bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks
Authors: Voznica J , Zhukova A , Boskova V , Saulnier E , Lemoine F , Moslonka-Lefebvre M , Gascuel O 
Published: March 2021

ABSTRACTWidely applicable, accurate and fast inference methods in phylodynamics are needed to fully profit from the richness of genetic data in uncovering the dynamics of epidemics. Standard methods, including maximum-likelihood and Bayesian approaches, generally rely on complex mathematical formulae and approximations, and do not scale with dataset size. We develop a likelihood-free, simulation-based approach, which combines deep learning with (1) a large set of summary statistics measured on phylogenies or (2) a complete and compact representation of trees, which avoids potential limitations of summary statistics and applies to any phylodynamics model. Our method enables both model selection and estimation of epidemiological parameters from very large phylogenies. We demonstrate its speed and accuracy on simulated data, where it performs better than the state-of-the-art methods. To illustrate its applicability, we assess the dynamics induced by superspreading individuals in an HIV dataset of men-having-sex-with-men in Zurich. Our tool PhyloDeep is available ongithub.com/evolbioinfo/phylodeep.
Reconciliation of theoretical and empirical brain criticality via network heterogeneity
Authors: Gu Lei , Wu Ruqian 
Published: March 2021

AbstractInspired by heterogeneity in biological neural networks, we explore a heterogeneous network consisting of receipt, transmission and computation layers. It reconciles the dilemma that the data analysis scheme for empirical records yields non-power laws when applied to microscopic simulation of critical neural dynamics. Detailed analysis shows that the reconciliation is due to synchronization effect of the feedforward connectivity. The network favours avalanches with denser activity in the first half of life, and the result is consistent with the experimental observation. This heterogeneous structure facilitates robust criticality against external stimuli, which implies the inappropriateness of interpreting the subcritcality signature as an indication of subcrtical dynamics. These results propose the network heterogeneity as an essential piece for understanding the brain criticality.
Inhibitors of the Small Membrane (M) Protein Viroporin Prevent Zika Virus Infection
Authors: Brown Emma , Swinscoe Gemma , Lefteri Daniella , Singh Ravi , Moran Amy , Thompson Rebecca , Maskell Daniel , Beaumont Hannah , Bentham Matthew , Donald Claire , Kohl Alain , Macdonald Andrew , Ranson Neil , Foster Richard , McKimmie Clive S. , Kalli Antreas C. , Griffin Stephen 
Published: March 2021

Flaviviruses, including Zika virus (ZIKV), are a significant global health concern, yet no licensed antivirals exist to treat disease. The small Membrane (M) protein plays well-defined roles during viral egress and remains within virion membranes following release and maturation. However, it is unclear whether M plays a functional role in this setting. Here, we show that M forms oligomeric membrane-permeabilising channelsin vitro, with increased activity at acidic pH and sensitivity to the prototypic channel-blocker, rimantadine. Accordingly, rimantadine blocked an early stage of ZIKV cell culture infection.Structure-based channel models, comprising hexameric arrangements of twotrans-membrane domain protomers were shown to comprise more stable assemblages than other oligomers using molecular dynamics (MD) simulations. Models contained a predicted lumenal rimantadine binding site, as well as a second druggable target region on the membrane-exposed periphery.In silicoscreening enriched for repurposed drugs/compounds predicted to bind to either one site or the other. Hits displayed superior potencyin vitroand in cell culture compared with rimantadine, with efficacy demonstrably linked to virion-resident channels. Finally, rimantadine effectively blocked ZIKV viraemia in preclinical models, supporting that M constitutes a physiologically relevant target. This could be explored by repurposing rimantadine, or development of new M-targeted-therapies.
Sars-CoV-2 attack rate in reception and accommodation centres for asylum seekers: systematic review of outbreak media reports in Germany
Authors: Jahn Rosa , Hintermeier Maren , Bozorgmehr Kayvan 
Published: March 2021

ABSTRACTObjectivesDespite concerns about the impact of the severe acute respiratory syndrome corona virus (Sars-CoV-2) in refugee camps, data on attack rates and effectiveness of containment measures are lacking. We aimed to (1) quantify the attack rate of Sars-CoV-2 during outbreaks in reception and accommodation centres in Germany, (2) assess differences in the attack rate based on containment measures, and (3) provide an overview of testing strategies, communication, conflicts, and protection measures for refugees with special needs.MethodsSystematic web-based review of outbreak media reports (until June 2020) on confirmed Sars-CoV-2 cases in reception centers for asylum seekers in Germany using the google search engine. Reports were screened for pre-defined inclusion criteria and complemented by snowball searches. Data on facility name, location, confirmed cases, containment measures, communication, protection strategies, and conflicts was extracted for each outbreak and reporting date. Evidence synthesis: meta-analysis and negative binomial regression.FindingsWe identified 337 media reports on 101 Sars-CoV-2 outbreaks in 99 reception and accommodation centers in Germany. The pooled Sars-CoV-2 attack rate was 13.1% (95% confidence interval, CI: 9.8-16.7). Outbreak sites implementing mass quarantine (n=76) showed higher rates (15.7; 95% CI: 11.6 - 20.2) compared to sites using conventional strategies (6.6; 95%CI: 3.1 - 11.2), yielding a rate ratio of 0.44 (95%CI: 0.27-0.72) adjusted for testing strategies, type and size of accommodation. Conflicts occurred in at least 11.8% of all outbreaks. Few sites reported specific measures to protect refugees with special needs.ConclusionMass quarantine is associated with higher attack rates, and appears to be a counter-productive containment measure in overcrowded camps. Although further research with individual-level data is required to rule out residual confounding, reception centers and refugee camps should follow the available guidelines on Covid-19 response and refrain from mass quarantine if physical distancing cannot be guaranteed.
“I was facilitating everybody else’s life. And mine had just ground to a halt”: the COVID-19 pandemic and its impact on women in the UK
Authors: Herten-Crabb Asha , Wenham Clare 
Published: March 2021

AbstractA growing body of research has highlighted the disproportionately negative impact of the COVID-19 pandemic on women globally. This paper contributes to this work by interrogating the lived realities of 64 women in the UK through semi-structured interviews, undertaken during the first and second periods of lockdown associated with COVID-19 in 2020. Categorising the data by theme and type of gendered disadvantage, this paper explores the normative and policy-imposed constraints experienced by women in 2020, highlighting the role that government can and should proactively play in attending to gender inequalities throughout its COVID-19 response.
YAP1 Regulates the Self-organized Fate Patterning of hESCs-Derived Gastruloids
Authors: Giraldez Servando , Stronati Eleonora , Huang Ling , Hsu Hui-Ting , Abraham Elizabeth , Jones Kathy A. , Estaras Conchi 
Published: March 2021

ABSTRACTDuring gastrulation, the coordinated activity of BMP, WNT and NODAL signaling pathways guide the differentiation of the pluripotent epiblast into the three germinal layers. Recent studies underline the role of the Hippo-effector YAP1 regulating WNT and NODAL signaling pathways and repressing mesoendodermal differentiation in human embryonic stem cells (hESCs). However, the contribution of YAP1 to the cell-fate patterning decisions that transform the epiblast in a three-germ layer gastrula remains unknown. We address this question by analyzing micropatterned 2D-gastruloids derived from hESCs, in the presence and absence of YAP1. Our findings show that YAP1 is necessary for gastrulation. YAP1 KO-gastruloids display reduced ectoderm layer and enlarged mesoderm and endoderm layers, compared to WT. Furthermore, YAP1 regulates the self-organized patterning of the hESCs, as the discrete position of the three germ layers is altered in the YAP1 KO-gastruloids. Our epigenome (single-nuclei ATACseq) and transcriptome (RNA-seq) analysis revealed that YAP1 directly represses the chromatin accessibility and transcription of key genes in the NODAL pathway, including the NODAL and FOXH1 genes. In WT gastruloids, a gradient of NODAL: SMAD2.3 signaling from the periphery to the center of the colony regulates the exit of pluripotency toward endoderm, mesoderm and ectoderm, respectively. Hence, in the absence of YAP1, a hyperactive NODAL signaling retains SMAD2.3 in the nuclei impeding the self-organized differentiation of hESCs. Accordingly, the partial inhibition of NODAL signaling is sufficient to rescue the differentiation and pattern -defective phenotypes of the YAP1 KO gastruloids. Our work revealed that YAP1 is a master regulator of NODAL signaling, essential to instruct germ layer fate patterning in human gastruloids.
When shared concept cells support associations: theory of overlapping memory engrams
Authors: Gastaldi Chiara , Schwalger Tilo , De Falco Emanuela , Quiroga Rodrigo Quian , Gerstner Wulfram 
Published: March 2021

AbstractAssemblies of neurons, called concepts cells, encode acquired concepts in human Medial Temporal Lobe. Those concept cells that are shared between two assemblies have been hypothesized to encode associations between concepts. Here we test this hypothesis in a computational model of attractor neural networks. We find that for concepts encoded in sparse neural assemblies there is a minimal fractioncminof neurons shared between assemblies below which associations cannot be reliably implemented; and a maximal fractioncmaxof shared neurons above which single concepts can no longer be retrieved. In the presence of a periodically modulated background signal, such as hippocampal oscillations, recall takes the form of association chains reminiscent of those postulated by theories of free recall of words. Predictions of an iterative overlap-generating model match experimental data on the number of concepts to which a neuron responds.Authors contributionsAll authors contributed to conception of the study and writing of the manuscript. CG and TS developed the theory. CG wrote the code for all figures. EDF and RQQ provided the experimental data. EDF and CG analyzed the data. WG and CG developed algorithms to fit the experimental data.
Central tendency biases must be accounted for to consistently capture Bayesian cue combination in continuous response data
Authors: Aston Stacey , Negen James , Nardini Marko , Beierholm Ulrik 
Published: March 2021

AbstractObservers in perceptual tasks are often reported to combine multiple sensory cues in a weighted average that improves precision – in some studies, approaching statistically-optimal (Bayesian) weighting, but in others departing from optimality, or not benefitting from combined cues at all. To correctly conclude which combination rules observers use, it is crucial to have accurate measures of their sensory precision and cue weighting. Here, we present a new approach for accurately recovering these parameters in perceptual tasks with continuous responses. Continuous responses have many advantages, but are susceptible to a central tendency bias, where responses are biased towards the central stimulus value. We show such biases lead to inaccuracies in estimating both precision gains and cue weightings, two key measures used to assess sensory cue combination. We introduce a method that estimates sensory precision by regressing continuous responses on targets and dividing the variance of the residuals by the squared slope of the regression line, “correcting-out” the error introduced by the central bias and increasing statistical power. We also suggest a complementary analysis that recovers the sensory cue weights. Using both simulations and empirical data, we show that the proposed methods can accurately estimate sensory precision and cue weightings in the presence of central tendency biases. We conclude that central tendency biases should be (and can easily be) accounted for to consistently capture Bayesian cue combination in continuous response data.
Nicotinamide riboside alleviates Parkinson’s disease symptoms but downregulates dopamine metabolism upon lactacystin-induced proteostasis failure
Authors: Turconi Giorgio , Alam Farhan , SenGupta Tanima , Pirnes-Karhu Sini , Olfat Soophie , Schmidt Mark S. , Mätlik Kärt , Montaño-Rodriguez Ana , Heiskanen Vladimir , Piepponen Petteri T. , Brenner Charles , Holmberg Carina I. , Nilsen Hilde , Andressoo Jaan-Olle , Pirinen Eija 
Published: March 2021

AbstractActivation of mitochondrial metabolism and proteostasis with the NAD+precursor nicotinamide riboside (NR) has emerged as a potential therapeutic approach for neurodegenerative disorders including Parkinson’s disease (PD). However, despite recently started clinical trials, studies on NR in animal models of PD are scarce. In this study, we investigated the effect of NR in multiple models of PD. In transgenicC. elegansoverexpressing α-synuclein, a protein of which aggregation is believed to promote PD, NR rescued PD-like phenotypes including mitochondrial dysfunction and motility defects, decreased oxidative stress, and age-related dopamine (DA) neuron loss. We found that NR eased symptoms of disease by activating the mitochondrial unfolded protein response (UPRmt) via the transcription factoratfs-1. Similarly, in a proteasome inhibitor, lactacystin, -induced mouse model of PD, NR rescued mitochondrial dysfunction and behavioural deficits caused by lactacystin lesion. However, long-term NR supplementation, in conjunction with proteasome inhibition, resulted in decreased DA levels in both the lesioned and unlesioned sides of the substantia nigra with concomitant downregulation of key genes in DA metabolism. Our results suggest specific endpoints that should be monitored in ongoing NR clinical trials.
Platforms' partner networks: the missing link in crowdfunding performance
Authors: Cosma Stefano , Grasso Alessandro Giovanni , Pattarin Francesco , Pedrazzoli Alessia 
Published: March 2021

PurposeA network of partners helps and assists a crowdfunding platform (CFP) in scouting, assessing and selecting projects. This cooperation increases the number of successful projects by attracting a sizable number of investors, proponents and attracting marginal investors when a campaign falls short of the threshold for success. This study examines the role of partner networks in a platform ecosystem, specifically in terms of number of different partners and their diversity in the performance of the crowdfunding campaign.Design/methodology/approachUsing logistic and linear regressions, we analyze a sample of 233 projects, both funded and not funded, launched by 10 Italian equity CFPs between 2014 and 2018.FindingsOur findings indicate that the variety of partners in a platform's network influence the probability of campaign success and how much capital the proponent company raises. CFPs are resource-constrained new ventures, and a network with a wider variety of partners ensures the strategic resources and competencies that are required in an early stage market, thus facilitating campaign funding.Practical implicationsThe variety of partner networks could help CFPs to offer unique and strategic value propositions and define the competitive positioning of platforms.Originality/valueThis study provides a deeper understanding of the determinants of equity crowdfunding campaign performance by emphasizing the role of CFP's network of partners on the entire crowdfunding ecosystem and its underlying organizational elements.
Impact of smart logistics on smart city sustainable performance: an empirical investigation
Authors: Shee Himanshu Kumar , Miah Shah J. , De Vass Tharaka 
Published: March 2021

PurposeTechnologies continue to disrupt logistics and freight transport (known as smart logistics), but their impacts on smart city sustainability is underinvestigated. Drawing on technology, organisation and environment (TOE) perspective, the objective of this study is to empirically investigate the hierarchical effects of smart logistics on smart city sustainable dimensions (i.e. environmental, social and economic).Design/methodology/approachThe study used cross-sectional survey to collect data from urban transporters, warehouse managers, retailers and information technology (IT) managers in Australia. Data were analysed using structural equation modeling (SEM) to test the hypothesised relationship between constructs of smart logistics and smart city sustainable performance.FindingsThe findings reveal that information and communications technologies (ICTs) use and IT capability (ITC) have positive and significant effects on smart logistics. Technology-enabled smart logistics have an immediate positive effect on smart city environment, which in turn has positive impacts on social and economic performance.Practical implicationsThe study informs managers that smart logistics equipped with freight transport telematics can improve smart city environment through enhanced tracking and tracing of goods movement. The improved environmental stewardship is likely to support social and economic performance.Originality/valueSmart city research remains primarily theoretical and focussed on concerns surrounding sustainable growth amid urbanisation and digitalisation. City logistics and urban freights play key role in smart city economic growth, but vehicular pollution pose social and environmental challenges. Technology-assisted smart logistics are likely to improve smart city sustainable performance but yet to find how they affect each other.
Simulation-based search for optimal designs of accelerated life tests through response surface methodology
Authors: Ayasse Daniel , Seo Kangwon 
Published: March 2021

PurposePlanning an accelerated life test (ALT) for a product is an important task for reliability practitioners. Traditional methods to create an optimal design of an ALT are often computationally burdensome and numerically difficult. In this paper, the authors introduce a practical method to find an optimal design of experiments for ALTs by using simulation and empirical model building.Design/methodology/approachInstead of developing the Fisher information matrix-based objective function and analytic optimization, the authors suggest “experiments for experiments” approach to create optimal planning. The authors generate simulated data to evaluate the quantity of interest, e.g. 10th percentile of failure time and apply the response surface methodology (RSM) to find an optimal solution with respect to the design parameters, e.g. test conditions and test unit allocations. The authors illustrate their approach applied to the thermal ALT with right censoring and lognormal failure time distribution.FindingsThe design found by the proposed approach shows substantially improved statistical performance in terms of the standard error of estimates of 10th percentile of failure time. In addition, the approach provides useful insights about the sensitivity of each decision variable to the objective function.Research limitations/implicationsMore comprehensive experiments might be needed to test its scalability of the method.Practical implicationsThis method is practically useful to find a reasonably efficient optimal ALT design. It can be applied to any quantities of interest and objective functions as long as those quantities can be computed from a set of simulated datasets.Originality/valueThis is a novel approach to create an optimal ALT design by using RSM and simulated data.
Humble leader behavior and team creativity: the team learning perspective
Authors: Chen Lifan , Liu Shengming , Wang Yue , Hu Xiaoli 
Published: March 2021

PurposeThis study argues that leader humility is an important facilitator of team creativity. Based on social learning theory, the study explores a new mechanism that links humble leader behavior to team creativity through a path of team learning.Design/methodology/approachData were collected in two private-owned technology companies located in South China. The two-time survey included 77 team leaders and 310 employees. An analysis of time-lagged, multisource data was conducted.FindingsEvidence shows that humble leader behavior promotes team learning behavior through a social learning process, with a subsequent increase in team creativity. This influence is also strengthened when leader effectiveness is high.Practical implicationsTeam creativity is an important determinant of organizational success. This research shows that humble leaders can motivate team creativity by acting as a role model. In addition, this research also reminds us that humble leader behavior loses its effect if the leader is incapable.Originality/valueThis research contributes to existing literature on humble leader behavior and team creativity, especially on the mechanisms and contingency effects between these factors.
Disrupting the brave new world: COVID-19 effects on organisations' sustainability efforts
Authors: Lozano Rodrigo , Barreiro-Gen María 
Published: March 2021

PurposeOrganisations have been working towards becoming more sustainable; where their efforts have been mainly on a steady state focussing on internal proactive changes. The purpose of this paper is to analyse how external events, e.g. COVID-19, affect organisations and their sustainability efforts.Design/methodology/approachA survey was sent to a database of 11,657 contacts, with a response rate of 5.60% obtained. The results were analysed using descriptive statistics, ranking and a ratio analysis comparing different types of organisations (corporations, higher education institutions, civil society and public sector organisations).FindingsCOVID-19 changed the organisation drivers for and barriers to sustainability perspective towards external stimuli, rather than internal factors. COVID-19 also affected the system elements negatively, with the exception of organisational systems. The results also show that the system elements are affected by an external event or crisis and are dependent on the type of organisation.Originality/valueThis paper proposes the “Organisational sustainability transition forced by exogenous events” framework to help organisations better understand and be prepared for unexpected external events. Organisations should learn from the experiences in dealing with COVID-19 and adopt a more humanistic approach to their sustainability efforts, rather than traditional approaches based on solipsism and techno-managerial centrism.