bluuebunny/crossref_metadata_2025_split huggingface dataset:
ZETA: a parameter-free statistical test for neuronal responsiveness
Authors: Montijn Jorrit S. , Seignette Koen , Howlett Marcus H. , Cazemier J. Leonie , Kamermans Maarten , Levelt Christiaan N. , Heimel J. Alexander 
Published: September 2020

AbstractNeurophysiological studies depend on a reliable quantification of whether and when a neuron responds to stimulation. Simple methods to determine responsiveness require arbitrary parameter choices, such as binning size, while more advanced model-based methods require fitting and hyperparameter tuning. These parameter choices can change the results, which invites bad statistical practice and reduces the replicability. New recording techniques that yield increasingly large numbers of cells would benefit from a test for cell-inclusion that requires no manual curation. Here, we present the parameter-free ZETA-test, which outperforms t-tests, ANOVAs, and renewal-process-based methods by including more cells at a similar false-positive rate. We show that our procedure works across brain regions and recording techniques, including calcium imaging and Neuropixels data. Furthermore, in illustration of the method, we show in mouse visual cortex that 1) visuomotor-mismatch and spatial location are encoded by different neuronal subpopulations; and 2) optogenetic stimulation of VIP cells leads to early inhibition and subsequent disinhibition.
Horizontal gene transfer-mediated bacterial strain variation affects host fitness
Authors: Wang Yun , Baumdicker Franz , Kuenzel Sven , Staubach Fabian 
Published: September 2020

AbstractHow microbes affect host fitness and environmental adaptation has become a fundamental research question in evolutionary biology. We tested for associations of bacterial genomic variation andDrosophila melanogasteroffspring number in a microbial Genome Wide Association Study (GWAS). Leveraging strain variation in the genusGluconobacter, a genus of bacteria that are commonly associated withDrosophilaunder natural conditions, we pinpoint the thiamine biosynthesis pathway (TBP) as contributing to differences in fitness conferred to the fly host. By tracing the evolutionary history of TBP genes inGluconobacter, we find that TBP genes were most likely lost and reacquired by horizontal gene transfer (HGT). We suggest that HGT might contribute to microbiome flexibility and speculate that it can also more generally contribute to host adaptation.
The intrinsically disordered N-terminus of the voltage-dependent anion channel
Authors: Preto Jordane , Krimm Isabelle 
Published: September 2020

AbstractThe voltage-dependent anion channel (VDAC) is a critical β-barrel membrane protein of the mitochondrial outer membrane, which regulates the transport of ions and ATP between mitochondria and the cytoplasm. In addition, VDAC plays a central role in the control of apoptosis and is therefore of great interest in both cancer and neurodegenerative diseases. Although not fully understood, it is presumed that the gating mechanism of VDAC is governed by its N-terminal region which, in the open state of the channel, exhibits an α-helical structure positioned midway inside the pore and strongly interacting with the β-barrel wall.In the present work, we performed molecular simulations with a recently developed force field for disordered systems to shed new light on known experimental results, showing that the N-terminus of VDAC is an intrinsically disordered region (IDR). First, simulation of the N-terminal segment as a free peptide highlighted its disordered nature and the importance of using an IDR-specific force field to properly sample its conformational landscape. Secondly, accelerated dynamics simulation of a double cysteine VDAC mutant under applied voltage revealed metastable low conducting states of the channel representative of closed states observed experimentally. Related structures were characterized by partial unfolding and rearrangement of the N-terminal tail, that led to steric hindrance of the pore. Our results indicate that the disordered properties of the N-terminus are crucial to properly account for the gating mechanism of VDAC.Author summaryThe voltage-dependent anion channel (VDAC) is a membrane protein playing a pivotal role in the transport of ions or ATP across the mitochondrial outer membrane as well as in the induction of apoptosis. At high enough membrane potential, VDAC is known to transition from an open state to multiple closed states, reducing the flow of ions through the channel and blocking the passage of large metabolites. While the structure of the open state was resolved more than a decade ago, a molecular description of the gating mechanism of the channel is still missing. Here we show that the N-terminus of VDAC is an intrinsically disordered region and that such a property has a profound impact on its dynamics either as a free peptide or as part of the channel. By taking disordered properties of the N-terminus into account, we managed to generate long-lived closed conformations of the channel at experimental values of the membrane potential. Our results provide new insights into the molecular mechanism driving the gating of VDAC.
A novel method for sensor-based quantification of single/multi-cellular traction dynamics and remodeling in 3D matrices
Authors: Emon Bashar , Li Zhengwei , Joy Md Saddam Hossain , Doha Umnia , Kosari Farhad , Saif M Taher A 
Published: September 2020

AbstractCellsin vivogenerate mechanical forces (traction) on surrounding 3D extra cellular matrix (ECM) and cells. Such traction and biochemical cues may remodel the matrix, e.g. increase stiffness, which in turn influences cell functions and forces. This dynamic reciprocity mediates development and tumorigenesis. Currently, there is no method available to directly quantify single cell traction and matrix remodeling in 3D. Here, we introduce a method to fulfil this long-standing need. We developed a high-resolution microfabricated sensor which hosts a 3D cell-ECM tissue formed by self-assembly. It measures cell forces and tissue-stiffness and can apply mechanical stimulation to the tissue. We measured single and multicellular force dynamics of fibroblasts (3T3), human colon (FET) and lung (A549) cancer cells and cancer associated fibroblasts (CAF05) with 1 nN resolution. Single cells show significant force fluctuations in 3D. FET/CAF co-culture system, mimicking cancer tumor microenvironment, increased tissue stiffness by 3 times within 24 hours.
A vaccine built from potential immunogenic pieces derived from the SARS-CoV-2 spike glycoprotein
Authors: Marchan Jose 
Published: September 2020

ABSTRACTCoronavirus Disease 2019 (COVID-19) represents a new global threat demanding a multidisciplinary effort to fight its etiological agent—severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this regard, immunoinformatics may aid to predict prominent immunogenic regions from critical SARS-CoV-2 structural proteins, such as the spike (S) glycoprotein, for their use in prophylactic or therapeutic interventions against this rapidly emerging coronavirus. Accordingly, in this study, an integrated immunoinformatics approach was applied to identify cytotoxic T cell (CTC), T helper cell (THC), and Linear B cell (BC) epitopes from the S glycoprotein in an attempt to design a high-quality multi-epitope vaccine. The best CTC, THC, and BC epitopes showed high viral antigenicity, lack of allergenic or toxic residues, and suitable HLA-viral peptide interactions. Remarkably, SARS-CoV-2 receptor-binding domain (RBD) and its receptor-binding motif (RBM) harbour several potential epitopes. The structure prediction, refinement, and validation data indicate that the multi-epitope vaccine has an appropriate conformation and stability. Three conformational epitopes and an efficient binding between Toll-like receptor 4 (TLR4) and the vaccine model were observed. Importantly, the population coverage analysis showed that the multi-epitope vaccine could be used globally. Notably, computer-based simulations suggest that the vaccine model has a robust potential to evoke and maximize both immune effector responses and immunological memory to SARS-CoV-2. Further research is needed to accomplish with the mandatory international guidelines for human vaccine formulations.Graphical Abstract
The susceptibility analysis ofEchinococcus multilocularisprotoscoleces tubulin to mebendazole and RNA interference
Authors: Shi Qiqi , Huo Lele , Jiang Bin , Gao Haijun , Zheng Jinxin , Tao Yi , Zhang Haobing 
Published: September 2020

ABSTRACTAlveolar echinococcosis, caused by the larval (metacestode) stage of the tapewormEchinococcus multilocularis, is a lethal parasitosis of the liver prevalent in the Northern Hemisphere. For chemotherapy the benzimidazole derivatives mebendazole and albendazole were introduced, which were found to disrupt the microtubules by inhibition of the polymerization of tubulin into microtubules, and β-tubulin was determined to be the drug target molecule. In the present study, we evaluated the chemosensitivity ofE. multilocularisprotoscoleces tubulin to mebendazole and RNA interference in vitro, and to explore whether the molecular level and ultrastructure ofE. multilocularisprotoscoleces microtubules change post-mebendazole and RNA interference. We identified that mebendazole is parasitostatic toE. multilocularisprotoscoleces through suppression the tubulin expression and change the flame cell morphology in molecular level, besides RNA interference indicated thatβ 2tubulin is probably one of the vital tubulin gene to form the flame cell and the protonephridial system tubules (collective tubes) ofE. multilocularisprotoscoleces. Molecular level and ultrastructure detection were performed by reverse transcription-PCR, western blotting and transmission electron microscope. The RNA interference would be probably as a parasitocidal method to disrupt the survival of PSCs, extend that the relevant tubulin maybe as potential target for drug development against AE.
An easy, reliable and rapid SARS-CoV2 RT-LAMP based test for Point-of-Care and diagnostic lab
Authors: Gouilh Meriadeg AR , Cassier Renaud , Maille Elodie , Schanen Cécile , Rocque Louis-Marie , Vabret Astrid 
Published: September 2020

ABSTRACTThis study presents and evaluates a rapid and all-in-one SARS-CoV-2 RT-LAMP based molecular detection system, including RNA extraction or not, for point-of-care or massive testing of naso-pharyngeal swabs. The point-of-care format uses LoopX©, a small portative device ensuring optimal LAMP reaction and automated reading with 95.2% and 95.5% sensitivity and specificity respectively. This system might also be useful for testing other sample types such as saliva.
Guiding the student entrepreneur – Considering the emergent adult within the pedagogy–andragogy continuum in entrepreneurship education
Authors: Hägg Gustav , Kurczewska Agnieszka 
Published: September 2020

PurposeThe purpose of the paper is to build on current discussions about the need for and role of guidance in learning and teaching, as well as to theoretically develop its specifics to further advance our scholarly understanding of how to structure and enhance entrepreneurship education.Design/methodology/approachThe paper takes a synthesizing conceptual approach, built on developmental psychology, instructional science, expertise research as well as the pedagogy–andragogy discussion and the role of guidance in contemporary entrepreneurship education research. In addition, a new term, odigogy, is developed.FindingsOdigogy, from the Greek word odigós (to guide), addresses how to navigate student entrepreneurs in higher education. The term seeks to correspond both to the specifics of entrepreneurship as a subject and the characteristics of students in the classroom who are in a transitional phase between adolescence and adulthood.Practical implicationsThe paper contributes to current entrepreneurship education discussions by offering a more balanced terminology positioned between how to teach (pedagogy) and how adults learn (andragogy). The paper provides insights for teachers when developing teaching methods and learning activities in higher education.Originality/valueBy introducing the term odigogy the paper seeks to contribute an enhanced understanding of the entrepreneurial learning process in higher education, which does not match pedagogical assumptions on how to teach children or adolescents, nor andragogical assumptions on how adults learn, or how to engage students in self-directed learning as presented in heutagogy.
Links between influence strategies and satisfaction: reexamination from the dyadic and network perspectives
Authors: Liu Yi , Liu Ting , Li Yuan , Ruan Liyang 
Published: September 2020

Purpose
Previous studies have investigated the influence strategy–economic satisfaction links within a pairwise framework. This study aims to reexamine this issue in a network context from both the structural and relational embeddedness perspectives.

Design/methodology/approach
An ego network approach in which the network consists of a focal distributor, other distributors and alternate manufacturers is adopted to measure the distributor’s network. Drawing on data from 124 distributors from China’s tire industry, a hierarchical multiple regression analysis is used to test the hypotheses.

Findings
The empirical results find a positive relationship between a manufacturer’s noncoercive influence strategies and the distributor’s economic satisfaction and an inverse U-shaped relationship between coercive influence strategies and economic satisfaction. It discusses the joint effects of coercive and noncoercive influence strategies and finds that the former mitigate the positive effects of the latter and that the latter flatten the inverse-U shaped effect of the former. Further, when a distributor spans rich structural holes, the effects of coercive and noncoercive influence strategies on economic satisfaction weaken. When a distributor has strong ties with its network members, the effects of noncoercive influence strategies are mitigated, while the effects of coercive influence strategies are enhanced.

Practical implications
This study provides implications for manufacturers, particularly concerning how to properly exert influence strategies to improve distributors’ economic satisfaction. Manufacturers should consider the attributes of the networks in which the distributors are embedded, involving structural holes and tie strength. They should also carefully use the two influence strategies simultaneously.

Originality/value
This study contributes to the influence strategy literature by incorporating a network perspective by empirically examining the different moderating effects of structural holes and tie strength; provides a new and powerful explanation for the effects that coercive influence strategies have on economic satisfaction by testing an inverse U-shaped effect; and examines the effects of the interaction of two strategies.
Fire resistance of corroded high-strength structural concrete
Authors: Sobhan Khaled , Reddy Dronnadula V. , Martinez Fernando 
Published: September 2020

Purpose
The exposure of reinforced concrete structures such as high-rise residential buildings, bridges and piers to saline environments, including exposure to de-icing salts, increases their susceptibility to corrosion of the reinforcing steel. The exposure to fire can further deteriorate the structural integrity of corroded concrete structures. This combined effect of corrosion damage and fire exposure is not generally addressed in the structural concrete design codes. The synergistic combination of the effects of corrosion and fire forms the basis of this paper.

Design/methodology/approach
Concrete beam specimens with different strengths were prepared, moist-cured and corroded with impressed current. Later, they were “crack-scored” for corrosion evaluation, after which half were exposed to fire in a gas kiln. The fire damage was evaluated by nondestructive testing using ultrasonic pulse velocity. Next, all specimens were tested for residual flexural strength. They were then autopsied, and the level of corrosion was determined based on mass loss of the reinforcement.

Findings
For corroded specimens, the flexural capacity loss because of fire exposure increases as the compressive strength increases. In general, the higher the crack score, the higher the corresponding mass loss, unless some partial/segmental debonding of the reinforcement occurred. The degree of corrosion increases with decreasing compressive strength. The residual moment capacity, based on analytically determined capacities of uncorroded and nonfire-exposed beams, was significantly lower than those of uncorroded beams exposed to fire.

Originality/value
The combined effects of corrosion and fire on the mechanical properties of structural concrete are relatively unknown, and no guidance is available in the existing design codes to address this issue. Accordingly, the findings of the paper are expected to be valuable to both researchers and design engineers and can be regarded as the initial investigation on this topic.
Functional traits explain trophic allometries of cephalopods
Authors: Murphy Kieran J. , Pecl Gretta T. , Richards Shane A. , Semmens Jayson M. , Revill Andrew T. , Suthers Iain M. , Everett Jason D. , Trebilco Rowan , Blanchard Julia L. 
Published: September 2020

Abstract

Individual body size strongly influences the trophic role of marine organisms and the structure and function of marine ecosystems. Quantifying trophic position–individual body size relationships (trophic allometries) underpins the development of size‐structured ecosystem models to predict abundance and the transfer of energy through ecosystems. Trophic allometries are well studied for fishes but remain relatively unexplored for cephalopods.

Cephalopods are important components of coastal, oceanic and deep‐sea ecosystems, and they play a key role in the transfer of biomass from low trophic positions to higher predators. It is therefore important to resolve cephalopod trophic allometries to accurately represent them within size‐structured ecosystem models.

We assessed the trophic positions of cephalopods in an oceanic pelagic (0–500 m) community (sampled by trawling in a cold‐core eddy in the western Tasman Sea), comprising 22 species from 12 families, using bulk tissue stable isotope analysis and amino acid compound‐specific stable isotope analysis. We assessed whether ontogenetic trophic position shifts were evident at the species‐level and tested for the best predictor of community‐level trophic allometry among body size, taxonomy and functional grouping (informed by fin and mantle morphology).

Individuals in this cephalopod community spanned two trophic positions and fell into three functional groups on an activity level gradient: low, medium and high. The relationship between trophic position and ontogeny varied among species, with the most marked differences evident between species from different functional groups. Activity‐level‐based functional group and individual body size are best explained by cephalopod trophic positions (marginal R2 = 0.43).

Our results suggest that the morphological traits used to infer activity level, such as fin‐to‐mantle length ratio, fin musculature and mantle musculature are strong predictors of cephalopod trophic allometries. Contrary to established theory, not all cephalopods are voracious predators. Low activity level cephalopods have a distinct feeding mode, with low trophic positions and little‐to‐no ontogenetic increases. Given the important role of cephalopods in marine ecosystems, distinct feeding modes could have important consequences for energy pathways and ecosystem structure and function. These findings will facilitate trait‐based and other model estimates of cephalopod abundance in the changing global ocean.
Transcriptomic reprogramming of the oceanic diatom Skeletonema dohrnii under warming ocean and acidification
Authors: Thangaraj Satheeswaran , Sun Jun 
Published: September 2020

SummaryUnder ocean warming and acidification, diatoms use a unique acclimation and adaptation strategy by saving energy and utilizing it for other cellular processes. However, the molecular mechanisms that underlie this reprogramming of energy utilization are currently unknown. Here, we investigate the metabolic reprogramming of the ecologically important diatom Skeletonema dohrnii grown under two different temperature (21°C and 25°C) and pCO2 (400 and 1000 ppm) levels, utilizing global transcriptomic analysis. We find that evolutionary changes in the baseline gene expression, which we termed transcriptional up‐ and downregulation, is the primary mechanism used by diatoms to acclimate to the combined conditions of ocean warming and acidification. This transcriptional regulation shows that under higher temperature and pCO2 conditions, photosynthesis, electron transport and carboxylation were modified with increasing abundances of genes encoding ATP, NADPH and carbon gaining for the carbon‐dioxide‐concentrating mechanisms (CCMs). Our results also indicate that changes in the transcriptional regulation of CCMs led to a decrease in the metabolic cost to save energy by promoting amino acid synthesis and nitrogen assimilation for the active protein processing machinery to adapt to warming and ocean acidification. This study generated unique metabolic insights into diatoms and suggests that future climate change conditions will cause evolutionary changes in oceanic diatoms that will facilitate their acclimation strategy.
Receipt of opioids and patient care experiences among nonsurgical hospitalized adults
Authors: Mazurenko Olena , Blackburn Justin , Bair Matthew J. , Kara Areeba Y. , Harle Christopher A. 
Published: September 2020

AbstractObjectiveTo examine the association between receipt of opioids and patient care experiences among nonsurgical hospitalized adults.Data SourcesA total of 17 691 patient‐level responses to the Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) patient care experience survey linked to medical records from nonsurgical hospitalizations in an 11‐hospital health care system in a Midwestern state, years 2011‐2016.Study DesignWe conducted a pooled cross‐sectional study that used propensity score matching analyses and logistic regression to estimate the relationship between patients’ care experience measures (overall and pain‐specific) and their receipt of opioids while hospitalized. In supplementary analyses, we used the same propensity score matching methods to estimate the relationship between patient care experience measures and receipt of opioids in four patient subgroups based on average patient‐reported pain during hospitalization (no pain; mild pain; moderate pain; and severe pain).Principal FindingsReceipt of opioids was not associated with patient care experience measures in our main analysis. In our supplementary analysis, we found lower ratings for pain control among hospitalizations for patients who reported moderate pain (Marginal Effects = −4.5 percent; P value = .015).ConclusionsCounter to some previous studies, we observed that receipt of opioids was not associated with patient care experience measures for nonsurgical hospitalized adults. These findings may be due to different pain experiences of adults hospitalized for nonsurgical versus surgical reasons.