tags:
- ANDDigest
- ANDSystem
extra_gated_fields:
I agree to share my contact information: checkbox
widget:
- text: >-
Deficient Mismatch Repair and Lymphocytic Response to Tumor as Prognostic
Markers in Stage II Colon Cancer Patients. OBJECTIVE: To investigate the
relationship between colon cancer subtypes defined by the status of
tumor-infiltrating lymphocytes and mismatch repair (MMR) combination with
clinicopathological features and survival. STUDY DESIGN: Observational
study. PLACE AND DURATION OF STUDY: Department of Medical Oncology,
HaydarpaAŸa Numune Research and Training Hospital, Istanbul, Turkey, from
July 2010 to March 2020. METHODOLOGY: Eighty-three patients with operated
stage II colon cancer were included in the study. Pathology, surgery and
oncological treatment and follow-up information were obtained from patient
files; And statistical analyses were performed on overall survival .
Tumor-infiltrating lymphocytes and mismatch repair status was determined
with the help of immunohistochemistry. RESULTS: TIL-high and deficient
<andsystem-candidate> status were detected in 26 patients (31.3%) and 21
patients (25.3%), respectively. Tumors were divided into four subgroups
according to tumor-infiltrating lymphocytes and MMR status.
TIL-high/deficient mmr tumors had the most favourable prognosis, while
TIL-low/proficient MMR tumors exhibited poor overall survival. CONCLUSION:
The combination of tumor-infiltrating lymphocytes and MMR could enable us
to differentiate patients' survival outcomes in more details. Therefore,
considering that the tumor-infiltrating lymphocytes and MMR status,
evaluated by IHC, may be a cost-effective and effective option for risk
classification in patients with stage II colon cancer. Key Word:
Lymphocytic response, Mismatch repair, Prognosis, Tumor-infiltrating
lymphocytes, Stage II cancer, Colon cancer.
example_title: MMR
- text: >-
Rapid alkalinization factor peptide signaling controls the polytubey block
in Arabidopsis. Fertilization of an egg by multiple sperm (polyspermy)
leads to lethal genome imbalance and chromosome segregation defects. In
Arabidopsis thaliana, the block to polyspermy is facilitated by a
mechanism that prevents polytubey (the arrival of multiple pollen tubes to
one ovule). We show here that FERONIA, ANJEA, and HERCULES RECEPTOR KINASE
1 receptor-like kinases located at the septum interact with pollen
tube-specific RALF6, 7, 16, 36, and 37 peptide ligands to establish this
polytubey block. The same combination of rapid alkalinization factor
peptides and receptor complexes controls pollen tube reception and rupture
inside the targeted ovule. Pollen tube rupture releases the polytubey
block at the septum, which allows the emergence of secondary pollen tubes
upon <andsystem-candidate> failure. Thus, orchestrated steps in the
fertilization process in Arabidopsis are coordinated by the same signaling
components to guarantee and optimize reproductive success.
example_title: fertilization
This model is a fine-tuned model of BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext (hugging-face card). The current model was developed for the web-based ANDDigest system for the classification of the names of biological pathways in texts on the basis of their context. The analyzed name should be replaced in text with tag.
Input:
Any biomedical text where a name of classified object is replaced with tag, for example, this pubmed abstract:
Deficient Mismatch Repair and Lymphocytic Response to Tumor as Prognostic Markers in Stage II Colon Cancer Patients. OBJECTIVE: To investigate the relationship between colon cancer subtypes defined by the status of tumor-infiltrating lymphocytes and mismatch repair (MMR) combination with clinicopathological features and survival. STUDY DESIGN: Observational study. PLACE AND DURATION OF STUDY: Department of Medical Oncology, HaydarpaAŸa Numune Research and Training Hospital, Istanbul, Turkey, from July 2010 to March 2020. METHODOLOGY: Eighty-three patients with operated stage II colon cancer were included in the study. Pathology, surgery and oncological treatment and follow-up information were obtained from patient files; And statistical analyses were performed on overall survival . Tumor-infiltrating lymphocytes and mismatch repair status was determined with the help of immunohistochemistry. RESULTS: TIL-high and deficient <andsystem-candidate> status were detected in 26 patients (31.3%) and 21 patients (25.3%), respectively. Tumors were divided into four subgroups according to tumor-infiltrating lymphocytes and MMR status. TIL-high/deficient mmr tumors had the most favourable prognosis, while TIL-low/proficient MMR tumors exhibited poor overall survival. CONCLUSION: The combination of tumor-infiltrating lymphocytes and MMR could enable us to differentiate patients' survival outcomes in more details. Therefore, considering that the tumor-infiltrating lymphocytes and MMR status, evaluated by IHC, may be a cost-effective and effective option for risk classification in patients with stage II colon cancer. Key Word: Lymphocytic response, Mismatch repair, Prognosis, Tumor-infiltrating lymphocytes, Stage II cancer, Colon cancer.
In this example MMR abbreviation, which refers to the mismatch repair, was replaced with <andsystem-candidate>. Please keep in mind that maximum length of input sequence for BERT is limited to 512 tokens.
Output:
LABEL_0 refers to the probability of the FALSE recognition, i.e. if the context of <andsystem-candidate> doesn't corresponds to the context specific for biological pathways.
LABEL_1 refers to the probability of the TRUE recognition, i.e. when the context of <andsystem-candidate> corresponds to the context specific for biological pathways.
The optimal threshold value for the short names of biological pathways for the LABEL_1, was calculated using a gold standard (add link). It is >= 0.999702513217926.
The Mathew Correlation Coefficient of the model for the long names (>= 15 symbols) is 0.987.
The ROC AUC value of the model, calculated for the short names (<= 4 symbols) is 0.877.
Citing
If you found the developed models to be useful in your research, please cite the following articles:
Ivanisenko, T.V., Saik, O.V., Demenkov, P.S. et al. ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature. BMC Bioinformatics 21 (Suppl 11), 228 (2020). https://doi.org/10.1186/s12859-020-03557-8
Ivanisenko, T.V.; Demenkov, P.S.; Kolchanov, N.A.; Ivanisenko, V.A. The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition. Int. J. Mol. Sci. 2022, 23, 14934. https://doi.org/10.3390/ijms232314934