Miracle-dz/UniFAR-FTUs huggingface dataset:
Studying the expression rate and methylation of Reprimo gene in the blood of patients suffering from gastric cancer

As gastric cancer has no exclusive signals in its initial phases, it is usually diagnosed in advanced phases. Although many researches have been conducted on methylation and diagnosis of cancer’s markers, the methylation and expression of Reprimo gene and its correlation with gastric cancer has not been thoroughly studied. Methylation of Reprimo promoter is a repetitive procedure exclusive to cancer which nullifies its expression and performance. The present research seeks to study the expression and methylation of Reprimo among people suffering with gastric cancer so that it may be used as a biomarker for early diagnosis. Fifty blood samples taken from healthy people (normal samples) and 50 blood samples obtained from gastric cancer patients were analyzed using Real-Time PCR. The methylation status of the promoter of Reprimo was studied using Methylation Specific PCR technique in normal samples and in gastric cancer Iranian patients. We observed reduction in expression rate of Reprimo in the blood samples of patients suffering with gastric cancer in comparison to normal blood samples. A significant correlation was also observed between the expression rate of this gene, age and methylation of its promoter among patients suffering with gastric cancer and various analysis points to a correlation between reduced expressions of Reprimo gene in gastric cancer patients. In conclusion, reduced expression of Reprimo gene and greater levels of methylation of its promoter seems to be promising biomarkers for early diagnosis of gastric cancer.
EPINETLAB: A Software for Seizure-Onset Zone Identification From Intracranial EEG Signal in Epilepsy

The pre-operative workup of patients with drug-resistant epilepsy requires in some candidates the identification from intracranial EEG (iEEG) of the seizure-onset zone (SOZ), defined as the area responsible of the generation of the seizure and therefore candidate for resection. High-frequency oscillations (HFOs) contained in the iEEG signal have been proposed as biomarker of the SOZ. Their visual identification is a very onerous process and an automated detection tool could be an extremely valuable aid for clinicians, reducing operator-dependent bias, and computational time. In this manuscript, we present the EPINETLAB software, developed as a collection of routines integrated in the EEGLAB framework that aim to provide clinicians with a structured analysis pipeline for HFOs detection and SOZ identification. The tool implements an analysis strategy developed by our group and underwent a preliminary clinical validation that identifies the HFOs area by extracting the statistical properties of HFOs signal and that provides useful information for a topographic characterization of the relationship between clinically defined SOZ and HFO area. Additional functionalities such as inspection of spectral properties of ictal iEEG data and import and analysis of source-space magnetoencephalographic (MEG) data were also included. EPINETLAB was developed with user-friendliness in mind to support clinicians in the identification and quantitative assessment of HFOs in iEEG and source space MEG data and aid the evaluation of the SOZ for pre-surgical assessment.
Novichok agents: a historical, current, and toxicological perspective

Abstract The Novichok, or “newcomer” class of nerve agents are lesser characterized, weaponized organophosphate agents. The use of known Novichok agents in warfare is banned under the Chemical Weapons Convention of 1997. Novichok agents are considered more potent than VX gas and can be applied in unitary and binary forms. Like other nerve agents, Novichok agents irreversibly bind acetylcholinesterase and produce a cholinergic toxidrome. Uniquely, these agents are thought to also target neurons in the peripheral nervous system. Delayed treatment or massive exposure may therefore cause a debilitating neuropathy. The recent 2018 assassination attempt of Russian dissident Sergei Skripal and his daughter Yulia in the United Kingdom highlights the importance of recognizing the potential lethal effects of these nerve agents. Treatment of Novichok agent poisoning is similar to management of other nerve agents. Given increasing worldwide incidents attributed to chemical weapons such as Novichok agents, clinicians should know how to rapidly recognize symptoms of acute poisoning and administer life-saving antidotal therapy, when indicated.
CIST@CLSciSumm-18: Methods for Computational Linguistics Scientific Citation Linkage, Facet Classification and Summarization

Our system makes contributions to the shared Task 1A (citation linkage), Task 1B (facet classification) and Task 2 (summarization) in CLSciSumm-18@SIGIR2018. We develop it based on our former one called CIST@CLSciSumm-17 [7]. We try to improve the methods for all the shared tasks. We adopt Word Mover’s Distance (WMD) and improve LDA model to calculate sentence similarity for citation linkage. We try more methods for facet classification. And in order to improve the performance of summarization, we also add WMD sentence similarity to construct new kernel matrix used in Determinantal Point Processes (DPPs).
Role of Oxidative Stress in Pathophysiology of Nonalcoholic Fatty Liver Disease

Liver steatosis without alcohol consumption, namely, nonalcoholic fatty liver disease (NAFLD), is a common hepatic condition that encompasses a wide spectrum of presentations, ranging from simple accumulation of triglycerides in the hepatocytes without any liver damage to inflammation, necrosis, ballooning, and fibrosis (namely, nonalcoholic steatohepatitis) up to severe liver disease and eventually cirrhosis and/or hepatocellular carcinoma. The pathophysiology of fatty liver and its progression is influenced by multiple factors (environmental and genetics), in a “multiple parallel-hit model,” in which oxidative stress plays a very likely primary role as the starting point of the hepatic and extrahepatic damage. The aim of this review is to give a comprehensive insight on the present researches and findings on the role of oxidative stress mechanisms in the pathogenesis and pathophysiology of NAFLD. With this aim, we evaluated the available data in basic science and clinical studies in this field, reviewing the most recent works published on this topic.
Surface functionalization of polyurethane scaffolds mimicking the myocardial microenvironment to support cardiac primitive cells

Scaffolds populated with human cardiac progenitor cells (CPCs) represent a therapeutic opportunity for heart regeneration after myocardial infarction. In this work, square-grid scaffolds are prepared by melt-extrusion additive manufacturing from a polyurethane (PU), further subjected to plasma treatment for acrylic acid surface grafting/polymerization and finally grafted with laminin-1 (PU-LN1) or gelatin (PU-G) by carbodiimide chemistry. LN1 is a cardiac niche extracellular matrix component and plays a key role in heart formation during embryogenesis, while G is a low-cost cell-adhesion protein, here used as a control functionalizing molecule. X-ray photoelectron spectroscopy analysis shows nitrogen percentage increase after functionalization. O1s and C1s core-level spectra and static contact angle measurements show changes associated with successful functionalization. ELISA assay confirms LN1 surface grafting. PU-G and PU-LN1 scaffolds both improve CPC adhesion, but LN1 functionalization is superior in promoting proliferation, protection from apoptosis and expression of differentiation markers for cardiomyocytes, endothelial and smooth muscle cells. PU-LN1 and PU scaffolds are biodegraded into non-cytotoxic residues. Scaffolds subcutaneously implanted in mice evoke weak inflammation and integrate with the host tissue, evidencing a significant blood vessel density around the scaffolds. PU-LN1 scaffolds show their superiority in driving CPC behavior, evidencing their promising role in myocardial regenerative medicine.
The Forward Effect of Testing: Behavioral Evidence for the Reset-of-Encoding Hypothesis Using Serial Position Analysis

The forward effect of testing refers to the finding that retrieval practice of previously studied information increases retention of subsequently studied other information. It has recently been hypothesized that the forward effect (partly) reflects the result of a reset-of-encoding (ROE) process. The proposal is that encoding efficacy decreases with an increase in study material, but testing of previously studied information resets the encoding process and makes the encoding of the subsequently studied information as effective as the encoding of the previously studied information. The goal of the present study was to verify the ROE hypothesis on an item level basis. An experiment is reported that examined the effects of testing in comparison to restudy on items’ serial position curves. Participants studied three lists of items in each condition. In the testing condition, participants were tested immediately on non-target lists 1 and 2, whereas in the restudy condition, they restudied lists 1 and 2. In both conditions, participants were tested immediately on target list 3. Influences of condition and items’ serial learning position on list 3 recall were analyzed. The results showed the forward effect of testing and furthermore that this effect varies with items’ serial list position. Early target list items at list primacy positions showed a larger enhancement effect than middle and late target list items at non-primacy positions. The results are consistent with the ROE hypothesis on an item level basis. The generalizability of the ROE hypothesis across different experimental tasks, like the list-method directed-forgetting task, is discussed.
Association Between Specific Internet Activities and Life Satisfaction: The Mediating Effects of Loneliness and Depression

The current study examined the associations between specific Internet activities (online shopping, pornography use, social networking site use, and Internet gaming), life satisfaction, and the mediating effects of loneliness and depression for these associations. Participants were 5,215 students (2,303 male participants, Mage = 16.20 years; ranging in age from 10 to 23 years) from various school types (546 elementary school students, 1710 junior high school students, 688 senior high school students, and 2271 university students) who provided self-report data on demographic variables, online shopping, pornography use, social networking site use, loneliness, depression, and life satisfaction. The results indicated that after controlling for demographic variables (gender and age) (a) loneliness and depression had fully positive mediating effects on the association between social networking site use and life satisfaction; (b) loneliness and depression played fully negative mediating effects on life satisfaction associations with online shopping, pornography use, and Internet gaming. Therefore, loneliness and depression were the underlying mechanisms that caused life satisfaction to be affected by online shopping, pornography use, social networking site use, and Internet gaming.
Semi-automatic Extraction of Plants Morphological Characters from Taxonomic Descriptions Written in Spanish

Abstract Taxonomic literature keeps records of the planet's biodiversity and gives access to the knowledge needed for its sustainable management. Unfortunately, most of the taxonomic information is available in scientific publications in text format. The amount of publications generated is very large; therefore, to process it in order to obtain high structured texts would be complex and very expensive. Approaches like citizen science may help the process by selecting whole fragments of texts dealing with morphological descriptions; but a deeper analysis, compatible with accepted ontologies, will require specialised tools. The Biodiversity Heritage Library (BHL) estimates that there are more than 120 million pages published in over 5.4 million books since 1469, plus about 800,000 monographs and 40,000 journal titles (12,500 of these are current titles). It is necessary to develop standards and software tools to extract, integrate and publish this information into existing free and open access repositories of biodiversity knowledge to support science, education and biodiversity conservation. This document presents an algorithm based on computational linguistics techniques to extract structured information from morphological descriptions of plants written in Spanish. The developed algorithm is based on the work of Dr. Hong Cui from the University of Arizona; it uses semantic analysis, ontologies and a repository of knowledge acquired from the same descriptions. The algorithm was applied to the books Trees of Costa Rica Volume III (TCRv3), Trees of Costa Rica Volume IV (TCRv4) and to a subset of descriptions of the Manual of Plants of Costa Rica (MPCR) with very competitive results (more than 92.5% of average performance). The system receives the morphological descriptions in tabular format and generates XML documents. The XML schema allows documenting structures, characters and relations between characters and structures. Each extracted object is associated with attributes like name, value, modifiers, restrictions, ontology term id, amongst other attributes. The implemented tool is free software. It was developed using Java and integrates existing technology as FreeLing, the Plant Ontology (PO), the Plant Glossary, the Ontology Term Organizer (OTO) and the Flora Mesoamericana English-Spanish Glossary.
Clinical Evaluation of Preventive Effect of Fissure Sealants on Initial Carious Lesion of Permanent Mandibular Molars Pretreated with and without Fluoride Varnish by Fluorescence Camera

The important armamentarium in the present day scenario against caries prevention is considered to be a combination of preventive methods. The present study was conducted to evaluate the preventive effect of pit and fissure sealant pretreated with fluoride varnish on initial carious lesion by fluorescence camera (FC). How to cite this article: Lakshmi MS, Srilatha KT, Nandlal B, Deshmukh S. Clinical Evaluation of Preventive Effect of Fissure Sealants on Initial Carious Lesion of Permanent Mandibular Molars Pretreated with and without Fluoride Varnish by Fluorescence Camera. Int J Clin Pediatr Dent 2018;11(2):89-93.
Diagnostic Approach for Classic Compared With Localized Whipple Disease

Abstract Background Whipple disease (WD), a rare systemic infection caused by Tropheryma whipplei, can be a diagnostic challenge due to its variable presentation. The role of T. whipplei polymerase chain reaction (PCR) is unclear as small bowel biopsy with Periodic acid-Schiff (PAS) staining remains the diagnostic gold standard. Individualized diagnostic approaches based on variable clinical manifestations are underutilized. We investigated the methodologies employed at our institution to diagnose WD. Methods We retrospectively collected all cases of WD diagnosed from 1994 to 2016. Microbiology laboratory and anatomic pathology databases were queried. Case characteristics and disease clinical phenotypes (classical, localized WD arthritis, and localized central nervous system [CNS] disease) were described. The diagnostic approach and testing yield were analyzed and reported. Results Thirty-three cases of WD were diagnosed (18 classic WD [CWD], 9 localized WD arthritis [LWD], 6 CNS WD). Misdiagnosis and delay in diagnosis were frequent. Diagnostic approach and test yield differed by classical vs localized WD involvement. Small bowel tissue biopsy PAS stain/PCR was overwhelmingly positive (86%/92%) in CWD, yet seldom positive (12%/42%) in LWD (P < .001). Affected joint synovial fluid PCR was frequently positive in both CWD (100%, 3/3) and LWD (85%, 6/7). Conclusions These results support the role of small bowel biopsy PAS stain/PCR in the diagnosis of CW, though this approach may be of limited utility in LWD or CNS WD without gastrointestinal symptoms. Affected joint synovial fluid or cerebrospinal fluid PCR was frequently positive in both CWD and LWD, supporting its diagnostic usefulness.
RecA Regulation by RecU and DprA During Bacillus subtilis Natural Plasmid Transformation

Natural plasmid transformation plays an important role in the dissemination of antibiotic resistance genes in bacteria. During this process, Bacillus subtilis RecA physically interacts with RecU, RecX, and DprA. These three proteins are required for plasmid transformation, but RecA is not. In vitro, DprA recruits RecA onto SsbA-coated single-stranded (ss) DNA, whereas RecX inhibits RecA filament formation, leading to net filament disassembly. We show that a null recA (ΔrecA) mutation suppresses the plasmid transformation defect of competent ΔrecU cells, and that RecU is essential for both chromosomal and plasmid transformation in the ΔrecX context. RecU inhibits RecA filament growth and facilitates RecA disassembly from preformed filaments. Increasing SsbA concentrations additively contributes to RecU-mediated inhibition of RecA filament extension. DprA is necessary and sufficient to counteract the negative effect of both RecU and SsbA on RecA filament growth onto ssDNA. DprA-SsbA activates RecA to catalyze DNA strand exchange in the presence of RecU, but this effect was not observed if RecU was added prior to RecA. We propose that DprA contributes to RecA filament growth onto any internalized SsbA-coated ssDNA. When the ssDNA is homologous to the recipient, DprA antagonizes the inhibitory effect of RecU on RecA filament growth and helps RecA to catalyze chromosomal transformation. On the contrary, RecU promotes RecA filament disassembly from a heterologous (plasmid) ssDNA, overcoming an unsuccessful homology search and favoring plasmid transformation. The DprA–DprA interaction may promote strand annealing upon binding to the complementary plasmid strands and facilitating thereby plasmid transformation rather than through a mediation of RecA filament growth.
Microbial and host immune factors as drivers of COPD

Compartmentalisation of the respiratory tract microbiota in patients with different chronic obstructive pulmonary disease (COPD) severity degrees needs to be systematically investigated. In addition, it is unknown if the inflammatory and emphysematous milieux in patients with COPD are associated with changes in the respiratory tract microbiota and host macrophage gene expression. We performed a cross-sectional study to compare non-COPD controls (n=10) to COPD patients (n=32) with different disease severity degrees. Samples (n=187) were obtained from different sites of the upper and lower respiratory tract. Microbiota analyses were performed by 16S ribosomal RNA gene sequencing and host gene expression analyses by quantitative real-time PCR of distinct markers of bronchoalveolar lavage cells. Overall, the microbial communities of severe COPD (Global Initiative for Chronic Obstructive Lung Disease (GOLD) grade 3/4) patients clustered significantly differently to controls and less severe COPD (GOLD 1/2) patients (permutational multivariate ANOVA (MANOVA), p=0.001). However, we could not detect significant associations between the different sampling sites in the lower airways. In addition, the chosen set of host gene expression markers significantly separated COPD GOLD 3/4 patients, and we found correlations between the composition of the microbiota and the host data. In conclusion, this study demonstrates associations between host gene expression and microbiota profiles that may influence the course of COPD. Associations of the host immune response and a disordered microbiota in patients with different COPD severity degrees http://ow.ly/h2mW30k9Nua
Methodologies for in vitro and in vivo evaluation of efficacy of antifungal and antibiofilm agents and surface coatings against fungal biofilms

Unlike superficial fungal infections of the skin and nails, which are the most common fungal diseases in humans, invasive fungal infections carry high morbidity and mortality, particularly those associated with biofilm formation on indwelling medical devices. Therapeutic management of these complex diseases is often complicated by the rise in resistance to the commonly used antifungal agents. Therefore, the availability of accurate susceptibility testing methods for determining antifungal resistance, as well as discovery of novel antifungal and antibiofilm agents, are key priorities in medical mycology research. To direct advancements in this field, here we present an overview of the methods currently available for determining (i) the susceptibility or resistance of fungal isolates or biofilms to antifungal or antibiofilm compounds and compound combinations; (ii) the in vivo efficacy of antifungal and antibiofilm compounds and compound combinations; and (iii) the in vitro and in vivo performance of anti-infective coatings and materials to prevent fungal biofilm-based infections.
Contribution of Oxidative Stress and Inflammation to the Neurogenic Hypertension Induced by Intermittent Hypoxia

Chronic intermittent hypoxia (CIH), the hallmark of obstructive sleep apnea, is the main risk factor to develop systemic hypertension. Oxidative stress, inflammation, and sympathetic overflow have been proposed as possible mechanisms underlying the CIH-induced hypertension. CIH potentiates the carotid body (CB) chemosensory discharge leading to sympathetic overflow, autonomic dysfunction, and hypertension. Oxidative stress and pro-inflammatory molecules are involved in neurogenic models of hypertension, acting on brainstem and hypothalamic nuclei related to the cardiorespiratory control, such as the nucleus of the solitary tract, which is the primary site for the afferent inputs from the CB. Oxidative stress and pro-inflammatory molecules contribute to the activation of the CB chemoreflex pathway in CIH-induced hypertension. In this brief review, we will discuss new evidence for a critical role of oxidative stress and neuro-inflammation in development of the CIH-induced hypertension through activation of the CB chemoreflex pathway.
University of Houston @ CL-SciSumm 2018

In this paper we present our methods and their results on the CL-SciSumm tasks of 2018. In this round, for Task 1A, we tried deep learning methods, a variation of the Positional Language Model and also our methods from BIRNDL 2017. The results show that the deep learning method outperforms the positional language model method and TFIDF method from BRINDL 2017 yields the best F1 score. For Task 1B, we used rule-based methods and classifiers.