bluuebunny/crossref_metadata_2025_split huggingface dataset:
DecentTree: Scalable Neighbour-Joining for the Genomic Era
Authors: Wang Weiwen , Barbetti James , Wong Thomas , Thornlow Bryan , Corbett-Detig Russ , Turakhia Yatish , Lanfear Robert , Minh Bui Quang 
Published: April 2022

AbstractSummaryNeighbour-Joining is one of the most widely used distance-based phylogenetic inference methods. However, current implementations do not scale well for datasets with more than 10,000 sequences. Given the increasing pace of generating new sequence data, particularly in outbreaks of emerging diseases, and the already enormous existing databases of sequence data for which NJ is a useful approach, new implementations of existing methods are warranted.Here we present DecentTree, which provides highly optimised and parallel implementations of Neighbour-Joining and several of its variants. DecentTree is designed as a stand-alone application and a header-only library easily integrated with other phylogenetic software (e.g. it is integral in the popular IQ-TREE software). We show that DecentTree shows similar or improved performance over existing software (BIONJ, Quicktree, FastME, and RapidNJ), especially for handling very large alignments. For example, DecentTree is up to 6-fold faster than the fastest existing Neighbour-Joining software (e.g. RapidNJ) when generating a tree of 64,000 SARS-CoV-2 genomes.Availability and implementationDecentTree is open source and freely available at https://github.com/iqtree/decenttree.ContactMinh Bui: m.bui@anu.edu.au; Robert Lanfear: rob.lanfear@anu.edu.auSupplementary informationSupplementary data are available at Bioinformatics online.
Photodynamic inactivation of pathogenic bacteria on human skin by applying a potent photosensitizer in a hydrogel
Authors: Eckl Daniel Bernhard , Hoffmann Anja Karen , Landgraf Nicole , Kalb Larissa , Bäßler Pauline , Wallner Susanne , Eichner Anja , Huber Harald , Bäumler Wolfgang 
Published: April 2022

AbstractThe antibiotic crisis increasingly threatens the health systems world-wide. Especially as there is an innovation gap in the development of novel antibiotics, treatment options for bacterial infections become fewer. The photodynamic inactivation (PDI) of bacteria appears to be a potent, new technology that may support the treatment of colonized or infected skin. In photodynamic inactivation, a dye – called photosensitizer – absorbs light and generates reactive singlet oxygen. This singlet oxygen is then capable of killing bacteria independent of species or strain and their antibiotic resistance profile. In order to provide a practical application for the skin surface, the photosensitizer was included in an aqueous hydrogel (photodynamically active hydrogel). The efficacy of this gel was initially tested on an inanimate surface and then on the human skin ex vivo. NBTC staining and TUNEL assays were carried out on skin biopsies to investigate potential harmful effects of the surface PDI to the underlying skin cells. The photosensitizer in the gel sufficiently produced singlet oxygen while showing only little photobleaching. On inanimate surfaces as well as on the human skin, the number of viable bacteria was reduced by over or nearly up to 4 log10 steps, equal to 99.99% reduction or even more. Furthermore, histological staining showed no harmful effects of the gel towards the tissue. The application of this hydrogel represents a valuable method in decolonizing human skin including the potential to act against superficial skin infections. The presented results are promising and should lead to further investigation in a clinical study to check the effectivity of the photodynamically active hydrogel on patients.
Multishot Tomography for High-Resolution In Situ Subtomogram Averaging
Authors: Khavnekar S. , Wan W. , Majumder P. , Wietrzynski W. , Erdmann P. S. , Plitzko J. M. 
Published: April 2022

AbstractCryo-electron tomography (cryo-ET) and subtomogram averaging (STA) can resolve protein complexes at near atomic resolution, and when combined with focused ion beam (FIB) milling, macromolecules can be observed within their native context. Unlike single particle acquisition (SPA), cryo-ET can be slow, which may reduce overall project throughput. We here propose a fast, multi-position tomographic acquisition scheme based on beam-tilt corrected beam-shift imaging along the tilt axis, which yields sub-nanometer in situ STA averages.
New molecular signatures defining the differential proteostasis response in ALS-resistant and -sensitive motor neurons
Authors: Petisco Fiore Ana Paula Zen , Maity Shuvadeep , An Disi , Rendleman Justin , Iannitelli Dylan , Choi Hyungwon , Mazzoni Esteban , Vogel Christine 
Published: April 2022

AbstractAmyotrophic Lateral Sclerosis (ALS) is a fatal adult neurodegenerative disease characterized by proteostasis dysregulation, resulting in progressive loss of spinal and upper motor neurons. A subset of cranial motor neurons resistant to ALS-stress survive until late stages of the disease. To investigate these differences, we exploited a unique platform of induced cranial and spinal motor neurons (iCrMNs and iSpMNs, respectively). Exposing both cell types to proteotoxic stress, we quantified transcriptome and proteome changes over 36 hours for a core set of >8,200 genes. While mRNA and protein changes under stress were congruent for many genes, cell-type specific differences manifested at either the RNA or protein level, but less at both. At the protein level, iCrMNs and iSpMNs differed significantly with respect to abundance of many membrane proteins, including synaptic proteins, solute carriers, adhesion molecules, and signaling molecules suggesting that the superior stress survival of iCrMNs involve diverse pathways supporting neuronal function. Other differences included genes involved in ribosome biogenesis and subunits of the core proteasome. We investigated the role of proteasomal degradation in more detail. Our data showed that although stress reduces proteasome activity in both neuronal types, iCrMNs had significantly more abundant and active 26S proteasome than iSpMNs, which indicate a higher capacity for the degradation of ubiquitinated proteins. We identified a new regulator of this better performance, i.e. the nuclear proteasome activator Ublcp1, whose inhibition sensitized iCrMNs, but not iSpMNs, to stress and abolished their higher survival rates. The results suggest that the two neuronal cell types regulate and use the degradation machinery differently under normal and stress conditions. Overall, this work demonstrates the value of unbiased system-wide analyses in generating hypotheses on differential proteostasis regulation in cranial and spinal motor neurons.
Learning inverse folding from millions of predicted structures
Authors: Hsu Chloe , Verkuil Robert , Liu Jason , Lin Zeming , Hie Brian , Sercu Tom , Lerer Adam , Rives Alexander 
Published: April 2022

AbstractWe consider the problem of predicting a protein sequence from its backbone atom coordinates. Machine learning approaches to this problem to date have been limited by the number of available experimentally determined protein structures. We augment training data by nearly three orders of magnitude by predicting structures for 12M protein sequences using AlphaFold2. Trained with this additional data, a sequence-to-sequence transformer with invariant geometric input processing layers achieves 51% native sequence recovery on structurally held-out backbones with 72% recovery for buried residues, an overall improvement of almost 10 percentage points over existing methods. The model generalizes to a variety of more complex tasks including design of protein complexes, partially masked structures, binding interfaces, and multiple states.
A fuzzy-based competitiveness assessment tool for construction SMEs
Authors: Khouja Ahmed , Lehoux Nadia , Cimon Yan 
Published: April 2022

PurposeIn highly competitive industries such as the construction sector, companies with limited capabilities struggle to maintain their current standing, let alone acquire more market share. Before they are able to address their shortcomings, these companies need to pinpoint where their performance stands when it comes to market demand. Furthermore, competitiveness is strongly linked with companies' ability to win tenders and deliver the associated construction projects. Tenders are, therefore, a mechanism that reflects the strengths and weaknesses of construction firms and can be deemed an indicator of competitiveness. This paper aims to help small and medium-sized enterprises (SMEs) increase their presence in the construction sector by suggesting a systematic approach to evaluate their competitiveness.Design/methodology/approachParticipation requirements were extracted from 11 calls for tenders and organized into categories using a qualitative content analysis. These requirements along with winning assets deduced from the literature constitute the basis of the tool. The qualitative evaluation of the difficulty in satisfying requirements or acquiring assets was transformed into unified, quantifiable scores by means of fuzzy numbers.FindingsA total of 233 requirements were found and classified in 3 main categories. In addition, a list of 54 assets organized into five categories was compiled. The entire methodology led to a five-step assessment tool whose output can be depicted on the proposed competitiveness readiness matrix (CRM).Research limitations/implicationsThis study contributes to the limited number of articles discussing the contractor's side in the tendering process. Furthermore, it combines three theoretical perspectives (i.e. resource-based view, relational view, and industry structure perspective), which are scarcely applied in the construction management field. Consideration of the calls for tenders when developing solutions is also a unique aspect of this research when compared to previous studies.Practical implicationsThis tool may help practitioners navigate the rather elusive tendering process by outlining the necessary elements to participate in and win tenders. It may also allow construction firms to better position themselves in the market with respect to customers' requirements and competitors' performances.Originality/valueThis study provides an approach of both self-assessment and market benchmarking. It assists companies in formulating strategies to become more competitive in general and make better bidding decisions. This is especially interesting because of three aspects: the study is based on a fundamental element of the construction competitiveness concept, i.e. calls for tenders; it offers a mechanism to transform systematically qualitative attributes into quantifiable scores; and it provides a practical and reliable display of the assessment results.
Enhancing the performance of Indian micro, small and medium enterprises by implementing supply chain finance: challenges emerging from COVID-19 pandemic
Authors: Sahoo P.S. Biswa Bhusan , Thakur Vikas 
Published: April 2022

PurposeThe already scarce financial resources coupled with the current COVID-19 pandemic have created the worst scenario for Indian micro, small and medium enterprises (MSMEs). The application of supply chain finance (SCF) solutions to MSMEs can enhance the performance and growth of the sector. But, the implementation of SCF solutions faces various obstacles which restrict the MSMEs' ability to meet their financial requirements. The purpose of this paper is to explore and prioritize the various important barriers hindering SCF application in Indian MSMEs.Design/methodology/approachLiterature on SCF and MSMEs are critically reviewed and barriers affecting the SCF application in Indian MSMEs are scrutinized with the consultation of the experts. The present study applies intuitionistic fuzzy-analytic hierarchy process (IF-AHP) methodology to prioritize the identified barriers and thereafter, the sensitivity analysis is also done to observe the identified barriers under different situations.FindingsThe results of the study have revealed that poor cash flow management and working capital management disruption are acting as the most prioritized barriers of SCF. The external factor of cultural challenges has been prioritized as the minimum-influence factor that has least negative influence on the operations of SCF in MSMEs.Practical implicationsThe present study bears an important practical and managerial implication to solve real world problems of financial constraints of MSMEs. The managers should emphasize upon the importance smooth flow of cash and working capital management across the supply chains by which better SCF solution can be implemented in MSMEs.Originality/valueThe study conducted is an effort to address the barriers of SCF in Indian MSMEs during the COVID-19 pandemic. The implementation of IF-AHP and sensitivity analysis would help managers and policymakers to comprehend and resolve the prioritized barriers and sub-barriers of SCF in the MSMEs.
Rethinking lean synergistically in practice for construction industry improvements
Authors: Pan Wei , Pan Mi 
Published: April 2022

PurposeLean construction is widely known as a theory or methodology of organizational management, while seldom been studied as a solution for industry improvements through practice. This paper explores the practical role of lean for construction industry improvements beyond its theoretical inspirations by empirically examining the industry understanding and practice with the case of Hong Kong.Design/methodology/approachThe research was designed as a mixed-method study by combining a critical literature review, semi-structured interviews with relevant professionals, and a follow-up research workshop that includes eight focus group discussions over two break-out sessions with Hong Kong construction stakeholders.FindingsThe research results indicate a low awareness of the term “lean construction” in use, but its principles were implicitly embedded in relevant practices and techniques, particularly building information modeling (BIM), low or zero carbon building (L/ZCB), and prefabrication and modular construction. Practitioners perceived wide-ranging benefits of lean for construction industry improvements but were reluctant to pioneer its adoption and concerned the multi-level challenges.Originality/valueThe paper provides a new practical perspective to rethink lean for construction industry improvements through its synergies with emerging practices, i.e. BIM and ICT, L/ZCB and sustainability, and prefabrication and modular construction.
Determinants of immersive technology acceptance in the construction industry: management perspective
Authors: Okoro Chioma Sylvia , Nnaji Chukwuma , Adediran Abdulrauf 
Published: April 2022

PurposeThe usefulness of technology for managing projects in the construction industry is indisputable. The potential utility of immersive technologies (ImTs), including virtual and augmented reality, has recently received significant attention. However, the construction industry, especially in developing countries, lags on the implementation of technology generally and ImTs specifically. Forecasting the potential successful ImTs acceptance at the individual level is essential to strategic planning. The study's objective was to develop and test a conceptual model of factors influencing ImTs acceptance at the individual level in the construction industry.Design/methodology/approachA survey of construction management-level professionals in South Africa was undertaken. The study extended two complementary models, the technology acceptance model (TAM) and the theory of planned behavior (TPB), to analyze behavior towards technology acceptance using structural equation modelling.FindingsResults indicated that attitude significantly influenced the intention to use ImTs and perceived usefulness (PU) positively and significantly predicted the intention to use and usage attitude (UA). Further, the effects of perceived enjoyment (PEn) on UA, and social norms (SNs) and perceived behavioral control (PBC) on intention to use were positive and significant. Perceived ease of use (PEU) had negative and non-significant effects on intention to use and UA. By explaining 82% of the variance, the study established that the proposed model successfully evaluates how management-level professionals in the construction industry accept ImTs.Practical implicationsThe study provides valuable insight into the acceptance of ImTs from the perspective of management-level stakeholders in the South African construction industry. It offers fundamental direction to create a general theory on integrating ImTs in construction.Originality/valueThis study systematically surveyed the intention to accept ImTs in the South African construction industry using an extension of the TAM and TPB models.
A science mapping approach-based review of near-miss research in construction
Authors: Duan Pinsheng , Zhou Jianliang 
Published: April 2022

PurposeNear misses are important references for the construction industry to move toward zero injuries, and are of great significance in reducing accidents and improving safety education. To fully improve the construction industry's understanding and standardize the management process of near-miss events, this paper describes a systematic review of the research front and intellectual basis of near-miss events based on scientometric technique and CiteSpace.Design/methodology/approachThe authors reviewed and summarized the research wave and definitions of near-miss events in construction. The science mapping approach is used to conduct quantitative analyses of 120 relevant articles published between 2009 and 2019. Three research themes are identified via author analysis, keyword analysis and co-citation analysis: the construction of near-miss management systems, near-miss events research and characteristic research.FindingsIt is found that improving the data collection method to maximize the quality of near-miss reports, optimizing and verifying the event analysis model considering the characteristics of near-miss events in construction, establishing a more comprehensive framework for the analysis of near-miss events and building a highly inclusive technology integration platform are the four main development directions for the future.Originality/valueAccording to Heinrich's law, incidents are mainly blamed on near-miss events such as workers' unsafe behaviors. Due to the complexity and variability of the construction site, near-miss events in construction may have different features. This article helps promote the understanding of near misses in academia, standardizing the management process of near-miss events, which is conducive to mining the potential value of such events in practice. Some insights into the research front and the intellectual base of near-miss research in construction are proposed.
Continuous learning during crises: achieving change-efficacy, meaningful work and adaptive performance
Authors: Budhiraja Sunil , Rathi Neerpal 
Published: April 2022

PurposeThe study aims to examine the association between learning culture and adaptive performance of delivery employees during crises situation. The study develops and tests a model that explains how learning culture, through change-efficacy and meaningful work, influences employees' adaptive performance (including how they handle crisis situations and deal with uncertainty).Design/methodology/approachData was collected from 298 delivery employees working in e-commerce companies throughout India in a time-lagged manner. Regression analysis and structural equation modeling were performed to assess the influence of learning culture, change-efficacy and meaningful work on adaptive performance using SPSS 24. Further, PROCESS macro was used to test the parallel mediation effects through bootstrapping approach.FindingsThe study establishes a significant direct and indirect relationship between learning culture and adaptive performance for employees. Further, underpinning the transformative learning theory (Mezirow, 1997), and job characteristics theory (1976), this study came across two pathways for organizations to transform their learning efforts into improved adaptive performance for employees.Practical implicationsOrganizations, particularly in crisis situations, can leverage employees' change-efficacy and meaningful work to connect learning efforts with employees' adaptive performance.Originality/valueThe study contributes significantly to existing theory on transformative learning and job characteristics theory while strengthening the literature on antecedents of employees' adaptive performance, particularly in crises situation.
“Should offensively oriented players receive a salary premium in the national basketball association?”
Authors: Potter Joel , Ehrlich Justin A. 
Published: April 2022

PurposeSince recent research has found that offensively oriented players receive a salary premium, the current study recognizes this observed premium might exist because offense is worth more in terms of revenue generation. Given the popular sports saying, “Offense sells tickets, defense wins championships,” the authors quantify whether offense really does sell more “tickets” than defense in the NBA.Design/methodology/approachUsing NBA team revenue data as well as team offensive and defensive win shares, the authors estimate several econometric specifications to test if teams generate more revenue for offensive wins compared to defensive wins. The authors also employ a multi-year free agency study to identify if NBA players receive more compensation for offensive production than they do for defensive production.FindingsThe authors find no statistical difference in revenue generation from offense compared to defense. The authors confirm these findings both before and after revenue sharing. These results are also robust to alternative specifications. Therefore, the authors conclude that fans do not prefer offense to defense in terms of their spending. Contrary to previous research, the authors find no evidence of an offensive premium paid to NBA players.Originality/valueBased on their findings, offensively oriented players should not receive a salary premium. The clear implication for team decision makers is that offensive production should be compensated at a similar rate as defensive production. Since the authors do not find evidence of an offensive premium for offensive production, their research suggests a likely labor market equilibrium in the NBA for both profit-maximizing and win-maximizing teams.