bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal environments drive convergent evolution of a faster pace-of-life in tropical butterflies
Authors: Halali Sridhar , van Bergen Erik , Breuker Casper J , Brakefield Paul M , Brattström Oskar 
Published: May 2020

ABSTRACTGlobal change can trigger shifts in habitat stability and shape the evolution of organismal life-history strategies, with unstable habitats typically favouring a faster pace-of-life. We test this hypothesis in species-rich Mycalesina butterflies that have undergone parallel radiations in Africa, Asia, and Madagascar. First, our ancestral state reconstruction of habitat preference, using ~85% of extant species, revealed that early forest-linked lineages began to invade seasonal savannahs during the Late Miocene-Pliocene. Second, rearing replicate pairs of forest and savannah species from the African and Malagasy radiation in a common garden experiment, and utilising published data from the Asian radiation, demonstrated that savannah species consistently develop faster, have smaller bodies, higher fecundity with an earlier investment in reproduction, and reduced longevity, compared to forest species across all three radiations. We argue that time-constraints for reproduction favoured the evolution of a faster pace-of-life in savannah species that facilitated their persistence in seasonal habitats.
Orderly assembly underpinning built-in asymmetry in the yeast centrosome duplication cycle requires cyclin-dependent kinase
Authors: Geymonat Marco , Peng Qiuran , Guo Zhiang , Yu Zulin , Unruh Jay R. , Jaspersen Sue L. , Segal Marisa 
Published: May 2020

ABSTRACTAsymmetric astral microtubule organization drives the polarized orientation of theS. cerevisiaemitotic spindle and primes the invariant inheritance of the old spindle pole body (SPB, the yeast centrosome) by the bud. This model has anticipated analogous centrosome asymmetries featuring in self-renewing stem cell divisions. We previously implicated Spc72, the cytoplasmic receptor for the gamma-tubulin nucleation complex, as the most upstream determinant linking SPB age, functional asymmetry and fate. Here we used structured illumination microscopy and biochemical analysis to explore the asymmetric landscape of nucleation sites inherently built into the spindle pathway and under the control of cyclin-dependent kinase (CDK). We show that CDK enforces Spc72 asymmetric docking by phosphorylating Nud1/centriolin. Furthermore, CDK-imposed order in the construction of the new SPB promotes the correct balance of nucleation sites between the nuclear and cytoplasmic faces of the SPB. Together these contributions by CDK inherently link correct SPB morphogenesis, age and fate.
No fruits without color: Cross-modal priming and EEG reveal different roles for different features across semantic categories
Authors: Argiris Georgette , Rumiati Raffaella I. , Crepaldi Davide 
Published: May 2020

AbstractCategory-specific impairments witnessed in patients with semantic deficits have broadly dissociated into natural and artificial kinds. However, how the category of food (more specifically, fruits and vegetables) fits into this distinction has been difficult to interpret, given a pattern of deficit that has inconsistently mapped onto either kind, despite its intuitive membership to the natural domain. The present study explores the effects of a manipulation of a visual sensory (i.e., color) or functional (i.e., orientation) feature on the consequential semantic processing of fruits and vegetables (and tools, by comparison), first at the behavioral and then at the neural level. The categorization of natural (i.e., fruits/vegetables) and artificial (i.e., utensils) entities was investigated via cross–modal priming. Reaction time analysis indicated a reduction in priming for color-modified natural entities and orientation-modified artificial entities. Standard event-related potentials (ERP) analysis was performed, in addition to linear classification. For natural entities, a N400 effect at central channel sites was observed for the color-modified condition compared relative to normal and orientation conditions, with this difference confirmed by classification analysis. Conversely, there was no significant difference between conditions for the artificial category in either analysis. These findings provide strong evidence that color is an integral property to the categorization of fruits/vegetables, thus substantiating the claim that feature-based processing guides as a function of semantic category.
A Study of Secondary School Students’ Participation in a Novel Course on Genomic Principles and Practices
Authors: Stefanile Adam 
Published: May 2020

AbstractThis paper presents the design, development, and validation of a study among secondary school students’ participation in a novel course on genomic principles and practices by analyzing and documenting evidence of their participation, and educational outcomes, in a novel course on genomic principles and practices. A mixed methods approach, using qualitative and quantitative methods, was used to address three research questions. 1) Based on affective evidence, how did secondary school students perceive and critically judge, content topics learned in a course on modern genomic principles and practices? 2) Based on cognitive evidence, how much of the content did secondary school students learn when they participated in a course on modern genomic principles and practices? 3) Using individual interview evidence, what are the major perceptions that the secondary school students expressed throughout the duration of the course? The participants were provided an opportunity to comment on the course through individual and collaborative interviews, in order to find out to what extent they perceived the course to be interesting and challenging. Future inquiry expanding from this research would help to establish the foundational pathway for designing a more inclusive genomics curriculum. In conclusion, the course offered real-life/real-world applications that encourage all students to conceptualize genomics, human health, diseases, medicine, ethics, beliefs, research, and careers.
Effect of mechanical properties of monofilament twines on the catch efficiency of biodegradable gillnets
Authors: Grimaldo Eduardo , Herrmann Bent , Jacques Nadine , Vollstad Jørgen , Su Biao 
Published: May 2020

AbstractGillnets made of the biodegradable resin polybutylene succinate co-adipate-co-terephthalate (PBSAT) were tested under commercial fishing conditions to compare their fishing performance with that of conventional nylon polyamide (PA) gillnets. Both types of gillnets were made of 0.55 mm Ø monofilaments. However, since the biodegradable nets are weaker than nylon PA nets when using the same monofilament diameter, we also used biodegradable nets made of 0.60 mm Ø monofilament that had a similar tensile strength to the 0.55 mm Ø nylon PA nets. The relative catch efficiency of the different gillnet types was evaluated over the 2018 autumn fishing season for saithe and cod in northern Norway. For cod, both biodegradable gillnets (0.55 and 0.60 mm) had a significantly lower catch efficiency compared to the traditional nylon PA net (0.55 mm) with estimated catch efficiencies of 62.38% (CI: 50.55–74.04) and 54.96% (CI: 35.42–73.52) compared with the nylon PA net, respectively. Similarly for saithe, both biodegradable gillnets (0.55 and 0.60 mm) had a lower estimated catch efficiency compared to the traditional nylon PA net (0.55 mm) with estimated catch efficiencies of 83.40% (71.34–94.86) and 83.87% (66.36–104.92), compared with the nylon PA net, respectively. Tensile strength does not explain the differences in catch efficiency between the two gillnet types, since increasing the twine diameter of the biodegradable gillnets (to match the strength of nylon PA gillnets) did not yield similar catch efficiencies. However, the elasticity and stiffness of the materials may be responsible for the differences in catch efficiency between the nylon PA and biodegradable gillnets.
Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2
Authors: Anderson Cole , Castillo Fritz , Koenig Michael , Managbanag Jim 
Published: May 2020

AbstractThe recent emergence of SARS-CoV-2 has lead to a global pandemic of unprecedented proportions. Current diagnosis of COVID-19 relies on the detection of SARS-CoV-2 RNA by RT-PCR in upper and lower respiratory specimens. While sensitive and specific, these RT-PCR assays require considerable supplies and reagents, which are often limited during global pandemics and surge testing. Here, we show that a nasopharyngeal swab pooling strategy can detect a single positive sample in pools of up to 10 samples without sacrificing RT-PCR sensitivity and specificity. We also report that this pooling strategy can be applied to rapid, moderate complexity assays, such as the BioFire COVID-19 test. Implementing a pooling strategy can significantly increase laboratory testing capacity while simultaneously reducing turnaround times for rapid identification and isolation of positive COVID-19 cases in high risk populations.
In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19
Authors: Phan Isabelle Q. , Subramanian Sandhya , Kim David , Carter Lauren , King Neil , Anishchenko Ivan , Barrett Lynn K. , Craig Justin , Tillery Logan , Shek Roger , Harrington Whitney E. , Koelle David M. , Wald Anna , Boonyaratanakornkit Jim , Isoherranen Nina , Greninger Alexander L. , Jerome Keith R. , Chu Helen , Staker Bart , Stewart Lance , Myler Peter J. , Van Voorhis Wesley C. 
Published: May 2020

AbstractRapid generation of diagnostics is paramount to understand epidemiology and to control the spread of emerging infectious diseases such as COVID-19. Computational methods to predict serodiagnostic epitopes that are specific for the pathogen could help accelerate the development of new diagnostics. A systematic survey of 27 SARS-CoV-2 proteins was conducted to assess whether existing B-cell epitope prediction methods, combined with comprehensive mining of sequence databases and structural data, could predict whether a particular protein would be suitable for serodiagnosis. Nine of the predictions were validated with recombinant SARS-CoV-2 proteins in the ELISA format using plasma and sera from patients with SARS-CoV-2 infection, and a further 11 predictions were compared to the recent literature. Results appeared to be in agreement with 12 of the predictions, in disagreement with 3, while a further 5 were deemed inconclusive. We showed that two of our top five candidates, the N-terminal fragment of the nucleoprotein and the receptor-binding domain of the spike protein, have the highest sensitivity and specificity and signal-to-noise ratio for detecting COVID-19 sera/plasma by ELISA. Mixing the two antigens together for coating ELISA plates led to a sensitivity of 94% (N=80 samples from persons with RT-PCR confirmed SARS-CoV2 infection), and a specificity of 97.2% (N=106 control samples).
Bayesian analysis of tests with unknown specificity and sensitivity
Authors: Gelman Andrew , Carpenter Bob 
Published: May 2020

AbstractWhen testing for a rare disease, prevalence estimates can be highly sensitive to uncertainty in the specificity and sensitivity of the test. Bayesian inference is a natural way to propagate these uncertainties, with hierarchical modeling capturing variation in these parameters across experiments. Another concern is the people in the sample not being representative of the general population. Statistical adjustment cannot with- out strong assumptions correct for selection bias in an opt-in sample, but multilevel regression and poststratification can at least adjust for known differences between the sample and the population. We demonstrate hierarchical regression and poststratification models with code in Stan and discuss their application to a controversial recent study of SARS-CoV-2 antibodies in a sample of people from the Stanford University area. Wide posterior intervals make it impossible to evaluate the quantitative claims of that study regarding the number of unreported infections. For future studies, the methods described here should facilitate more accurate estimates of disease prevalence from imperfect tests performed on non-representative samples.
COVID-19 Outcomes in 4712 consecutively confirmed SARS-CoV2 cases in the city of Madrid
Authors: Heili-Frades Sarah , Minguez Pablo , Fernández Ignacio Mahillo , Prieto-Rumeau Tomás , González Antonio Herrero , de la Fuente Lorena , Nieto María Jesús Rodríguez , Romero Germán Peces-Barba , Peces-Barba Mario , del Pilar Carballosa de Miguel María , Ormaechea Itziar Fernández , prieto Alba Naya , de Blas Farah Ezzine , Hiscock Luis Jiménez , Calvo Cesar Perez , Santos Arnoldo , Alameda Luis Enrique Muñoz , Bueno Fredeswinda Romero , Hernández-Mora Miguel Górgolas , Úbeda Alfonso Cabello , Álvarez Beatriz Álvarez , Petkova Elizabet , Carrasco Nerea , Ríos Dolores Martín , Mangado Nicolás González , Pernaute Olga Sánchez ,   and the COVID FJD-TEAM
Published: May 2020

ABSTRACTThere is limited information describing features and outcomes of patients requiring hospitalization for COVID19 disease and still no treatments have clearly demonstrated efficacy. Demographics and clinical variables on admission, as well as laboratory markers and therapeutic interventions were extracted from electronic Clinical Records (eCR) in 4712 SARS-CoV2 infected patients attending 4 public Hospitals in Madrid. Patients were stratified according to age and stage of severity. Using multivariate logistic regression analysis, cut-off points that best discriminated mortality were obtained for each of the studied variables. Principal components analysis and a neural network (NN) algorithm were applied.A high mortality incidence associated to age >70, comorbidities (hypertension, neurological disorders and diabetes), altered vitals such as fever, heart rhythm disturbances or elevated systolic blood pressure, and alterations in several laboratory tests. Remarkably, analysis of therapeutic options either taken individually or in combination drew a universal relationship between the use of Cyclosporine A and better outcomes as also a benefit of tocilizumab and/or corticosteroids in critically ill patients.We present a large Spanish population-based study addressing factors influencing survival in current SARS CoV2 pandemic, with particular emphasis on the effectivity of treatments. In addition, we have generated an NN capable of identifying severity predictors of SARS CoV2. A rapid extraction and management of data protocol from eCR and artificial intelligence in-house implementations allowed us to perform almost real time monitoring of the outbreak evolution.
Bi-allelic variants inTSPOAP1, encoding the active zone protein RIMBP1, cause autosomal recessive dystonia
Authors: Mencacci Niccolò E. , Brockmann Marisa M. , Dai Jinye , Pajusalu Sander , Atasu Burcu , Gonzalez-Latapi Paulina , Patzke Christopher , Schwake Michael , Tucci Arianna , Pittman Alan , Simon-Sanchez Javier , Carvill Gemma L. , Balint Bettina , Wiethoff Sarah , Warner Thomas T. , Papandreou Apostolos , Soo Audrey , Rein Reet , Kadastik-Eerme Liis , Puusepp Sanna , Reinson Karit , Tomberg Tiiu , Campos Joaquin , Pino Gabriela , Hanagasi Hasmet , Gasser Thomas , Bhatia Kailash P. , Kurian Manju A. , Lohmann Ebba , Õunap Katrin , Rosenmund Christian , Südhof Thomas C. , Wood Nicholas W. , Krainc Dimitri , Acuna Claudio 
Published: May 2020

ABSTRACTDystonia is a debilitating hyperkinetic movement disorder, frequently transmitted as a monogenic trait. Here, we describe homozygous frameshift, nonsense and missense variants inTSPOAP1, encoding the active zone RIM-binding protein 1 (RIMBP1), as a novel genetic cause of autosomal recessive dystonia in seven subjects from three unrelated families. Subjects carrying loss-of-function variants presented with juvenile- onset progressive generalized dystonia, associated with intellectual disability and cerebellar atrophy. Conversely, subjects carrying a pathogenic missense variant (p.Gly1808Ser) presented with isolated adult-onset focal dystonia. In mice, complete loss of RIMBP1, known to reduce neurotransmission, led to motor abnormalities reminiscent of dystonia, decreased Purkinje cell dendritic arborization, and reduced numbers of cerebellar synapses. In vitro analysis of the p.Gly1808Ser variant showed larger spike-evoked calcium transients and enhanced neurotransmission, suggesting that RIMBP1-linked dystonia can be caused by either reduced or enhanced rates of spike-evoked release in relevant neural networks. Our findings establish a direct link between presynaptic RIMBP1 dysfunction and dystonia and highlight the critical role played by well-balanced neurotransmission in motor control and disease pathogenesis.
Nanopore sequencing enables comprehensive transposable element epigenomic profiling
Authors: Ewing Adam D. , Smits Nathan , Sanchez-Luque Francisco J. , Faivre Jamila , Brennan Paul M. , Cheetham Seth W. , Faulkner Geoffrey J. 
Published: May 2020

AbstractWe apply long-read nanopore sequencing and a new tool, TLDR (Transposons from Long Dirty Reads), to directly infer CpG methylation of new and extant human transposable element (TE) insertions in hippocampus, heart, and liver, as well as paired tumour and non-tumour liver. Whole genome TLDR analysis greatly facilitates studies of TE biology as complete insertion sequences and their epigenetic modifications are readily obtainable.
Gut microbial ecology of Xenopus tadpoles across life stages
Authors: Scalvenzi Thibault , Clavereau Isabelle , Bourge Mickaël , Pollet Nicolas 
Published: May 2020

ABSTRACTBackgroundThe microorganism world living in amphibians is still largely under-represented and under-studied in the literature. Among anuran amphibians, African clawed frogs of theXenopusgenus stand as well-characterized models with an in-depth knowledge of their developmental biological processes including their metamorphosis. In this study, we analyzed the succession of microbial communities and their activities across diverse body habitats ofXenopus tropicalisusing different approaches including flow cytometry and 16s rDNA gene metabarcoding. We also evaluated the metabolic capacity of the premetamorphic tadpole’s gut microbiome using metagenomic and metatranscriptomic sequencing.ResultsWe analyzed the bacterial components of theXenopusgut microbiota, the adult gut biogeography, the succession of communities during ontogeny, the impact of the alimentation in shaping the tadpole’s gut bacterial communities and the transmission of skin and fecal bacteria to the eggs. We also identified the most active gut bacteria and their metabolic contribution to tadpole physiology including carbohydrate breakdown, nitrogen recycling, essential amino-acids and vitamin biosynthesis.ConclusionsWe present a comprehensive new microbiome dataset of a laboratory amphibian model. Our data provide evidences that studies on theXenopustadpole model can shed light on the interactions between a vertebrate host and its microbiome. We interpret our findings in light of bile acids being key molecular components regulating the gut microbiome composition during amphibian development and metamorphosis. Further studies into the metabolic interactions between amphibian tadpoles and their microbiota during early development and metamorphosis should provide useful information on the evolution of host-microbiota interactions in vertebrates.This article has been peer-reviewed and recommended byPeer Community in Genomicshttps://doi.org/10.24072/pci.genomics.100005
A non-parametric analysis of the effect of the configuration of competitive pillars on competitive efficiency
Authors: Horváth Krisztina , Lafuente Esteban 
Published: May 2020

Purpose
This study aims to evaluate how the configuration of competitive pillars impacts businesses' competitive efficiency by using a non-parametric model, namely, data envelopment analysis (DEA), with a single constant input.

Design/methodology/approach
The proposed DEA model evaluates technical inefficiency, which results from differences in the availability and allocation of resources, and configuration inefficiency, which we link to differences in the way businesses amalgamate their competitive pillars. The sample includes 115 Spanish businesses operating in manufacturing, construction, retail and knowledge-intensive business services (KIBS) sectors.

Findings
The results reveal that, on an average, firms can improve their overall competitive efficiency by 53.53%. The findings suggest that the configuration of competitive pillars has important implications for efficiency analyses: human capital and strategy are the most relevant aspects shaping competitive efficiency in manufacturing and construction firms; whereas innovation emerges as the most relevant competitive aspect driving competitive efficiency in KIBS firms.

Originality/value
The novelty of this study lies in the analysis of competitive efficiency in a model where efficiency can be explained by overall (industry-specific) competitive efficiency within the industry and by strategic choices on how resources and capabilities are combined within the business.
Entrepreneurial learning as practice: a video-ethnographic analysis
Authors: Thompson Neil Aaron , Illes Edina 
Published: May 2020

PurposeDespite the gains that have been made by adopting contemporary theories of practice in entrepreneurship studies, the field still lacks a comprehensive practice theory of entrepreneurial learning. In this article, we develop a practice theory of entrepreneurial learning by elaborating on the relations between practicing, knowing and learning.Design/methodology/approachUsing a video ethnography of a two-day “Startup Weekend for Refugees” event in Amsterdam, our aim is to further theorise the relational, material and embodied nature of entrepreneurial learning through analysing video fragments of naturally occurring practices.FindingsOur findings demonstrate that entrepreneurial learning transpires through, and is emergent from, practices and their relations. On the one hand, practitioners learn to competently participate in various practices by sensing, observing and experimenting with the meaning of others' gestures and utterances. On the other, the learning of new opportunities for value creation emerges as practitioners connect various practices to one another through translation.Originality/valueThis article contributes by illustrating and explaining real-time instances of learning to develop a practice theory of entrepreneurial learning. This contributes to the literature by detailing the relations between learning, knowing and practising entrepreneurship, which leads to a novel alternative to existing individual- and organisational-level learning theories.