bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping splice QTLs reveals distinct transcriptional and post-transcriptional regulatory variation of gene expression in pigs
Authors: Zhang Fei , Velez-Irizarry Deborah , Ernst Catherine W , Huang Wen 
Published: November 2022

AbstractBackgroundAlternative splicing is an important step in gene expression, generating multiple isoforms for the same genes and greatly expanding the diversity of proteomes. Genetic variation in alternative splicing contributes to phenotypic diversity in natural populations. However, the genetic basis of variation in alternative splicing in livestock animals including pigs remains poorly understood.ResultsIn this study, using a Duroc x Pietrain F2 pig population, we performed genome-wide analysis of alternative splicing estimated from stranded RNA-Seq data in skeletal muscle. We characterized the genetic architecture of alternative splicing and compared its basic features with overall gene expression. We detected a large number of novel alternative splicing events that were not previously annotated. We found heritability of quantitative alternative splicing scores (percent spliced in or PSI) to be lower than that of overall gene expression. In addition, heritabilities showed little correlation between alternative splicing and overall gene expression. Finally, we mapped expression QTLs (eQTLs) and splice QTLs (sQTLs) and found them to be largely non-overlapping.ConclusionsOur results suggest that regulatory variation exists at multiple levels and that their genetic controls are distinct, offering opportunities for genetic improvement.
scFormer: A Universal Representation Learning Approach for Single-Cell Data Using Transformers
Authors: Cui Haotian , Wang Chloe , Maan Hassaan , Duan Nan , Wang Bo 
Published: November 2022

AbstractSingle-cell sequencing has emerged as a promising technique to decode cellular heterogeneity and analyze gene functions. With the high throughput of modern techniques and resulting large-scale sequencing data, deep learning has been used extensively to learn representations of individual cells for downstream tasks. However, most existing methods rely on fully connected networks and are unable to model complex relationships between both cell and gene representations. We hereby propose scFormer, a novel transformer-based deep learning framework to jointly optimize cell and gene embeddings for single-cell biology in an unsupervised manner. By drawing parallels between natural language processing and genomics, scFormer applies self-attention to learn salient gene and cell embeddings through masked gene modelling. scFormer provides a unified framework to readily address a variety of downstream tasks such as data integration, analysis of gene function, and perturbation response prediction. Extensive experiments using scFormer show state-of-the-art performance on seven datasets across the relevant tasks. The scFormer model implementation is available athttps://github.com/bowang-lab/scFormer.
Subacute changes in brain functional network connectivity after nocturnal sodium oxybate intake are associated with anterior cingulate GABA/glutamate balance
Authors: Bavato Francesco , Esposito Fabrizio , Dornbierer Dario A. , Zölch Niklaus , Quednow Boris B. , Staempfli Philipp , Landolt Hans-Peter , Seifritz Erich , Bosch Oliver G. 
Published: November 2022

AbstractSodium oxybate (γ-hydroxybutyrate, GHB) is an endogenous GHB/GABABreceptor agonist, clinically used to promote slow-wave sleep and reduce next-day sleepiness in disorders such as narcolepsy and fibromyalgia. The neurobiological signature of these unique therapeutic effects remains elusive. Promising current neuropsychopharmacological approaches to understand the neural underpinnings of specific drug effects address cerebral resting-state functional connectivity (rsFC) patterns and neurometabolic alterations. Hence, we performed a placebo-controlled, double-blind, randomized, cross-over pharmacological magnetic resonance imaging study with a nocturnal administration of GHB, combined with magnetic resonance spectroscopy of GABA and glutamate (Glu) in the anterior cingulate cortex (ACC). Sixteen healthy male volunteers received 50mg/kg GHB p.o. or placebo at 02:30am to maximize deep sleep enhancement and multi-modal brain imaging was performed at 09:00am of the following morning. Independent component analysis of whole-brain rsFC revealed a significant increase of rsFC between the salience network (SN) and the right central executive network (rCEN) after GHB intake compared to placebo. This SN-rCEN coupling was significantly associated with changes in GABA and GABA/Glu levels in the ACC (pall<0.05). The proposed framework allows to identify a neural pattern of pharmacological modulation of the SN, which may serve as a neurobiological signature of the wake-promoting effects of GHB.
An updated evolutionary history and taxonomy ofMycobacterium tuberculosislineage 5, also calledM. africanum
Authors: Sahal Muhammed Rabiu , Senelle Gaetan , La Kevin , Molina-Moya Barbara , Dominguez Jose , Panda Tukur , Cambau Emmanuelle , Refregier Guislaine , Sola Christophe , Guyeux Christophe 
Published: November 2022

AbstractContrarily to other lineages such as L2 and L4, there are still scarce whole-genome-sequence data on L5-L6 MTBC clinical isolates in public genomes repositories. Recent results suggest a high complexity of L5 history in Africa. It is of importance for an adequate assessment of TB infection in Africa, that is still related to the presence of L5-L6 MTBC strains. This study reports a significant improvement of our knowledge of L5 diversity, phylogeographical history, and global population structure ofMycobacterium africanumL5. To achieve this aim, we sequenced new clinical isolates from Northern Nigeria and from proprietary collections, and used a new powerful bioinformatical pipeline,TB-Annotatorthat explores not only the shared SNPs but also shared missing genes, identical IS6110insertion sites and shared regions of deletion. This study using both newly sequenced genomes and available public genomes allows to describe new L5 sublineages. We report that the MTBC L5 tree is made-up of at least 12 sublineages from which 6 are new descriptions. We confront our new classification to the most recent published one and suggest new naming for the discovered sublineages. Finally, we discuss the phylogeographical specificity of sublineages 5.1 and sublineage 5.2 and suggest a new hypothesis of L5-L6 emergence in Africa.Impact statementRecent studies onMycobacterium africanum(L5-L6-L9 of MTBC) genomic diversity and its evolution in Africa discovered three new lineages of theMycobacterium tuberculosiscomplex (MTBC) in the last ten years (L7, L8, L9). These discoveries are symptomatic of the delay in characterizing the diversity of the MTBC on the African continent. Another understudied part of MTBC diversity is the intra-lineage diversity of L5 and L6. This study unravels an hidden diversity of L5 in Africa and provides a more exhaustive description of specific genetic features of each sublineage by using a proprietary “TB-Annotator” pipeline. Furthermore, we identify different phylogeographical localization trends between L5.1 and L5.2, suggesting different histories. Our results suggest that a better understanding of the spatiotemporal dynamics of MTBC in Africa absolutely requires a large sampling effort and powerful tools to dig into the retrieved diversity.Data summary[A section describing all supporting external data, software or code, including the DOI(s) and/or accession numbers(s), and the associated URL. If no data was generated or reused in the research, please state this.]The search was done in the TB-Annotator 15901 genomes version which is available at: http://(to be added). The new sequenced genomes are available via NCBI Bioproject accession number: (to be added). The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
Learning Fast and Slow: Increased cortical plasticity leads to memory interference and enhanced hippocampal-cortical interactions
Authors: Navarro-Lobato Irene , Aleman-Zapata Adrian , Samanta Anumita , Bogers Milan , Narayanan Shekhar , Rayan Abdelrahman , Alonso Alejandra , van der Meij Jacqueline , Khamassi Mehdi , Khan Zafar , Genzel Lisa 
Published: November 2022

SummaryOur brain is continuously challenged by daily experiences. Thus, how to avoid systematic erasing of previously encoded memories? While it has been proposed that a dual-learning system with “slow” learning in the cortex and “fast” learning in the hippocampus could protect previous knowledge from interference, this has never been observed in the living organism. Here, we report that increasing plasticity via the viral-induced overexpression of RGS14414 in the prelimbic cortex leads to better one-trial memory, but that this comes at the price of increased interference in semantic-like memory. Indeed, electrophysiological recordings showed that this manipulation also resulted in shorter NonREM-sleep bouts, smaller delta-waves and decreased neuronal firing rates. In contrast, hippocampal-cortical interactions in form of theta coherence during wake and REM-sleep as well as oscillatory coupling during NonREM-sleep were enhanced. Thus, we provide the first experimental evidence for the long-standing and unproven fundamental idea that high thresholds for plasticity in the cortex protects preexisting memories and modulating these thresholds affects both memory encoding and consolidation mechanisms.
Defects in the HIV immature lattice support essential lattice remodeling within budded virions
Authors: Guo Sikao , Saha Ipsita , Saffarian Saveez , Johnson Margaret E 
Published: November 2022

ABSTRACTFor HIV virions to become infectious, the immature lattice of Gag polyproteins attached to the virion membrane must be cleaved. Cleavage cannot initiate without the protease formed by the homo-dimerization of domains linked to Gag. However, only 5% of the Gag polyproteins, termed Gag-Pol, carry this protease domain, and they are embedded within the structured lattice. The mechanism of Gag-Pol dimerization is unknown. Here, we use reaction-diffusion simulations of the immature Gag lattice as derived from experimental structures, showing that dynamics of the lattice on the membrane is unavoidable due to the missing 1/3 of the spherical protein coat. These dynamics allow for Gag-Pol molecules carrying the protease domains to detach and reattach at new places within the lattice. Surprisingly, dimerization timescales of minutes or less are achievable for realistic binding energies and rates despite retaining most of the large-scale lattice structure. We derive a formula allowing extrapolation of timescales as a function of interaction free energy and binding rate, thus predicting how additional stabilization of the lattice would impact dimerization times. We further show that during assembly, dimerization of Gag-Pol occurs stochastically and therefore must be actively suppressed to prevent early activation. By direct comparison to recent biochemical measurements within budded virions, we find that only moderately stable hexamer contacts (−12kBT<ΔG<-8kBT) retain both the dynamics and lattice structures that are consistent with experiment. These dynamics are likely essential for proper maturation, and our models quantify and predict lattice dynamics and protease dimerization timescales that define a key step in understanding formation of infectious viruses.Statement of SignificanceFor retroviruses such as HIV-1, the Gag polyprotein assembles an immature lattice that ensures successful budding from the cell plasma membrane. The first step in the subsequent maturation requires a pair of protease domains embedded within the lattice to form a homodimer. We show here that this homo-dimerization can proceed within minutes despite involving a small subset of Gag monomers, due to the incompleteness of the immature lattice. Using reaction-diffusion simulations, we quantify timescales of first dimerization events between the protease domains and define a formula to extrapolate across a range of energies and rates. Our models illustrate how protein contacts can be weakened to disrupt lattice assembly or stabilized to slow the remodeling essential for viral infectivity.
Risk Factors for 30-day Postoperative Surgical Site Hematoma Requiring Evacuation After Resection of Brain Metastases
Authors: Zheng Yilong , Teo Kejia , Nga Vincent Diong Weng , Yeo Tseng Tsai , Lim Mervyn Jun Rui 
Published: November 2022

AbstractObjectiveTo identify the risk factors for a 30-day postoperative surgical site hematoma requiring evacuation (POH) after surgical resection of brain metastases.MethodsPatients who underwent surgical resection of brain metastases between 2011 and 2019 at our institution were included. Risk factors for a 30-day POH were identified using a multivariate logistic regression model.ResultsA total of 158 patients were included in the analysis. The mean (SD) age of the study population was 59.3 (12.0) years, and 82 (53.2%) patients were female. The incidence of a 30-day POH was 8.2% (13 patients). There was no statistically significant association between the occurrence of a 30-day POH and overall mortality (p=0.100). On multivariate analysis, there was a statistically significant association between a 30-day POH and younger age (OR=0.91; 95% CI=0.83, 0.99; p=0.035), higher BMI (OR=1.61; 95% CI=1.16, 2.46; p=0.010), and blood type AB (OR=21.7; 95% CI=1.66, 522; p=0.031). On receiver operating characteristic analysis, a threshold BMI of 25.1 kg/m2and threshold age of 57 gave the optimum balance of sensitivity and specificity in predicting the occurrence of a 30-day POH.ConclusionsPatients below 57 years old, who have a BMI of above 25, and/or have blood type AB were at higher risk of developing a 30-day POH after surgical resection of brain metastases. Additional care in intraoperative hemostasis and postoperative monitoring may be indicated among patients who have these risk factors.
A new structure for line-start non-slotted axial-flux permanent magnet motor, proposing a novel 3D FEA-based demagnetization reduction approach
Authors: Karimi Aliabad Hadi , Baghayipour Mohammadreza 
Published: November 2022

Purpose
This paper aims to propose a novel simple and efficient structure for line-start axial-flux permanent magnet (LSAFPM) synchronous motor, especially regarding the permanent magnets (PMs) demagnetization reduction.

Design/methodology/approach
At first, a primitive raw scheme of the new structure for the LSAFPM motor is introduced. Considering this raw scheme, the levels of irreversible demagnetization in various regions throughout the entire volume of each PM are evaluated using 3 dimensional (3D) finite elements analysis (3D FEA) in full loading condition during startup until reaching steady state. Based on the results of these analyses, the primitive structural scheme is then modified through segmenting (cutting into four pieces) each PM from where the worst irreversible demagnetization levels occurred.

Findings
As will be demonstrated by the results of 3D FEA, the proposed modified structure is not only capable of successful startup and synchronization of the motor but also it considerably reduces the PM demagnetization level. Thus, the performance of the motor is significantly improved.

Originality/value
The demagnetization of PMs is an important effect in PM synchronous motors, which can greatly affect motor performance. Therefore, it is necessary to be considered in the motor design processes. This effect becomes much more significant in the line-start PM motors because the usual high-magnitude startup induction current produces a strong armature-reaction magnetic field, which may cause the PMs to be irreversibly demagnetized. The approach proposed in this paper provides a structural solution to mitigate the PM demagnetization effect and thereby improve the performance of an LSAFPM motor through modifying the structure of the LSAFPM motor according to an FEA-based PM demagnetization analysis. As a considerable contribution, in this analysis, the variation of demagnetization level between different areas inside each PM is computed and is considered as a basis for proposing an appropriate structural modification to mitigate the PM demagnetization effect as much as possible.
The differential impact of user- and firm-generated content on online brand advocacy: customer engagement and brand familiarity matter
Authors: Aljarah Ahmad , Sawaftah Dima , Ibrahim Blend , Lahuerta-Otero Eva 
Published: November 2022

PurposeThe aim of this study is first, to investigate the relative effect of user-generated content (UGC) and firm-generated content (FGC) on online brand advocacy, and second, to examine the mediation effect of customer engagement and the moderation effect of brand familiarity in the relationship between UGC and FGC and online brand advocacy. The differential impact of UGC and FGC on consumer behavior has yet to receive sufficient academic attention among hospitality scholars.Design/methodology/approachBased on social learning theory, cognitive consistency theory and schema theory, this study established an integrated research framework to explain the relationship between the constructs of the study. This study adopts a scenario-based experimental design in two separate studies within contexts to examine the proposed hypotheses.FindingsThe results revealed that UGC is a stronger predictor of online brand advocacy than FGC. A mediation analysis supported that the effect of digital content marketing types on online brand advocacy occurs because of customer engagement. Further, when the brand was familiar, participants showed a higher level of online brand advocacy than when they were exposed to FGC (vs. unfamiliar brand), whereas the effect of familiar and unfamiliar brands on online brand advocacy remains slightly close to each other when the participants were exposed to UGC. Brand familiarity positively enhanced participants’ engagement when they were exposed to UGC. Further, customer engagement is only a significant mediator when the brand is unfamiliar.Practical implicationsThis paper presents significant managerial implications for hospitality companies about how they can effectively enhance brand advocacy in the online medium.Originality/valueThis research provides a novel contribution by examining the differential impact of UGC and FGC on online brand advocacy as well as uncovering the underlying mechanism of how and under what conditions user- and firm-generated content promotes online brand advocacy in the hospitality context.
Impact of big data analytics on banking: a case study
Authors: He Wu , Hung Jui-Long , Liu Lixin 
Published: November 2022

PurposeThe paper aims to help enterprises gain valuable knowledge about big data implementation in practice and improve their information management ability, as they accumulate experience, to reuse or adapt the proposed method to achieve a sustainable competitive advantage.Design/methodology/approachGuided by the theory of technological frames of reference (TFR) and transaction cost theory (TCT), this paper describes a real-world case study in the banking industry to explain how to help enterprises leverage big data analytics for changes. Through close integration with bank's daily operations and strategic planning, the case study shows how the analytics team frame the challenge and analyze the data with two analytic models – customer segmentation (unsupervised) and product affinity prediction (supervised), to initiate the adoption of big data analytics in precise marketing.FindingsThe study reported relevant findings from a longitudinal data analysis and identified some key success factors. First, non-technical factors, for example intuitive analytics results, appropriate evaluation baseline, multiple-wave implementation and selection of marketing channels critically influence big data implementation progress in organizations. Second, a successful campaign also relies on technical factors. For example, the clustering analytics could promote customers' response rates, and the product affinity prediction model could boost efficient transaction and lower time costs.Originality/valueFor theoretical contribution, this paper verified that the outstanding characteristics of online mutual fund platforms brought up by Nagle, Seamans and Tadelis (2010) could not guarantee organizations' competitive advantages from the aspect of TCT.
Automating tourism online reviews: a neural network based aspect-oriented sentiment classification
Authors: Li Nao , Yang Xiaoyu , Wong IpKin Anthony , Law Rob , Xu Jing Yang , Zhang Binru 
Published: November 2022

PurposeThis paper aims to classify the sentiment of online tourism-hospitality reviews at an aspect level. A new aspect-oriented sentiment classification method is proposed based on a neural network model.Design/methodology/approachThis study constructs an aspect-oriented sentiment classification model using an integrated four-layer neural network: the bidirectional encoder representation from transformers (BERT) word vector model, long short-term memory, interactive attention-over-attention (IAOA) mechanism and a linear output layer. The model was trained, tested and validated on an open training data set and 92,905 reviews extrapolated from restaurants in Tokyo.FindingsThe model achieves significantly better performance compared with other neural networks. The findings provide empirical evidence to validate the suitability of this new approach in the tourism-hospitality domain.Research limitations/implicationsMore sentiments should be identified to measure more fine-grained tourism-hospitality experience, and new aspects are recommended that can be automatically added into the aspect set to provide dynamic support for new dining experiences.Originality/valueThis study provides an update to the literature with respect to how a neural network could improve the performance of aspect-oriented sentiment classification for tourism-hospitality online reviews.