Miracle-dz/UniFAR-FTUs huggingface dataset:
GLIDER: function prediction from GLIDE-based neighborhoods

Abstract Motivation Protein function prediction, based on the patterns of connection in a protein–protein interaction (or association) network, is perhaps the most studied of the classical, fundamental inference problems for biological networks. A highly successful set of recent approaches use random walk-based low-dimensional embeddings that tend to place functionally similar proteins into coherent spatial regions. However, these approaches lose valuable local graph structure from the network when considering only the embedding. We introduce GLIDER, a method that replaces a protein–protein interaction or association network with a new graph-based similarity network. GLIDER is based on a variant of our previous GLIDE method, which was designed to predict missing links in protein–protein association networks, capturing implicit local and global (i.e. embedding-based) graph properties. Results GLIDER outperforms competing methods on the task of predicting GO functional labels in cross-validation on a heterogeneous collection of four human protein–protein association networks derived from the 2016 DREAM Disease Module Identification Challenge, and also on three different protein–protein association networks built from the STRING database. We show that this is due to the strong functional enrichment that is present in the local GLIDER neighborhood in multiple different types of protein–protein association networks. Furthermore, we introduce the GLIDER graph neighborhood as a way for biologists to visualize the local neighborhood of a disease gene. As an application, we look at the local GLIDER neighborhoods of a set of known Parkinson’s Disease GWAS genes, rediscover many genes which have known involvement in Parkinson’s disease pathways, plus suggest some new genes to study. Availability and implementation All code is publicly available and can be accessed here: https://github.com/kap-devkota/GLIDER. Supplementary information Supplementary data are available at Bioinformatics online.
Vitamin D: sources, physiological role, biokinetics, deficiency, therapeutic use, toxicity, and overview of analytical methods for detection of vitamin D and its metabolites

Abstract Vitamin D has a well-known role in the calcium homeostasis associated with the maintenance of healthy bones. It increases the efficiency of the intestinal absorption of dietary calcium, reduces calcium losses in urine, and mobilizes calcium stored in the skeleton. However, vitamin D receptors are present ubiquitously in the human body and indeed, vitamin D has a plethora of non-calcemic functions. In contrast to most vitamins, sufficient vitamin D can be synthesized in human skin. However, its production can be markedly decreased due to factors such as clothing, sunscreens, intentional avoidance of the direct sunlight, or the high latitude of the residence. Indeed, more than one billion people worldwide are vitamin D deficient, and the deficiency is frequently undiagnosed. The chronic deficiency is not only associated with rickets/osteomalacia/osteoporosis but it is also linked to a higher risk of hypertension, type 1 diabetes, multiple sclerosis, or cancer. Supplementation of vitamin D may be hence beneficial, but the intake of vitamin D should be under the supervision of health professionals because overdosing leads to intoxication with severe health consequences. For monitoring vitamin D, several analytical methods are employed, and their advantages and disadvantages are discussed in detail in this review.
Ultrasound Targeted Microbubble Destruction Promotes the Therapeutic Effect of HUMSC Transplantation on Glaucoma-Caused Optic Nerve Injury in Rabbits

Purpose The purpose of this study was to explore the therapeutic effect of human umbilical cord mesenchymal stem cell (HUMSC) transplantation alone or assisted with ultrasound targeted microbubble destruction (UTMD) on optic neuropathy in a novel and practical model of experimental glaucoma in rabbits. Methods Eight New Zealand white healthy rabbits were used as the control group (group A). Twenty-four experimental glaucomatous rabbits were established as described previously and randomly divided into three groups: (1) received no treatment (group B); (2) received intravitreal transplantation of HUMSCs (group C); and (3) received UTMD-assisted intravitreal transplantation of HUMSCs (group D). After 4 weeks of treatment, the distribution of HUMSCs, retinal thickness, layer structure, retinal ganglion cells (RGCs), and their axons were examined. Results After 4 weeks of treatment, HUMSCs were successfully scattered under the retina. HUMSC transplantation significantly increased the regeneration of RGCs and their axons, and restored the retinal structure in glaucomatous rabbits. Moreover, the application of UTMD enhances HUMSC distribution and achieved more significant therapeutic effect. Conclusions Intravitreal transplantation of HUMSCs effectively repaired glaucomatous optic nerve injury, and UTMD enhanced the successful delivery of HUMSCs into injured retina, promoting its therapeutic effects remarkably. Translational Relevance This study demonstrated that HUMSC transplantation repaired the glaucoma-caused nerve injury significantly and the combination of UTMD can augment the therapeutic effect further, which has important clinical guiding significance for the development of therapeutic strategies of glaucoma.
Genome Sequences of Two Methicillin-Sensitive Staphylococcus aureus Healthy Skin Isolates

The USA300 and USA600 clonal lineages are the cause of many serious Staphylococcus aureus infections. Here, we report the complete genomes of two methicillin-sensitive S. aureus strains isolated from the healthy skin of adults in Colorado, which are most phylogenetically similar to the USA300 and USA600 lineages. ABSTRACT The USA300 and USA600 clonal lineages are the cause of many serious Staphylococcus aureus infections. Here, we report the complete genomes of two methicillin-sensitive S. aureus strains isolated from the healthy skin of adults in Colorado, which are most phylogenetically similar to the USA300 and USA600 lineages.
Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis

Atopic dermatitis (AD) is one of the most common skin disorders among children. Disease etiology involves genetic and environmental factors, with 29 independent AD risk loci enriched for risk allele-dependent gene expression in the skin and CD4+ T cell compartments. We investigated the potential epigenetic mechanisms responsible for the genetic susceptibility of CD4+ T cells. To understand the differences in gene regulatory activity in peripheral blood T cells in AD, we measured chromatin accessibility (an assay based on transposase-accessible chromatin sequencing, ATAC-seq), nuclear factor kappa B subunit 1 (NFKB1) binding (chromatin immunoprecipitation with sequencing, ChIP-seq), and gene expression levels (RNA-seq) in stimulated CD4+ T cells from subjects with active moderate-to-severe AD, as well as in age-matched non-allergic controls. Open chromatin regions in stimulated CD4+ T cells were highly enriched for AD genetic risk variants, with almost half of the AD risk loci overlapping AD-dependent ATAC-seq peaks. AD-specific open chromatin regions were strongly enriched for NF-κB DNA-binding motifs. ChIP-seq identified hundreds of NFKB1-occupied genomic loci that were AD- or control-specific. As expected, the AD-specific ChIP-seq peaks were strongly enriched for NF-κB DNA-binding motifs. Surprisingly, control-specific NFKB1 ChIP-seq peaks were not enriched for NFKB1 motifs, but instead contained motifs for other classes of human transcription factors, suggesting a mechanism involving altered indirect NFKB1 binding. Using DNA sequencing data, we identified 63 instances of altered genotype-dependent chromatin accessibility at 36 AD risk variant loci (30% of AD risk loci) that might lead to genotype-dependent gene expression. Based on these findings, we propose that CD4+ T cells respond to stimulation in an AD-specific manner, resulting in disease- and genotype-dependent chromatin accessibility alterations involving NFKB1 binding.
A national study of moral distress among U.S. internal medicine physicians during the COVID-19 pandemic

Background There have been no studies to date of moral distress during the COVID-19 pandemic in national samples of U.S. health workers. The purpose of this study was to determine, in a national sample of internal medicine physicians (internists) in the U.S.: 1) the intensity of moral distress; 2) the predictors of moral distress; 3) the outcomes of moral distress. Methods We conducted a national survey with an online panel of internists, representative of the membership of the American College of Physicians, the largest specialty organization of physicians in the United States, between September 21 and October 8, 2020. Moral distress was measured with the Moral Distress Thermometer, a one-item scale with a range of 0 (“none”) to 10 (“worst possible”). Outcomes were measured with short screening scales. Results The response rate was 37.8% (N = 810). Moral distress intensity was low (mean score = 2.4, 95% CI, 2.2–2.6); however, 13.3% (95% CI, 12.1% - 14.5%) had a moral distress score greater than or equal to 6 (“distressing”). In multiple linear regression models, perceived risk of death if infected with COVID-19 was the strongest predictor of higher moral distress (β (standardized regression coefficient) = 0.26, p < . 001), and higher perceived organizational support (respondent belief that their health organization valued them) was most strongly associated with lower moral distress (β = -0.22, p < .001). Controlling for other factors, high levels of moral distress, but not low levels, were strongly associated (adjusted odds ratios 3.0 to 11.5) with screening positive for anxiety, depression, posttraumatic stress disorder, burnout, and intention to leave patient care. Conclusions The intensity of moral distress among U.S. internists was low overall. However, the 13% with high levels of moral distress had very high odds of adverse mental health outcomes. Organizational support may lower moral distress and thereby prevent adverse mental health outcomes.
Context-dependent parasite infection affects trophic niche in populations of sympatric stickleback species

Abstract Abstract How parasites alter host feeding ecology remains elusive in natural populations. A powerful approach to investigate the link between infection and feeding ecology is quantifying unique and shared responses to parasite infection in related host species within a common environment. Here, 9 pairs of sympatric populations of the three-spined and nine-spined stickleback fishes were sampled across a range of freshwater and brackish habitats to investigate how parasites alter host feeding ecology: (i) biotic and abiotic determinants of parasite community composition, and (ii) to what extent parasite infection correlates with trophic niche specialization of the 2 species, using stable isotope analyses (δ15N and δ13C). It was determined that parasite community composition and host parasite load varied among sites and species and were correlated with dissolved oxygen. It was also observed that the digenean Cyathocotyle sp. 's abundance, a common directly infecting parasite with a complex life cycle, correlated with host δ13C in a fish species-specific manner. In 6 sites, correlations were found between parasite abundance and their hosts' feeding ecology. These effects were location-specific and occasionally host species or host size-specific. Overall, the results suggest a relationship between parasite infection and host trophic niche which may be an important and largely overlooked ecological factor. The population specificity and variation in parasite communities also suggest this effect is multifarious and context-dependent.
Predictors for intracerebral hemorrhage after intravenous or intraarterial recanalization in acute major cerebral artery occlusion in Korean patients

Abstract Objective To evaluate predictors for intracerebral hemorrhage (ICH) and 1-month mortality after intravenous (IV) or intraarterial (IA) recanalization therapy for major cerebral artery occlusion in Korean patients. Methods From 2011 to 2015, we prospectively gathered data from consecutive patients treated with IV/IA recanalization within 8 h of symptoms in a single center. The effects of demographic, clinical, laboratory, and radiological factors on ICH within 2 weeks were assessed, as well as 1-month mortality. Results From a total of 183 patients, symptomatic intracerebral hemorrhage (SICH) occurred in 32 patients (17.5%), and asymptomatic ICH occurred in 37 patients (20.2%). The mortality rate at 1 month in ICH patients was 37.7%. The international normalized ratio (INR) (OR, 4.9; 95% CI, 1.03–23.4; p = 0.046), glucose (OR, 1.119 per mmol/L; 95% CI, 1.015–1.233; p = 0.023), medium-volume infarct (15–69.9 mL) (OR, 2.62; 95% CI, 1.1–6.26; p = 0.03), large-volume infarct (≥70 mL) (OR, 5.54; 95% CI, 2.1–14.6; p = 0.001), and angioplasty or stenting (OR, 6.29; 95% CI, 1.71–23.22; p = 0.006) were predictors of any ICH. Hyperlipidemia or statin medication (OR, 4.17; 95% CI, 1.38–12.59; p = 0.011), INR (OR, 7.13; 95% CI, 0.94–54.22 p = 0.058), and large-volume infarct (≥70 mL) (OR, 7.96; 95% CI, 2.31–27.39; p = 0.001) were predictors of SICH. Hypertension (OR, 5.77; 95% CI, 1.43-23.3; p = 0.014), initial NIHSS score (OR, 1.09; 95% CI, 1.01–1.18; p = 0.27), and SICH (OR, 15.7; 95% CI, 4.04–61.08; p < 0.001) were predictors of 1-month mortality. Conclusion INR and glucose may be strong modifiable predictors of critical ICH leading to death after IV/IA recanalization therapy in acute cerebral artery occlusion.
Study on driver's eye fatigue state detection technique

Locating driver's eyes exactly firstly to judge driver's eye state.Then by counting eye area and area's reduction extent,noting eye's continual closure time and closure frequency to detect driver's eye fatigue state.Secondly,by skin color segmentation in RGB space,removing the object connected to the border and minishing the range of eye area gradually together with shape validation to locate driver' eye,and then the eye closure times and time are computed.The test proves this method is simple and fast,and it can't be influenced by complex background,faces of different skin color or guise.
Neurotoxic 18-kDa apolipoprotein E fragment production contributes to anesthetic sevoflurane-induced tau phosphorylation and neuroinflammation in vitro

Anesthesia may induce neuronal tau phosphorylation and neurotoxicity in the developing brain. Apolipoprotein E (ApoE) may play a protective role in neuronal activity and injury repair, whereas its 18-kDa fragments are reported to induce neurodegeneration and neuroinflammation in Alzheimer’s disease patients. We aimed to test the hypothesis that differences in 18-kDa ApoE fragment levels, but not full-length ApoE, in primary neurons contribute to differences in tau phosphorylation and neuroinflammation with or without sevoflurane administration. Neurons extracted from wild-type (WT), ApoE knockout (ApoE-KO), and ApoE ε3-and ε2-targeted replacement (ApoE ε3, ApoE ε2) mice were divided into control and sevoflurane groups. Neurons in the sevoflurane group were treated with 21% O2, 5% CO2, and 4.1% sevoflurane, whereas those in the control group were treated with 21% O2 and 5% CO2 only on day 5 of neuronal culture. ApoE mRNA, full-length ApoE, 18-kDa ApoE fragments, Tau-PS202/PT205 (AT8), Tau-PSer396/404 (PHF1), tumor necrosis factor (TNF)-α, and interleukin (IL)-6 and IL-1β levels were measured. The data showed that sevoflurane-induced AT8 and PHF1 increases, and TNF-α, IL-6, and IL-1β increases in WT or ApoE ε3 neurons (both expressing full-length and 18-kDa fragmented ApoE) could be mitigated in ApoE ε2 (only expressing full-length ApoE), but not in ApoE-KO neurons, indicating that differences in 18-kDa ApoE fragments, but not full-length ApoE, in primary mouse neurons contributed to differences in tau phosphorylation and neuroinflammation with or without 4.1% sevoflurane administration.
Wi-Fi 환경에서 센서 및 정규분포 확률을 적용한 실내 위치추정 알고리즘

In this paper, the localization algorithm for improving the accuracy of the positioning using the Wi-Fi fingerprint using the normal distribution probability and the built-in typed accelerometer sensor, the gyroscope sensor of smartphone in the indoor environment is proposed. The experiments for analyzing the performance of the proposed algorithm were carried out at the region of the horizontal and vertical 20m * 10m in the engineering school building of our university
Effects of “It Gets Better” Suicide Prevention Videos on Youth Identifying as Lesbian, Gay, Bisexual, Transgender, Queer, or Other Sexual or Gender Minorities: A Randomized Controlled Trial

Purpose: The “It Gets Better” project (IGBP) features video narratives of lesbian, gay, bisexual, transgender, queer persons or persons with other sexual or gender minority identities (LGBTQ+) of overcoming coming-out-related difficulties. This is the first experimental study investigating effects of these videos. Methods: We conducted a double-blind randomized controlled trial on-site in Austria and online in German-language settings from January to November 2020 with LGBTQ+ youth (14–22 years; n = 483), randomized to an IGBP (n = 242) or control video (n = 241). Suicidal ideation (primary outcome), help-seeking intentions, hopelessness, mood, and sexual identity were assessed at baseline (T1), postexposure (T2), and 4-week follow-up (T3). We assessed differences among gender identities, sexual orientations, with regard to depressive symptoms, and the role of identification. Data were analyzed with linear mixed models and mediation analysis. Results: There was no overall effect on suicidal ideation, but nonbinary/transgender individuals experienced a small-sized improvement (T2: mean change [MC] from baseline MC = −0.06 [95% confidence interval {CI} −0.16 to 0.05], p = 0.60; mean difference [MD] to controls MD = −0.42 [95% CI −0.79 to −0.06], p = 0.02, d = −0.10). An indirect preventive effect on suicidal ideation at T2 through the degree of identification with the protagonist in the video was observed. There was improvement in help-seeking intentions in the intervention group (T2: MC = 0.25 [95% CI 0.15 to 0.35], p < 0.001; MD = 0.28 [95% CI 0.01 to 0.54], p < 0.05, d = 0.09). Conclusion: Video narratives featuring coping might have some potential to decrease suicidal ideation and encourage help-seeking among vulnerable youth identifying with videos, but effects are small and short-lived. Study Registration: German Clinical Trial Registry (DRKS00019913).
An Experimental Study of Squeal Noise Characteristics for Railway Using a Scale Model Test Rig

Squeal noise is a harsh, high-pitched sound that occurs when railways are running at sharp curve tracks. The cause of squeal noise is known to be the transient lateral traction force between wheel and rail. Field measurements are too difficult to control the parameters. Thus, the scaled test rig should have been made in order to investigate the generating mechanism of squeal noise. The unique feature of our test rig, HSTR(Hongik Squeal Testing Rig), is that DOFs of its wheelset are as close to as
The Design of Continuous Observation Work on Mining Failure Feature in the Floor of Mine and Its Practice

This paper introduced the design of continuously observing the mining failure feature in the floor of inclined thin seams and its practice,and made a study of the depth and form of mining failure in the floor of inclined thin seams in combination with analysis by fracture mechanics on the basis of actual measurements,thus providing scientific basis for the safe mining of Huafeng Mine and other similar mines.
Numerical simulation of flexible blank drawer formation

This paper presents a finite element model for a technology of Fexible Blank Drawer Formation (FBDF) for the forming process.In order to verify the feasibility and versatility of the FBDF technology, we performed numerical simulations for multi-point saddle-shaped parts, and for convex curved surface and hemispherical parts. We analysed the effect of different forming methods on wrinkling and cracking, stress and strain distribution as well as circulating and spring back. Also, we studied the effect on the FBDF result caused by the chucking power, blank drawer force, friction coefficient and material parameters. The results showed that under the same conditions, the parts formed by FBDF technology showed uniform stress and strain distribution with little spring back. The blank drawer force can efficiently restrain the defects such as wrinkling and crack.
Breaking Barriers with Bread: Using the Sourdough Starter Microbiome to Teach High-Throughput Sequencing Techniques

Widespread usage of high-throughput sequencing (HTS) in the LIFE SCIENCES has produced a demand for undergraduate and graduate institutions to offer classes exposing students to all aspects of HTS (sample acquisition, laboratory work, sequencing technologies, bioinformatics, and statistical analyses). Despite the increase in demand, many challenges exist for these types of classes. ABSTRACT Widespread usage of high-throughput sequencing (HTS) in the LIFE SCIENCES has produced a demand for undergraduate and graduate institutions to offer classes exposing students to all aspects of HTS (sample acquisition, laboratory work, sequencing technologies, bioinformatics, and statistical analyses). Despite the increase in demand, many challenges exist for these types of classes. We advocate for the usage of the sourdough starter microbiome for implementing meta-amplicon sequencing. The relatively small community, dominated by a few taxa, enables potential contaminants to be easily identified, while between-sample differences can be quickly statistically assessed. Finally, bioinformatic pipelines and statistical analyses can be carried out on personal student laptops or in a teaching computer lab. In two semesters adopting this system, 12 of 14 students were able to effectively capture the sourdough starter microbiome, using the instructor’s paired sample as reference.