effect of socio-economic status on case fatality has mainly been studied following myocardial infarction. Macintyre et al et al 26 28 Increased use of hospital services by the more disadvantaged in our population reflect their greater health need and, in many cases, also a greater severity of illness [ 23 29 25 Conclusion This study has shown that the socially disadvantaged within Western Australia are more intensive users of health services and their outcomes following hospitalisation are worse. Comparison of hospital admission rates and premature mortality rates suggest that the increased admission rates in the most disadvantaged are not sufficient to account for their increased need. Some examples of overuse in the least disadvantaged and under use in the most disadvantaged were also identified. These factors together with the discrepancy in the gradient between medical and surgical admissions are suggestive of inequity in treatment between socio-economic groups, specifically the greatest and the least disadvantaged. The WA data linkage system provides an effective mechanism for ongoing monitoring of equity in hospital utilisation and outcomes. Further research is required to identify the need for health services according to socio-economic groups and to identify how services can be made more easily accessible for these groups. Competing interests The author(s) declare that they have no competing interests. Authors' contributions KJB participated in the conception and design of the study, performed the analysis and drafted the paper. CDJH participated in the conception and design of the study and in revising the paper. Pre-publication history The pre-publication history for this paper can be accessed here: Acknowledgements The authors wish to acknowledge all staff who maintain the Western Australian Hospital Morbidity Data System and the Data Linkage System on which this study was based. The study was funded by the National Health and Medical Research Council, Australia. Grant No. 139071.",
"bibliography": "Turrell, G, Oldenburg, B, McGuffog, I, Dent, R, Socioeconomic determinants of health: towards a national research program and a policy and intervention agenda, 1999, Canberra: Queensland University of technology\nTurrell, G, Mathers, C, Socioeconomic status and health in Australia, Med J Aust, 2000, 172, 434, 438, 10870537\nTaylor, R, Quine, S, Lyle, D, Bilton, A, Socioeconomic correlates of mortality and morbidity in Sydney, 1985–88, Aust J Public Health, 1992, 16, 305, 314, 1482725\nWiggers, J, Sanson-Fisher, R, Halpin, S, Prevalence and frequency of health service use: Associations with occupational prestige and educational attainment, Aust J Public Health, 1995, 19, 512, 519, 8713203\nGittelsohn, A, Powe, N, Small area variation in health care delivery in Maryland, Health Serv Res, 1995, 30, 295, 317, 7782218\nRoyston, P, Altman, D, Regression using fractional polynomials of continuous covariates: parsimonious parametric modelling (with discussion), Appl Stat, 1994, 43, 429, 467\nCharlson, M, Pompei, P, Ales, K, Mackenzie, C, A new method of classifying prognostic comorbidity in longitudinal studies: development and validation, J Chronic Dis, 1987, 40, 373, 383, 3558716, 10.1016/0021-9681(87)90171-8\nRomano, PS, Roos, LL, Jollis, JG, Adapting a clinical comorbidity index for use with ICD-9-CM administrative data: differing perspectives, J Clin Epidemiol, 1993, 46, 1075, 9, discussion 1081–90, 8410092, 10.1016/0895-4356(93)90103-8\nABS, 1996 Census of Population and Housing. Socio-economic indexes for areas, 1998, Canberra: Australian Bureau of Statistics\nCDHAC, Measuring Remoteness: Accessibility/remoteness index of Australia (ARIA), 2001, Canberra: Commonwealth Dept of Health and Aged Care\nABS, 1996 Census of Population and Housing. CDATA96, 1997, Canberra: Australian Bureau of Statistics\nABS, Health Insurance Survey, Australia, 1999, Canberra: Australian Bureau of Statistics\nDuckett, S, The Australian Health Care System, 2004, 2, Melbourne: Oxford University Press\nMooney, G, Economics, medicine and health care, 2003, 3, London: Prentice Hall\nBraverman, P, Gruskin, S, Poverty, equity, human rights, and health, Bulletin World Health Organ, 2003, 81, 539, 545\nKeskimaki, I, How did Finland's economic recession in the early 1990s affect socio-economic equity in the use of hospital care?, Soc Sci Med, 2003, 56, 1517, 1530, 12614702, 10.1016/S0277-9536(02)00153-3\nTaylor, R, Chey, T, Bauman, A, Webster, I, Socio-economic, migrant and geographic differentials in coronary heart disease occurence in New South Wales, Aust N Z J Public Health, 1999, 23, 20, 26, 10083685\nCarriere, K, Roos, L, Dover, D, Across time and space: variations in hospital use during Canadian health reform, Health Serv Res, 2000, 35, 467, 87, 10857472\nRoos, N, Mustard, C, Variation in health and health care use by socioeconomic status in Winnipeg, Canada: Does the system work well? Yes and no, Milbank Q, 1997, 75, 89, 111, 9063301, 10.1111/1468-0009.00045\nABS, Private Health Insurance, 2003, Canberra: Australian Bureau of Statistics\nDraper, G, Turrell, G, Oldenburg, B, Health inequalities in Australia: Mortality, 2004, Canberra: Queensland Institute of Technology and the Australian Institute of Health and Welfare\nCarstairs, V, Morris, R, Deprivation and Health in Scotland, 1991, Aberdeen: Aberdeen University Press\nEpstein, A, Stern, R, Weissman, J, Do the poor cost more? A multihospital study of patients' socioeconomic status and use of hospital resources, N Engl J Med, 1990, 322, 1122, 8, 2108331\nAshton, CM, Wray, NP, A conceptual framework for the study of early readmission as an indicator of quality of care, Soc Sci Med, 1996, 43, 1533, 41, 8961397, 10.1016/S0277-9536(96)00049-4\nWeissman, J, Stern, R, Epstein, A, The Impact of Patient Socioeconomic Status and Other Social Factors on Readmission: a Prospective Study in Four Massachusetts Hospitals, Inquiry, 1994, 31, 163, 172, 8021022\nMacintyre, K, Stewart, S, Chalmers, J, Pell, J, Finlayson, A, Boyd, J, Relation between socioeconomic deprivation and death from a first myocardial infarction in Scotland: population based analysis, BMJ, 2001, 322, 1152, 53, 11348909, 10.1136/bmj.322.7295.1152\nSalomaa, V, Niemela, M, Miettinen, H, Ketonen, M, Immonen-Raija, P, Koskinene, S, Relationship of socioeconomic status to the incidence and prehospital, 28-Day, and 1-Year mortality rates of acute coronary events in the FINMONICA myocardial infarction register study, Circulation, 2000, 101, 1913, 1918, 10779456\nAlter, D, CD, N, Austin, P, Tu, J, Effects of socioeconomic status on access to invasive cardiac procedures and on mortality after acute myocardial infarction, N Engl J Med, 1999, 341, 1359, 67, 10536129, 10.1056/NEJM199910283411806\nEachus, J, Chan, P, Pearson, N, Propper, C, Davey Smith, G, An additional dimension to health inequalities: disease severity and socioeconomic position, J Epidemiol Community Health, 1999, 53, 603, 611, 10616672"
} |
10.1371/journal.ppat.0010016 | [] | http://creativecommons.org/licenses/by/4.0/ | {
"title": "\n",
"authors": "Wong, Ka-Wing, 1, Isberg, Ralph R, 1, 2, *",
"abstract": "Yersinia pseudotuberculosis",
"body_text": "Introduction After ingestion by a host, Yersinia pseudotuberculosis 1 Y. enterocolitica, 2 3 1 1 4 Yersinia 5 6 7 8 Invasin-mediated uptake by cultured cells involves internalization of bacteria into membrane-bound compartments [ 9 4 10 11 10 12 10 13 14 Yersinia 15 16 17 Pseudomonas aeruginosa Samonella typhimurium 18 19 20 Y. pestis Yersinia Y. enterocolitica 21 Y. pseudotuberculosis- 22 Enteropathogenic Yersinia Y. pseudotuberculosis Results Use of Fluorescent Resonance Energy Transfer Measurements to Monitor Rac1 Activation Several strategies based on fluorescence resonance energy transfer (FRET) have been described to visualize Rac1 activation [ 23 25 Y. pseudotuberculosis 23 Figure 1 26 Materials and Methods Materials and Methods Figure 1 Activation of Rac1 in Single Cells as Demonstrated by FRET (A) Schematic representation of intermolecular FRET from Rac1-GTP to PBD. In the absence of GTP loading, mCFP-Rac1 is unable to bind mYFP-PBD. Upon GTP loading (activation) of Rac1, mCFP-Rac1-GTP is able to bind to the downstream effector construction mYFP-PBD. This allows the emission from mCFP to excite mYFP, resulting in emission at 527 nm. (B) Display of fluorescence emission and sensitized FRET in individual transfectants. COS1 cells cotransfected with various mCFP-Rac1 derivatives and either mYFP-PBD or mYFP-PBD(LL) were subjected to FRET analysis, and sensitized FRET was calculated ( Materials and Methods Materials and Methods (C) FRET is dependent on coexpression of active mCFP-Rac1 and mYFP-PBD. FRET from ten ROIs, which represented two cytoplasmic regions from each of five cells, were plotted as a function of the intensity of the mCFP-Rac1 donor. (D) Activation of Rac1 increases normalized levels of FRET. Data from (C) were normalized to amount of mCFP-Rac1 in each region of interest and displayed. Displayed are means ± standard errors of the mean (SEMs) (E) Enhanced emission of the mCFP-Rac1 donor resulting from acceptor photobleaching requires Rac1 activation. The acceptor mYFP-PBD was selectively photobleached for 2 min, and amount of mCFP-Rac1 donor emission was compared before and after irradiation ( Materials and Methods To determine if GTP loading was the specific readout of this system, a series of mutant Rac1 and PBD derivatives were transfected into COS1 cells in the absence of incubation with Y. pseudotuberculosis Table 1 Table 1 Figure 1 1 Figure 1 Figure 1 Figure 1 1 Table 1 Figure 1 Table 1 Figure 1 Table 1 Predicted Properties of Fluorescent Proteins Used in this Study To give further support to the hypothesis that FRET was due to binding of Rac1-GTP to PBD, photobleaching was performed ( Figure 1 Materials and Methods 27 Figure 1 Figure 1 GTP-Loaded Rac1 Is Recruited to Nascent Phagosomes Rac1 is activated after engagement of integrin receptors by Y. pseudotuberculosis 10 Y. pseudotuberculosis Y. pseudotuberculosis Yersinia Figure 2 Materials and Methods Figure 2 Figure 2 Figure 2 Figure 2 p Figure 2 Figure 2 Figure 2 Figure 2 Figure 2 Figure 2 Figure 2 Localized Activation of Rac1 on the Phagosomal Membrane during Y. pseudotuberculosis (A–D) Transfected COS1 cells were incubated with Y. pseudotuberculosis − Y. pseudotuberculosis Materials and Methods Materials and Methods Figure 1 Materials and Methods (E) FRET in response to Y. pseudotuberculosis (F) The pool of Rac1 surrounding incoming bacteria is preferentially activated. The intensity of FRET that surrounded nascent phagosomes was compared to that found in nearby cytoplasmic areas, normalized against the concentration of mCFP-Rac1 found in each area, and then used to calculate the ratio of normalized Rac1 activity of nascent phagosome to that of background ( Materials and Methods p Selective Inactivation of Membrane-Targeted Rac1 by YopE The ability to localize activated Rac1 to specific sites within target cells facilitated spatial analysis of the targeting of Rac1 by Yersinia Figure 3 16 17 Materials and Methods Figure 3 3 Table 1 28 Y. pseudotuberculosis Figure 3 3 Figure 3 3 Figure 3 YopE Selectively Inactivates Membrane-Associated Rac1. COS1 cells cotransfected with plasmids expressing mYFP-PBD and noted plasmids were challenged at 37 °C for 30 min with Y. pseudotuberculosis (yopH − − − Materials and Methods (A and B) Displayed are images of typical cells showing phase contrast, mCFP fluorescence and color-scaled sensitized FRET or normalized (Rac1 activation) for YP17 (A) or Yp17/pYopE (A and B) infected cells ( Materials and Methods (C) Cytoplasmic Rac1 is not a YopE target. Normalized FRET was determined ( Materials and Methods Materials and Methods p −6 The Y. pseudotuberculosis We next wished to analyze the interplay between YopE and another translocated effector that targets Rac1 in vitro. Both YopE and YopT inhibit uptake of enteropathogenic Yersinia 17 Y. enterocolitica 21 Y. pseudotuberculosis Y. pseudotuberculosis 17 To investigate the possibility that Y. pseudotuberculosis Figure 4 Figure 4 4 Y. pseudotuberculosis Figure 4 4 14 29 Figure 4 4 Y. pseudotuberculosis, Figure 4 Y. pseudotuberculosis (A–D) COS1 cells transfected with plasmids encoding T7-Rac1, T7-Rac1C189S, myc-Cdc42, myc-RhoA, or HA-Arf6 were incubated at 37 °C for 30 min with Y. pseudotuberculosis Materials and Methods Materials and Methods n n n n n (E) Representative localization of uninfected cells expressing mYFP-Rac1(WT), mYFP-Rac1C189S, or mYFP-Rac16Q, as well as a mYFP-Rac1(WT) transfectant challenged with YP17/pYopT for 30 min (WT; +YopT). White bar represents 1 μm. (F) The presence of excess RhoGDI interferes with the activity of YopT. Y. pseudotuberculosis Rac1 has a strong nuclear localization signal in the polybasic domain located immediately upstream of the CAAX prenylation motif [ 22 20 Y. pseudotuberculosis, n Figure 4 Figure 4 n Table 1 Figure 4 As observed for YopE, membrane-associated Rac1 was the target of YopT. Bacterial translocation of YopT failed to result in nuclear accumulation of the cytoplasmically localized Rac16Q (unpublished data). Furthermore, if Rac1 were localized in a cytoplasmic pool as a result of overproduction of RhoGDI, then YopT-promoted nuclear accumulation of Rac1 was blocked ( Figure 4 YopT Cleavage Does Not Block Rac1 Activation Based on the biochemical properties of the Yersinia Y. pseudotuberculosis Figure 5 Figure 5 22 30 Figure 5 Figure 5 5 Figure 5 YopT Cleavage Does Not Prevent Rac1 Activation COS1 cells were cotransfected with plasmids expressing mYFP-PBD and either mCFP-Rac1 or mCFP-Rac1C189S followed by exposure to Y. pseudotuberculosis Materials and Methods (A–C) Cells expressing mCFP-Rac1(WT) challenged with either YP17 (control) (A) or mCFP-Rac1(WT) challenged with YP17/pYopT (+YopT) (B). Rac1 activation is maintained in the presence of YopT cleavage (C). Data for normalized Rac1 activity from eight cells described in (A) and (B) were quantitated as mean ± SEM. (D) Cytoplasmic localization of Rac1 does not affect activation. FRET was analyzed in ROIs from cytoplasmic regions of uninfected cells transfected with mCFP-Rac1(WT) or mCFP-Rac1C189S and normalized versus amount of mCFP observed in each cell. NS, no significant difference between control and experimental. (E) Example of normalized FRET observed in uninfected cell expressing mCFP-Rac1C189S. White bar represents 10 μm. The Combined Action of YopE and YopT Generate Two Different Pools of Rac1 The above results indicate that the nonprenylated form of Rac1 is a poor substrate for YopE. Therefore, the removal of prenylation by YopT should protect a pool of Rac1 from inactivation by YopE, and that pool should move into the nucleus. To test this prediction, a strain expressing both YopE and YopT was used to challenge COS1 cells, and levels of Rac1 activation were compared to the parental strain lacking YopT ( Figure 6 Figure 6 Figure 6 Figure 6 31 Figure 6 Figure 6 Figure 6 Overexpression of YopT Interferes with YopE-Mediated Inactivation of Rac1 by Blocking YopE Translocation COS1 cells were cotransfected with plasmids expressing mYFP-PBD and mCFP-Rac1, challenged for 30 min with Y. pseudotuberculosis (yopE + (yopE + + (yopE − + Figure 5 Materials and Methods (A) Typical FRET images of cells incubated with denoted strains. (B) The presence of pYopT interferes with the ability of YopE to inactivate cytoplasmically localized Rac1. Data represent normalized FRET, using ROIs within the cytoplasms of ten cells. ***** p −5 p Materials and Methods (C) Plasmid-expressed YopT promotes translocation of active Rac1 into the nucleus in the presence of YopE. Nuclear accumulation of Rac1 was determined by presence of mCFP-Rac1 fluorescence (bar graph), and activation was determined in that population showing accumulation using FRET analysis of nuclear regions (data below bar graph; Materials and Methods (D) Overexpression of YopT blocks translocation of YopE from bacteria into host cells. After 1 h of infection with Y. pseudotuberculosis 6 Materials and Methods yscU To directly study the effects of simultaneous deposition of YopT and YopE on Rac1 dynamics without changing translocation rates, two alternate strategies were pursued. First, strains expressing only YopT (“T,” Figure 7 Figure 7 Yersinia 32 Figure 7 7 Figure 7 7 Figure 7 7 Figure 7 Figure 7 Temporally Regulated Interference of YopE Activity by YopT COS1 cells cotransfected with mCFP-Rac1 and mYFP-PBD were incubated with the noted strains and processed for FRET analysis using ROIs located within the cytoplasm as in Figure 6 Materials and Methods (A) YopE can inactivate cytosolic Rac1 in the presence of YopT. FRET was determined after 30 min of infection with COS1 cells for the following strains. E, YP15 (yopT − + (yopT + − (yopT + − (yopT − + (B) Injection of YopT prior to YopE interferes with Rac1 inactivation by YopE. Control → E, cells were infected with YP17 for 30 min and then incubated with YP15 ( yopE + (yopT + + (yopE − (yopE + p −5 p (C) Examples of sensitized FRET and normalized FRET for cells infected with denoted strains, as above. (D) YopT-promoted Rac1 nuclear localization occurs after YopE pretreatment. COS1 cells were incubated with bacteria using the above conditions, with the added protocol of incubating the cells with bacteria expressing YopE for 30 min prior to infection with bacteria that express YopT. E → T, YP15 ( yopE + yopT − yopT + yopE − Materials and Methods (E) Translocation of YopE is unaffected by the presence of YopT in either a serogroup I strain or using coinfection conditions. Infection conditions were as indicated above; translocation was assayed, and the amount of protein was determined by immunoblotting using an anti-YopE antibody in an NP-40 extractible fraction ( Materials and Methods Despite the fact that cytoplasmically-localized Rac1 was inactivated in cells simultaneously exposed to YopT and YopE, YopT still exerted effects on these cells. Nucleus-localized Rac1 could be detected for any experimental procedure that introduced YopT into cells, even if a YopT-expressing strain was added 30 min after the addition of the YopE expressing strain (“E → T,” Figure 7 Figure 7 As the YopT-cleaved Rac1 may be protected from YopE and come in contact with Rac1-specific guanosine exchange factor (RacGEF) proteins in the nucleus [ 22 30 33 Figure 8 Figure 8 Figure 8 Figure 8 8 Figure 7 Figure 8 Nuclear Localization of Rac1 Protects It from Inactivation by YopE COS1 cells expressing the probes for Rac1 activity (mCFP-Rac1 and mYFP-PBD) were challenged with the indicated strains and then analyzed for nuclear-localized Rac1 activation using FRET. To account for differences in PBD and Rac1 concentrations in the nucleus relative to the cytoplasm, FRET was normalized to both proteins ( Materials and Methods (A) The FRET readout in the nucleus requires Rac1 activation. Translocation of various mutants of mCFP-Rac1 was promoted by incubating COS1 cells with YP17/pYopT2 for 30 min. (B) YopE is not able to reverse or prevent the accumulation of active nuclear Rac1 promoted by YopT. Control, 30-min incubation with YP17 (yopE − − (yopE − − (yopE + − (yopE + − (yopT + − (yopT + − (yopE − (yopE + − p −5 (C) IP32953 inactivates cytosolic Rac1 and activates nuclear Rac1. Two examples of cells infected with IP32953 for 1 h show intense Rac1 activity (displayed as Nuclear FRET) that corresponds to the nucleus shown in phase contrast images. Discussion Enteropathogenic Yersinia Y. pseudotuberculosis Y. pseudotuberculosis Figure 2 10 Figure 3 34 35 Figure 6 All standard criteria, including the use of Rac1 dominant inhibitory mutants and effector binding-defective derivatives, indicate that our FRET system faithfully monitored the localization of Rac1 activation within the cell and gave activation readouts similar to previously described analysis (see Figure 1 23 13 13 Figure 2 A signal that induces the release of Rac1 from RhoGDI is the first step in activation after integrin engagement, followed by GTP loading by guanine nucleotide exchange factors and translocation of Rac1 to the membrane [ 13 36 37 38 39 It has been argued that misregulation of the host cell cytoskeleton by the Yersinia 35 P. aeruginosa 40 Yersinia Rac1 released from the plasma membrane by YopT resulted in an active pool of the GTPase within the nucleus (see Figures 4 8 22 Figure 7 Y. pseudotuberculosis Figures 7 8 Yersinia Y. pestis Y. enterocolitica Y. pseudotuberculosis, Y. enterocolitica 41 Although competition between YopT and YopE can be observed in this work, it is possible that the two proteins have a collaborative relationship that is more difficult to measure. YopT could collaborate with YopE by releasing Rac1-GDP from the membrane after YopE action but prior to that of RhoGDI, causing accumulation of inactive Rac1 in the nucleus. This should bypass any need for RhoGDI to support the function of YopE as previously reported [ 40 As a final note, the translocation of Rac1 into the nucleus that results from YopT cleavage may be a strategy to cause misregulation of the host cell transcription program. As the nuclear Rac1 population includes active protein, it is able to bind downstream effectors. Furthermore, it is known that several GEFs, such as SmgGDS and Dock180, can be similarly localized in this compartment, maintaining Rac1 in the active conformation to bind nuclear factors [ 22 30 42 43 Yersinia Materials and Methods Cell culture, DNA constructs, and transfections. COS1 cells were cultured and transfected as previously described [ 10 26 14 Table 1 14 Y. pseudotuberculosis Y. pseudotuberculosis − Y. pseudotuberculosis + yopT − yopE kan yopH cam Y. pseudotuberculosis + yopT − yopH cam yopE + 32 Y. pseudotuberculosis Growth conditions of YPIII(P − 600 2 600 − COS1 cells incubated with bacteria were processed for immunofluorescence staining using anti- Y. pseudotuberculosis 10 To detect localization of Rac1, Cdc42, or Arf6-HA, cells were stained using mouse monoclonal antibodies directed against Rac1, Cdc42 (BD Transduction Laboratories, San Diego, California, United States), or the HA tag (Santa Cruz Biotechnology, Santa Cruz, California, United States) followed by probing with goat anti-mouse IgG-Alexa Fluor 488 (Molecular Probes). To analyze partially engulfed organisms, bacteria were identified in which only a portion of the rod showed staining with anti- Y. pseudotuberculosis 14 FRET image analysis to determine levels of Rac1 activation. To determine levels of Rac1 activation within COS1 cells, monolayers grown on 12-mm untreated round glass coverslips (Fisher Scientific, Pittsburgh, Pennsylvania, United States) were washed three times in PBS, fixed in PBS containing 3% paraformaldehyde, and then immunostained, if appropriate. The coverslips were then mounted on glass slides in the presence of antifade reagent (BioRad, Hercules, California, United States). Individual cells were analyzed using a Plan Apo 100×/1.4 objective fitted on a Nikon Eclipse TE300 inverted microscope (Nikon, Tokyo, Japan) with a 100-W Hg light source, using neutral density filter-4 (25% transmittance). Images were captured using a Hamamatsu Orca II camera (Hamamatsu Photonics, Hamamatsu City, Japan), with scripts controlled by IPLab v 3.5 software (Scanalytics, Rockville, Maryland, United States) capturing, in order, the YFP, CFP, and FRET channels at a bin setting of 2 × 2 with 200 msec exposure time. Filter sets (Chroma, Rockingham, Vermont, United States) consisted of: YFP excitation/emission set with HQ500/20× (exciter), Q515LP (beamsplitter), and HQ535/30m (emitter) filters; CFP excitation/emission set, with D436/10×, 455DCLP, and D480/40m filters; and a FRET set, with D436/10×, 455DCLP, and HQ535/30m filters. Photobleaching of YFP was performed using the D535/50 excitation filter and a Q515LP beamsplitter (Chroma). The ROI chosen to determine FRET was dependent on whether or not transfectants were incubated with bacteria. For all experiments in which transfectants were incubated in the absence of bacteria, two random fields (each about 10% of the area of a whole cell) located within cytoplasmic regions were chosen. Nucleus-localized protein was avoided, unless stated otherwise. To determine the amount of FRET surrounding nascent phagosomes, the ROI chosen was around partially internalized bacteria [ 14 To quantitate sensitized FRET, correction coefficients were derived to account for bleedthrough of CFP emission and cross-excitation of YFP during FRET measurements. The background level of fluorescence on the coverslip was determined, and then cells that were singly transfected with either mCFP-Rac1 or mYFP-PBD were analyzed. The correction coefficient for a particular fluor was determined by capturing images from the singly transfected cells. The mean intensities (I) from two randomly-chosen cytoplasmic regions of interests from single cells were determined, and the fraction of emission observed with the FRET filter relative to the appropriate excitation/emission filter set (I FRET filter fluor filter FRET filter CFP filter FRET filter YFP filter sensitized FRET FRET CFP YFP 33 sensitized FRET CFP YFP 1/2 33 Photobleaching was determined after grabbing the images required for FRET determinations. The sample was the exposed for 3 min to a 100-W Hg lamp using a 535 nm excitation filter but no neutral density filter. An image was then grabbed using the CFP filter set. Images obtained before and after photobleaching were background subtracted, and the CFP fluorescence in two ROIs from each image were obtained to calculate the percentage increase in CFP emission. Detergent fractionation of COS1 cells infected with Y. pseudotuberculosis Freshly diluted Y. pseudotuberculosis 6 2 2 4 We would like to thank Drs. Molly Bergman, Vicki Auerbuch, and Marion Dorer for review of the text; Drs. Jim Bliska, Jonathan Chernoff, Ulla Knaus, and Kit Wong for supplying plasmids; Drs. Jim Bliska and Emilio Garcia for supplying Yersinia",
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} |
10.1186/ar1776 | [] | http://creativecommons.org/licenses/by/2.0 | {
"title": "Differential expression of chemokine receptors on peripheral blood B cells from patients with rheumatoid arthritis and systemic lupus erythematosus",
"authors": "Henneken, Maren, 1, [email protected], Dörner, Thomas, 2, [email protected], Burmester, Gerd-Rüdiger, 2, [email protected], Berek, Claudia, 1, [email protected]",
"abstract": "Chemokines and their receptors are essential in the recruitment and positioning of lymphocytes. To address the question of B cell migration into the inflamed synovial tissue of patients with rheumatoid arthritis (RA), peripheral blood naive B cells, memory B cells and plasma cells were analyzed for cell surface expression of the chemokine receptors CXCR3, CXCR4, CXCR5, CCR5, CCR6, CCR7 and CCR9. For comparison, B cells in the peripheral blood of patients with the autoimmune disease systemic lupus erythematosus (SLE) or with the degenerative disease osteoarthritis (OA) were analyzed. Expression levels of chemokine receptors were measured by flow cytometry and were compared between the different patient groups and healthy individuals. The analysis of chemokine receptor expression showed that the majority of peripheral blood B cells is positive for CXCR3, CXCR4, CXCR5, CCR6 and CCR7. Whereas a small fraction of B cells were positive for CCR5, practically no expression of CCR9 was found. In comparison with healthy individuals, in patients with RA a significant fraction of B cells showed a decreased expression of CXCR5 and CCR6 and increased levels of CXCR3. The downregulation of CXCR5 correlated with an upregulation of CXCR3. In patients with SLE, significant changes in CXCR5 expression were seen. The functionality of the chemokine receptors CXCR3 and CXCR4 was demonstrated by transmigration assays with the chemokines CXCL10 and CXCL12, respectively. Our results suggest that chronic inflammation leads to modulation of chemokine receptor expression on peripheral blood B cells. However, differences between patients with RA and patients with SLE point toward a disease-specific regulation of receptor expression. These differences may influence the migrational behavior of B cells.",
"body_text": "Introduction Rheumatoid arthritis (RA) is a complex autoimmune disease of unknown etiology. It is characterized by chronic inflammation of the synovial membrane and the formation of a pannus, which leads to swollen joints and finally to joint destruction. Inflammatory cells such as monocytes and neutrophils, together with T and B cells, infiltrate the synovial membrane [ 1 2 3 About 50 chemokines have been identified in humans and are divided into four groups according to their cysteine motifs [ 4 5 6 Under pathological conditions, such as RA, chemokines direct lymphocytes into the chronically inflamed synovial tissue [ 7 8 2 9 13 Contradictory results have been reported for chemokine receptor expression on peripheral blood T cells of patients with RA [ 13 14 15 6 11 17 18 19 CXCR3 is a chemokine receptor for the inflammatory chemokines CXCL9, CXCL10 and CXCL11. It has been described as a marker for malignant B cells and is absent from the majority of normal peripheral blood B cells [ 20 21 20 To address the question of B cell migration, we analyzed chemokine receptor expression on peripheral blood B cells. Expression profiles of patients with RA were compared with those from patients with systemic lupus erythematosus (SLE), who – in contrast to patients with RA – usually show no or very little B cell accumulation at the site of chronic inflammation [ 22 Methods Patients and controls Heparinized whole blood (9 ml) from patients with RA, patients with SLE and patients with OA was obtained from the Departments of Rheumatology and Orthopedics (Charité, Humboldt University, Berlin, Germany). Patients with RA were diagnosed in accordance with the American College of Rheumatology criteria [ 23 1 Cell isolation and flow cytometry Peripheral blood mononuclear cells (PBMC) were isolated by gradient centrifugation with Ficoll (Amersham Biosciences) and then stained (30 min at 4°C) with a biotin-coupled B cell-specific mAb against CD19 (clone SJ25-C1; Southern Biotechnology Associates), with the Cy5-labeled mAb against CD27 (clone 2E4; gift from RA van Lier, Academic Medical Center, Amsterdam) and with fluorescein isothiocyanate (FITC)-labeled mAb specific for one of the chemokine receptors CXCR3 (clone 49801.111; R&D Systems), CXCR5 (clone 51505.111; R&D Systems), CCR5 (clone 45523.111; R&D Systems), CCR6 (clone 53103.111; R&D Systems), CCR7 (clone 3D12; a gift from M Lipp, Max Delbrück Center, Berlin) or CCR9 (clone 112509.111; R&D Systems). Antibody against CXCR4 was labeled with phycoerythrin (PE; clone 12G5; BD Pharmingen). Before incubation with streptavidin-PE or streptavidin-FITC (for CXCR4) (0.5 μg/ml; Pharmingen), cells were washed twice in phosphate-buffered saline/2% BSA/4 mM EDTA. To determine the frequency of CD5 + + Propidium iodide (1 μg/ml; Sigma) was added immediately before cytometric analysis for the exclusion of dead cells. Flow cytometric analyses were performed by fluorescence-activated cell sorting (FACS) software (FACSCalibur and CellQuest; Becton Dickinson). Measurement of CXCL10 concentrations For further analysis, sera of controls and those of patients analyzed for chemokine receptor expression were stored at -20°C. The concentration of CXCL10 was determined by using a sensitive ELISA test kit (HyCult Biotechnology). Samples were tested in duplicate and values were compared with a standard curve. Transmigration assay Cell migration was examined in Transwell™ inserts (Corning Costar) with a diameter of 6.5 mm and 5 μm pores, by using fibronectin-precoated membranes as described previously [ 24 5 2 Statistical analyses Statistical analyses were performed with GraphPad Prism software (Prism 3.0 software for windows; GraphPad). Frequencies of B cells were calculated with CellQuest software (Becton Dickinson) and variations in chemokine receptor expression on B cells within the analyzed group were compared in a hierarchic statistic analysis, using Kruskal–Wallis and the nonparametric Mann–Whitney U P Results Chemokine receptor expression on peripheral blood B cells of healthy controls To analyze chemokine receptor expression on B cells of normal healthy volunteers PBMC were double-stained with antibodies specific for the B cell marker CD19 and for the chemokine receptors CXCR3, CXCR4, CXCR5, CCR5, CCR6, CCR7 or CCR9. Data from a representative experiment are depicted in Fig. 1 Analyses of chemokine receptor expression on peripheral blood B cell subsets of patients with RA, with SLE and with OA To assess changes in the pattern of B cell chemokine receptor expression associated with RA ( n n n n - + hi 25 2a 2b In healthy individuals most B cells (median value 93.8%, range 66.9 to 99.3%) were positive for CXCR5 (CXCR5 + 3 3 + P 7 In contrast to the patients with OA, a decrease in the fraction of CXCR5 + + P P 3 + 3 3 The analysis of the different B cell subsets revealed that the fraction of CXCR5 + + 3 + 3 Similar results were obtained when B cells were tested for the chemokine receptor CXCR4. In both healthy controls and patients with OA, most B cells expressed high levels of this chemokine receptor, and little individual variation was seen (Fig. 4 + n + n + 4 When B cells from patients with RA and patients with SLE were tested for the expression of CCR6, again a reduction in the frequency of CCR6 + + P 5 A great variation in chemokine receptor expression was obtained when B cells were tested for CXCR3, which is a receptor for chemokines that is upregulated in inflammation. We found that in healthy individuals most B cells are positive for CXCR3; however, the mean fluorescence intensity was rather low and only a few B cells expressed CXCR3, at a level comparable to that seen after staining with mAb specific for CXCR5 (Figs 1 7 hi 6 hi 6 The results obtained for CXCR3 suggest that its expression is upregulated as B cells differentiate into memory B cells and plasma cells. In most healthy controls the fraction of CXCR3 hi 6 7 P P 6 hi Furthermore, we addressed the question of whether there is a significant correlation between the expression of CXCR5 with that of CXCR4, CCR6 and CXCR3. In patients with RA a decreased fraction of CXCR5-expressing B cells correlated with the expression of CCR6 ( r P r P 8 Chemokine receptor expression on CD5+ B cells Staining of PBMC of healthy controls showed that on average 20% of B cells were positive for CD5 (data not shown). Comparable frequencies of CD5 expression were found for patients with RA (range 12 to 23% of B cells). To assess chemokine receptor expression on CD5 + + + + hi + - + The level of CXCL10 may influence CXCR3 expression PBMC were isolated by Ficoll gradient centrifugation. In the supernatant the concentration of CXCL10 was measured with a standard ELISA test. In both sera from the different patient groups and from healthy controls only low levels of CXCL10 were detectable (about 200 pg/ml; Fig. 9 Influence of medication on chemokine receptor expression To determine a potential influence of medication, five blood samples of newly diagnosed patients with RA were analyzed before treatment. In three of the samples, B cells showed a pattern of chemokine receptor expression as described above, in that the median value for the frequency of B cells with high levels of CXCR5 was decreased from 93.8% (range 66.9 to 99.3%) to 79.4% (range 2.6 to 96.8%) (Fig. 10 n n + 10 The analysis of CXCR3 expression on B cells revealed that in comparison with healthy individuals, untreated patients with RA had an increase in the frequency of CXCR3 hi hi The influence of chemokine receptor expression on B cell migration To test whether low expression of CXCR3 on B cells is sufficient to respond to the inflammatory chemokine CXCL10, PBMC from patients with RA were tested with the use of a transmigration assay (Fig. 11 hi lo 11 + - 11 in vitro Discussion The analysis of peripheral blood B cells from patients with RA and patients with SLE showed significant differences in their chemokine receptor expression when compared with B cells from healthy individuals and also from patients with OA. In patients with RA and patients with SLE a fraction of B cells showed decreased expression of CXCR5, CXCR4 and CCR6, chemokine receptors that have been associated with B cell homing into follicles [ 26 27 4 10 CXCR5 was previously shown to be expressed on most mature circulating B cells [ 8 28 3 in vitro 29 + 30 Lower levels of chemokine receptor CXCR5 and higher levels of CXCR3 on peripheral blood B cells may represent a generalized change in the profile and might be seen on all of the activated B cells in the systemic compartment or these changes in chemokine receptor expression might serve in selective recruitment into the inflamed tissue. In line with this interpretation we observed CXCR3 expression on synovial tissue B cells. However, comprehensive studies are under way to further delineate the expression of chemokine receptors and their function in migration into the effected tissue. CXCR3 was described as a marker for malignant B cells, and its expression on normal peripheral blood B cells has been controversial [ 20 21 hi in vitro 31 32 hi A significant increase in the fraction of CXCR3 hi 6 33 9 hi Using a transmigration assay we were able to show that low levels of CXCR3 expression are sufficient to permit a response to the migrational stimulus of the chemokine CXCL10. However, these chemotaxis results in vitro in vivo 10 + Whereas B cells from healthy controls and patients with OA showed little inter-individual variation in the expression of chemokine receptors, individual patients with RA and patients with SLE gave a rather heterogeneous picture (Fig. 7 Little is known about the mechanisms controlling chemokine receptor expression and what might cause the variability in their expression level on peripheral blood B cells. One possibility might be that the modulation of chemokine receptor expression is associated with rheumatoid factor (RF) antibody titers. The majority of patients with RA analyzed were positive for RF. A correlation of chemokine receptor expression and the level of RF was therefore not seen. An attempt to correlate the level of chemokine receptor expression with age or sex of the patients, with disease duration or with disease activity failed. There was no clear-cut correlation to be seen. Furthermore, from our data it seems unlikely that the variability in chemokine receptor expression results from the different treatment regimes of individual patients with RA (Fig. 10 RA and SLE are chronic inflammatory diseases, and both are characterized by a continuous activation of B cells. Whereas SLE is a more systemic inflammatory disease, in most patients with RA the inflammation is localized primarily to the synovial membrane. To what extent the described differences in chemokine receptor expression between B cells from patients with RA and patients with SLE might influence the migrational pattern of B cells needs to be delineated by continuing studies, potentially permitting new therapeutic avenues. Conclusion Here we show that chronic inflammation influences chemokine receptor expression on peripheral blood B cells. Receptors for homeostatic chemokines, like CXCL13 and CXCL12 showed reduced levels of expression whereas CXCR3 a receptor for inflammatory chemokines becomes unregulated. Differences between RA and SLE patients suggest a disease specific regulation of chemokine receptor expression, which may influence the migrational behavior of B cells. Abbreviations BSA = bovine serum albumin; ELISA = enzyme-linked immunosorbent assay; FITC = fluorescein isothiocyanate; FACS = fluorescence-activated cell sorting, mAb = monoclonal antibody; OA = osteoarthritis; PBMC = peripheral blood mononuclear cells; PE = phycoerythrin; RA = rheumatoid arthritis; RF = rheumatoid factor; SLE = systemic lupus erythematosus; TNF = tumor necrosis factor. Competing interests The author(s) declare that they have no competing interests. Authors' contributions MH made acquisition of data and their interpretation, performed the statistical analysis and drafted the article. TD was responsible for assessment of patients and revising the article critically. G-RB was involved in the analysis and careful discussion of the data. CB coordinated the study, was involved in the critical discussion of results and their interpretation and helped to draft the article. All authors read and approved the final manuscript. Acknowledgements The work was supported by the SFB 421 and by the Network of Competence, Rheumatology (BMBF grant C2.2 to CB). The DRFZ is supported by the Berlin Senate of Research and Education.",
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P, Moser, B, Homing chemokines in rheumatoid arthritis, Arthritis Res, 2002, 4, 233, 236, 12106492, 10.1186/ar412\nKatschke, KJ, Jr, Rottman, JB, Ruth, JH, Qin, S, Wu, L, LaRosa, G, Ponath, P, Park, CC, Pope, RM, Koch, AE, Differential expression of chemokine receptors on peripheral blood, synovial fluid, and synovial tissue monocytes/macrophages in rheumatoid arthritis, Arthritis Rheum, 2001, 44, 1022, 1032, 11352233, 10.1002/1529-0131(200105)44:5<1022::AID-ANR181>3.0.CO;2-N\nPatel, DD, Zachariah, JP, Whichard, LP, CXCR3 and CCR5 ligands in rheumatoid arthritis synovium, Clin Immunol, 2001, 98, 39, 45, 11141325, 10.1006/clim.2000.4957\nShi, K, Hayashida, K, Kaneko, M, Hashimoto, J, Tomita, T, Lipsky, PE, Yoshikawa, H, Ochi, T, Lymphoid chemokine B cell-attracting chemokine-1 (CXCL13) is expressed in germinal center of ectopic lymphoid follicles within the synovium of chronic arthritis patients, J Immunol, 2001, 166, 650, 655, 11123349\nNanki, T, Hayashida, K, El-Gabalawy, HS, Suson, 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} |
10.1186/1743-8977-2-8 | [] | http://creativecommons.org/licenses/by/2.0 | {"title":"Principles for characterizing the potential human health effects from exposure to nanomate(...TRUNCATED) |
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Scientific Openly-Licensed Publications
This repository contains companion material for the following publication:
Tim Tarsi, Heike Adel, Jan Hendrik Metzen, Dan Zhang, Matteo Finco, Annemarie Friedrich. SciOL and MuLMS-Img: Introducing A Large-Scale Multimodal Scientific Dataset and Models for Image-Text Tasks in the Scientific Domain. WACV 2024.
Please cite this paper if using the dataset, and direct any questions regarding the dataset to Tim Tarsi
Summary
Scientific Openly-Licensed Publications (SciOL) is the largest openly-licensed pre-training corpus for multimodal models in the scientific domain, covering multiple sciences including materials science, physics, and computer science. It consists of over 2.7M scientific scientific publications converted into semi-structured data. SciOL contains over 14 Billion tokens of extracted and structured text.
Note: This repository only contains the textual data of SciOL. For the figures and captions see:
SciOL-CI
Data Format
We provide the annotations of our dataset in the JSON format. Files are grouped and compressed as zip files. We provide a basic index to find annotations by DOI, PMID or DOAJ id and keywords.
Annotation Schema
Annotations are structured as in the following schema:
{
"$schema": "http://json-schema.org/draft-07/schema#",
"type": "object",
"properties": {
"doi": {
"type": "string"
},
"keywords": {
"type": "array",
"items": {
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}
},
"license": {
"type": "string"
},
"article": {
"type": "object",
"properties": {
"title": {
"type": "string"
},
"authors": {
"type": "array",
"items": {
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}
},
"abstract": {
"type": "string"
},
"body_text": {
"type": "string"
},
"bibliography": {
"type": "string"
}
}
}
}
}
Citation
If you use our dataset in your scientific, please cite our paper:
@InProceedings{Tarsi_2024_WACV,
author = {Tarsi, Tim and Adel, Heike and Metzen, Jan Hendrik and Zhang, Dan and Finco, Matteo and Friedrich, Annemarie},
title = {SciOL and MuLMS-Img: Introducing a Large-Scale Multimodal Scientific Dataset and Models for Image-Text Tasks in the Scientific Domain},
booktitle = {Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV)},
month = {January},
year = {2024},
pages = {4560-4571}
}
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