MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature

<p>Abstract</p> <p>Background</p> <p>DNA methylation is regarded as a potential biomarker in the diagnosis and treatment of cancer. The relations between aberrant gene methylation and cancer development have been identified by a number of recent scientific studies. In a previous work, we used co-occurrences to mine those associations and compiled the MeInfoText 1.0 database. To reduce the amount of manual curation and improve the accuracy of relation extraction, we have now developed MeInfoText 2.0, which uses a machine learning-based approach to extract gene methylation-cancer relations.</p> <p>Description</p> <p>Two maximum entropy models are trained to predict if aberrant gene methylation is related to any type of cancer mentioned in the literature. After evaluation based on 10-fold cross-validation, the average precision/recall rates of the two models are 94.7/90.1 and 91.8/90% respectively. MeInfoText 2.0 provides the gene methylation profiles of different types of human cancer. The extracted relations with maximum probability, evidence sentences, and specific gene information are also retrievable. The database is available at <url>http://bws.iis.sinica.edu.tw:8081/MeInfoText2/</url>.</p> <p>Conclusion</p> <p>The previous version, MeInfoText, was developed by using association rules, whereas MeInfoText 2.0 is based on a new framework that combines machine learning, dictionary lookup and pattern matching for epigenetics information extraction. The results of experiments show that MeInfoText 2.0 outperforms existing tools in many respects. To the best of our knowledge, this is the first study that uses a hybrid approach to extract gene methylation-cancer relations. It is also the first attempt to develop a gene methylation and cancer relation corpus.</p

Dimethyl 1-(4-cyano­benz­yl)-1H-pyrazole-3,5-dicarboxyl­ate

The title compound, C15H13N3O4, was synthesized from dimethyl 1H-pyrazole-3,5-dicarboxyl­ate and 4-(bromo­meth­yl)benzonitrile. The inter­planar angle between the pyrazole and cyano­benzyl ring planes is 71.74 (17)° and an intramolecular C—H⋯O interaction occurs. The crystal structure is stabilized by π–π stacking inter­actions between the neighbouring pyrazole and benzene rings [centroid–centroid distances of 3.5074 (16) and 3.9401 (15) Å, respectively]. One of the methyl groups is disordered over two positions of equal occupancy

Protection of SH-SY5Y Neuronal Cells from Glutamate-Induced Apoptosis by 3,6′-Disinapoyl Sucrose, a Bioactive Compound Isolated from Radix Polygala

The neuroprotective effects of 3,6′-disinapoyl sucrose (DISS) from Radix Polygala against glutamate-induced SH-SY5Y neuronal cells injury were evaluated in the present study. SH-SY5Y neuronal cells were pretreated with glutamate (8 mM) for 30 min followed by cotreatment with DISS for 12 h. Cell viability was determined by (3,4,5-dimethylthiazol-2-yl)-2,5-diphenylte-trazolium bromide (MTT) assay, and apoptosis was confirmed by cell morphology and flow cytometry assay, evaluated with propidium iodide dye. Treatment with DISS (0.6, 6, and 60 μmol/L) increased cell viability dose dependently, inhibited LDH release, and attenuated apoptosis. The mechanisms by which DISS protected neuron cells from glutamate-induced excitotoxicity included the downregulation of proapoptotic gene Bax and the upregulation of antiapoptotic gene Bcl-2. The present findings indicated that DISS exerts neuroprotective effects against glutamate toxicity, which might be of importance and contribute to its clinical efficacy for the treatment of neurodegenerative diseases

A new species of Fordiophyton (Sonerileae, Melastomataceae) from Yunnan, China

Fordiophyton jinpingense (Melastomataceae; Sonerileae), a species occurring in south-eastern Yunnan, China, is described as new, based on morphological and molecular data. Phylogenetic analyses, based on nrITS sequence data, showed that, except F. breviscapum, all species sampled in Fordiophyton formed a strongly supported clade in which two geographical lineages were recovered. The generic placement of F. jinpingense is well supported by phylogenetic analyses and a character combination of 4-merous flowers, distinctly dimorphic stamens and the connectives basally not calcarate. Molecular divergence and morphological evidence indicate that F. jinpingense is well separated from other members of the genus, thus justifying its recognition as a distinct species. Fordiophyton jinpingense is phylogenetically closest to F. repens, but differs markedly from the latter in stem morphology (short, obtusely 4-sided vs. long, 4-angular), habit (erect vs. creeping), leaf size (6–16.5 × 4.5–13 cm vs. 4–7.5 × 4–6.5 cm) and flower number per inflorescence (5–13 vs. 3–6)

The impact of gum-chewing on postoperative ileus following gynecological cancer surgery: A systematic review and meta-analysis of randomized controlled trials

ObjectiveTo assess the effect and safety of gum-chewing on the prevention of postoperative ileus after gynecological cancer surgery.MethodsWe conducted a systematic review of randomized controlled trials (RCTs) published between 2000 and 2022 in English and Chinese, using the EBSCO, Web of Science, Scopus, Cochrane Central Register of Controlled Trials (Cochrane database), PubMed, Medline (via Ovid), Chinese National Knowledge Infrastructure (CNKI), China Science and Technology Journal Database, and Wan Fang databases. A total of 837 studies were screened using Endnote software, and those that met the inclusion criteria were selected for analysis. The main outcome of interest was the incidence of postoperative ileus, and secondary outcomes included time to first flatus, time to first bowel movement, and length of hospital stay.ResultsTwo authors extracted data and performed quality assessment independently. The review included six RCTs with a total of 669 patients. Compared with routine care, gum-chewing could significantly reduce the incidence of postoperative ileus (RR 0.46, 95% CI: 0.30, 0.72, P=0.0006), shorten the time to first flatus (WMD -9.58, 95% CI: -15.04, -4.12, P=0.0006), first bowel movement (WMD -11.31, 95% CI: -21.05, -1.56, P=0.02), and the length of hospital stay (WMD -1.53, 95% CI: -2.08, -0.98, P&lt;0.00001).ConclusionsGum-chewing is associated with early recovery of gastrointestinal function after gynecological cancer surgery and may be an effective and harmless intervention to prevent postoperative ileus.Systemaic review registrationhttps://www.crd.york.ac.uk/prospero/#searchadvanced, identifier CRD42022384346