Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting Citation Count of Scientists as a Link Prediction Problem

The studies dealing with the problem of predicting scientific impacts in the scientific world mostly focus on predicting citation count of papers (PCCP). However, in the literature, only a little bit of research has been conducted on estimating the future influence of scientists individually. Estimating the impact of scientists individually is a worthwhile task for the following scientific research and cooperatives. From this point of view, a new supervised link prediction method is proposed to predict the citation count of scientists (PCCS). Many PCCP studies employ document-based attributes, such as titles, abstracts, and keywords of papers; institutions of scientists; impact factors of publishers; etc. and they do not take advantage of any topological features of complex networks formed with citations among papers. However, citation networks include valuable features for PCCP and PCCS. Therefore, we formulate the problem of PCCS as a link prediction problem in directed, weighted, and temporal citation networks. The proposed approach predicts not only links but also its weights. Our supervised link prediction method is tested on two citation networks in Experiment 1. The results of Experiment 1 confirm that our method achieves promising performances when considering prediction links with its weights are addressed for the first time in terms of link prediction in directed, weighted, and temporal networks. In Experiment 2, the performance of the proposed link prediction metric and five well-known link prediction metrics are compared in terms of prediction new links in complex networks. The results of Experiment 2 demonstrate that the proposed link prediction metric outperforms all baseline link prediction metrics.
Binding of BRACO19 to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent

Although BRACO19 is a potent G-quadruplex binder, its potential for clinical usage is hindered by its low selectivity towards DNA G-quadruplex over duplex. High-resolution structures of BRACO19 in complex with neither single-stranded telomeric DNA G-quadruplexes nor B-DNA duplex are available. In this study, the binding pathway of BRACO19 was probed by 27.5 µs molecular dynamics binding simulations with a free ligand (BRACO19) to a DNA duplex and three different topological folds of the human telomeric DNA G-quadruplex (parallel, anti-parallel and hybrid). The most stable binding modes were identified as end stacking and groove binding for the DNA G-quadruplexes and duplex, respectively. Among the three G-quadruplex topologies, the MM-GBSA binding energy analysis suggested that BRACO19′s binding to the parallel scaffold was most energetically favorable. The two lines of conflicting evidence plus our binding energy data suggest conformation-selection mechanism: the relative population shift of three scaffolds upon BRACO19 binding (i.e., an increase of population of parallel scaffold, a decrease of populations of antiparallel and/or hybrid scaffold). This hypothesis appears to be consistent with the fact that BRACO19 was specifically designed based on the structural requirements of the parallel scaffold and has since proven effective against a variety of cancer cell lines as well as toward a number of scaffolds. In addition, this binding mode is only slightly more favorable than BRACO19s binding to the duplex, explaining the low binding selectivity of BRACO19 to G-quadruplexes over duplex DNA. Our detailed analysis suggests that BRACO19′s groove binding mode may not be stable enough to maintain a prolonged binding event and that the groove binding mode may function as an intermediate state preceding a more energetically favorable end stacking pose; base flipping played an important role in enhancing binding interactions, an integral feature of an induced fit binding mechanism.
Multiple CH/π Interactions Maintain the Binding of Aflatoxin B1 in the Active Cavity of Human Cytochrome P450 1A2

Human cytochrome P450 1A2 (CYP1A2) is one of the key CYPs that activate aflatoxin B1 (AFB1), a notorious mycotoxin, into carcinogenic exo-8,9-epoxides (AFBO) in the liver. Although the structure of CYP1A2 is available, the mechanism of CYP1A2-specific binding to AFB1 has not been fully clarified. In this study, we used calculation biology to predict a model of CYP1A2 with AFB1, where Thr-124, Phe-125, Phe-226, and Phe-260 possibly participate in the specific binding. Site-directed mutagenesis was performed to construct mutants T124A, F125A, F226A, and F260A. Escherichia coli-expressed recombinant proteins T124A, F226A, and F260A had active structures, while F125A did not. This was evidenced by Fe2+∙Carbon monoxide (CO)-reduced difference spectra and circular dichroism spectroscopy. Mutant F125A was expressed in HEK293T cells. Steady kinetic assays showed that T124A had enhanced activity towards AFB1, while F125A, F226A, and F260A were significantly reduced in their ability to activate AFB1, implying that hydrogen bonds between Thr-124 and AFB1 were not important for substrate-specific binding, whereas Phe-125, Phe-226, and Phe-260 were essential for the process. The computation simulation and experimental results showed that the three key CH/π interactions between Phe-125, Phe-226, or Phe-260 and AFB1 collectively maintained the stable binding of AFB1 in the active cavity of CYP1A2.
Dietary Fiber from Chickpea (Cicer arietinum) and Soybean (Glycine max) Husk Byproducts as Baking Additives: Functional and Nutritional Properties

Dietary fiber extracted from soybean and chickpea husks was used in the formulation of white bread. Treatments at different concentrations of dietary fiber (DF): bread + 0.15%, 0.3%, 1.5%, 2% soybean dietary fiber (SDF); bread + 0.15%, 0.3%, 1.5%, 2% chickpea dietary fiber (CDF), and a control treatment (Bread 0% DF) were used initially. However, the treatments that showed the greatest improvement effects were: bread + 2% SDF and bread + 2% CDF. The functionality and the nutritional contribution in the treatments were evaluated during four days of storage. The weight loss on the third day of storage was 30% higher in the control treatment than the products with 2% SDF and 2% CDF, while for the evaluation of firmness, the control obtained a hardness of 86 N, and treatments with 2% SDF and 2% CDF 60 N and 45 N, respectively. The presence of phenolic compounds and their antioxidant activity was evident, mainly in the 2% SDF treatment, which had a total phenolic content of 1036, while in the Bread 0% DF it was 232 mgEAC/kg. The antioxidant activity for 2% SDF by DPPH (2,2-diphenyl-1-picrylhydrazyl), ABTS (3-ethyl-benzothiazoline-6-sulfonic acid), and FRAP (ferric reducing antioxidant power) was 1096, 2567, and 1800 µmolTE/kg, respectively. Dietary fiber addition favored the reduction of weight loss and firmness of white bread during storage. In addition, color was not affected and the content calcium, phenolics, as well as antioxidant capacity were slightly improved.
Arsenic Trioxide and (−)-Gossypol Synergistically Target Glioma Stem-Like Cells via Inhibition of Hedgehog and Notch Signaling

Glioblastoma is one of the deadliest malignancies and is virtually incurable. Accumulating evidence indicates that a small population of cells with a stem-like phenotype is the major culprit of tumor recurrence. Enhanced DNA repair capacity and expression of stemness marker genes are the main characteristics of these cells. Elimination of this population might delay or prevent tumor recurrence following radiochemotherapy. The aim of this study was to analyze whether interference with the Hedgehog signaling (Hh) pathway or combined Hh/Notch blockade using small-molecule inhibitors can efficiently target these cancer stem cells and sensitize them to therapy. Using tumor sphere lines and primary patient-derived glioma cultures we demonstrate that the Hh pathway inhibitor GANT61 (GANT) and the arsenic trioxide (ATO)-mediated Hh/Notch inhibition are capable to synergistically induce cell death in combination with the natural anticancer agent (-)-Gossypol (Gos). Only ATO in combination with Gos also strongly decreased stemness marker expression and prevented sphere formation and recovery. These synergistic effects were associated with distinct proteomic changes indicating diminished DNA repair and markedly reduced stemness. Finally, using an organotypic brain slice transplantation model, we show that combined ATO/Gos treatment elicits strong growth inhibition or even complete elimination of tumors. Collectively, our data show for the first time that ATO and Gos, two drugs that can be used in the clinic, represent a promising targeted therapy approach for the synergistic elimination of glioma stem-like cells.
The juvenility-associated long noncoding RNA Gm14230 maintains cellular juvenescence

ABSTRACT Juvenile animals possess distinct properties that are missing in adults. These properties include capabilities for higher growth, faster wound healing, plasticity and regeneration. However, the molecular mechanisms underlying these juvenile physiological properties are not fully understood. To obtain insight into the distinctiveness of juveniles from adults at the molecular level, we assessed long noncoding RNAs (lncRNAs) that are highly expressed selectively in juvenile cells. The noncoding elements of the transcriptome were investigated in hepatocytes and cardiomyocytes isolated from juvenile and adult mice. Here, we identified 62 juvenility-associated lncRNAs (JAlncs), which are selectively expressed in both hepatocytes and cardiomyocytes from juvenile mice. Among these common (shared) JAlncs, Gm14230 is evolutionarily conserved and is essential for cellular juvenescence. Loss of Gm14230 impairs cell growth and causes cellular senescence. Gm14230 safeguards cellular juvenescence through recruiting the histone methyltransferase Ezh2 to Tgif2, thereby repressing the functional role of Tgif2 in cellular senescence. Thus, we identify Gm14230 as a juvenility-selective lncRNA required to maintain cellular juvenescence. Summary: Cellular juvenescence is maintained by Gm14230 juvenility-associated lncRNA (JAlnc).
A Declining Trend of Leishmaniasis Based on Previous Data in Larstan, South of Iran 2007–2017

Introduction: Cutaneous Leishmaniasis is a unicellular of the Leishmania type, and 0.7 to 1.2 million people are annually infected by Cutaneous Leishmaniasis. Larestan is one of the southern cities of Fars Province. Every year, some issues of Cutaneous Leishmaniasis are reported from Larestan. This study aims to analyze the prevalence of Cutaneous Leishmaniasis in Larestan from 2007 to 2017. Methodology: The present study is a cross-sectional descriptive-analytical study which is carried out in Larestan. The study population consists of those people who are infected by Cutaneous Leishmaniasis during 2007 to 2017 and are referred to health care centers. The methodology and data collection are done based on the recorded information. Results: Among 4,965 Cutaneous Leishmaniasis infected patients who referred to health care centers of Larestan, 2407 patients (48.47%) are males and 2558 patients (51.53%) are females. In the ten-year time period of the study, 1,315 (26.6%) were infected to Cutaneous Leishmaniasis in 2010. The maximum infected group consisted of 1,303 patients ranging from 0–5 years old, and the minimum infected group consisted of 90 patients ranging from 55–60 years old. Discussion: This study showed that female subjects were more polluted in Larestan city. There is also a significant relationship between age and cutaneous leishmaniasis. Finally, it was found that the disease in the city of Larestan has been decreasing.
A Longitudinal Study of Emotional and Behavioral Problems among Malaysian School Children

Background: Emotional and behavioral problems (EBD) or mental health problems in children and adolescents are an important public health issue, but there has been no evaluation to date of the extent of such problems in near-developed countries. This study evaluated the prevalence and stability of EBD among children in Malaysia. Methods: This research comprises a longitudinal population-based study that measured the prevalence and 6-month stability of EBD in children aged seven to eight years and thirteen to fourteen years attending public schools in Malaysia based on parents, teachers and children’s (aged 13 to 14 years) report of the Strengths and Difficulties Questionnaire (SDQ) at baseline and 6 months later. Findings: The prevalence of EBD in Malaysian school children was 9.3% for teacher-report, 8.5% for parent-report and 3.9% for child-report. There was no significance difference in the prevalence of emotional and behavioral problems over six-months for all informants, except for teacher-report Emotional and Conduct problems scores which increased significantly and child-report Total Difficulties and Emotional problems scores which decreased significantly (p < 0.05). Conclusions: This study shows that the prevalence of EBD among Malaysian children is almost similar to the Western countries and stable over a 6-month period. These findings suggest the need for policy makers in near-developed countries to provide services aimed at preventing EBD and treating children identified as having such problems.
Retinoic acid receptor plays both sides of homeostatic plasticity

Retinoic acid (RA) was originally identified as a morphogen, a signaling molecule that is produced by a specific region but diffuses away, thereby producing a concentration gradient. The morphogen’s nonuniform distribution governs embryo patterning during development. In its role as a morphogen, RA was shown to bind to the RA receptor (RAR) to directly modulate transcription in the nucleus. Recently, though, a noncanonical role for the RARα subtype was identified at neuronal synapses. At the synapse, RARα promotes local translation of AMPA receptors in response to persistently low neuronal activity (1). Increasing AMPA receptors in this way strengthens synapses in a form of homeostatic synaptic plasticity (HSP). HSP shifts the overall synaptic strengths across the neuron while maintaining relative synaptic weights. HSP is bidirectional; synapse may “scale up” in response to decreased neuronal activity or “scale down” in response to increased neuronal activity. HSP is thought to play a vital role in holding synaptic activity within the physiological range and preventing information loss due to a “maxed-out” signal. The mechanistic basis of HSP is poorly understood, particularly in relation to synaptic downscaling. In PNAS, Hsu et al. (2) discover that RARα, through its effects on the ERK-mammalian target of rapamycin complex 1 (mTORC1) pathway, also plays a pivotal role in synaptic downscaling. In an exhaustive series of experiments, the authors show that loss of RARα in the CA1 region of the dorsal hippocampus has no effect on baseline electrophysiological or behavioral properties of mice. However, after a manipulation that elicits HSP [environmental enrichment (EE)], Hebbian long-term potentiation (LTP) is enhanced while long-term depression (LTD) is repressed (a sign of “runaway plasticity”). This imbalance results in improved performance in spatial memory tests but reduced capacity for reversal … [↵][1]1To whom correspondence should be addressed. Email: sheena.josselyn{at}sickkids.ca. [1]: #xref-corresp-1-1
The effects of umblical cord clamping time on lymphocyte subgroups in term and late preterm infants.

Aim To evaluate the effect of umblical cord clamping time on lymphocyte subgroups in term and late preterm infants. Material and Methods Seventy-four infants between 34 and 41 weeks of gestation were included in the study. Of these, 37 were umbilical cord clamped immediately after birth and the remaining 37 were clamped after waiting one minute. Babies were divided into two groups as term and preterm. The prenatal, natal, postnatal characteristics of the infants were recorded. Hematologic and lymphocyte subgroups were investigated in cord blood and venous blood at day 7. Lymphocyte subgroups were evaluated using flow cytometry. Results With the delay of cord clamping, the leucocytes count and the percentage of CD3+T lymphocytes in cord blood of preterm infants decreased and this decrease continued at day 7. On the contrary, CD19+B lymphocyte levels in the cord blood of preterm infants increased, and this increase continued at day 7. Also, the percentage of CD4+T lymphocytes of preterm infants decreased with the delay of cord clamping at day 7. There was no difference between groups for the rate of sepsis development. Conclusion With the delay of cord clamping, the leucocytes count, the percentage of CD3+T, and CD4+T lymphocytes decreased, and the percentage of CD19+B lymphocytes increased in preterm infants. The delay in cord clamping time in term and preterm infants seems to have no impact on the rate of sepsis development. Larger series of studies are needed to assess the effect of these findings on the development of infection in late preterm infants who have delayed cord clamping.
Harnessing the Power of Machine Learning in Dementia Informatics Research: Issues, Opportunities, and Challenges

Dementia is a chronic and degenerative condition affecting millions globally. The care of patients with dementia presents an ever-continuing challenge to healthcare systems in the 21st century. Medical and health sciences have generated unprecedented volumes of data related to health and wellbeing for patients with dementia due to advances in information technology, such as genetics, neuroimaging, cognitive assessment, free texts, routine electronic health records, etc. Making the best use of these diverse and strategic resources will lead to high-quality care of patients with dementia. As such, machine learning becomes a crucial factor in achieving this objective. The aim of this paper is to provide a state-of-the-art review of machine learning methods applied to health informatics for dementia care. We collate and review the existing scientific methodologies and identify the relevant issues and challenges when faced with big health data. Machine learning has demonstrated promising applications to neuroimaging data analysis for dementia care, while relatively less effort has been made to make use of integrated heterogeneous data via advanced machine learning approaches. We further indicate future potential and research directions in applying advanced machine learning, such as deep learning, to dementia informatics.
The thousand faces of autism spectrum disorder.

Autism Spectrum Disorder (ASD) is a lifelong clinical condition that severely impacts on the life of affected individuals and their families, due to the impairment of social interaction and communication, as well as to the presence of repetitive interests and activities (1). According to the most recent epidemiologic studies, ASD has reached the prevalence of 16.8 per 1000 children aged 8 years (2); the dramatic increase in cases diagnosed during the last decades is only partly attributable to a better knowledge of this condition (3). A real increase in affected individuals is unquestionable and urgently requires answers because it leads us to hypothesize that in the etiopathogenesis of the disorder, important roles are played by a genetic predisposition (strongly supported by literature data), and by environmental factors that may be positively influenced through an effective prevention action. It is still a matter of study as to exactly what these environmental factors are, but it is possible that a large number of heterogeneous pollutants are involved (4). The Diagnostic and Statistical Manual of Mental Disorders 5th edition (DSM-5) subdivides patients with ASD into 3 groups of increasing severity (from 1 to 3), depending on the level of required support. Unfortunately, this subdivision appears to be too crude to adequately characterize these individuals, both for clinical purposes and for research purposes. It is no coincidence that most health professionals who deal with autism usually use in spoken and written language the expression “Autism Spectrum Disorders” in the plural and not in the singular as proposed by the DSM-5 (see the title of the respective chapter). In fact, they perceive these conditions as very heterogeneous entities, with differences among patients that are quantitative and qualitative.
Threat reduces value-driven but not salience-driven attentional capture.

What we direct our attention to is strongly influenced by both bottom-up and top-down processes. Moreover, the control of attention is biased by prior learning, such that attention is automatically captured by stimuli previously associated with either reward or threat. It is unknown whether value-oriented and threat-oriented mechanisms of selective information processing function independently of one another, or whether they interact with each other in the selection process. Here, we introduced the threat of electric shock into the value-driven attentional capture paradigm to examine whether the experience of threat influences the attention capturing quality of previously reward-associated stimuli. The results showed that value-driven attentional capture was blunted by the experience of threat. This contrasts with previous reports of threat potentiating attentional capture by physically salient stimuli, which we replicate here. Our findings demonstrate that threat selectively interferes with value-based but not salience-based attentional priority, consistent with a competitive relationship between value-based and threat-based information processing. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Functional Anatomy of the Craniomedial and Caudolateral Bundles of the Cranial Cruciate Ligament in Beagle Dogs

Abstract Objective The aim of this study was to investigate detailed functional anatomy of the craniomedial bundle (CrMB) and caudolateral bundle (CdLB) of cranial cruciate ligament (CrCL) for application of intra-articular anatomical reconstruction in dogs. Materials and Methods Twelve stifle joint of 12 Beagle cadavers were used. Anatomical characteristics of femoral attachment regions of the CrCL were determined. Then, the location and area of the footprints of the CrMB and CdLB were objectively measured. Each bundle was equally divided into four fibre bundles, and changes in the fibre arrangement were recorded during stifle range of motion. Additionally, the tension of each fibre bundle at various stifle joint angles was objectively measured. Results The attachment region of the CrCL clearly differed from that reported in humans. The centre of the CdLB attachment site was located craniodistal to that of the CrMB on the femur and slightly caudal to that of the CrMB on the tibia. The area of the CrMB on the femoral and tibial attachment sites was larger than that of the CdLB. During stifle range of motion, each divided fibre bundle in the CrMB and CdLB was twisted intricately. The tension of the CrMB was higher than that of CdLB. The central part of the CrMB was always tense during stifle range of motion. Clinical Significance These results may contribute to the application of anatomical reconstruction surgery for CrCL deficient stifle in dogs.