bluuebunny/crossref_metadata_2025_split huggingface dataset:
New gene association measures by joint network embedding of multiple gene expression datasets
Authors: Wu Guiying , Li Xiangyu , Guo Wenbo , Wei Zheng , Hu Tao , Gu Jin 
Published: March 2020

ABSTRACTLarge number of samples are required to construct a reliable gene co-expression network, the samples from a single gene expression dataset are obviously not enough. However, batch effect may widely exist among datasets due to different experimental conditions. We proposed JEBIN (Joint Embedding of multiple BIpartite Networks) algorithm, it can learn a low-dimensional representation vector for each gene by integrating multiple bipartite networks, and each network corresponds to one dataset. JEBIN owns many inherent advantages, such as it is a nonlinear, global model, has linear time complexity with the number of genes, dataset or samples, and can integrate datasets with different distribution. We verified the effectiveness and scalability of JEBIN through a series of simulation experiments, and proved better performance on real biological data than commonly used integration algorithms. In addition, we conducted a differential co-expression analysis of hepatocellular carcinoma between the single-cell and bulk RNA-seq data, and also a contrast between the hepatocellular carcinoma and its adjacency samples using the bulk RNA-seq data. Analysis results prove that JEBIN can obtain comprehensive and stable gene co-expression networks through integrating multiple datasets and has wide prospect in the functional annotation of unknown genes and the regulatory mechanism inference of target genes.
Brain network motifs are markers of loss and recovery of consciousness
Authors: Duclos Catherine , Nadin Danielle , Mahdid Yacine , Tarnal Vijay , Picton Paul , Vanini Giancarlo , Golmirzaie Goodarz , Janke Ellen , Avidan Michael S. , Kelz Max B. , Mashour George A. , Blain-Moraes Stefanie 
Published: March 2020

AbstractMotifs are patterns of inter-connections between nodes of a network, and have been investigated as building blocks of directed networks. This study explored the re-organization of 3-node motifs during loss and recovery of consciousness. Nine healthy subjects underwent a 3-hour anesthetic protocol while 128-channel electroencephalography (EEG) was recorded. In the alpha (8–13 Hz) band, five-minute epochs of EEG were extracted for: baseline; induction; unconscious; 30-, 10- and 5-minutes pre-recovery of responsiveness; 30- and 180-minutes post-recovery of responsiveness. We constructed a functional brain network using the weighted and directed phase lag index, on which we calculated the frequency and topology of 3-node motifs. Three motifs (motifs 1, 2 and 5) were significantly present across participants and epochs, when compared to random networks (p<0.05). The topology of motifs 1 and 5 changed significantly between responsive and unresponsive epochs (p<0.01). Motif 1 was constituted by long-range chain-like connections, while motif 5 was constituted by short-range, loop-like connections. Our results suggest that anesthetic-induced unconsciousness is associated with a topological re-organization of network motifs. As motif topological re-organization may precede (motif 5) or accompany (motif 1) the return of responsiveness, motifs could contribute to the understanding of the neural correlates of consciousness.
IsOculudentavisa bird or even archosaur?
Authors: Li Zhiheng , Wang Wei , Hu Han , Wang Min , Yi Hongyu , Lu Jing 
Published: March 2020

AbstractRecent finding of a fossil –Oculudentavis khaungraaeXing et al. 2020, entombed in a Late Cretaceous amber – was claimed to represent a humming bird-sized dinosaur1. Regardless of the intriguing evolutionary hypotheses about the bauplan of Mesozoic dinosaurs (including birds) posited therein, this enigmatic animal demonstrates various morphologies resembling lizards. IfOculudentaviswas a bird, it challenges several fundamental morphological differences between Lepidosauria and Archosauria. Here we reanalyze the original computed tomography scan data ofOculudentavis. Morphological evidences demonstrated here highly contradict the avian or even archosaurian phylogenetic placement ofOculudentavis. In contrast, our analysis revealed multiple synapomorphies of the Squamata in this taxon, including pleurodont marginal teeth and an open infratemporal fenestra, which suggests a squamate rather than avian or dinosaurian affinity ofOculudentavis.
Negative effects characterization and comparative transcriptomics elucidation on the lag phase of an industrialS. cerevisiaeunder the corn stover hydrolysate stress
Authors: Kuang Xiaolin , Guo Yaping , Zhang Zhengyue , Hu Xiangdong , Han Xuebing , Ouyang Yidan , Xiao Difan , Li Qian , Wang Hanyu , Li Xi , Chen Qiang , Ma Menggen 
Published: March 2020

AbstractDuring biofuels fermentation from pretreated lignocellulosic biomass, the strong toxicity of the lignocellulose hydrolysate is resulted from the synergistic effect of multiple lignocellulosic inhibitors, which far exceeds the sum of effects caused by every single inhibitor. Meanwhile, the synergistic effect is unclear and the underlying response mechanism of the industrial yeast towards the actual pretreated lignocellulose hydrolysate is still under exploration. Here, we employed an industrialS. cerevisiaefor the transcriptomic analysis in two time points (early and late) of the lag phase under the corn stover hydrolysate stress. As investigation, the corn stover hydrolysate caused the accumulation of reactive oxygen species (ROS), damages of mitochondrial membrane and endoplasmic reticulum (ER) membrane in the industrialS. cerevisiaeYBA_08 during the lag phase, especially these negative effects were more significant at the early lag phase. Based on the transcriptome profile, the industrialS. cerevisiaeYBA_08 might recruit stress-related transcription factors (MSN4,STE12,SFL1,CIN5,COM2,MIG3, etc.) through the mitogen-activated protein kinase (MAPK)-signaling pathway to induce a transient G1/G2 arrest, and to activate defense bioprocesses like protectants metabolism, sulfur metabolism, glutaredoxin system, thioredoxin system, heat shock proteins chaperone and oxidoreductase detoxification, resisting those compounded stresses including oxidative stress, osmotic stress and structural stress. Surprisingly, this defense system might be accompanied with the transient repression of several bioprocesses like fatty acid metabolism, purinede novobiosynthesis and ergosterol biosynthesis.ImportanceThis research systematically demonstrated the lag phase response of an industrial yeast to the lignocellulosic hydrolysate in transcriptional level, providing a molecular fundament for understanding the synergistic effect of various lignocellulosic inhibitors and the regulatory mechanism of tolerance for industrial yeasts under this stress.
Depression of heart rate in fish at critically high temperatures is due to atrioventricular block
Authors: Haverinen Jaakko , Vornanen Matti 
Published: March 2020

ABSTRACTAt critically high temperature, cardiac output in fish collapses due to depression of heart rate (bradycardia). However, the cause of bradycardia remains unresolved. Here we provide a mechanistic explanation for the temperature induced bradycardia. To this end rainbow trout (Oncorhynchus mykiss; acclimated at +12°C) were exposed to acute warming, while cardiac function was followed from electrocardiograms. From +12°C to +25.3°C, electrical excitation between different parts of the heart was coordinated but above +25.3°C atrial and ventricular beating rates became partly dissociated due to 2:1 atrioventricular (AV) block. With further warming atrial rate increased to the peak value of 188 ± 22 bpm at +27°C, while the rate of the ventricle reached the peak value of 124 ± 10 bpm at +25.3°C and thereafter dropped to 111 ± 15 bpm at +27°C. In single ventricular myocytes, warming from +12°C to +25°C attenuated electrical excitability as evidenced by increases in rheobase current and critical depolarization required to trigger action potential. The depression of excitability was caused by temperature induced decrease in input resistance (sarcolemmal K+leak via the outward IK1current) of resting myocytes and decrease in inward charge transfer by the Na+current (INa) of active myocytes. Collectively these findings show that at critically high temperatures AV block causes ventricular bradycardia which is an outcome from the increased excitation threshold of the ventricle due to changes in passive (resting ion leak) and active (inward charge movement) electrical properties of ventricular myocytes. The sequence of events from the level of ion channels to the cardiac functionin vivoprovides a mechanistic explanation for the depression of cardiac output in fish at critically high temperature.
Highly Sensitive Identification of Lymphatic and Hematogenous Metastasis Routes of Novel Radiolabeled Exosomes Using Non-invasive PET Imaging
Authors: Jung Kyung Oh , Kim Young-Hwa , Chung Seock-Jin , Kang Keon Wook , Rhee Siyeon , Pratx Guillem , Chung June-Key , Youn Hyewon 
Published: March 2020

Clinically, there has been significant interest in the use of exosomes for diagnostic applications as promising biomarkers and therapeutic applications as therapeutic vehicles. However, knowledge ofin vivophysiological biodistribution of exosomes was difficult to assess until now. Physiological distribution of exosomes in the body must be elucidated for clinical application. In this study, we aimed to develop reliable and novel methods to monitor biodistribution of exosomes usingin vivoPET and optical imaging.MethodsExosomes were isolated from cultured medium of 4T1, mouse breast cancer cells. Exosomes were labeled with Cy7 and64Cu (or68Ga). In mice, radio/fluorescent dye-labeled exosomes were injected through the lymphatic routes (footpad injection) and hematogenous metastatic routes (tail vein injection). Fluorescence and PET images were obtained and quantified. Radio-activity ofex vivoorgans was measured by gamma counter.ResultsPET signals from exosomes in the lymphatic metastatic route were observed in the draining lymph nodes, which are not distinguishable with optical imaging. Immunohistochemistry revealed greater uptake of exosomes in brachial and axillary lymph nodes than inguinal lymph node. After administration through the hematogenous metastasis pathway, accumulation of exosomes was clearly observed in PET images in the lungs, liver, and spleen, showing results similar toex vivogamma counter data.ConclusionExosomes from tumor cells were successfully labeled with64Cu (or68Ga) and visualized by PET imaging. These results suggest that this cell type-independent, quick, and easy exosome labeling method using PET isotopes could provide valuable information for further application of exosomes in the clinic.
Delivering equitable distance library services to off-campus users at the University of the Free State in South Africa
Authors: Coetzer Lianda , Mapulanga Patrick 
Published: March 2020

PurposeThe purpose of this study is to assess the perceived satisfaction of Advanced Certificate in Teaching students and facilitators regarding online library services offered by the University of the Free State (UFS) in South Africa.Design/methodology/approachThe study adopted a quantitative approach with open-ended questions that generated some qualitative data. Data has been presented using descriptive statistics in the form of tables, graphs and charts and thematic content analysis for some qualitative data.FindingsAll learners in this study were adults between 45 and 55 years of age. Of the respondents, 13% lacked online experience, while about 85% had never used online library services and 35% indicated that Google was their primary source of information. The majority of respondents indicated information literacy as a core function of the academic library. High data cost in South Africa came out as one of the major issues affecting distance learners as well as login and password frustrations. The study confirmed computer anxiety, physical discomfort, information overflow and prompt response as some of the perceived challenges and levels of satisfaction respectively of Advanced Certificate in Teaching students and facilitators regarding online library services offered by the University of the Free State (UFS) in South Africa.Practical implicationsThe study revealed that a distance learning library policy is of the essence because it helps to put in place rules and regulations that guide the delivery of distance library services.Originality/valueThe offering of online and distance library services is a fairly new concept to the UFS library. This study bridges the gap between theory and practice regarding the perceived satisfaction of distance users on online library services and how to improve the current practice.
Attractive and facilitating store atmospheric stimuli
Authors: Bhatt Gaurav , Sarkar Abhigyan , Sarkar Juhi Gahlot 
Published: March 2020

PurposeThe majority of past studies on the physical store environment have focused on the impacts of distinct store environmental cues like music, crowding and décor on consumers' responses. However, recent research posits that consumer is more likely to experience several cues in a combination, rather than in isolation, i.e. different categories of store environmental cues are likely to impact consumer psychology holistically. Hence, our study aims to identify the relevant factors of store atmospheric cues impacting consumer's attitude in physical retail store context and validate scales to measure such factors.Design/methodology/approachThis research develops and validates psychometrically reliable scales to measure two broad store stimuli factors namely: attractive and facilitating store stimuli, following the scale development method suggested by Churchill (1979).FindingsThe study shows that attractive store stimuli predict affective and sensory store brand experiences. The facilitating store stimuli moderate the effects of attractive store stimuli on affective and sensory store brand experiences. Affective and sensory store brand experiences predict store satisfaction.Originality/valueThis research contributes to the existing body of store ambience research by empirically understanding the psychological mechanism through which customers perceive different store cues holistically leading to the elicitation of store satisfaction.
Modelling Twitter conversations in #favela towards the conceptualization of the eVoice of the unheard
Authors: Inversini Alessandro , Williams Nigel L. , Rega Isabella , Samakovlis Ioanna 
Published: March 2020

PurposeThe purpose of this study to shed light on the importance of social media hosted content related to socially-motivated discussions. Moving from the field of communication for development, the research leverages social media as a powerful tool for collecting and analyse peer-to-peer communication towards the conceptualization of eVoices of Unheard. The deep understanding of these conversation can generate recommendations for organizations and governments designing and providing interventions fostering local socio-economic development.Design/methodology/approachThe study presents a large-scale analysis of social media interactions on the topic “#favela” to generate insights into a social network structure, narrative contents and meaning generated.FindingsStructurally, the analysed networks are comparable with those presented in current academic literature; automatic text analysis confirmed the promise of the inner value of communication for development opening the floor to conceptualization of the “eVoices of unheard”, which is the collective and conscious use of social media to mediate community discussions about tangible and intangible issues related to socio-economic development.Originality/valueFramed within the rise of interactive communication for development this research show that social media an support the notion of voice proposed by Couldry (2010) moving from process (i.e. the recording of the voice) towards value (i.e. the possibility of giving an account of one’s life and its conditions to have an impact on human life and resources) thereby understanding intangible issues related with socio-economic development.
Navigating the campus past: college yearbook controversies
Authors: Batchelor Oliver 
Published: March 2020

Purpose
This paper is about the controversies stemming from digitized college and university yearbook photos and the professional values of librarians and archivists in helping higher education communities to confront their unsettling pasts. The actions taken by college librarians and archivists reveal their dedication to core values.

Design/methodology/approach
The approach taken in this concept paper includes a review of various college yearbook controversies in higher education and the strategies used by librarians to address the controversy.

Findings
My findings revealed that librarians and archivists play a crucial role in assisting higher education institutions in coming to terms with their histories.

Originality/value
Although various news outlets have reported on college yearbook controversies, very few (if any) library publications have addressed this issue. This document will serve as a comprehensive evaluation of the controversies and how librarians have taken action.
Increased risk of dementia in patients with genital warts: A nationwide cohort study in Taiwan
Authors: Lin Chia‐Hua , Chien Wu‐Chien , Chung Chi‐Hsiang , Chiang Chien‐Ping , Wang Wei‐Ming , Chang Hsin‐An , Kao Yu‐Chen , Tzeng Nian‐Sheng 
Published: March 2020

AbstractGenital warts are a common sexually transmitted disease caused by human papillomavirus (HPV) infections. The prevalence of dementia is 4–8% in those aged 65 years or older in Taiwanese community studies, with a high social and economic burden for patients, family caregivers, the community and society. Previous studies have shown that viral infections such as herpes simplex and herpes zoster were associated with dementia. This study aimed to investigate the association between dementia and HPV infections. A population‐based cohort study using data from Taiwan’s National Health Insurance Research Database was conducted. Fine and Grays’s survival analysis was employed to estimate the hazard ratios (HR) and 95% confidence intervals (CI) for the association between genital warts and dementia. From all of the potential participants aged 50 years or more, a total of 16 116 patients were enrolled, including 4029 genital warts‐infected patients, with 12 087 sex‐, age‐ and indexed date‐matched controls (1:3). The cumulative incidences of dementia were 10.72 per 103 person‐years and 6.43 per 103 person‐years in the genital warts and control group, respectively. There were 475 dementia cases from the genital warts cohort during the follow‐up period of 15 years. The adjusted HR for dementia was 1.485 (95% CI, 1.321–1.668;P < 0.001) for genital warts patients after adjusting for all of the covariates. Our study indicates that genital warts infection may increase the risk of dementia.
Plant diversity in hedgerows and road verges across Europe
Authors: Vanneste Thomas , Govaert Sanne , De Kesel Willem , Van Den Berge Sanne , Vangansbeke Pieter , Meeussen Camille , Brunet Jörg , Cousins Sara A. O. , Decocq Guillaume , Diekmann Martin , Graae Bente J. , Hedwall Per‐Ola , Heinken Thilo , Helsen Kenny , Kapás Rozália E. , Lenoir Jonathan , Liira Jaan , Lindmo Sigrid , Litza Kathrin , Naaf Tobias , Orczewska Anna , Plue Jan , Wulf Monika , Verheyen Kris , De Frenne Pieter 
Published: March 2020

Abstract

Linear landscape elements such as hedgerows and road verges have the potential to mitigate the adverse effects of habitat fragmentation and climate change on species, for instance, by serving as a refuge habitat or by improving functional connectivity across the landscape. However, so far this hypothesis has not been evaluated at large spatial scales, preventing us from making generalized conclusions about their efficacy and implementation in conservation policies.

Here, we assessed plant diversity patterns in 336 vegetation plots distributed along hedgerows and road verges, spanning a macro‐environmental gradient across temperate Europe. We compared herb‐layer species richness and composition in these linear elements with the respective seed‐source (core) habitats, that is, semi‐natural forests and grasslands. Next, we assessed how these differences related to several environmental drivers acting either locally, at the landscape level or along the studied macro‐ecological gradient.

Across all regions, about 55% of the plant species were shared between forests and hedgerows, and 52% between grasslands and road verges. Habitat‐specialist richness was 11% lower in the linear habitats than in the core habitats, while generalist richness was 14% higher. The difference in floristic composition between both habitat types was mainly due to species turnover, and not nestedness. Most notably, forest‐specialist richness in hedgerows responded positively to tree cover, tree height and the proportion of forests in the surrounding landscape, while generalist richness was negatively affected by tree height and buffering effect of trees on subcanopy temperatures. Grassland and road verge diversity was mainly influenced by soil properties, with positive effects of basic cation levels on the number of specialists and those of bioavailable soil phosphorus on generalist diversity.

Synthesis and applications. We demonstrate that linear landscape elements provide a potential habitat for plant species across Europe, including slow‐colonizing specialists. Additionally, our results stress the possibility for land managers to modify local habitat features (e.g. canopy structure, subcanopy microclimate, soil properties, mowing regime) through management practices to enhance the colonization success of specialists in these linear habitats. These findings underpin the management needed to better conserving the biodiversity of agricultural landscapes across broad geographical scales.
Association of FcγRIIA‐R/H131 polymorphism and systemic lupus erythematosus lupus nephritis risk: A meta‐analysis
Authors: Xu Yuan , Wei Hui‐Ting , Zou Jun‐Ju , Ma Yue‐Rong 
Published: March 2020

AbstractAimPrevious studies have discussed association of FcγRIIA‐R/H131 polymorphism and systemic lupus erythematosus (SLE), lupus nephritis (LN) risk. However, conclusions were inconsistent.MethodsA meta‐analysis was performed in this study with allelic contrast (allele R vs H), additive model (genotype RR vs HH), recessive model (genotype RR vs RH + HH), and dominant model (genotype RR + RH vs HH).ResultsA total of 33 studies discussed the correlation between FcγRIIA‐R/H131 polymorphism and SLE, involving 5652 SLE patients and 6322 controls. Allele R was significantly related to SLE in the overall population (odds ratio [OR] = 1.238, P < .001), Asian (OR = 1.237, P < .001) and European population (OR = 1.212, P = .012). Additive, recessive and dominant models were correlating with SLE in the overall population (OR = 1.448, P < .001; OR = 1.303, P < .001; OR = 1.310, P < .001), Asian population (OR = 1.640, P = .001; OR = 1.437, P < .001; OR = 1.344, P = .005), respectively. In addition, 22 studies evaluated relation of FcγRIIA‐R/H131 polymorphism with LN, involving 2065 patients with LN, and 2023 patients without LN. Results showed that allele R and the other 3 models related to LN susceptibility in the overall population when discussing differences of polymorphism between patients with/without LN. We further compared differences of polymorphism between patients with LN and controls, showing that additive and recessive models related to LN risk in the overall population, Asian, European and North American populations.ConclusionIn summary, FcγRIIA‐R/H131 polymorphism is associated with SLE and LN.