bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unsupervised cluster analysis of SARS-CoV-2 genomes reflects its geographic progression and identifies distinct genetic subgroups of SARS-CoV-2 virus
Authors: Hahn Georg , Lee Sanghun , Weiss Scott T. , Lange Christoph 
Published: May 2020

AbstractOver 10,000 viral genome sequences of the SARS-CoV-2 virus have been made readily available during the ongoing coronavirus pandemic since the initial genome sequence of the virus was released on the open access Virological website (http://virological.org/) early on January 11. We utilize the published data on the single stranded RNAs of 11, 132 SARS-CoV-2 patients in the GISAID (Elbe and Buckland-Merrett, 2017; Shu and McCauley, 2017) database, which contains fully or partially sequenced SARS-CoV-2 samples from laboratories around the world. Among many important research questions which are currently being investigated, one aspect pertains to the genetic characterization/classification of the virus. We analyze data on the nucleotide sequencing of the virus and geographic information of a subset of 7, 640 SARS-CoV-2 patients without missing entries that are available in the GISAID database. Instead of modelling the mutation rate, applying phylogenetic tree approaches, etc., we here utilize a model-free clustering approach that compares the viruses at a genome-wide level. We apply principal component analysis to a similarity matrix that compares all pairs of these SARS-CoV-2 nucleotide sequences at all loci simultaneously, using the Jaccard index (Jaccard, 1901; Tan et al., 2005; Prokopenko et al., 2016; Schlauch et al., 2017). Our analysis results of the SARS-CoV-2 genome data illustrates the geographic and chronological progression of the virus, starting from the first cases that were observed in China to the current wave of cases in Europe and North America. This is in line with a phylogenetic analysis which we use to contrast our results. We also observe that, based on their sequence data, the SARS-CoV-2 viruses cluster in distinct genetic subgroups. It is the subject of ongoing research to examine whether the genetic subgroup could be related to diseases outcome and its potential implications for vaccine development.
Cadherin Preserves Cohesion Across Involuting Tissues DuringC. elegansNeurulation
Authors: Barnes Kristopher , Fan Li , Moyle Mark W. , Brittin Christopher , Xu Yichi , Colón-Ramos Daniel , Santella Anthony , Bao Zhirong 
Published: May 2020

AbstractThe internalization of the central nervous system, termed neurulation in vertebrates, is a critical step in embryogenesis. Open questions remain as to how force propels coordinated tissue movement during the process, and little is known as to how internalization happens in invertebrates. We show that inC. elegansmorphogenesis, apical constriction in the retracting pharynx drives involution of the adjacent neuroectoderm. Localized HMR-1/Cadherin mediates the inter-tissue attachment, as well as within the neuroectoderm to maintain intratissue cohesion. Our results demonstrate that localized HMR-1 is capable of mediating embryo wide reorganization driven by a centrally located force generator, and indicate a non-canonical use of Cadherin on the basal side of an epithelium that may apply to vertebrate neurulation. Additionally, we highlight shared morphology and gene expression in tissues driving involution, which suggests that neuroectoderm involution inC. elegansis potentially homologous with vertebrate neurulation and thus may help elucidate the evolutionary origin of the brain.
Condensed chromatin behaves like a solid on the mesoscale in vitro and in living cells
Authors: Strickfaden Hilmar , Tolsma Thomas , Sharma Ajit , Underhill D. Alan , Hansen Jeffrey C. , Hendzel Michael J 
Published: May 2020

SUMMARYThe association of nuclear DNA with histones to form chromatin is essential to the temporal and spatial control of eukaryotic genomes. In this study, we examined the physical state of chromatin in vitro and in vivo. Our in vitro studies demonstrate that MgCl2-dependent self-association of native chromatin fragments or reconstituted nucleosomal arrays produced supramolecular condensates whose constituents are physically constrained and solid-like. Liquid chromatin condensates could be generated in vitro, but only using non-physiological conditions. By measuring DNA mobility within heterochromatin and euchromatin in living cells, we show that chromatin also exhibits solid-like behavior in vivo. Representative heterochromatin proteins, however, displayed liquid-like behavior and coalesced around a solid chromatin scaffold. Remarkably, both euchromatin and heterochromatin showed solid-like behavior even when transmission electron microscopy revealed limited interactions between chromatin fibers. Our results therefore argue that chromatin is not liquid but exists in a solid-like material state whose properties are tuned by fiber-fiber interactions.
Keratinocytes are required for normal cold and heat sensation
Authors: Sadler Katelyn E. , Moehring Francie , Stucky Cheryl L. 
Published: May 2020

AbstractKeratinocytes are the most abundant cell type in the epidermis, the most superficial layer of the skin. Historically, epidermal-innervating sensory neurons were thought to be the exclusive detectors and transmitters of environmental stimuli. However, recent work from our lab and others has demonstrated that keratinocytes are also critical for normal mechanotransduction and mechanically-evoked behavioral responses in mice. Here, we asked whether keratinocyte activity is also required for normal cold and heat sensation. We first observed cold-induced activity in mouse, rat, hibernating 13-lined ground squirrel, and human keratinocytes and determined that keratinocyte cold activity is conserved across mammalian species. Next, using transgenic mouse tissues and pharmacological tools, we determined that keratinocyte cold responses require the release of intracellular calcium through one or more unknown cold-sensitive proteins. This cold-induced keratinocyte activity is required for normal cold sensation as optogenetic inhibition of epidermal cells reduced reflexive behavioral responses to cold stimuli. Keratinocyte inhibition also decreased reflexive behavioral responses to heat stimuli. Lastly, we demonstrated that epidermal ATP-P2X4 signaling is required for normal cold and heat sensation. Based on these data and our previous findings, keratinocyte purinergic signaling is a modality-conserved amplification system that is required for normal somatosensationin vivo.
Exploring the conformational space of a receptor for drug design: an ERαcase study
Authors: Schneider Melanie , Pons Jean-Luc , Labesse Gilles 
Published: May 2020

ABSTRACTMotivationProtein flexibility is challenging for both experimentalists and modellers, especially in the field of drug design. Estrogen Receptor alpha (ERα) is an extensively studied Nuclear Receptor (NR) and a well-known therapeutic target with an important role in development and physiology. It is also a frequent off-target in standard toxicity tests for endocrine disruption. Here, we aim to evaluate the degree to which the conformational space and macromolecular flexibility of this well-characterized drug target can be described. Our approach exploits hundreds of crystallographic structures by means of molecular dynamics simulations and of virtual screening.ResultsThe analysis of hundreds of crystal structures confirms the presence of two main conformational states, known as ‘agonist’ and ‘antagonist’, that mainly differ by the orientation of the C-terminal helix H12 which serves to close the binding pocket. ERαalso shows some loop flexibility, as well as variable side-chain orientations in its active site. We scrutinized the extent to which standard molecular dynamics simulations or crystallographic refinement as ensemble recapitulate most of the variability features seen by the array of available crystal structure. In parallel, we investigated on the kind and extent of flexibility that is required to achieve convincing docking for all high-affinity ERαligands present in BindingDB. Using either only one conformation with a few side-chains set flexible, or static structure ensembles in parallel during docking led to good quality and similar pose predictions. These results suggest that the several hundreds of crystal structures already known can properly describe the whole conformational universe of ERα’s ligand binding domain. This opens the road for better drug design and affinity computation.Contactlabesse@cbs.cnrs.fr
In Vitro Reconstitution of Dynein Force Exertion in Bulk Cytoplasm
Authors: Palenzuela Héliciane , Lacroix Benjamin , Sallé Jérémy , Minami Katsuhiko , Shima Tomohiro , Jegou Antoine , Romet-Lemonne Guillaume , Minc Nicolas 
Published: May 2020

SUMMARYThe forces generated by Microtubules (MTs) and their associated motors orchestrate essential cellular processes ranging from vesicular trafficking to centrosome positioning [1, 2]. To date, most studies have focused on force exertion from motors anchored on a static surface, such as the cell cortexin vivoor glass surfacesin vitro[2–4]. However, motors also transport large cargos and endomembrane networks, whose hydrodynamic interactions with the viscous cytoplasm should generate sizable forces in bulk. Such forces may contribute to MT aster centration, organization and orientation [5–14], but have yet to be evidenced and studied in a minimal reconstituted system. By developing a bulk motility assay, based on stabilized MTs and dynein-coated beads freely floating in a viscous medium away from any surface, we demonstrate that the motion of a cargo exerts a pulling force on the MT and propels it in opposite direction. Quantification of resulting MT movements for different motors, motor velocities, over a range of cargo size and medium viscosities, shows that the efficiency of this mechanism is primarily determined by cargo size and MT length. Forces exerted by cargos are additive, allowing us to recapitulate tug-of-war situations, or bi-dimensional motions of minimal asters. These data also reveal unappreciated effects of the nature of viscous crowders and hydrodynamic interactions between cargos and MTs, likely relevant to understand this mode of force exertion in living cells. This study places endomembrane transport as a significant mode of MT force exertion with far-reaching consequences for cellular organization.
h-adaptive topology optimization considering variations of material properties and energy error density recovery
Authors: da Silva Jéderson , Pereira Jucélio Tomás , Torres Diego Amadeu F. 
Published: May 2020

Purpose
The purpose of this paper is to propose a new scheme for obtaining acceptable solutions for problems of continuum topology optimization of structures, regarding the distribution and limitation of discretization errors by considering h-adaptivity.

Design/methodology/approach
The new scheme encompasses, simultaneously, the solution of the optimization problem considering a solid isotropic microstructure with penalization (SIMP) and the application of the h-adaptive finite element method. An analysis of discretization errors is carried out using an a posteriori error estimator based on both the recovery and the abrupt variation of material properties. The estimate of new element sizes is computed by a new h-adaptive technique named “Isotropic Error Density Recovery”, which is based on the construction of the strain energy error density function together with the analytical solution of an optimization problem at the element level.

Findings
Two-dimensional numerical examples, regarding minimization of the structure compliance and constraint over the material volume, demonstrate the capacity of the methodology in controlling and equidistributing discretization errors, as well as obtaining a great definition of the void–material interface, thanks to the h-adaptivity, when compared with results obtained by other methods based on microstructure.

Originality/value
This paper presents a new technique to design a mesh made with isotropic triangular finite elements. Furthermore, this technique is applied to continuum topology optimization problems using a new iterative scheme to obtain solutions with controlled discretization errors, measured in terms of the energy norm, and a great resolution of the material boundary. Regarding the computational cost in terms of degrees of freedom, the present scheme provides approximations with considerable less error if compared to the optimization process on fixed meshes.
The multi resource leveling and materials procurement problem: an integrated approach
Authors: Almatroushi Hessa , Hariga Moncer , As'ad Rami , Al-Bar AbdulRahman 
Published: May 2020

PurposeThis paper proposes an integrated approach that seeks to jointly optimize project scheduling and material lot sizing decisions for time-constrained project scheduling problems.Design/methodology/approachA mixed integer linear programming model is devised, which utilizes the splitting of noncritical activities as a mean toward leveling the renewable resources. The developed model minimizes renewable resources leveling costs along with consumable resources related costs, and it is solved using IBM ILOG CPLEX optimization package. A hybrid metaheuristic procedure is also proposed to efficiently solve the model for larger projects with complex networks structure.FindingsThe results confirmed the significance of the integrated approach as both the project schedule and the material ordering policy turned out to be different once compared to the sequential approach under same parameter settings. Furthermore, the integrated approach resulted in substantial total costs reduction for low values of the acquiring and releasing costs of the renewable resources. Computational experiments conducted over 240 test instances of various sizes, and complexities illustrate the efficiency of the proposed metaheuristic approach as it yields solutions that are on average 1.14% away from the optimal ones.Practical implicationsThis work highlights the necessity of having project managers address project scheduling and materials lot sizing decisions concurrently, rather than sequentially, to better level resources and minimize materials related costs. Significant cost savings were generated through the developed model despite the use of a small-scale example which illustrates the great potential that the integrated approach has in real life projects. For real life projects with complex network topology, practitioners are advised to make use of the developed metaheuristic procedure due to its superior time efficiency as compared to exact solution methods.Originality/valueThe sequential approach, wherein a project schedule is established first followed by allocating the needed resources, is proven to yield a nonoptimized project schedule and materials ordering policy, leading to an increase in the project's total cost. The integrated approach proposed hereafter optimizes both decisions at once ensuring the timely completion of the project at the least possible cost. The proposed metaheuristic approach provides a viable alternative to exact solution methods especially for larger projects.
After encounters: revealing patients’ unseen work through their pathways to care
Authors: Humphris Rachel , Bradby Hannah , Padilla Beatriz , Phillimore Jenny , Pemberton Simon , Samerski Silja 
Published: May 2020

Purpose
Research has long focused on the notion of access and the trajectory towards a healthcare encounter but has neglected what happens to patients after these initial encounters. This paper focuses attention on what happens after an initial healthcare encounter leading to a more nuanced understanding of how patients from a diverse range of backgrounds make sense of medical advice, how they mix this knowledge with other forms of information and how they make decisions about what to do next.

Design/methodology/approach
Drawing on 160 in-depth interviews across four European countries the paper problematizes the notion of access; expands the definition of “decision partners”; and reframes the medical encounter as a journey, where one encounter leads to and informs the next.

Findings
This approach reveals the significant unseen, unrecognised and unacknowledged work that patients undertake to solve their health concerns.

Originality/value
De-centring the professional from the healthcare encounter allows us to understand why patients take particular pathways to care and how resources might be more appropriately leveraged to support both patients and professionals along this journey.
What do project management practitioners think governance is? A study on perceptions in Queensland, Australia
Authors: McGrath Stephen Keith , Whitty Stephen Jonathan 
Published: May 2020

PurposeTo determine if there is confusion in governance terminology amongst experienced management and project management practitioners.Design/methodology/approachPractitioner interviews and subsequent analysis.FindingsSignificant differences in governance terminology were found. The participants had nevertheless arrived at similar operating arrangements for their committees, even though they came from different segments of different industries and did not agree on the definition of governance. It was possible to develop a list of working parameters for operation of these committees from their responses. The labelling of committees associated with governance as steering or decision-making was found to be problematic and various causes/motivations for the differing definitions of governance having arisen were detected. These ranged from altruism, through dogmatic belief in particular frameworks, to enhancing career prospects/ego.Research limitations/implicationsThe sample came from organisations and industries in one state in one country. The need for review of governance terminology used in various project management practitioner reference documents and methodologies was identified.Practical implicationsProjects and business alike can potentially achieve improvements in efficiency and effectiveness through consistency of terminology and the clarity this brings to governance arrangements and committee operations.Social implicationsCreation of a unifying feature within the project and management literature, shifting the understanding of governance and its boundaries and limitations. This will help progress governance from complexity to simplicity, from an art to an understandable practice, from a concept that has been hijacked for partisan and political gain to a lean social tool which can be put to use for the benefit of organisations, whether public, charitable or private.Originality/valueThe value is clarity – resulting in the avoidance of confusion and misunderstanding together with their consequent waste of time, resources and money.
Estimation of Armington elasticities for trade-policy analysis
Authors: Liu Kai , Yamazaki Masato , Koike Atsushi 
Published: May 2020

Purpose
The purpose of this paper is to compare the Armington elasticities for world average values and country-specific values and obtain evidence for whether the world average elasticities and the “rule of two”, which have been applied in many papers, are accurate for cereals in trade policy studies related to an individual country.

Design/methodology/approach
The authors use panel data with a nested model to estimate and compare Armington elasticities based on world average values and country-specific values from 10 countries and regions.

Findings
The results suggest that cereals’ elasticities vary between world average values and country-specific values, and the “rule of two” is not strictly applicable. In fact, the “less than two” concept fits well in many cases.

Originality/value
This study sheds light on the effects of country heterogeneity on the elasticities and the accuracy of using world average elasticities in a trade policy study for an individual country. In addition, this paper offers estimated values of country-specific elasticities for 10 countries and regions.
Push–pull factors influencing international return migration intentions: a systematic literature review
Authors: Mohamed Mohamed-Abdullahi , Abdul-Talib Asmat-Nizam 
Published: May 2020

PurposeThe purpose of this paper is to review motivational factors driving migration return by assessing both push and pull factors that influence return intentions. The study aims to expand current literature of migration return, and proposes a conceptual framework.Design/methodology/approachA systematic literature review was conducted to determine the push–pull factors that influence international return migration. The authors did a comprehensive search of electronic databases using relevant key terms.FindingsThe findings highlight motivational factors in detail and classify them into three categories: economic, psychological and situational. Most of the literature concerning motives of migration return discussed economic and psychological as the two major factors, but here other motivational factors are presented, which are named as situational factors in this study.Research limitations/implicationsThe paper adopts a systematic literature review method to probe into existing literature, inevitably lacking some empirical studies; thus, the results may not be generalizable. Therefore, future research is suggested to test the proposed propositions.Practical implicationsThe paper offers compelling propositions, which could be a useful reference for migrants’ repatriation motives. It will shed light on motivational factors beyond economic and physiological factors.Originality/valueTo the best of the authors’ knowledge, this study is the first to provide a comprehensive review of motivational factors of migration return using push–pull theory and propose beyond psychological and economic factors.
Investigating quality of life by residents of social housing in eastern Algeria: a structural equation modelling
Authors: Djafri Riadh , Mohamed Osman Mariana , Suzilawati Rabe Noor , Shuid Syafiee 
Published: May 2020

PurposeThe purpose of this paper is to identify, confirm and validate a model appropriate to capture the interrelationships between different variables to develop and improve social housing quality, adequacy, provision and residents’ quality of life (RQOL).Design/methodology/approachThis research adopted a quantitative approach to examine the research objectives of this study. The proposed conceptual framework was tested using primary data collected from a survey of 418 residents of the new urban center of Hamla. The data were analyzed using descriptive analysis and exploratory factor analysis through SPSS. In addition, confirmatory factor analysis was performed using AMOS before validating the measurement model and testing the hypotheses through structural equation modeling (SEM).FindingsThe results of SEM indicated acceptable high goodness-of-fit indices. The results revealed that three out of six hypotheses were supported. Consequently, residential quality and housing adequacy appeared to have a vital role in the conceptual framework, as it influenced social housing provision andRQOLand was influenced by socio-economic characteristics.Practical implicationsThe present study illustrates the interrelationships between the proposed variables using SEM analysis. In addition, by understanding the direct relationships between the selected variables, the findings would be useful for the concerned authorities to ameliorate and upgrade the social housing quality and adequacy along with surpassing the current shortage, which would enhance and contribute to the amelioration of theRQOLand throughout Algeria.Originality/valueThis paper aims to establish, examine, validate the relationships and develop a conceptual framework in the context of Algerian social housing that contributes to the assessment and amelioration of social housing.