bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variation in the transcriptome response and detoxification gene diversity drives pesticide tolerance in fishes
Authors: Lawrence M.J. , Grayson P. , Jeffrey J.D. , Docker M.F. , Garroway C.J. , Wilson J.M. , Manzon R.G. , Wilkie M.P. , Jeffries K.M. 
Published: December 2021

AbstractPesticides are critical for invasive species management, but often have negative effects on non-target native biota. Tolerance to pesticides should have an evolutionary basis, but this is poorly understood. Invasive sea lamprey (Petromyzon marinus) populations in North America have been controlled with a pesticide lethal to them at lower concentrations than native fishes. We addressed how interspecific variation in gene expression and detoxification gene diversity confer differential pesticide sensitivity in two fish species. We exposed sea lamprey and bluegill (Lepomis macrochirus), a tolerant native species, to TFM, a pesticide commonly used in sea lamprey control, and used whole-transcriptome sequencing of gill and liver to characterize the cellular response. Comparatively, bluegill exhibited a larger number of detoxification genes expressed and a larger number of responsive transcripts overall, which likely contributes to greater tolerance to TFM. Understanding the genetic and physiological basis for pesticide tolerance is crucial for managing invasive species.
LTBP1 promotes fibrillin incorporation into the extracellular matrix
Authors: Przyklenk Matthias , Georgieva Veronika S. , Metzen Fabian , Mostert Sebastian , Kobbe Birgit , Sengle Gerhard , Brachvogel Bent , Mecham Robert P. , Paulsson Mats , Wagener Raimund , Koch Manuel , Schiavinato Alvise 
Published: December 2021

AbstractLTBP1 is a large extracellular matrix protein and an associated ligand of fibrillinmicrofibrils. Knowledge of LTBP1 functions is largely limited to its role in targeting and sequestering TGFβ growth factors within the extracellular matrix, thereby regulating their bioavailability. However, the recent description of a wide spectrum of phenotypes in multiple tissues in patients harboring LTBP1 pathogenic variants suggests a multifaceted role of the protein in the homeostasis of connective tissues. To better understand the human pathology caused by LTBP1 deficiency it is important to investigate its functional role in extracellular matrix formation. In this study, we show that LTBP1 coordinates the incorporation of fibrillin-1 and −2 into the extracellular matrix in vitro. We also demonstrate that this function is differentially exerted by the two isoforms, the short and long forms of LTBP1. Thereby our findings uncover a novel TGFβ-independent LTBP1 function potentially contributing to the development of connective tissue disorders.
Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model
Authors: Suter Polina , Dazert Eva , Kuipers Jack , Ng Charlotte K.Y. , Boldanova Tuyana , Hall Michael N. , Heim Markus H. , Beerenwinkel Niko 
Published: December 2021

AbstractComprehensive molecular characterization of cancer subtypes is essential for predicting clinical outcomes and searching for personalized treatments. We present bnClustOmics, a statistical model and computational tool for multi-omics unsupervised clustering, which serves a dual purpose: Clustering patient samples based on a Bayesian network mixture model and learning the networks of omics variables representing these clusters. The discovered networks encode interactions among all omics variables and provide a molecular characterization of each patient subgroup. We conducted simulation studies that demonstrated the advantages of our approach compared to other clustering methods in the case where the generative model is a mixture of Bayesian networks. We applied bnClustOmics to a hepatocellular carcinoma (HCC) dataset comprising genome (mutation and copy number), transcriptome, proteome, and phosphoproteome data. We identified three main HCC subtypes together with molecular characteristics, some of which are associated with survival even when adjusting for the clinical stage. Cluster-specific networks shed light on the links between genotypes and molecular phenotypes of samples within their respective clusters and suggest targets for personalized treatments.Author summaryMulti-omics approaches to cancer subtyping can provide more insights into molecular changes in tumors compared to single-omics approaches. However, most multi-omics clustering methods do not take into account that gene products interact, for example, as parts of protein complexes or signaling networks. Here we present bnClustOmics, a Bayesian network mixture model for unsupervised clustering of multi-omics data, which can represent dependencies among molecular changes of various omics types explicitly. Unlike other approaches that use data from public interaction databases as ground truth, bnClustOmics learns the dependencies between genes from the analyzed multi-omics dataset. At the same time, our approach can also account for prior knowledge from public interaction databases and use it to guide network learning without losing the ability to learn new dependencies. We applied bnClustOmics to a multi-omics HCC dataset and identified three subtypes similar to those identified in other HCC studies. The cluster-specific networks learned by bnClustOmics revealed additional insights into the molecular characterization of the discovered subgroups and highlighted the changes in signaling networks leading to distinct HCC phenotypes.
Numerical methods for the detection of phase defect structures in excitable media
Authors: Kabus Desmond , Arno Louise , Leenknegt Lore , Panfilov Alexander V. , Dierckx Hans 
Published: December 2021

AbstractElectrical waves that rotate in the heart organize dangerous cardiac arrhythmias. Finding the region around which such rotation occurs is one of the most important practical questions for arrhythmia management. For many years, the main method for finding such regions was so-called phase mapping, in which a continuous phase was assigned to points in the heart based on their excitation status and defining the rotation region as a point of phase singularity. Recent analysis, however, showed that in many rotation regimes there exist phase discontinuities and the region of rotation must be defined not as a point of phase singularity, but as a phase defect line. In this paper, we use this novel methodology and perform a comparative study of three different phase definitions applied to in silico data and to experimental data obtained from optical voltage mapping experiments on monolayers of human atrial myocytes. We introduce new phase defect detection algorithms and compare them with those that appeared in literature already. We find that the phase definition is more important than the algorithm to identify sudden spatial phase variations. Sharp phase defect lines can be obtained from a phase derived from local activation times observed during one cycle of arrhythmia. Alternatively, similar quality can be obtained from a reparameterization of the classical phase obtained from observation of a single timeframe of transmembrane potential. We found that the phase defect line length was (35.9 ± 6.2) mm in the Fenton-Karma model and (4.01 ± 0.55) mm in cardiac human atrial myocyte monolayers. As local activation times are obtained during standard clinical cardiac mapping, the methods are also suitable to be applied to clinical datasets. All studied methods are publicly available and can be downloaded from an institutional web-server.
Psilocybin modulation of dynamic functional connectivity is associated with plasma psilocin and subjective effects
Authors: Olsen Anders S. , Lykkebo-Valløe Anders , Ozenne Brice , Madsen Martin K. , Stenbæk Dea S. , Armand Sophia , Mørup Morten , Ganz Melanie , Knudsen Gitte M. , Fisher Patrick M. 
Published: December 2021

AbstractBackgroundPsilocin, the neuroactive metabolite of psilocybin, is a serotonergic psychedelic that induces an acute altered state of consciousness, evokes lasting changes in mood and personality in healthy individuals, and has potential as an antidepressant treatment. Examining the acute effects of psilocin on resting-state dynamic functional connectivity implicates network-level connectivity motifs that may underlie acute and lasting behavioral and clinical effects.AimEvaluate the association between resting-state dynamic functional connectivity (dFC) characteristics and plasma psilocin level (PPL) and subjective drug intensity (SDI) before and right after intake of a psychedelic dose of psilocybin in healthy humans.MethodsFifteen healthy individuals completed the study. Before and at multiple time points after psilocybin intake, we acquired 10-minute resting-state blood-oxygen-level-dependent functional magnetic resonance imaging scans. Leading Eigenvector Dynamics Analysis (LEiDA) and diametrical clustering were applied to estimate discrete, sequentially active brain states. We evaluated associations between the fractional occurrence of brain states during a scan session and PPL and SDI using linear mixed-effects models. We examined associations between brain state dwell time and PPL and SDI using frailty Cox proportional hazards survival analysis.ResultsFractional occurrences for two brain states characterized by lateral frontoparietal and medial fronto-parietal-cingulate coherence were statistically significantly negatively associated with PPL and SDI. Dwell time for these brain states was negatively associated with SDI and, to a lesser extent, PPL. Conversely, fractional occurrence and dwell time of a fully connected brain state was positively associated with PPL and SDI.ConclusionOur findings suggest that the acute perceptual psychedelic effects induced by psilocybin may stem from drug-level associated decreases in the occurrence and duration of lateral and medial frontoparietal connectivity motifs in exchange for increases in a uniform connectivity structure. We apply and argue for a modified approach to modeling eigenvectors produced by LEiDA that more fully acknowledges their underlying structure. Together these findings contribute to a more comprehensive neurobiological framework underlying acute effects of serotonergic psychedelics.HighlightsWe examined psilocybin effects on resting-state fMRI dynamic functional connectivityDiametrical clustering described as improved strategy for LEiDA-defined brain statesIndividual brain state dynamics defined by fractional occurrence and dwell timeTwo frontoparietal states and a fully connected brain state affected by psilocybinBrain state dynamics associated with psilocin level and subjective experience
Molecular mechanisms governing circulating immune cell heterogeneity across different species revealed by single cell sequencing
Authors: Li Zhibin , Sun Chengcheng , Wang Fei , Wang Xiran , Zhu Jiacheng , Luo Lihua , Ding Xiangning , Zhang Yanan , Ding Peiwen , Wang Haoyu , Pu Mingyi , Li Yuejiao , Wang Shiyou , Qin Qiuyu , Wei Yanan , Sun Jian , Wang Xiangdong , Luo Yonglun , Chen Dongsheng , Qiu Wei 
Published: December 2021

AbstractBackgroundImmune cells play important roles in mediating immune response and host defense against invading pathogens. However, insights into the molecular mechanisms governing circulating immune cell diversity among multiple species are limited.MethodsIn this study, we compared the single-cell transcriptomes of 77□957 immune cells from 12 species using single-cell RNA-sequencing (scRNA-seq). Distinct molecular profiles were characterized for different immune cell types, including T cells, B cells, natural killer cells, monocytes, and dendritic cells.ResultsResults revealed the heterogeneity and compositions of circulating immune cells among 12 different species. Additionally, we explored the conserved and divergent cellular crosstalk and genetic regulatory networks among vertebrate immune cells. Notably, the ligand and receptor pair VIM-CD44 was highly conserved among the immune cells.ConclusionsThis study is the first to provide a comprehensive analysis of the cross-species single-cell atlas for peripheral blood mononuclear cells (PBMCs). This research should advance our understanding of the cellular taxonomy and fundamental functions of PBMCs, with important implications in evolutionary biology, developmental biology, and immune system disorders.
Global plant-frugivore trait matching is shaped by climate and biogeographic history
Authors: McFadden Ian R. , Fritz Susanne A. , Zimmermann Niklaus E. , Pellissier Loïc , Kissling W. Daniel , Tobias Joseph A. , Schleuning Matthias , Graham Catherine H. 
Published: December 2021

ABSTRACTSpecies interactions are influenced by the trait structure of local multi-trophic communities. However, it remains unclear whether mutualistic interactions in particular can drive trait patterns at the global scale, where climatic constraints and biogeographic processes gain importance. Here we evaluate global relationships between traits of frugivorous birds and palms (Arecaceae), and how these relationships are affected, directly or indirectly, by assemblage richness, climate and biogeographic history. We leverage a new and expanded gape size dataset for nearly all avian frugivores, and find a positive relationship between gape size and fruit size, i.e., trait matching, which is influenced indirectly by palm richness and climate. We also uncover a latitudinal gradient in trait matching strength, which increases towards the tropics and varies among zoogeographic realms. Taken together, our results suggest trophic interactions have consistent influences on trait structure, but that abiotic, biogeographic and richness effects also play important, though sometimes indirect, roles in shaping the functional biogeography of mutualisms.
Passive epidemiological surveillance in wildlife in Costa Rica identifies pathogens of zoonotic and conservation importance
Authors: Aguilar-Vargas Fernando , Solorzano-Scott Tamara , Baldi Mario , Barquero-Calvo Elías , Jiménez-Rocha Ana , Jiménez Carlos , Piche-Ovares Marta , Dolz Gaby , León Bernal , Corrales-Aguilar Eugenia , Santoro Mario , Alfaro-Alarcón Alejandro 
Published: December 2021

AbstractEpidemiological surveillance systems for pathogens in wild species have been proposed as a preventive measure for epidemic events. These systems can minimize the detrimental effects of an outbreak, but most importantly, passive surveillance systems are the best adapted to countries with limited resources. Therefore, the present study aims to evaluate the technical and infrastructural feasibility to establish this type of scheme in Costa Rica targeting thedetection of pathogens of zoonotic and conservation importance in wildlife. Between 2018 and 2020, 85 carcasses of free-ranging vertebrates were admitted for post mortem analysis and complementary laboratory analysis, representing a solid basis for the implementation of a passive surveillance system for wildlife diseases in the country. However, we encounter during this research significant constraints that affected the availability of carcasses for analysis, mainly related to the initial identification of cases, detection biases towards events in populated- or easily accessible-areas with nearby located wildlife management centers, further associated with financial disincentives, and limited local logistics capacity. Thus resulting in the exclusion of some geographic regions of the country. This epidemiological surveillance scheme allowed us to estimate the general state of health of the country’s wildlife, establishing the cause of death of the analyzed animals as follows: (i) 46 (54.1%) traumatic events, (ii) 23 (27.1%) infectious agents, (iii) two (2.4%) degenerative illness, (iv) three (3.5%) presumably poisoning, and (v) in 11 (12.9%)undetermined. It also allowed the detection of pathogens such as, canine distemper virus, Klebsiella pneumoniae, Toxoplasma gondii, Trypanosoma spp., Angiostrongylus spp., Dirofilaria spp., Baylisascaris spp., among others. As well as recognizing the circulation of these pathogens around national territory and also on those analyzed species. This strategy is crucial in geographical regions defined as critical for the appearance of diseases due to their great biodiversity and social conditions.
Mobile phone communication for improving uptake of antiretroviral therapy in HIV-infected pregnant women: updated systematic review and meta-analysis
Authors: Tamuzi Jacques L. , Lulendo Gomer , Mbuesse Patrick , Ntambwe Thierry 
Published: December 2021

AbstractObjectiveThe aim of this systematic review is to provide some evidence on the use of mobile phone communication for improving ARV adherence during pregnancy, as well as to investigate whether text messaging on mobile phones could improve follow-up in HIV-exposed infants.MethodsWe did a systematic review and meta-analysis, using CENTRAL (Cochrane Central Register of Controlled Trials), Scopus, MEDLINE via PubMed, Web of Science, and CINAHL to search for studies in English published between 5 may 2016 to May 2021 that assessed the effects of mobile phone in HIV-infected pregnant women. We used MetaPro version 3.0 to compute the OR and RR and their 95%CI. We performed random-effects model meta-analysis for estimating pooled outcomes.ResultsNine studies were included in the meta-analysis. The pooled maternal post-partum retention was (OR 2.20, 95%CI: 1.55 – 3.13, I2 = 53.20%, P < 0.001).In the same line, the pooled odds of ART uptake was (OR 1.5, 95%CI: 1.07-2.11, I2 =0%, P = 0.020) and we found statistically significant impact of mobile phone on HIV testing at 6 weeks and above among HIV exposed children (OR 1.89, 95%CI: 1.04 – 3. 48, I2 = OR 1.89, 95%CI: 1.04 – 3. 48, I2 =88.04%, P = 0.032).ConclusionIn comparison to our previous review, this updated review focuses on moderate evidence for mobile phone communication in HIV-infected pregnant women. The results showed that using a mobile phone improved maternal post-partum retention, ART uptake, and infant HIV testing at 6 weeks and older.
Research on collaborative task assignment method of assembly line
Authors: Shen Weilei , Jiang Qiangqiang , Yang Yang 
Published: December 2021

Purpose
The purpose of this paper is to construct a task assignment model for U-shaped production lines with collaborative task, which is optimized by minimizing the number of workers and balancing the workload of the operators. The ultimate goal is to increase productivity by increasing the U-line balance and balancing the load on the operators.

Design/methodology/approach
First, task selection and update mechanism are analyzed and the task selection mechanism suitable for collaborative task is proposed. Second, M-COMOSAL is obtained by improving the original COMOSAL. Finally, The M-COMOSAL algorithm and the COMAOSAL algorithm are used to perform job assignment on the double-acting clutch U-shaped assembly line.

Findings
According to the allocation scheme obtained by M-COMSOAL, the beat can be adjusted according to the change of order demand. The final allocation scheme is superior to the COMSOAL algorithm in terms of number of workers, working time, production tempo and balance rate. In particular, compared with the old scheme, the new scheme showed a decrease of 16.7% in the number of employees and a 18.8% increase in the production line balance rate. Thus, the method is helpful to reduce the number of operators and balance the workload.

Originality/value
The new algorithm proposed in this paper for the assignment of collaborative task can minimize the number of workers and balance the load of operators, which is of great significance for improving the balance rate of U-shaped production lines and the utilization of personnel or equipment.
Examining the impact of relational benefits on continuance intention of PBS services: mediating roles of user satisfaction and engagement
Authors: Pattnaik Pinaki Nandan , Shukla Mahendra Kumar 
Published: December 2021

PurposeThe purpose of this study is to examine the dimensionality of relational benefits in public bike sharing (PBS) and explore the mediating role of user satisfaction and engagement on the linkage between relational benefits and continuance intention.Design/methodology/approachThis study used a mixed method approach. Data were collected using convenience sampling technique from 411 users of PBS in Bhubaneswar, India. In the first part of the study, in-depth interviews were conducted to identify a set of relational benefits for scale development. In the second part, CB-SEM was used to establish the reliability and validity of the scale and test the hypotheses linking relational benefits with user satisfaction, engagement and continuance intention.FindingsThe analysis suggests that relational benefit is a second order construct having five distinct yet related dimensions namely economic, convenience, environmental, identity related and health and safety benefits. Also, the impact of relational benefits on continuance intention is positively and significantly mediated through user satisfaction and engagement.Research limitations/implicationsThis study is conducted in only one Indian city and is limited to PBS, which, is one of the elements of green transportation and does not cover other modes of transportation. Therefore, generalization of findings beyond this region and the mode of transportation should be done with caution.Originality/valueThis study contributes to the extant management literature by examining the mediating role of user satisfaction and engagement on the linkage between relational benefits and continuance intention which is an unexplored area of research. The study adds to existing knowledge by exploring the dimensionality of relational benefits in PBS context.
Impact of information risk and cost of equity: moderating role of investor attention
Authors: Saleem Sana , Usman Muhammad 
Published: December 2021

PurposeThe purpose of this study is to finds out how investor attention plays the moderating role between the relation of information risk and COE by considering the effect of three different types of information risk, that is private information, lack of quality and transparent information.Design/methodology/approachFor that purpose, data is collected from all the non-financial firms listed on PSX from 2007 to 2019. Two-step system GMM dynamic panel estimators are applied to test the dynamic nature of the proposed model.FindingsThe findings of the study show that investor attention reduces these three information risks by increasing the stock liquidity and decreasing the crash risk which ultimately decreases the COE. Also, this study examined the role of investor attention between the relations of information risk and corporate investment in the dynamic panel model, where the two-step system generalized method of the moment has been applied. The finding of the study shows that investor attention stimulates the innovative investment by increasing investor confidence and decreasing the agency conflict.Originality/valueThis study contributes to the literature by providing the novel findings by considering the role of investor attention in reducing the effect of three different types of information risk, that is private information, less quality as well as less transparency of information and further their effect on the cost of equity.