Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracting chemical-protein interactions from literature

Chemical compound and protein interaction information is indispensable for understanding the regulation of biological processes and development of therapeutic drugs. Manually extracting such information from biomedical literature is very time and resource consuming. In this study, we proposed a computational method to automatically extract chemicalprotein interactions (CPI) from a given text. Our method extracts CPI-pairs and CPI-triplets from sentences, where a CPI-pair is defined as a chemical compound and a protein name in a sentence, and a CPI-triplet is defined as a chemical compound name, a protein name, and a word describing their relationship (interaction word) in a sentence. We formulate the task as a machine learning problem and extract a diverse set of features from sentences, which were used to build multiple machine learning models. Our models contain both simple features, which can be directly computed from sentences and also more sophisticated features derived using natural language processing (NLP) techniques. For example, one set of features are extracted based on the shortest paths between the CPI-pairs or among the CPI-triplets in the dependency graphs obtained from sentence parsing. To predict the multiple categories of CPI types, we designed a three-stage approach to divide-and-conquer the challenging multi-class prediction problem. Our method obtained good performance on the BioCreative VI track 5 data with F1-scores of 0.7641, 0.7912, and 0.7798 for train set, development set and the combination of them, respectively, on 10-fold cross validation. Keywords—Protein-protein interactions; chemical-protein relations; text mining; CPI triplets;
BIOINFORMATICS ORIGINAL PAPER

Motivation: Genome-wide association studies (GWAS) involving half a million or more single nucleotide polymorphisms (SNPs) allow genetic dissection of complex diseases in a holistic manner. The common practice of analyzing one SNP at a time does not fully realize the potential of GWAS to identify multiple causal variants and to predict risk of disease. Existing methods for joint analysis of GWAS data tend to miss causal SNPs that are marginally uncorrelated with disease and have high false discovery rates (FDRs). Results: We introduce GWASelect, a statistically powerful and computationally efﬁcient variable selection method designed to tackle the unique challenges of GWAS data. This method searches iteratively over the potential SNPs conditional on previously selected SNPs and is thus capable of capturing causal SNPs that are marginally correlated with disease as well as those that are marginally uncorrelated with disease. A special resampling mechanism is built into the method to reduce false positive ﬁndings. Simulation studies demonstrate that the GWASelect performs well under a wide spectrum of linkage disequilibrium patterns and can be substantially more powerful than existing methods in capturing causal variants while having a lower FDR. In addition, the regression models based on the GWASelect tend to yield more accurate prediction of disease risk than existing methods. The advantages of the GWASelect are illustrated with the Wellcome Trust Case-Control Consortium (WTCCC) data.
Characterizing Spatial Resolution of a Fringe Projection System for Measuring Additively Manufactured Surfaces

INTRODUCTION One of the biggest challenges for metal additive manufacturing is the inability to control surface quality. An approach to solve this problem is to use in-situ metrology systems. Fast data acquisition and a relatively long working distance make fringe projection a viable solution for in-situ metrology of layered metal additive manufacturing process [1], [2]. Surfaces created by metal additive processes, particularly the laser powder bed fusion (LPBF) process, are rough, porous and textured. The roughness and texture are the results of laser scanning and are related to the process parameters such as laser power, scan velocity, and hatch distance (laser step over). The combination of the parameters creates a unique surface texture with rich spatial frequency content. Figure 1 shows such a texture with a fused square on a layer of Inconel-625 metal powder. The laser scan path is along the vertical axis with a step over of 90 μm. The laser power is 290 W, and the scan speed is 110 mm/s. The fused surface is measured in situ by a fringe projection system. The measured topography shows clear periodic structures near the bottom edge along the x-axis (Figure 1 (d)). Fourier analysis of the measured profile shows a strong peak at the spatial frequency corresponding to twice the hatch distance, suggesting a merge of two scans due to the closeness (time-wise) of the two scan paths.
Diffusion Based Network Embedding

In network embedding, random walks play a fundamental role in preserving network structures. However, random walk based embedding methods have two limitations. First, random walk methods are fragile when the sampling frequency or the number of node sequences changes. Second, in disequilibrium networks such as highly biases networks, random walk methods often perform poorly due to the lack of global network information. In order to solve the limitations, we propose in this paper a network diffusion based embedding method. To solve the first limitation, our method employs a diffusion driven process to capture both depth information and breadth information. The time dimension is also attached to node sequences that can strengthen information preserving. To solve the second limitation, our method uses the network inference technique based on cascades to capture the global network information. To verify the performance, we conduct experiments on node classification tasks using the learned representations. Results show that compared with random walk based methods, diffusion based models are more robust when samplings under each node is rare. We also conduct experiments on a highly imbalanced network. Results shows that the proposed model are more robust under the biased network structure.
Validation of Traditional Methods of Genotoxicity with Liver Tyrosine Aminotransferase Activity Induced by Metribuzin Treatment in Albino Rats

The genotoxicity of pesticides give a potential role in population health and ecosystem safety and here the we would like to explore genotoxicity of metribuzin herbicide. Metribuzin dosed orally in albino rats twice per week for 3 months at dose level 0, 110, 220, and 440 mg/kg. All rats were sacrificed and liver was preserved in liquid nitrogen and bone marrow cells was obtained from femur bone. It was founded that chromosomal aberrations were dose dependent with significant increase in all doses (1/20, 1/10 and ⅕ of the LD50% of metribuzin herbicide) specially higher doses represented by structural abnormalities as chromosomal break, fragments, gap, association and a centromeric chromosomes beside numerical abnormalities as polyploidy and hypoploidy. Additionally, DNA quantity was dose dependent significant increase. Notably, there was significant increase in micronuclei level in respect to control that considered as a clastogenic signal and defect in mitotic activity that founded to be decreased in bone marrow cell where the mitotic index had decreased drastically in comparison to control value. Notably, metribuzin enhanced expression of TAT gene at all doses when compared with control group. on conclusion, metribuzin herbicide had a genotoxic properties that constitute hazard and great concern to population and TAT gene expression could be a potential role in detection of toxicity.
Synthesis and Characterization of Biodegradable Hydrogels for Oral Delivery of 5-Fluorouracil Targeted to Colon: Screening with Preliminary In Vivo Studies

In this communication, we developed a thermally stable, biocompatible, and colonically degradable hydrogel-based device [pectin-co-poly(MAA)] for oral delivery of 5-fluorouracil (5-FU) to treat colon cancer with minimal upper gastrointestinal invasion. Toward this end, ethylene glycol dimethacrylate (EGDMA) cross-linked hydrogels of pectin were synthesized. Methacrylic acid (MAA) was grafted to impart pH-responsive character, whereas benzoyl peroxide (BPO) was applied for simultaneous grafting and cross-linking polymerization. The hydrogels were characterized by Fourier transform infrared , thermogravimetric analysis, differential scanning calorimetry, and X-ray diffractometry. Scanning electron microscopic photographs were taken to analyze the surface morphology. Swelling behavior was analyzed to assess better performance of biodegradable hydrogels for optimized loading and release of the drug targeted to the colon. Gel fraction, swelling ratio, diffusion coefficient, drug loading, and cumulative release increased with an increase of pectin ratio and decreased with an increase of MAA and EGDMA ratio. Strategically, hydrogels with higher amounts of pectin were prepared for complete degradation in the colon. Our investigations indicate that pectin-co-poly(MAA) hydrogel is a suitable delivery system developed for oral delivery of the drug targeted to the colon.
DNA Microarray Analysis of Hypothermic Murine Myocardium to Study Pathophysiology and Identify Forensic Biomarkers

We used DNA microarray technology to analyze the myocardial transcriptome of mice killed via experimentally induced hypothermia. This analysis identified significant differential regulation of 3438 genes; specifically, 1704 genes were upregulated, and 1734 were downregulated in response to hypothermia. The gene encoding granzyme A was the most upregulated gene, and that encoding solute carrier family 41 member 3 was the most downregulated. Geneset analysis identified significant hypothermia-induced variation in 79 pathways, and we suggest that pathways related to granzyme A and cell death may be involved in cardiac pathogenesis of hypothermia. Gene-function-category analysis demonstrated the most highly represented categories among the upregulated and downregulated genes were cellular process (biological process), binding (molecular function), and cell and cell part (cellular component). The presented findings clearly demonstrated that acute myocardial responses to hypothermia did occur; they also indicated several cardiac-related candidate genes as forensic biomarkers of hypothermia. Hypothermiainduced myocardial cell death would be an irreversible change that, we believe, may explain the circulatory failure, resistance to treatment, and high mortality associated with hypothermia. Furthermore, the present microarray data may facilitate development of immunohistochemical analysis and protocols to be used for human forensics and may be beneficial in clinical research on hypothermia.
Evaluation, treatment, and prevention of vitamin D deficiency: an Endocrine Society clinical practice guideline.

OBJECTIVE The objective was to provide guidelines to clinicians for the evaluation, treatment, and prevention of vitamin D deficiency with an emphasis on the care of patients who are at risk for deficiency. PARTICIPANTS The Task Force was composed of a Chair, six additional experts, and a methodologist. The Task Force received no corporate funding or remuneration. CONSENSUS PROCESS Consensus was guided by systematic reviews of evidence and discussions during several conference calls and e-mail communications. The draft prepared by the Task Force was reviewed successively by The Endocrine Society's Clinical Guidelines Subcommittee, Clinical Affairs Core Committee, and cosponsoring associations, and it was posted on The Endocrine Society web site for member review. At each stage of review, the Task Force received written comments and incorporated needed changes. CONCLUSIONS Considering that vitamin D deficiency is very common in all age groups and that few foods contain vitamin D, the Task Force recommended supplementation at suggested daily intake and tolerable upper limit levels, depending on age and clinical circumstances. The Task Force also suggested the measurement of serum 25-hydroxyvitamin D level by a reliable assay as the initial diagnostic test in patients at risk for deficiency. Treatment with either vitamin D(2) or vitamin D(3) was recommended for deficient patients. At the present time, there is not sufficient evidence to recommend screening individuals who are not at risk for deficiency or to prescribe vitamin D to attain the noncalcemic benefit for cardiovascular protection.
Salivary analysis in oral cancer patients

Free radicals such as reactive oxygen species (ROS) and reactive nitrogen species (RNS), which induce oxidative and nitrative stress, are main contributors to oral carcinogenesis. The RNS (nitrosamines: nitrates, NO3, and nitrites, NO2) are also produced by the reaction of ROS and other free radicals with nitric oxide (NO) and are therefore in equilibrium with it.
Heart arrhythmia classification using the prediction by partial matching algorithm

This paper describes a method for heart arrhythmia classification based on the heart rate variability HRV signal and the compression algorithm PPM. The arrhythmias to be identified are: atrial fibrillation, second heart block, normal sinus rhythm, premature ventricular contraction, ventricular fibrillation and sinus bradycardia. In the learning stage the PPM algorithm builds statistical models for the extracted tachogram. In the classification stage, the tachograms are compressed by the obtained models and attributed to the class whose models results in the best compression rate. The tests were performed with 1367 segments from the MIT-BIH Arrhythmia Database and Creighton University Ventricular Tachyarrhythmia Database. The classifier was tested for several context sizes and different training/classification sets. The performance of the classifier was measured according to sensitivity, specificity and accuracy, obtaining 96.93, 99.47 and 98.73% respectively, with the context size equal to one. These results are comparable to those of the best modern classifiers.
Factors Associated with Cesarean Section in Tehran, Iran using Multilevel Logistic Regression Model

Objectives Over the past few decades, the prevalence of cesarean sections (CS) have risen dramatically worldwide, particularly in Iran. The aim of this study was to determine the prevalence of CS in Tehran, and to examine the associated risk factors. Methods A cross-sectional study of 4,308 pregnant women with singleton live-births in Tehran, Iran, between July 6–21, 2015 was performed. Multilevel logistic regression analysis was performed using demographic and obstetrical variables at the first level, and hospitals as a variable at the second level. Results The incidence of CS was 72.0%. Multivariate analysis showed a significant relationship between CS and the mother’s age, socioeconomic status, body mass index, parity, type of pregnancy, preeclampsia, infant height, and baby’s head circumference. The intra-class correlation using the second level variable, the hospital was 0.292, indicating approximately 29.2% of the total variation in the response variable accounted for by the hospital. Conclusion The incidence of CS was substantially higher than other countries. Therefore, educational and psychological interventions are necessary to reduce CS rates amongst pregnant Iranian women.
Differences in Pelvic Floor Symptoms During Pregnancy Between Hispanic and Non-Hispanic White Women.

OBJECTIVES This study aimed to describe and compare pelvic floor symptoms and symptom burden between nulliparous Hispanic and non-Hispanic white women in the third trimester of pregnancy and to determine, in women with stress urinary incontinence (SUI), whether bother differs between groups, adjusted for UI severity. METHODS In this cross-sectional analysis, participants completed the Epidemiology of Prolapse and Incontinence and Incontinence Severity Index questionnaires. We compared differences in symptom domains between groups using logistic regression and tested the effect of ethnicity on bother in women with SUI using linear regression. RESULTS The sample comprised 418 non-Hispanic white and 154 Hispanic women. Prevalence rates of symptom domains ranged from 5.0% and 7.1% for pelvic organ prolapse to 95.2% and 94.2% for overactive bladder in non-Hispanic white and Hispanic women, respectively. After adjusting age, height, weight, education, physical activity, and gestational age, non-Hispanic whites had 2.37-fold increased odds (95% confidence interval, 1.44-3.92) for defecatory dysfunction and had nonsignificant increases in other symptom domains. Non-Hispanic whites were more likely to endorse symptoms in 3 or more domains than Hispanic women (58.9% vs 40.3%, respectively; P = 0.0001). Given the same UI severity (Incontinence Severity Index), Hispanic women with SUI reported 7.5 points greater bother (Epidemiology of Prolapse and Incontinence) than non-Hispanic white women (P = 0.07). CONCLUSIONS After adjustment, we found few differences in the prevalence of pelvic floor symptom domains between Hispanic and non-Hispanic white women, apart from defecatory dysfunction. If differences by ethnicity in other pelvic floor symptoms exist, they do not seem to originate during the first pregnancy.
A comparative assessment of bite marks in analyzing the overlay generation using styrofoam sheet and modeling wax with the dental casts as one of the adjuncts for archiving the forensic records: An in vivo study

Introduction: Bite mark evidence is unique to an individual and plays an important role in the legal system. There has always been the need to develop newer materials for bite mark analysis that will have excellent reproducibility as well as reliability. Aim: The present study aimed to evaluate the efficacy of styrofoam sheets and modeling wax with time-dependent changes when compared to the routine dental cast models. Materials and Methods: The present study included thirty volunteers and their bite marks were taken on the styrofoam and wax sheet materials that were traced on the transparent sheet and evaluation of the bite marks on the two materials were carried out at an interval of 1 day for 3 alternate days and grades were given, respectively. ANOVA test and t-test were used for statistical analysis. Results: The comparison between the styrofoam sheet and wax sheet with the dental cast on day 1 proved to be excellent materials for reproducibility, but from day 3 onward, the styrofoam sheet showed changes in bite registered area; whereas wax sheet maintained its registered dimensions. Conclusion: The study concludes that bite mark registration on styrofoam and wax sheet had excellent reproducibility on day 1, which makes these two materials advantageous in bite mark registration and overlay generation on the same day, whereas on day 3 and day 5, the styrofoam sheet showed changes with respect to bite registration and overlay generation, which questions the reliability of the styrofoam sheet for long-term record keeping when compared with the modeling wax.
Why Do Young People Consume Marijuana? Extending Motivational Theory via the Dualistic Model of Passion

We evaluated an extended model of motivation for consuming marijuana by combining motivational theory and the dualistic model of passion. An online sample of 524 young, frequent marijuana consumers (Mage = 24; 88% male; Mpast-30-days = 21; Mode = 31; 50% used 25–31 days) self-administered several questionnaires including the Marijuana-Harmonious and Obsessive Passion Scale and the Marijuana Motives Measure. Intercorrelations among the obsessive and harmonious passion and motives subscales were small to medium. A canonical correlation analysis revealed that obsessive passion was significantly positively associated with coping and conformity motives while controlling for marijuana use, other motives, and harmonious passion scores. In addition, harmonious passion was significantly positively associated with expansion, social, enhancement, and coping motives while controlling for marijuana use and obsessive passion scores. A second canonical correlation analysis revealed that, when motive and passion subscales were included as independent predictors of recent marijuana use and related consequences, high obsessive passion and coping motives emerged as significant predictors of recent use and related consequences. Moreover, high harmonious passion and using less for conformity motives emerged as significant predictors of recent marijuana use. These results demonstrate that passion is related to, but not a proxy for, previously established motives for marijuana use and that, when examined simultaneously, both types of passion predict recent consumption but appear to differentiate whether one will experience use-related consequences. Researchers and clinicians could evaluate whether addressing obsessive passion and coping motives reduces or ameliorates negative outcomes associated with consumption.
A Quantitative Investigation on the Effect of Edge Enhancement for Improving Visual Acuity at Different Levels of Contrast

Background: The major limitation in human vision is refractive error. Auxiliary equipment and methods for these people are not always available. In addition, limited range of accommodation in adult people when switching from a far point to a near point is not simply possible. In this paper, we are looking for solutions to use the facilities of digital image processing and displaying to improve visual acuity when using digital display devices. We quantitatively investigate the effect of edge enhancement on improving the visual acuity at different levels of contrast. We can improve visual acuity for people such as emmetropia, myopia and hyperopia when they utilize display devices. Materials and Methods: According to the objective of this research, 24 visual acuity optical charts were designed using MATLAB software, based on logMAR standard. The charts have different levels of contrast with enhanced edges of optotypes at two brightness levels: 0 and 255. The proposed patterns were tested on 20 human subjects. The obtained results for each chart were analyzed in SPSS software. Results: The results show that at all contrast levels, edge enhancement improves visual acuity. The degree of improvement where the edges have brightness level of 0 is higher than where the edges have brightness level of 255. Conclusion: Based on the results, enhancing the edges of optotypes in the background image improves visual acuity by about 16.1% on logMAR scale.
Child prosociality within HIV-affected contexts: the impact of carer ill-health and orphan status

ABSTRACT Considerable attention has been provided to the potential adverse outcomes for youth in the context of HIV and AIDS. Using data from a large community-based study on the psychosocial well-being of youth affected by HIV and AIDS, this paper advances a strength-based, resiliency perspective that is centred on the construct of prosociality. Data was derived from the Young Carers South Africa Project, where a cross-sectional household survey was conducted with 2477 child–carer pairs in an HIV-endemic community in the province of KwaZulu-Natal, South Africa. Analysis in this paper focuses on a subset of 2136 child–carer pairs. Perceptions of child prosociality were assessed using the Prosocial Scale of the Strengths and Difficulties Questionnaire (SDQ). Both child and carer responses were obtained to provide insight into the functioning of carer–child dyads. Descriptive and inferential analysis was conducted to explore ratings of child prosociality across different relational contexts affected by HIV and involving care for orphaned youths. Dual-affected households, where carers are ill with opportunistic infections and youth are orphaned due to AIDS, yielded the highest discrepancies with carers reporting low child prosociality and children self-reporting high prosociality. Carer ill health appears to play a role in differentiating child prosociality across relational contexts involving non-orphaned youth. Further research is needed to explore child prosociality as a protective mechanism in high HIV-endemic communities.