bluuebunny/crossref_metadata_2025_split huggingface dataset:
GLIDER: function prediction from GLIDE-based neighborhoods
Authors: Devkota Kapil , Schmidt Henri , Werenski Matt , Murphy James M , Erden Mert , Arsenescu Victor , Cowen Lenore J 
Published: May 2022

AbstractMotivationProtein 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.ResultsGLIDER 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 implementationAll code is publicly available and can be accessed here: https://github.com/kap-devkota/GLIDER.Supplementary informationSupplementary data are available at Bioinformatics online.
Learning when effort matters: neural dynamics underlying updating and adaptation to changes in performance efficacy
Authors: Grahek Ivan , Frömer Romy , Prater Fahey Mahalia , Shenhav Amitai 
Published: May 2022

AbstractTo determine how much cognitive control to invest in a task, people need to consider whether exerting control matters for obtaining rewards. In particular, they need to account for the efficacy of their performance—the degree to which rewards are determined by performance or by independent factors. Yet it remains unclear how people learn about their performance efficacy in an environment. Here we combined computational modeling with measures of task performance and EEG, to provide a mechanistic account of how people (i) learn and update efficacy expectations in a changing environment and (ii) proactively adjust control allocation based on current efficacy expectations. Across 2 studies, subjects performed an incentivized cognitive control task while their performance efficacy (the likelihood that rewards are performance-contingent or random) varied over time. We show that people update their efficacy beliefs based on prediction errors—leveraging similar neural and computational substrates as those that underpin reward learning—and adjust how much control they allocate according to these beliefs. Using computational modeling, we show that these control adjustments reflect changes in information processing, rather than the speed–accuracy tradeoff. These findings demonstrate the neurocomputational mechanism through which people learn how worthwhile their cognitive control is.
Target-specific sentiment analysis method combining word-masking data enhancement and adversarial learning
Authors: Liu Xiaoyang , Dai Shanghong , Fiumara Giacomo , De Meo Pasquale 
Published: May 2022

Abstract
Target-specific sentiment analysis is an emerging topic in the field of text mining but current approaches to deriving the polarity of a sentence suffer from two main drawbacks: on one hand, we lack of a large and well-curated corpus, and on the other hand, current solutions based on deep learning are particularly vulnerable to the attack of adversarial samples. A novel target-specific sentiment classification method is proposed. Firstly, the method of masking target entities is applied to replace synonyms and insert words randomly; secondly, the target-specific sentiment classification model of adversarial learning is constructed with six baseline models; finally, we combine data enhancement and adversarial learning to construct target-specific sentiment classification model. Experimental results show that Macro-F1 values are improved by 0.30–2.91, 0.88–2.42 and 0.13–1.94% compared to the six baseline models by using Laptop14, Restaurant14 and Twitter original datasets, respectively, using Adversarial learning. Using word-masking data enhancement samples and Adversarial learning from Laptop14, Restaurant14 and Twitter shows that Macro-F1 values are improved by 0.9–2.64, 1.59–3.09 and 0.18–1.71% compared to the six baseline (SC), respectively. Our method can effectively improve the quality of samples, it improves the classification performance and the capability of adversarial samples defense.
The Gut Microbiota Metabolite Succinate Promotes Adipose Tissue Browning in Crohn’s Disease
Authors: Monfort-Ferré Diandra , Caro Aleidis , Menacho Margarita , Martí Marc , Espina Beatriz , Boronat-Toscano Albert , Nuñez-Roa Cati , Seco Jesús , Bautista Michelle , Espín Eloy , Megía Ana , Vendrell Joan , Fernández-Veledo Sonia , Serena Carolina 
Published: May 2022

Abstract

Background and Aims
Crohn’s disease [CD] is associated with complex microbe–host interactions, involving changes in microbial communities, and gut barrier defects, leading to the translocation of microorganisms to surrounding adipose tissue [AT]. We evaluated the presence of beige AT depots in CD and questioned whether succinate and/or bacterial translocation promotes white-to-beige transition in adipocytes.

Methods
Visceral [VAT] and subcutaneous [SAT] AT biopsies, serum and plasma were obtained from patients with active [n = 21] or inactive [n = 12] CD, and from healthy controls [n = 15]. Adipose-derived stem cells [ASCs] and AT macrophages [ATMs] were isolated from VAT biopsies.

Results
Plasma succinate levels were significantly higher in patients with active CD than in controls and were intermediate in those with inactive disease. Plasma succinate correlated with the inflammatory marker high-sensitivity C-reactive protein. Expression of the succinate receptor SUCNR1 was higher in VAT, ASCs and ATMs from the active CD group than from the inactive or control groups. Succinate treatment of ASCs elevated the expression of several beige AT markers from controls and from patients with inactive disease, including uncoupling protein-1 [UCP1]. Notably, beige AT markers were prominent in ASCs from patients with active CD. Secretome profiling revealed that ASCs from patients with active disease secrete beige AT-related proteins, and co-culture assays showed that bacteria also trigger the white-to-beige switch of ASCs from patients with CD. Finally, AT depots from patients with CD exhibited a conversion from white to beige AT together with high UCP1 expression, which was corroborated by in situ thermal imaging analysis.

Conclusions
Succinate and bacteria trigger white-to-beige AT transition in CD. Understanding the role of beige AT in CD might aid in the development of therapeutic or diagnostic interventions.
Impact of pre-existing vascular disease on clinical outcomes
Authors: Weight Nicholas , Moledina Saadiq , Zoccai Giuseppe Biondi , Zaman Sarah , Smith Triston , Siller-Matula Jolanta , Dafaalla Mohamed , Rashid Muhammad , Nolan James , Mamas Mamas A 
Published: May 2022

Abstract

Aims
Little is known about the outcomes and processes of care of patients with non-ST-segment myocardial infarction (NSTEMI) who present with ‘polyvascular’ disease.

Methods and results
We analysed 287 279 NSTEMI patients using the Myocardial Ischaemia National Audit Project registry. Clinical characteristics and outcomes were analysed according to history of affected vascular bed—coronary artery disease (CAD), cerebrovascular disease (CeVD), and peripheral vascular disease (PVD)—with comparison to a historically disease-free control group, comprising 167 947 patients (59%). After adjusting for demographics and management, polyvascular disease was associated with increased likelihood of major adverse cardiovascular events (MACEs) [CAD odds ratio (OR): 1.06; 95% confidence interval (CI): 1.01–1.12; P = 0.02] (CeVD OR: 1.19; 95% CI: 1.12–1.27; P &lt; 0.001) (PVD OR: 1.22; 95% CI: 1.13–1.33; P &lt; 0.001) and in-hospital mortality (CeVD OR: 1.24; 95% CI: 1.16–1.32; P &lt; 0.001) (PVD OR: 1.33; 95% CI: 1.21–1.46; P &lt; 0.001). Patients without vascular disease were less frequently discharged on statins (PVD 88%, CeVD 86%, CAD 90%, and control 78%), and those with moderate [ejection fraction (EF) 30–49%] or severe left ventricular systolic dysfunction (EF &lt; 30%) were less frequently discharged on angiotensin-converting enzyme (ACE) inhibitors or angiotensin receptor blockers (ARBs) (CAD 82%, CeVD 77%, PVD 77%, and control 74%). Patients with polyvascular disease were less likely to be discharged on dual antiplatelet therapy (DAPT) (PVD 78%, CeVD 77%, CAD 80%, and control 87%).

Conclusion
Polyvascular disease patients had a higher incidence of in-hospital mortality and MACEs. Patients with no history of vascular disease were less likely to receive statins or ACE inhibitors/ARBs, but more likely to receive DAPT.
Long noncoding RNA GAS5 alleviates the inflammatory response of human periodontal ligament stem cells by regulating the NF-κB signalling pathway
Authors: Yang Qiaolin , Liu Peng , Han Yineng , Wang Chenxin , Huang Yipeng , Li Xiaobei , Zheng Yunfei , Li Weiran 
Published: May 2022

Summary

Objectives
This study investigated the role of lncRNA growth arrest-specific transcript 5 (GAS5) in the inflammatory response of periodontal ligament stem cells (PDLSCs) during periodontitis with attempts to its possible mechanisms.

Materials and methods
Gingiva samples were collected from healthy people and patients with periodontitis. The ligature-induced periodontitis model was established in mice. Cell transfection was utilized to knock down and overexpress GAS5 in PDLSCs. Quantitative real-time polymerase chain reaction (qRT-PCR) and fluorescence in situ hybridization were performed to detect the GAS5 expression. In combination with high-throughput sequencing technology, qRT-PCR, Western blotting, and immunofluorescence were performed to detect the effects of GAS5 on cytokines and proteins in the NF-κB pathway.

Results
GAS5 expression decreased in PDLSCs subjected to compressive force. GAS5 expression was downregulated in the gingiva tissues from patients with periodontitis. Consistent with the results of clinical samples, GAS5 expression decreased in the mouse ligature-induced periodontitis model. GAS5 expression was downregulated in PDLSCs under tumour necrosis factor (TNF)-α stimulation. Knockdown and overexpression of GAS5 increased and decreased the expression of cytokines induced by TNF-α in PDLSCs, respectively. The sequencing results showed that overexpressing GAS5 was related to genes in the NF-κB pathway. Overexpressing GAS5 alleviated p65 phosphorylation and inhibited the entry of p65 into the nucleus in the TNF-α activated NF-κB pathway, whereas GAS5 knockdown resulted in contrasting results.

Conclusions
GAS5 alleviated the expression of cytokines in PDLSCs by inhibiting activation of the TNF-α-mediated NF-κB pathway. These findings provide new insight into the regulation of the PDLSCs inflammation response.
Post-transcriptional regulation during stress
Authors: Hernández-Elvira Mariana , Sunnerhagen Per 
Published: May 2022

AbstractTo remain competitive, cells exposed to stress of varying duration, rapidity of onset, and intensity, have to balance their expenditure on growth and proliferation versus stress protection. To a large degree dependent on the time scale of stress exposure, the different levels of gene expression control: transcriptional, post-transcriptional, and post-translational, will be engaged in stress responses. The post-transcriptional level is appropriate for minute-scale responses to transient stress, and for recovery upon return to normal conditions. The turnover rate, translational activity, covalent modifications, and subcellular localisation of RNA species are regulated under stress by multiple cellular pathways. The interplay between these pathways is required to achieve the appropriate signalling intensity and prevent undue triggering of stress-activated pathways at low stress levels, avoid overshoot, and down-regulate the response in a timely fashion. As much of our understanding of post-transcriptional regulation has been gained in yeast, this review is written with a yeast bias, but attempts to generalise to other eukaryotes. It summarises aspects of how post-transcriptional events in eukaryotes mitigate short-term environmental stresses, and how different pathways interact to optimise the stress response under shifting external conditions.
Genotype by environment interactions for chronic wasting disease in farmed US white-tailed deer
Authors: Seabury Christopher M , Lockwood Mitchell A , Nichols Tracy A 
Published: May 2022

AbstractDespite implementation of enhanced management practices, chronic wasting disease in US white-tailed deer (Odocoileus virginianus) continues to expand geographically. Herein, we perform the largest genome-wide association analysis to date for chronic wasting disease (n = 412 chronic wasting disease-positive; n = 758 chronic wasting disease-nondetect) using a custom Affymetrix Axiom single-nucleotide polymorphism array (n = 121,010 single-nucleotide polymorphisms), and confirm that differential susceptibility to chronic wasting disease is a highly heritable (h2= 0.611 ± 0.056) polygenic trait in farmed US white-tailed deer, but with greater trait complexity than previously appreciated. We also confirm PRNP codon 96 (G96S) as having the largest-effects on risk (P ≤ 3.19E-08; phenotypic variance explained ≥ 0.025) across 3 US regions (Northeast, Midwest, South). However, 20 chronic wasting disease-positive white-tailed deer possessing codon 96SS genotypes were also observed, including one that was lymph node and obex positive. Beyond PRNP, we also detected 23 significant single-nucleotide polymorphisms (P-value ≤ 5E-05) implicating ≥24 positional candidate genes; many of which have been directly implicated in Parkinson’s, Alzheimer’s and prion diseases. Genotype-by-environment interaction genome-wide association analysis revealed a single-nucleotide polymorphism in the lysosomal enzyme gene ARSB as having the most significant regional heterogeneity of effects on chronic wasting disease (P ≤ 3.20E-06); with increasing copy number of the minor allele increasing susceptibility to chronic wasting disease in the Northeast and Midwest; but with opposite effects in the South. In addition to ARSB, 38 significant genotype-by-environment single-nucleotide polymorphisms (P-value ≤ 5E-05) were also detected, thereby implicating ≥ 36 positional candidate genes; the majority of which have also been associated with aspects of Parkinson’s, Alzheimer’s, and prion diseases.
The dilemma of cytomegalovirus and hepatitis B virus interaction
Authors: Khan Muzammil M , Ali Mukarram J , Hanif Hira , Maqsood Muhammad H , Ahmad Imama , Alvarez Javier E G , Catana Maria-Andreea , Lau Daryl T Y 
Published: May 2022

Abstract
Hepatitis B virus (HBV) remains a global public health problem despite the availability of effective vaccine and antiviral therapy. Cytomegalovirus (CMV), another hepatotropic virus, is also very prevalent in the general population worldwide. Both HBV and CMV can persist in the host and have potential to reactivate especially with weakened host cellular immunity. Superimposed CMV infection can lead to severe HBV reactivation. The pathogenesis of the co-infection of HBV and CMV remains poorly understood. Studies reported conflicting results regarding the inhibitory effect of CMV on HBV replication. There is an unmet need on the management of co-infection of HBV and CMV; research initiatives dedicated to understanding their interactions are urgently needed.
Translational suppression via IFG-1/eIF4G inhibits stress-induced RNA alternative splicing in Caenorhabditis elegans
Authors: Chomyshen Samantha C , Tabarraei Hadi , Wu Cheng-Wei 
Published: May 2022

Abstract
Splicing of precursor mRNA is an essential process for dividing cells, and splicing defects have been linked to aging and various chronic diseases. Environmental stress has recently been shown to modify alternative splicing, and molecular mechanisms that influence stress-induced alternative splicing remain unclear. Using an in vivo RNA splicing reporter, we performed a genome-wide RNAi screen in Caenorhabditis elegans and found that protein translation suppression via silencing of the conserved eukaryotic initiation factor 4G (IFG-1/eIF4G) inhibits cadmium-induced alternative splicing. Transcriptome analysis of an ifg-1-deficient mutant revealed an overall decrease in intronic and intergenic reads and prevented cadmium-induced alternative splicing compared to the wild type. We found that the ifg-1 mutant up-regulates &gt;80 RNA splicing regulatory genes controlled by the TGF-β transcription factor SMA-2. The extended lifespan of the ifg-1 mutant is partially reduced upon sma-2 depletion and completely nullified when core spliceosome genes including snr-1, snr-2, and uaf-2 are knocked down. Depletion of snr-1 and snr-2 also diminished the enhanced cadmium resistance of the ifg-1 mutant. Together, these data describe a molecular mechanism through which translation suppression inhibits stress-induced alternative splicing and demonstrate an essential role for RNA splicing in promoting longevity and stress resistance in a translation-compromised mutant.
A network modeling approach provides insights into the environment-specific yield architecture of wheat
Authors: DeWitt Noah , Guedira Mohammed , Murphy Joseph Paul , Marshall David , Mergoum Mohamed , Maltecca Christian , Brown-Guedira Gina 
Published: May 2022

Abstract
Wheat (Triticum aestivum) yield is impacted by a diversity of developmental processes which interact with the environment during plant growth. This complex genetic architecture complicates identifying quantitative trait loci that can be used to improve yield. Trait data collected on individual processes or components of yield have simpler genetic bases and can be used to model how quantitative trait loci generate yield variation. The objectives of this experiment were to identify quantitative trait loci affecting spike yield, evaluate how their effects on spike yield proceed from effects on component phenotypes, and to understand how the genetic basis of spike yield variation changes between environments. A 358 F5:6 recombinant inbred line population developed from the cross of LA-95135 and SS-MPV-57 was evaluated in 2 replications at 5 locations over the 2018 and 2019 seasons. The parents were 2 soft red winter wheat cultivars differing in flowering, plant height, and yield component characters. Data on yield components and plant growth were used to assemble a structural equation model to characterize the relationships between quantitative trait loci, yield components, and overall spike yield. The effects of major quantitative trait loci on spike yield varied by environment, and their effects on total spike yield were proportionally smaller than their effects on component traits. This typically resulted from contrasting effects on component traits, where an increase in traits associated with kernel number was generally associated with a decrease in traits related to kernel size. In all, the complete set of identified quantitative trait loci was sufficient to explain most of the spike yield variation observed within each environment. Still, the relative importance of individual quantitative trait loci varied dramatically. Path analysis based on coefficients estimated through structural equation model demonstrated that these variations in effects resulted from both different effects of quantitative trait loci on phenotypes and environment-by-environment differences in the effects of phenotypes on one another, providing a conceptual model for yield genotype-by-environment interactions in wheat.
Thermal conductivity, density and porosity of sedimentary and metamorphic rocks from the Lower and Higher Himalaya, Western Himalaya, India
Authors: Rao S Eswara , Ray Labani , Khan Tavheed , Ravi G 
Published: May 2022

SUMMARY
Thermal conductivity at ambient conditions is a vital parameter in the determination of heat flow, thermal modelling and various geoengineering purposes. We have measured thermal conductivity in the laboratory at ambient conditions using a steady-state method on 69 samples of sedimentary and metamorphic rocks from the Western Himalaya, India, for the first time covering major lithologies of the region. Density and porosity measurements have been carried out along with petrographic and geochemical studies to characterize these rocks. The investigated rocks include sandstone, limestone, dolomitic limestone, quartzite, slate, phyllite and schist. The average thermal conductivity is found to be the highest (5.4 W m–1 K–1) for quartzite, moderate (ranges between 3.2 and 4.2 W m–1 K–1) for sandstone, limestone and dolomitic limestone and lowest (ranges between 2.6 and 2.9 W m–1 K–1) for the slate, phyllite and schist. The average values of the porosity for the rocks are less than 2 per cent. The variations in thermal conductivity within each rock type more or less reflect the compositional change, rather than the porosity. The measured thermal conductivity of the sandstone and limestone is found much higher than usually observed in such rocks, while it is on the lower side in the case of quartzite, phyllite and schist. Moreover, sedimentary rocks have higher density and lower porosity than usually found in such rocks. In fact, in this region, the sedimentary rocks show a similar density to that of the metamorphic rocks. The average density in sedimentary and metamorphic rocks varies from 2590 to 2780 kg m–3 and 2630 to 2740 kg m–3, respectively. The study region comes under the seismic gap, and several hot springs also exist here. Therefore, the obtained results will be useful in thermal modelling, which is critical for the understanding of earthquake nucleation.
Impact of counseling visual multimedia on use of family planning methods among displaced Nigerian families
Authors: Anibueze Anselm U , Ugwuanyi John Chidi , Ikwuemesi Chukwuezugo Krydz , Onuora Chijioke , Ugwuoke Joel C , Apuke Oberiri Destiny , Gever Verlumun Celestine 
Published: May 2022

Abstract
Although there is evidence of increasing childbirth in internally displaced person (IDP) camps, limited literature exists on how to promote knowledge and use of modern family planning methods among this vulnerable group. The objective of this study was to determine the efficacy of visual multimedia in promoting knowledge and use of modern family planning methods among families in IDP camps in Nigeria. This study was a quasi-experiment of 470 individuals in IDP camps to determine the impact of visual multimedia in enhancing knowledge and intention to use modern family planning. The result of the study showed that at the pre-stage, participants in both the control and treatment groups reported low scores on knowledge and use of modern family planning methods. After the intervention and follow-up assessment, participants in the experimental group reported higher mean scores regarding knowledge and intention to use modern family planning methods while participants in the control group did not significantly improve. Animated visuals were found to be more effective than static pictures.