bluuebunny/crossref_metadata_2025_split huggingface dataset:
The S1/S2 boundary of SARS-CoV-2 spike protein modulates cell entry pathways and transmission
Authors: Zhu Yunkai , Feng Fei , Hu Gaowei , Wang Yuyan , Yu Yin , Zhu Yuanfei , Xu Wei , Cai Xia , Sun Zhiping , Han Wendong , Ye Rong , Chen Hongjun , Ding Qiang , Cai Qiliang , Qu Di , Xie Youhua , Yuan Zhenghong , Zhang Rong 
Published: August 2020

SUMMARYThe global spread of SARS-CoV-2 is posing major public health challenges. One unique feature of SARS-CoV-2 spike protein is the insertion of multi-basic residues at the S1/S2 subunit cleavage site, the function of which remains uncertain. We found that the virus with intact spike (Sfull) preferentially enters cells via fusion at the plasma membrane, whereas a clone (Sdel) with deletion disrupting the multi-basic S1/S2 site instead utilizes a less efficient endosomal entry pathway. This idea was supported by the identification of a suite of endosomal entry factors specific to Sdel virus by a genome-wide CRISPR-Cas9 screen. A panel of host factors regulating the surface expression of ACE2 was identified for both viruses. Using a hamster model, animal-to-animal transmission with the Sdel virus was almost completely abrogated, unlike with Sfull. These findings highlight the critical role of the S1/S2 boundary of the SARS-CoV-2 spike protein in modulating virus entry and transmission.
The genusMicroniphargus(Crustacea, Amphipoda): evidence for three lineages distributed across northwestern Europe and transfer to Pseudoniphargidae
Authors: Weber Dieter , Stoch Fabio , Knight Lee R.F.D. , Chauveau Claire , Flot Jean-François 
Published: August 2020

AbstractMicroniphargus leruthiSchellenberg, 1934 (Amphipoda: Niphargidae) was first described based on samples collected in Belgium and placed in a monotypic genus within the family Niphargidae. However, some details of its morphology as well as recent phylogenetic studies suggest thatMicroniphargusmay be more closely related toPseudoniphargus(Amphipoda: Pseudoniphargidae) than toNiphargus.Moreover,M. leruthiranges over 1,469km from Ireland to Germany, which is striking since only a few niphargids have confirmed ranges in excess of 200km. To find out the phylogenetic position ofM. leruthiand check whether it may be a complex of cryptic species, we collected material from Ireland, England and Belgium then sequenced fragments of the mitochondrial cytochromecoxidase subunit 1 gene as well as of the nuclear 28S ribosomal gene. Phylogenetic analyses of both markers confirm thatMicroniphargusis closer toPseudoniphargusthan toNiphargus, leading us to reallocateMicroniphargusto Pseudoniphargidae. We also identify three congruent mito-nuclear lineages present respectively in Ireland, in both Belgium and England, and in England only (with the latter found in sympatry at one location), suggesting thatM. leruthiis a complex of at least three species with a putative centre of origin in England.
The high energetic cost of rapid force development in cyclic muscle contraction
Authors: van der Zee Tim J. , Kuo Arthur D. 
Published: August 2020

AbstractMuscles consume metabolic energy for active movement, particularly when performing mechanical work or producing force. Less appreciated is the cost for activating and deactivating muscle quickly, which adds considerably to the overall cost of cyclic force production (Chasiotis et al., 1987). But the cost relative to mechanical work, which features in many movements, is unknown. We therefore tested whether fast activation-deactivation is costly compared to performing work or producing isometric force. We hypothesized that metabolic cost would increase with a proposed measure termedforce-rate(rate of increase in muscle force) in cyclic tasks, separate from mechanical work or average force level. We tested humans (N = 9) producing cyclic knee extension torque against an isometric dynamometer (torque 22 N-m, cyclic waveform frequencies 0.5 – 2.5 Hz), while also quantifying the force and work of muscle fascicles against series elasticity (with ultrasonography), along with metabolic rate through respirometry. Net metabolic rate increased by more than fourfold (10.5 to 46.7 W) with waveform frequency. At high frequencies, the hypothesized force-rate cost accounted for nearly half (41%) of energy expenditure. This exceeded the cost for average force (17%) and was comparable to the cost for shortening work (42%). The energetic cost is explained by a simple first-order model of rate-limiting steps in muscle contraction, primarily crossbridge dynamics. The force-rate cost could contribute substantially to the overall cost of movements that require cyclic muscle activation, such as locomotion.Summary statementThe energetic cost of isometric muscle force production during cyclic muscle contraction increases sharply with cycle frequency and in proportion to the rate of force development
RNA promotes the formation of spatial compartments in the nucleus
Authors: Quinodoz Sofia A. , Bhat Prashant , Ollikainen Noah , Jachowicz Joanna W. , Banerjee Abhik K. , Chovanec Peter , Blanco Mario R. , Chow Amy , Markaki Yolanda , Plath Kathrin , Guttman Mitchell 
Published: August 2020

SUMMARYThe nucleus is a highly organized arrangement of RNA, DNA, and protein molecules that are compartmentalized within three-dimensional (3D) structures involved in shared functional and regulatory processes. Although RNA has long been proposed to play a global role in organizing nuclear structure, exploring the role of RNA in shaping nuclear structure has remained a challenge because no existing methods can simultaneously measure RNA-RNA, RNA-DNA, and DNA-DNA contacts within 3D structures. To address this, we developed RNA & DNA SPRITE (RD-SPRITE) to comprehensively map the location of all RNAs relative to DNA and other RNAs. Using this approach, we identify many RNAs that are localized near their transcriptional loci (RNA-DNA) together with other diffusible ncRNAs (RNA-RNA) within higher-order DNA structures (DNA-DNA). These RNA-chromatin compartments span three major classes of nuclear functions: RNA processing (including ribosome biogenesis, mRNA splicing, snRNA biogenesis, and histone mRNA processing), heterochromatin assembly, and gene regulation. More generally, we identify hundreds of ncRNAs that form stable nuclear compartments in spatial proximity to their transcriptional loci. We find that dozens of nuclear compartments require RNA to guide protein regulators into these 3D structures, and focusing on several ncRNAs, we show that these ncRNAs specifically regulate heterochromatin assembly and the expression of genes contained within these compartments. Together, our results demonstrate a unique mechanism by which RNA acts to shape nuclear structure by forming high concentration territories immediately upon transcription, binding to diffusible regulators, and guiding them into spatial compartments to regulate a wide range of essential nuclear functions.
The Population Genetics of Collateral Resistance and Sensitivity
Authors: Ardell Sarah M. , Kryazhimskiy Sergey 
Published: August 2020

AbstractResistance mutations against one drug can elicit collateral sensitivity against other drugs. Multi-drug treatments exploiting such trade-offs can help slow down the evolution of resistance. However, if mutations with diverse collateral effects are available, a treated population may evolve either collateral sensitivity or collateral resistance. How to design treatments robust to such uncertainty is unclear. We show that many resistance mutations inEscherichia coliagainst various antibiotics indeed have diverse collateral effects. We propose to characterize such diversity with a joint distribution of fitness effects (JDFE) and develop a theory for describing and predicting collateral evolution based on simple statistics of the JDFE. We show how to robustly rank drug pairs to minimize the risk of collateral resistance and how to estimate JDFEs. In addition to practical applications, these results have implications for our understanding of evolution in variable environments.
MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor
Authors: Forouzesh Negin , Onufriev Alexey V. 
Published: August 2020

AbstractThe ability to estimate protein-protein binding free energy in a computationally efficient via a physics-based approach is beneficial to research focused on the mechanism of viruses binding to their target proteins. Implicit solvation methodology may be particularly useful in the early stages of such research, as it can offer valuable insights into the binding process, quickly. Here we evaluate the potential of the related molecular mechanics generalized Born surface area (MMGB/SA) approach to estimate the binding free energy ΔGbindbetween the SARS-CoV-2 spike receptor-binding domain and the human ACE2 receptor. The calculations are based on a recent flavor of the generalized Born model, GBNSR6. Two estimates of ΔGbindare performed: one based on standard bondi radii, and the other based on a newly developed set of atomic radii (OPT1), optimized specifically for protein-ligand binding. We take the average of the resulting two ΔGbindvalues as the consensus estimate. For the well-studied Ras-Raf protein-protein complex, which has similar binding free energy to that of the SARS-CoV-2/ACE2 complex, the consensus ΔGbind= −11.8±1 kcal/mol, vs. experimental −9.7±0.2 kcal/mol.The consensus estimates for the SARS-CoV-2/ACE2 complex is ΔGbind= −9.4±1.5 kcal/mol, which is in near quantitative agreement with experiment (−10.6 kcal/mol). The availability of a conceptually simple MMGB/SA-based protocol for analysis of the SARS-CoV-2 /ACE2 binding may be beneficial in light of the need to move forward fast.
Global and Local Mutations in Bangladeshi SARS-CoV-2 Genomes
Authors: Hasan Md. Mahbub , Das Rasel , Rasheduzzaman Md. , Hussain Md Hamed , Muzahid Nazmul Hasan , Salauddin Asma , Rumi Meheadi Hasan , Rashid S M Mahbubur , Siddiki AMAM Zonaed , Mannan Adnan 
Published: August 2020

AbstractCorona Virus Disease-2019 (COVID-19) warrants comprehensive investigations of publicly available Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) genomes to gain new insight about their epidemiology, mutations and pathogenesis. Nearly 0.4 million mutations were identified so far in ∼60,000 SARS-CoV-2 genomic sequences. In this study, we compared 207 of SARS-CoV-2 genomes reported from different parts of Bangladesh and their comparison with 467 globally reported sequences to understand the origin of viruses, possible patterns of mutations, availability of unique mutations, and their apparent impact on pathogenicity of the virus in victims of Bangladeshi population. Phylogenetic analyses indicates that in Bangladesh, SARS-CoV-2 viruses might arrived through infected travelers from European countries, and the GR clade was found as predominant in this region. We found 2602 mutations including 1602 missense mutations, 612 synonymous mutations, 36 insertions and deletions with 352 other mutations types. In line with the global trend, D614G mutation in spike glycoprotein was predominantly high (95.6%) in Bangladeshi isolates. Interestingly, we found the average number of mutations in ORF1ab, S, ORF3a, M and N of genomes, having nucleotide shift at G614 (n=459), were significantly higher (p≤0.001) than those having mutation at D614 (n=215). Previously reported frequent mutations such as P4715L, D614G, R203K, G204R and I300F were also prevalent in Bangladeshi isolates. Additionally, 87 unique amino acid changes were revealed and were categorized as originating from different cities of Bangladesh. The analyses would increase our understanding of variations in virus genomes circulating in Bangladesh and elsewhere and help develop novel therapeutic targets against SARS-CoV-2.
Photobleaching step analysis for robust determination of protein complex stoichiometries
Authors: Hummert Johan , Yserentant Klaus , Fink Theresa , Euchner Jonas , Herten Dirk-Peter 
Published: August 2020

AbstractThe composition of cellular structures on the nanoscale is a key determinant of macroscopic functions in cell biology and beyond. Different fluorescence single-molecule techniques have proven ideally suited for measuring protein copy numbers of cellular structures in intact biological samples. Of these, photobleaching step analysis poses minimal demands on the microscope and its counting range has significantly improved with more sophisticated algorithms for step detection, albeit at an increasing computational cost. Here, we present a comprehensive framework for photobleaching step analysis, optimizing both data acquisition and analysis. To make full use of the potential of photobleaching step analysis, we evaluate various labelling strategies with respect to their molecular brightness and photostability. The developed analysis algorithm focuses on automation and computational efficiency. Moreover, we benchmark the framework with experimental data acquired on DNA origami labeled with defined fluorophore numbers to demonstrate counting of up to 35 fluorophores. Finally, we show the power of the combination of optimized trace acquisition and automated data analysis for robust protein counting by counting labelled nucleoporin 107 in nuclear pore complexes of intact U2OS cells. The successful in situ application promotes this framework as a new resource enabling cell biologists to robustly determine the stoichiometries of molecular assemblies at the single-molecule level in an automated fashion.
A heuristic method with a novel stability concept to perform parallel assembly sequence planning by subassembly detection
Authors: Gulivindala Anil Kumar , Bahubalendruni M.V.A. Raju , Varupala S.S. Vara Prasad , K. Sankaranarayanasamy 
Published: August 2020

Purpose
Parallel assembly sequence planning (PASP) reduces the overall assembly effort and time at the product development stage. Methodological difficulties at framework development and computational issues at their implementation made the PASP complex to achieve. This paper aims to propose a novel stability concept for subassembly detection to minimize the complexities in PASP.

Design/methodology/approach
In this research, a heuristic method is developed to identify, represent and implement the stability predicate to perform subassembly detection and assembly sequence planning (ASP) at the further stages. Stability is organized into static, dynamic, enriched and no stability between the mating assembly parts. The combination of parts that possesses higher fitness is promoted to formulate the final solution about PASP.

Findings
The results obtained by applying the proposed concept on complex configurations revealed that stability predicate plays a dominant role in valid subassembly detection and final sequence generation further.

Originality/value
The value of the presented study lies in the three types of stability conditions and effective integration to existed ASP method. Unlike the existed heuristics in subassembly detection, the proposed concept identifies the parallel subassemblies during ASP.
Automated guided vehicles in modular integrated construction: potentials and future directions
Authors: Yang Yi , Pan Wei 
Published: August 2020

Purpose
This paper aims to examine the potentials of using automated guided vehicle (AGV) technology in modular integrated construction (MiC) to realise logistics automation in module manufacturing and transport.

Design/methodology/approach
This paper adopts a scenario approach through three phases (i.e. scenario preparation, development and transfer), with six steps performed iteratively. The scenarios were systematically developed using a six-aspect socio-technical framework. Data were collected through a comprehensive literature review, site visits and interviews with relevant stakeholders and professionals. Implications regarding strength, weakness, opportunities and challenges and future research directions are provided.

Findings
The developed scenarios of “smart manufacturing” and “last-mile delivery” demonstrated how AGVs could be used to enhance efficiency and productivity in module manufacturing and transport. The synergies between AGVs and emerging information technologies should pave a good foundation for realising logistics automation in MiC. Future research should address: how to define the tasks of AGVs, how will the use of AGVs impact MiC practices, how to design AGV-integrated module manufacturing/transport systems and how to integrate people factors into the use of AGVs in MiC.

Practical implications
This paper reveals the socio-technical benefits and challenges of using AGVs in MiC.

Originality/value
This study extends the understanding of using logistics automation in MiC as emerging research directions, with the intention of directing scholars’ and practitioners’ interest into future exploration. It is the first attempt in its kind. Its findings could be extended to constitute a comprehensive development roadmap and prospects of automation in modular construction.
The competitive efficiency of Costa Rican small and medium-sized businesses: a data envelopment analysis approach
Authors: Alonso-Ubieta Suyen , Mora-Esquivel Ronald , Leiva Juan Carlos 
Published: August 2020

Purpose
Building on the resource-based view theory, this paper aims to evaluate the role of innovation on competitiveness and competitive efficiency among Costa Rican small and medium-size enterprises (SMEs).

Design/methodology/approach
The study uses a sample of 231 Costa Rican small and medium-size firms for 2019. The authors compute a competitiveness index that includes four pillars: innovation, strategy, markets and human capital. To estimate competitive efficiency, the authors use a non-parametric model, namely, data envelopment analysis, with a single constant input.

Findings
The results confirm that competitive and efficient SMEs present a more homogenous distribution of resources and capabilities. The innovation pillar is positively correlated with competitive efficiency. A positive correlation exists between market experience (business age) and innovation and between innovation and business size in terms of the number of employees.

Practical implications
The study contributes to the understanding on how SME managers’ decision-making processes affect resource allocation within the business, and on how SMEs can introduce strategic actions based on improvements of those resources that will likely have a greater impact on competitive efficiency.

Originality/value
This study contributes to better grasping how the configuration of resources and capabilities, in which innovation plays a decisive role, and contributes to shape the competitive efficiency of small and medium-sized businesses in a developing economy.
Climate change impacts on water resources in a rural community in Limpopo province, South Africa: a community-based adaptation to water insecurity
Authors: Rankoana Sejabaledi Agnes 
Published: August 2020

Purpose
The study explored the impacts of climate change on water resources, and the community-based adaptation practices adopted to ensure water security in a rural community in Limpopo Province, South Africa.

Design/methodology/approach
The study was conducted in Limpopo Province, South Africa. The participatory approach was used to allow community members to share their challenges of water scarcity, and the measures they have developed to cope with inconsistent water supply.

Findings
The study results show that the community obtains water for household consumption from the reticulation system supplied by Mutale River and the community borehole. These resources are negatively impacted by drought, change in the frequency and distribution of rainfall, and increased temperature patterns. The water levels in the river and borehole have declined, resulting in unsustainable water supply. The community-based adaptation practices facilitated by the water committee include observance of restrictions and regulations on the water resources use. Others involve securing water from neighbouring resources.

Originality/value
This type of community-based action in response to climate change could be used as part of rural water management strategies under climate change.
Recruitment, retention and resignation among Non-Career Firefighters
Authors: Lantz Emelie , Runefors Marcus 
Published: August 2020

PurposeThe purpose of this paper is to provide a review of literature about recruitment, retention and resignation among non-career firefighters.Design/methodology/approachA systematic review was conducted to identify factors associated with the recruitment, retention and resignation of non-career firefighters. The authors divided the results into three topics and four levels for further analysis.Findings27 articles are included in the review. Most research addresses retention at an organizational level and indicates a link between job satisfaction and factors such as supervisor support, recognition and close relationships within the workgroup. Further, a recurring reason that contributes to resignations seems to be family related (e.g. partner disapproval).Research limitations/implicationsThere is a lack of European and Asian research into non-career firefighters. The included research papers generally have low response rates and the sample is often mostly male and Caucasians from a limited area.Practical implicationsThe identified factors offer deeper understanding and can help practitioners in their pursuit of the sustainable retention of non-career firefighters.Originality/valueBecause securing adequate numbers of non-career firefighters is important, there is a need to synthesize current evidence to identify and further understand which factors contribute to retention. To the authors' knowledge, this is the first systematic review to synthesize such evidence about non-career firefighters.
What do practitioners expect from an evaluation report? A qualitative analysis of Dutch crisis management professionals' expectations
Authors: Beerens Ralf Josef Johanna , Haverhoek-Mieremet Karin 
Published: August 2020

PurposeThis paper seeks to overcome the mismatch between evaluation reports and the expectations of the target audience, by identifying crisis management professionals' expectations.Design/methodology/approachAn adapted stakeholder information analysis was used to survey the expectations of 84 crisis management professionals in the Netherlands. A general inductive analysis was applied to qualitative data, from which five main themes emerged: purpose; object or focus; reasoning and (meta) analysis; result or conclusion, and the overall design of the evaluation.FindingsCurrently, evaluation reports are seen merely as a way to share experience and support thinking about how to avoid repeating mistakes. However, most respondents expected them to contribute to learning and support improvement. They should provide actionable feedback on what could be done differently or better, and indicate how this can be achieved. Respondents emphasised the need to focus on the human factor and not neglect the context. The wide variety of views underlined that it is difficult to create one evaluation product that meets all expectations.Research limitations/implicationsAlthough some major themes clearly emerged from the data, it is unclear how they relate to each other, and their relative importance. In addition, no distinction is made between evaluations of real events and simulations.Practical implicationsUsers should be encouraged to provide input into the evaluation process by clarifying their needs and how they use evaluation reports.Originality/valueThis research is the first attempt to identify user expectations regarding what constitutes an effective evaluation.