bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new model of spinal cord injury by cryoapplication: Morphodynamics of histological changes of the spinal cord lesion
Authors: Telegin George B. , Minakov Alexey N. , Chernov Aleksandr S. , Kazakov Vitaly A. , Кalabina Elena A. , Belogurov Alexey A. , Konovalov Nikolay A. , Gabibov Aleksandr G 
Published: September 2020

AbstractUp to 500,000 people worldwide suffer from spinal cord injuries (SCI) annually, according to the WHO. Animal models are essential for searching novel methodological guidelines and therapeutic agents for SCI treatment. We developed an original model of posttraumatic spinal cord glial scar in rats using cryoapplication. The method is based on cryodestruction of spinal cord tissue with liquid nitrogen. Thirty six male SD linear rats of SPF category were included in this experimental study. A T13 unilateral hemilaminectomy was performed with an operating microscope, as it was extremely important not to penetrate the dura mater, and liquid nitrogen was applied into the bone defect for one minute. The animals were euthanized at various intervals ranging from 1 to 60 days after inducing cryogenic trauma, their Th12-L1 vertebrae were removed “en bloc” and the segment of the spinal cord exposed to the cryoapplicator was carefully separated for histological examination. The study results demonstrated that cryoapplication of liquid nitrogen, provoking a local temperature of approximately minus 20°C, produced a highly standardized transmural defect which extended throughout the dorsoventral arrangement of the spinal cord and had an “hour-glass” shape. During the entire study period (1-60 post-injury days), the glial scarring process and the spinal cord defect were located within the surgically approached vertebral space (Th13). Unlike other available experimental models of SCI (compression, contusion, chemical, etc.), the present option is characterized by a minimal invasiveness (the hemilaminectomy is less than 1 mm wide), high precision and consistency. Also, there was a low interanimal variability in histological lesions and dimensions of the produced defect. The original design of cryoapplicator used in the study played a major role in achieving these results. The original technique of high-precision cryoapplication for inducing consistent morphodynamic glial scarring could facilitate a better understanding of the self-recovery processes of injured spinal cord and would be helpful for proposing new platforms for the development of therapeutic strategies.
Adaptive dating and fast proposals: revisiting the phylogenetic relaxed clock model
Authors: Douglas Jordan , Zhang Rong , Bouckaert Remco 
Published: September 2020

AbstractUncorrelated relaxed clock models enable estimation of molecular substitution rates across lineages and are widely used in phylogenetics for dating evolutionary divergence times. In this article we delved into the internal complexities of the relaxed clock model in order to develop efficient MCMC operators for Bayesian phylogenetic inference. We compared three substitution rate parameterisations, introduced an adaptive operator which learns the weights of other operators during MCMC, and we explored how relaxed clock model estimation can benefit from two cutting-edge proposal kernels: the AVMVN and Bactrian kernels. This work has produced an operator scheme that is up to 65 times more efficient at exploring continuous relaxed clock parameters compared with previous setups, depending on the dataset. Finally, we explored variants of the standard narrow exchange operator which are specifically designed for the relaxed clock model. In the most extreme case, this new operator traversed tree space 40% more efficiently than narrow exchange. The methodologies introduced are adaptive and highly effective on short as well as long alignments. The results are available via the open source optimised relaxed clock (ORC) package for BEAST 2 under a GNU licence (https://github.com/jordandouglas/ORC).Author summaryBiological sequences, such as DNA, accumulate mutations over generations. By comparing such sequences in a phylogenetic framework, the evolutionary tree of lifeforms can be inferred. With the overwhelming availability of biological sequence data, and the increasing affordability of collecting new data, the development of fast and efficient phylogenetic algorithms is more important than ever. In this article we focus on the relaxed clock model, which is very popular in phylogenetics. We explored how a range of optimisations can improve the statistical inference of the relaxed clock. This work has produced a phylogenetic setup which can infer parameters related to the relaxed clock up to 65 times faster than previous setups, depending on the dataset. The methods introduced adapt to the dataset during computation and are highly efficient when processing long biological sequences.
Molecular evidence for the hybrid origin ofCryptocoryne ×purpureaRidl. nothovar.purpurea(Araceae)
Authors: Rosazlina Rusly , Jacobsen Niels , Ørgaard Marian , Othman Ahmad Sofiman 
Published: September 2020

AbstractNatural hybridization has been considered a source of taxonomic complexity inCryptocoryne. A combined study of DNA sequencing data from internal transcribed spacer (ITS) of nuclear ribosomal DNA andtrnK-matKregion of chloroplast DNA was used to identify the parents ofCryptocoryneputative hybrids from Peninsular Malaysia. Based on the morphological intermediary and sympatric distribution, the plants were tentatively identified as the hybridCryptocoryne ×purpureanothovar.purpurea;plants were pollen sterile and had long been considered to be hybrids, possibly between two related and co-existing species,C. cordatavar. cordataandC. griffithii. TheC. ×purpureanothovar.purpureastatus was independently confirmed by the presence of an additive ITS sequence pattern from these two parental species in hybrid individuals. Analysis of the chloroplasttrnK-matKsequences showed that the hybridization is bidirectional with the putative hybrids sharing identical sequences fromC. cordatavar. cordataandC. griffithii, indicating that both putative parental species had been the maternal parent in different accessions.
Fish harvesting advice under climate change: a risk-equivalent empirical approach
Authors: Duplisea Daniel E. , Roux Marie-Julie , Hunter Karen L. , Rice Jake 
Published: September 2020

1AbstractThe rate of climate change (CC) has accelerated to the point where it now affects the mid-to long-term sustainability of fishing strategies. Therefore, it is important to consider practical and effective ways to incorporate CC into fisheries advice so that the advice can be considered conditioned to CC. We developed a quantitative model to characterise the empirical relationship between a variable affected by climate and fish production. We then used model projections as a foundation for a risk analysis of CC effects on harvesting of Greenland halibutReinhardtius hippoglossoidesin the Gulf of St Lawrence, Canada. The risk-based approach quantified a) the relative change in risk of a status quo fishing strategy under various CC scenarios, and b) the change in fishery exploitation rates required to achieve a management objective over a specified time period at a level of risk considered acceptable (risk equivalent fishery exploitation advice). This empirical approach can be used to develop risk-based advice for any other external variable that affects stock production in addition to climate-related variables and it can be applied in most situations where there is an index of stock biomass and fisheries catch. Shifting the focus from process-based understanding of the responses of fish stocks to CC to quantification of how CC-contributed uncertainty can alter the risks associated with different fishing strategies and/or management options, can ensure timely delivery of robust scientific advice for fisheries under non-stationary environmental conditions.
Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks
Authors: Jones Beryl M. , Rao Vikyath D. , Gernat Tim , Jagla Tobias , Cash-Ahmed Amy , Rubin Benjamin E. R. , Comi Troy J. , Bhogale Shounak , Husain Syed S. , Blatti Charles , Middendorf Martin , Sinha Saurabh , Chandrasekaran Sriram , Robinson Gene E. 
Published: September 2020

AbstractUnderstanding the regulatory architecture of phenotypic variation is a fundamental goal in biology, but connections between gene regulatory network (GRN) activity and individual differences in behavior are poorly understood. We characterized the molecular basis of behavioral plasticity in queenless honey bee (Apis mellifera) colonies, where individuals engage in both reproductive and non-reproductive behaviors. Using high-throughput behavioral tracking, we discovered these colonies contain a continuum of phenotypes, with some individuals specialized for either egg-laying or foraging and “generalists” that perform both. Brain gene expression and chromatin accessibility profiles were correlated with behavioral variation, with generalists intermediate in behavior and molecular profiles. Models of brain GRNs constructed for individuals revealed that transcription factor (TF) activity was highly predictive of behavior, and behavior-associated regulatory regions had more TF motifs. These results provide new insights into the important role played by brain GRN plasticity in the regulation of behavior, with implications for social evolution.
Relative matching using low coverage sequencing
Authors: Petter Ella , Schweiger Regev , Shahino Bar , Shor Tal , Aker Malka , Almog Lior , Weissglas-Volkov Daphna , Naveh Yoav , Navon Oron , Carmi Shai , Li Jeremiah H. , Berisa Tomaz , Pickrell Joseph K. , Erlich Yaniv 
Published: September 2020

AbstractFinding familial relatives using DNA has multiple applications, in genetic genealogy, population genetics, and forensics. So far, most relative matching algorithms rely on detecting identity-by-descent (IBD) segments with high quality genotype data. Recently, low coverage sequencing (LCS) has received growing attention as a promising cost-effective method to ascertain genomic information. However, with higher error rates, it is unclear whether existing IBD detection can work on LCS datasets. Here, we developed and tested a framework for relative matching using sequencing with 1× coverage (1×LCS). We started by exploring the error characteristics of this method compared to array data. Our results show that after some optimization 1×LCS can exhibit the same genotyping discordance rates as the discordance between two array platforms. Using this observation, we developed a hybrid framework for relative matching and tuned this framework with >2,700 pairs of confirmed genealogical relatives that were genotyped using heterogenous datasets. We then obtained array and 1×LCS on 19 samples and use our framework to find relatives in a database of over 3 million individuals. The total length of shared segments obtained by 1×LCS was virtually indistinguishable to genotyping arrays for matches with a total sharing >200cM (second cousins or closer). For more distant relatives, as long as those were detected by both technologies, the total length obtained by LCS and by genotyping arrays was highly correlated, with no evidence of over- or underestimation. Taken together, our results show that 1×LCS can be a valid alternative to arrays for relative matching, opening the possibility for further democratization of genomic data.
Natural sensory context drives diverse brain-wide activity duringC. elegansmating
Authors: Susoy Vladislav , Hung Wesley , Witvliet Daniel , Whitener Joshua E. , Wu Min , Graham Brett J. , Zhen Mei , Venkatachalam Vivek , Samuel Aravinthan D.T. 
Published: September 2020

AbstractNatural goal-directed behaviors often involve complex sequences of many stimulus-triggered components. Understanding how brain circuits organize such behaviors requires mapping the interactions between an animal, its environment, and its nervous system. Here, we use continuous brain-wide neuronal imaging to study the full performance of mating by theC. elegansmale. We show that as each mating unfolds in its own sequence of component behaviors, the brain operates similarly between instances of each component, but distinctly between different components. When the full sensory and behavioral context is taken into account, unique roles emerge for each neuron. Functional correlations between neurons are not fixed, but change with behavioral dynamics. From the contribution of individual neurons to circuits, our study shows how diverse brain-wide dynamics emerge from the integration of sensory perception and motor actions within their natural context.
Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions
Authors: Radhakrishnan Chandni , Divakar Mohit Kumar , Jain Abhinav , Viswanathan Prasanth , Bhoyar Rahul C. , Jolly Bani , Imran Mohamed , Sharma Disha , Rophina Mercy , Ranjan Gyan , Jose Beena Philomina , Raman Rajendran Vadukkoot , Kesavan Thulaseedharan Nallaveettil , George Kalpana , Mathew Sheela , Poovullathil Jayesh Kumar , Govindan Sajeeth Kumar Keeriyatt , Nair Priyanka Raveendranadhan , Vadekkandiyil Shameer , Gladson Vineeth , Mohan Midhun , Parambath Fairoz Cheriyalingal , Mangla Mohit , Shamnath Afra ,   Indian CoV2 Genomics & Genetic Epidemiology (IndiCovGEN) Consortium, Sivasubbu Sridhar , Scaria Vinod 
Published: September 2020

ABSTRACTCoronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. Genomic approaches have been extensively used to understand the evolution and epidemiology of SARS-CoV-2 across the world. Kerala is a unique state in India well connected with the rest of the world through a large number of expatriates, trade, and tourism. The first case of COVID-19 in India was reported in Kerala in January 2020, during the initial days of the pandemic. The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. We sequenced a total of 200 samples from patients at a tertiary hospital in Kerala using COVIDSeq protocol at a mean coverage of 7,755X. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. The genomes formed a monophyletic distribution exclusively mapping to the A2a clade. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. To the best of our knowledge, this is the first and most comprehensive report of genetic epidemiology and evolution of SARS-CoV-2 isolates from Kerala.
A new mechanism of fibronectin fibril assembly revealed by live imaging and super-resolution microscopy
Authors: Tomer Darshika , Arriagada Cecilia , Munshi Sudipto , Alexander Brianna E. , French Brenda , Vedula Pavan , Caorsi Valentina , House Andrew , Guvendiren Murat , Kashina Anna , Schwarzbauer Jean E. , Astrof Sophie 
Published: September 2020

AbstractFn1 fibrils have long been viewed as continuous fibers composed of extended, periodically aligned Fn1 molecules. However, our live imaging and single-molecule localization microscopy (SMLM) are inconsistent with this traditional view and show that Fn1 fibrils are composed of roughly spherical nanodomains containing 6-11 Fn1 dimers. As they move toward the cell center, Fn1 nanodomains become organized into linear arrays, wherein nanodomains are spaced at the average periodicity of 105±17 nm. Periodical Fn1 nanodomain arrays are bona fide fibrils: they are resistant to deoxycholate treatment and retain nanodomain periodicity in the absence of cells. The nanodomain periodicity in fibrils remained constant when probed with antibodies recognizing distinct Fn1 epitopes or combinations of antibodies recognizing epitopes spanning the length of Fn1. FUD, a bacterial peptide that binds Fn1 N-terminus and disrupts Fn1 fibrillogenesis does not disrupt the formation of Fn1 nanodomains, instead, it blocks the organization of Fn1 nanodomains into periodical arrays. These studies establish a new paradigm of Fn1 fibrillogenesis.
rSWeeP: A R/Bioconductor package deal with SWeeP sequences representation
Authors: Fernandes Danrley , Kulik Mariane G. , Machado Diogo J. S. , Marchaukoski Jeroniza N. , Pedrosa Fabio O. , De Pierri Camilla R. , Raittz Roberto T. 
Published: September 2020

AbstractThe rSWeeP package is an R implementation of the SWeeP model, designed to handle Big Data. rSweeP meets to the growing demand for efficient methods of heuristic representation in the field of Bioinformatics, on platforms accessible to the entire scientific community. We explored the implementation of rSWeeP using a dataset containing 31,386 viral proteomes, performing phylogenetic and principal component analysis. As a case study we analyze the viral strains closest to the SARS-CoV, responsible for the current pandemic of COVID-19, confirming that rSWeeP can accurately classify organisms taxonomically. rSWeeP package is freely available athttps://bioconductor.org/packages/release/bioc/html/rSWeeP.html.
Corporate communication in open innovation: a case-study of three multinationals
Authors: Gutiérrez-García Elena , Recalde Mónica , Alfaro José A. 
Published: September 2020

PurposeThis article proposes a theoretical framework that synthesizes the main factors explaining the strategic contribution of communication department to open innovation (OI) processes. Because there is little or no research literature on communication and OI, the purpose is to fill this gap. A literature review and empirical qualitative research were conducted to weigh the significance of the framework in practice.Design/methodology/approachAn interdisciplinary literature review was necessary to identify the main factors that explain the communication contribution to OI. The analysis of three multinational case studies has helped to enrich the proposed framework. Six semi-structured interviews were conducted with in-company communication managers and innovation managers in order to capture their perceptions.FindingsCommunication emerges as a strategic function with the potential to be embedded in the whole OI process. The main conclusion is that it may play an increasingly central role in enhancing relationships with external partners. Moreover, it enacts its strategic role while facilitating the enhancement of the organization's overall communication capability – that is, trust, transparency and a coherently articulated narrative.Research limitations/implicationsThis article has not been designed as a comprehensive overview of the topic, nor it is designed to be statistically representative or generalizable. The study was conducted with the intention of exploring the theoretical and practical contributions of communication department to OI, as well as to raise awareness among scholars and practitioners on this new but neglected topic for research. Its qualitative approach serves to assess the value of the framework proposed, and the key issues highlighted here require further research.Practical implicationsThe theoretical framework proposed may enable innovation managers to identify the factors in which the communication function and its practitioners may play a role for facilitating OI processes. Likewise, communication practitioners may find it useful to foster their organizational role and capabilities within these processes.Originality/valueThis article underlines the significant contribution that the communication function may play in OI processes. Research on this topic has been neglected thus far, despite its significance for the competitiveness of companies and the economy as a whole.
Subnational institutions and EMNE acquisitions in advanced economies: institutional escapism or fostering?
Authors: Nayyar Rishika , Prashantham Shameen 
Published: September 2020

Purpose
The purpose of this paper is to examine whether subnational market-supporting institutions in Indian states affect the likelihood of Indian multinational enterprises (MNEs) to undertake acquisitions in advanced economies (AEs) rather than emerging economies (EEs) and, if so, which mechanism – institutional fostering or escapism – underlies the phenomenon.

Design/methodology/approach
The paper uses a logistic regression model on a dataset of 647 firm-level cross-border acquisitions (CBAs) undertaken by Indian MNEs during the period 2010–2016.

Findings
The paper finds support for the institutional escapism mechanism, as opposed to the institutional fostering mechanism, underlying Indian MNEs’ acquisitions in AEs (rather than EEs). That is, firms headquartered in Indian states where market-supporting institutions (such as economic liberalization and efficiency of legal systems) are weak are more likely to undertake CBAs in AEs than in EEs as an escapist response to weak subnational institutions at home.

Originality/value
The paper highlights the relevance of the mainstream international business (IB) concept of emerging market multinational enterprises (EMNEs) internationalization to critical IB scholarship by examining subnational institutional influences on EMNEs’ foreign market choice between AEs and EEs. In particular, by providing evidence for the institutional escapism mechanism which has potential negative socioeconomic consequences in the region of the investing firm, the paper adds to critical IB research which places great emphasis on the examination of inequalities and draws attention to the EMNE context as a suitable setting for further research on internationalization from a critical perspective.
Elaborating on modular interfaces in multi-provider contexts
Authors: Peters Vincent , Vähätalo Mervi , Meijboom Bert , Barendregt Alice , Bok Levinus , de Vries Esther 
Published: September 2020

PurposeThis study examines how modular interfaces manifest in multi-provider contexts and how they can improve coordination and customization of services. The aim of the study is to describe interfaces in multi-provider contexts and elaborate on how they support the delivery of integrated patient care.Design/methodology/approachA qualitative, multiple case study was conducted in two multi-provider contexts in healthcare services: one representing paediatric Down syndrome care in the Netherlands and one representing home care for the elderly in Finland. Data collection involved semi-structured interviews in both contexts.FindingsThis study provides insight into several types of interfaces and their role in multi-provider contexts. Several inter- and intra-organizational situations were identified in which the delivery of integrated patient care was jeopardized. This study describes how interfaces can help to alleviate these situations.Originality/valueThis study deepens the understanding of interfaces in service modularity by describing interfaces in multi-provider contexts. The multi-provider contexts studied inspired to incorporate the inter-organizational aspect into the literature on interfaces in service modularity. This study further develops the typology for interfaces in modular services by adding a third dimension to the typology, that is, the orientation of interfaces.