bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Interferon Resistance of Transmitted HIV-1 is a Consequence of Enhanced Replicative Fitness
Authors: Sugrue Elena , Wickenhagen Arthur , Mollentze Nardus , Aziz Muhamad Afiq , Sreenu Vattipally B , Truxa Sven , Tong Lily , Silva Filipe Ana da , Robertson David L , Hughes Joseph , Rihn Suzannah J , Wilson Sam J 
Published: December 2021

ABSTRACTHIV-1 transmission via sexual exposure is a relatively inefficient process. When successful transmission does occur, newly infected individuals are colonized by either a single or a very small number of establishing virion(s). These transmitted founder (TF) viruses are more interferon (IFN) resistant than chronic control (CC) viruses present 6 months after transmission. To identify the specific molecular defences that make CC viruses more susceptible to the IFN-induced ‘antiviral state’ than TF viruses, we established a pair of fluorescent GFP-IRES-Nef TF and CC viruses and used arrayed interferon-stimulated gene (ISG) expression screening. The relatively uniform ISG resistance of transmitted HIV-1 directed us to investigate the underlying mechanism. Our subsequent in silico simulations, modelling, and in vitro characterisation of a model TF/CC pair (closely matched in replicative fitness), revealed that small differences in replicative growth rates can explain the broad IFN resistance displayed by transmitted HIV-1. We propose that the apparent IFN resistance of transmitted HIV-1 is a consequence of enhanced replicative fitness, as opposed to specific resistance to individual IFN-induced defences.
Multiparameters dependance of tissue shape maintenance in myoblasts multicellular aggregates: the role of intermediate filaments
Authors: Nagle Irène , Delort Florence , Hénon Sylvie , Wilhelm Claire , Batonnet-Pichon Sabrina , Reffay Myriam 
Published: December 2021

AbstractLiquid and elastic behavior of tissues drives their morphology and their response to the environment. They appear as the first insight on tissue mechanics. We explore the role of individual cell properties on spheroids of mouse muscle precursor cells by developing a fully automated surface tension and Young’s modulus measurement system. Flattening multicellular aggregates under magnetic constraint, we show that rigidity and surface tension act as highly sensitive macroscopic reporters closely related to microscopic local tension and effective adhesion. Shedding light on the major contributions of acto-myosin contractility, actin organization and intercellular adhesions, we reveal the role of desmin organization on the macroscopic mechanics of this tissue model.
Predicting Nicotine Metabolism Across Ancestries Using Genotypes
Authors: Baurley James W , Bergen Andrew W , Ervin Carolyn M , Park Sung-shim Lani , Murphy Sharon E , McMahan Christopher S 
Published: December 2021

AbstractBackgroundThere is a need to match characteristics of tobacco users with cessation treatments and risks of tobacco attributable diseases such as lung cancer. The rate in which the body metabolizes nicotine has proven an important predictor of these outcomes. Nicotine metabolism is primarily catalyzed by the enzyme cytochrone P450 (CYP2A6) and CYP2A6 activity can be measured as the ratio of two nicotine metabolites:trans-3’-hydroxycotinine to cotinine (NMR). Measurements of these metabolites are only possible in current tobacco users and vary by biofluid source, timing of collection, and protocols; unfortunately, this has limited their use in clinical practice. The NMR depends highly on genetic variation nearCYP2A6on chromosome 19 as well as ancestry, environmental, and other genetic factors. Thus, we aimed to develop prediction models of nicotine metabolism using easy to obtain genotypes and individual characteristics.ResultsWe identified four multiethnic studies with nicotine metabolites and DNA samples. We constructed a 263 marker panel from filtering genome-wide association scans of the NMR in each study. We then applied seven machine learning techniques to train models of nicotine metabolism on the largest and most ancestrally diverse dataset (N=2239). The models were then validated out-of-sample in the other three studies (total N=1415). Using cross-validation, we found the correlations between the observed and predicted NMR ranged from 0.69 to 0.97 depending on the model. When predictions were averaged in an ensemble model, the correlation was 0.81. The ensemble model generalizes well out-of-sample across ancestries, despite differences in the measurements of NMR between studies, with correlations of: 0.52 for African ancestry, 0.61 for Asian ancestry, and 0.46 for European ancestry. The most influential predictors of NMR identified in more than two models were rs56113850, rs11878604, and 21 other genetic variants nearCYP2A6as well as age and ancestry.ConclusionsWe have developed an ensemble of seven models for predicting the NMR across ancestries from genotypes and age, gender and BMI. Predictions from these models validate out-of-sample in three datasets and associate with nicotine dosages. The knowledge of how an individual metabolizes nicotine could be used to help select the optimal path to reducing or quitting tobacco use, as well as, evaluating risks of tobacco use.
Gene expression is a poor predictor of the metabolite abundance in cancer cells
Authors: Li Huaping , Barbour Jayne A. , Zhu Xiaoqiang , Wong Jason W. H. 
Published: December 2021

AbstractMetabolic reprogramming is a hallmark of cancer characterized by global changes in metabolite levels. However, compared with the study of gene expression, profiling of metabolites in cancer samples remains relatively understudied. We obtained metabolomic profiling and gene expression data from 454 human solid cancer cell lines across 24 cancer types from the Cancer Cell Line Encyclopedia (CCLE) database, to evaluate the feasibility of inferring metabolite levels from gene expression data. For each metabolite, we trained multivariable LASSO regression models to identify gene sets that are most predictive of the level of each metabolite profiled. Even when accounting for cell culture conditions or cell lineage in the model, few metabolites could be accurately predicted. In some cases, the inclusion of the upstream and downstream metabolites improved prediction accuracy, suggesting that gene expression is a poor predictor of steady-state metabolite levels. Our analysis uncovered a single robust relationship between the expression of nicotinamide N-methyltransferase (NNMT) and 1-methylnicotinamide (MNA), however, this relationship could only be validated in cancer samples with high purity, as NNMT is not expressed in immune cells. Together, our findings reveal the challenge of inferring metabolite levels from metabolic enzyme levels and suggest that direct metabolomic profiling is necessary to study metabolism in cancer.
Molecular identification of bats from Wavulgalge cave, Wellawaya, Sri Lanka
Authors: Perera Thejanee , Schwarz Franziska , Muzeniek Therese , Siriwardana Sahan , Becker-Ziaja Beate , Perera Inoka C. , Handunnetti Shiroma , Weerasena Jagathpriya , Premawansa Gayani , Premawansa Sunil , Nitsche Andreas , Yapa Wipula , Kohl Claudia 
Published: December 2021

AbstractThis is the first report on the molecular identification and phylogeny of Rousettus leschenaultii, Rhinolophus rouxii, Hipposideros speoris, Hipposideros lankadiva, Miniopterus fuliginosus bat species in Sri Lanka, inferred from mitochondrially encoded cytochrome b gene sequences. Wellawaya Wavulgalge cave in Sri Lanka is one of the largest sympatric colonies found on the island, occupied by five species of bats. Recent research has indicated that bats show enormous cryptic genetic diversity. Moreover, even in the same species, acoustic properties of echolocation calls and morphological features such as fur colour could vary in different populations. Therefore, we have used molecular techniques for the accurate identification of five bat species recorded in one of the largest cave populations in Sri Lanka. Bats were caught using a hand net and saliva samples were collected non-invasively from each bat using a sterile oral swab. Nucleic acids were extracted from oral swab samples and mitochondrial DNA was amplified using primers targeting the mitochondrially encoded cytochrome b gene. This study identified the bat species recorded in the Wellawaya cave as Rousettus leschenaultii, Rhinolophus rouxii, Hipposideros speoris, Hipposideros lankadiva and Miniopterus fuliginosus. Our findings will contribute to future conservation and systematic studies of bats in Sri Lanka. This study will also provide the basis for a genetic database of Sri Lankan bats.
The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors
Authors: Gavish Avishai , Tyler Michael , Simkin Dor , Kovarsky Daniel , Gonzalez Castro L. Nicolas , Halder Debdatta , Chanoch-Myers Rony , Laffy Julie , Mints Michael , Greenwald Alissa R. , Wider Adi , Tal Rotem , Spitzer Avishay , Hara Toshiro , Tirosh Amit , Puram Sidharth V. , Suva Mario L. , Tirosh Itay 
Published: December 2021

AbstractEach tumor contains malignant cells that differ in genotype, phenotype, and in their interactions with the tumor micro-environment (TME). This results in distinct integrated cellular states that govern intra-tumor heterogeneity (ITH), a central challenge of cancer therapeutics. Dozens of recent studies have begun to describe ITH by single cell RNA-seq, but each study typically profiledonly a small number of tumors and provided a narrow view of transcriptional ITH. Here, we curate, annotate and integrate the data from 77 different studies to reveal the patterns of ITH across 1,163 tumor samples covering 24 tumor types. Focusing on the malignant cells, we find thousands of transcriptional ITH programs that can be described by 41 consensus meta-programs (MPs), each consisting of dozens of genes that are coordinately upregulated in subpopulations of cells within many different tumors. The MPs cover diverse cellular processes and differ in their cancer-type distribution. General MPs associated with processes such as cell cycle and stress vary within most tumors, while context-specific MPs reflect the unique biology of particular cancer types, often resembling developmental cell types and suggesting the co-existence of variable differentiation states within tumors. Some of the MPs are further associated with overall tumor proliferation or immune state, highlighting their potential clinical significance. Based on functional similarities among MPs, we propose a set of 11 hallmarks that together account for the majority of observed ITH programs. Given the breadth and scope of the investigated cohort, the MPs and hallmarks described here reflect the first comprehensive pan-cancer description of transcriptional ITH.
Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders
Authors: Porubsky David , Höps Wolfram , Ashraf Hufsah , Hsieh PingHsun , Rodriguez-Martin Bernardo , Yilmaz Feyza , Ebler Jana , Hallast Pille , Maria Maggiolini Flavia Angela , Harvey William T. , Henning Barbara , Audano Peter A. , Gordon David S. , Ebert Peter , Hasenfeld Patrick , Benito Eva , Zhu Qihui ,   Human Genome Structural Variation Consortium (HGSVC), Lee Charles , Antonacci Francesca , Steinrücken Matthias , Beck Christine R. , Sanders Ashley D. , Marschall Tobias , Eichler Evan E. , Korbel Jan O. 
Published: December 2021

AbstractUnlike copy number variants (CNVs), inversions remain an underexplored genetic variation class. By integrating multiple genomic technologies, we discover 729 inversions in 41 human genomes. Approximately 85% of inversions <2 kbp form by twin-priming during L1-retrotransposition; 80% of the larger inversions are balanced and affect twice as many base pairs as CNVs. Balanced inversions show an excess of common variants, and 72% are flanked by segmental duplications (SDs) or mobile elements. Since this suggests recurrence due to non-allelic homologous recombination, we developed complementary approaches to identify recurrent inversion formation. We describe 40 recurrent inversions encompassing 0.6% of the genome, showing inversion rates up to 2.7×10-4per locus and generation. Recurrent inversions exhibit a sex- chromosomal bias, and significantly co-localize to the critical regions of genomic disorders. We propose that inversion recurrence results in an elevated number of heterozygous carriers and structural SD diversity, which increases mutability in the population and predisposes to disease- causing CNVs.
A peg-in-hole controller for cable-driven serial robots with compliant wrist based on cable tensions and joint positions
Authors: Lou Ya'nan , Quan Pengkun , Lin Haoyu , Liang Zhuo , Wei Dongbo , Di Shichun 
Published: December 2021

Purpose
This purpose of this paper is to design a peg-in-hole controller for a cable-driven serial robot with compliant wrist (CDSR-CW) using cable tensions and joint positions. The peg is connected to the robot link through a CW. It is required that the controller does not rely on any external sensors such as 6-axis wrist force/torque (F/T) sensor, and only the compliance matrix’s estimated value of the CW is known.

Design/methodology/approach
First, the peg-in-hole assembly system based on a CDSR-CW is analyzed. Second, a characterization algorithm using micro cable tensions and joint positions to express the elastic F/T at the CW is established. Next, under the premise of only knowing the compliance matrix’s estimate, a peg-in-hole controller based on force/position hybrid control is proposed.

Findings
The experiment results show that the plug contact F/T can be tracked well. This verifies the validity and correctness of the characterization algorithm and peg-in-hole controller for CDSR-CWs in this paper.

Originality/value
First, to the authors’ knowledge, there is no relevant work about the peg-in-hole assembly task using a CDSR-CW. Besides, the proposed characterization algorithm for the elastic F/T makes the peg-in-hole controller get rid of the dependence on the F/T sensor, which expands the application scenarios of the peg-in-hole controller. Finally, the controller does not require an accurate compliance matrix, which also increases its applicability.
Inspiring workplace happiness: religiosity and organizational trust in the academic context
Authors: Mousa Mohamed , Chaouali Walid 
Published: December 2021

PurposeThis paper focuses on academics in public universities in Egypt. It explores the effect of perceptions of the rector's religiosity and trust on workplace happiness among academics.Design/methodology/approachA total of 600 academics are contacted. After two follow-ups, a total of 540 responses are collected, of which 525 are valid. This study uses SmartPLS 3 to test the hypotheses.FindingsThis paper finds that academics' perceptions of their rector's religiosity have a positive effect on engagement, job satisfaction and affective organizational commitment. Moreover, academics' perceptions of their rector's religiosity positively affect their perceptions of their rector's ability, benevolence and honesty. Furthermore, academics' trust in their rector has a positive effect on their engagement, job satisfaction and affective organizational commitment.Originality/valueThis paper contributes by filling a gap in management and organization literature, in which empirical studies of the relationship between religiosity, organizational trust and workplace happiness are limited or scarce.
Environmental regulation and location dynamics of the livestock industry: evidence from 279 Chinese prefecture-level cities
Authors: Pan Dan , Zhou Yingheng , Zhang Liguo 
Published: December 2021

PurposeThis paper examines the impact of livestock environment regulations (LERs) on the location dynamics of the livestock farming industry. Specifically, it tests whether a “pollution haven effect” (PHE) exists in the Chinese livestock industry.Design/methodology/approachThe authors manually collected LERs data based on the frequency of livestock-related vocabulary in government work reports from 279 prefecture-level cities from 2010 to 2017. Using China's implementation of LERs since 2014 as a natural experiment, the authors employed difference-in-difference (DID) to avoid the endogeneity problem.FindingsLERs have led to a decline in livestock production in regulated areas. Moreover, compared with areas with more stringent LERs – southern China and developed areas, areas where LERs are less stringent – northern China and undeveloped areas, attract more livestock industry. As a result, people in northern China and undeveloped areas are exposed to higher livestock pollution.Originality/valueFirst, most empirical studies on PHE focus on industrial firms. PHE in the livestock industry has received limited attention. This paper aims to fill this gap. Second, this paper regards LERs as an endogenous process and uses the DID method to generate unbiased results. Third, this paper introduces a novel measurement of LERs based on the frequency of livestock-related vocabulary in government work reports from each prefecture city. Fourth, this paper uses prefecture-level data to analyze the PHE of LERs, and thus obtains more reliable results.
Households' intentions under financial vulnerability conditions: is it likely for the COVID-19 pandemic to leave a permanent scar?
Authors: Alhenawi Yasser , Yazdanparast Atefeh 
Published: December 2021

PurposeThe authors draw on psychological reactance theory, collective mental programming, psychological profiles and financial vulnerability experiences to assess the possibility that the pandemic may induce transformative changes in households' behavioral intentions related to financial decisions after the pandemic is over.Design/methodology/approachUsing a unique survey data drawn from four different countries located in North America, Europe, Africa and Latin America, the authors show that the stressful conditions that accompanied the pandemic have instigated a state of financial vulnerability and stimulated instinctual defensive mechanisms among consumers.FindingsThe study results indicate that households have intentions to make defensive decisions in spending, consumption, planning and investment. Furthermore, the authors report evidence that personal psychological heterogeneity (as an individual factor) and collective mental programming (as a cultural factor) play a significant role in shaping households' postpandemic financial intentions.Research limitations/implicationsThe study findings carry important practical implications. For financial institutions, marketers and financial advisors, the authors’ work implies that individual and collective factors affect people's perception and behavioral intentions in response to financial adversities. For social planners and legislators, the authors’ work shows that they should expect not only short-term but also long-term reactions to the COVID-19 pandemic.Originality/valueMost research on the impact of COVID-19 pandemic on households' financial behavior focuses on transitional adjustments made during the pandemic, and little emphasis has been placed on potential postpandemic adjustments. The authors contend that it would be a mistake to analyze the pandemic-induced crisis as a temporary financial hardship.
The multilabel fault diagnosis model of bearing based on integrated convolutional neural network and gated recurrent unit
Authors: Han Shanling , Zhang Shoudong , Li Yong , Chen Long 
Published: December 2021

PurposeIntelligent diagnosis of equipment faults can effectively avoid the shutdown caused by equipment faults and improve the safety of the equipment. At present, the diagnosis of various kinds of bearing fault information, such as the occurrence, location and degree of fault, can be carried out by machine learning and deep learning and realized through the multiclassification method. However, the multiclassification method is not perfect in distinguishing similar fault categories and visual representation of fault information. To improve the above shortcomings, an end-to-end fault multilabel classification model is proposed for bearing fault diagnosis.Design/methodology/approachIn this model, the labels of each bearing are binarized by using the binary relevance method. Then, the integrated convolutional neural network and gated recurrent unit (CNN-GRU) is employed to classify faults. Different from the general CNN networks, the CNN-GRU network adds multiple GRU layers after the convolutional layers and the pool layers.FindingsThe Paderborn University bearing dataset is utilized to demonstrate the practicability of the model. The experimental results show that the average accuracy in test set is 99.7%, and the proposed network is better than multilayer perceptron and CNN in fault diagnosis of bearing, and the multilabel classification method is superior to the multiclassification method. Consequently, the model can intuitively classify faults with higher accuracy.Originality/valueThe fault labels of each bearing are labeled according to the failure or not, the fault location, the damage mode and the damage degree, and then the binary value is obtained. The multilabel problem is transformed into a binary classification problem of each fault label by the binary relevance method, and the predicted probability value of each fault label is directly output in the output layer, which visually distinguishes different fault conditions.
An optimized complex motion prediction approach based on a video synopsis
Authors: Thirumalaiah G. , Immanuel Alex Pandian S. 
Published: December 2021

PurposeThe space-time variants algorithm will not give good results in practical scenarios; when no tubes increase, these techniques will not give the results. It is challenging to reduce the energy of the output synopsis videos. In this paper, a new optimized technique has been implemented that models and covers every frame in the output video.Design/methodology/approachIn the video synopsis, condensing a video to produce a low frame rate (FR) video using their spatial and temporal coefficients is vital in complex environments. Maintaining a database is also feasible and consumes space. In recent years, many algorithms were proposed.FindingsThe main advantage of this proposed technique is that the output frames are selected by the user definitions and stored in low-intensity communication systems and also it gives tremendous support to the user to select desired tubes and thereby stops the criterion in the output video, which can be further suitable for the user's knowledge and creates nonoverlapping tube-oriented synopsis that can provide excellent visual experience.Research limitations/implicationsIn this research paper, four test videos are utilized with complex environments (high-density objects) and show that the proposed technique gives better results when compared to other existing techniques.Originality/valueThe proposed method provides a unique technique in video synopsis for compressing the data without loss.