bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular characterization ofMycobacterium ulceransDNA gyrase and identification of mutations reduced susceptibility against quinolonesin vitro
Authors: Kim Hyun , Mori Shigtarou , Kenri Tsuyoshi , Suzuki Yasuhiko 
Published: October 2021

ABSTRACTBuruli ulcer disease is a neglected necrotizing and disabling cutaneous tropical illness caused byMycobacterium ulcerans(Mul). Fluoroquinolone (FQ), used in the treatment of this disease, has been known to act by inhibiting the enzymatic activities of DNA gyrase; however, the detailed molecular basis of these characteristics and the FQ resistance mechanisms inMulremains unknown. This study investigated the detailed molecular mechanism ofMulDNA gyrase and the contribution of FQ resistancein vitrousing recombinant proteins from theMulsubsp. shinshuense and Agy99 strains with reduced sensitivity to FQs. The IC50of FQs against Ala91Vla and Asp95Gly mutants ofMulshinshuense and Agy99 GyrA subunits were 3.7- to 42.0-fold higher than those against wild-type enzyme. Similarly, the CC25was 10- to 210-fold higher than those for the WT enzyme. Furthermore, the interaction between the amino acid residues of WT/mutantMulDNA gyrase and FQ side chains was assessed via molecular docking studies. This is the first detailed study showing the contribution ofMulDNA GyrA subunit mutations to reduce the susceptibility against FQs.
Why can we detect lianas from space?
Authors: Visser Marco D. , Detto Matteo , Meunier Félicien , Wu Jin , Foster Jane R. , Marvin David C. , van Bodegom Peter M. , Bongalov Boris , Nunes Matheus Henrique , Coomes David , Verbeeck Hans , Guzmán Q J. Antonio , Sanchez-Azofeifa Arturo , Chandler Chris J. , van der Heijden Geertje M.F , Boyd Doreen S. , Foody Giles M. , Cutler Mark E.J. , Broadbent Eben N. , Serbin Shawn P. , Schnitzer Stefan , Rodríguez-Ronderos M. Elizabeth , Sterck Frank , Medina-Vega José A. , Pacala Steve 
Published: October 2021

AbstractLianas, woody vines acting as structural parasites of trees, have profound effects on the composition and structure of tropical forests, impacting tree growth, mortality, and forest succession. Remote sensing offers a powerful tool for quantifying the scale of liana infestation, provided the availability of robust detection methods. We analyze the consistency and global specificity of spectral signals from liana-infested tree crowns and forest stands, examining the underlying mechanisms. We compiled a database, including leaf reflectance spectra from 5424 leaves, fine-scale airborne reflectance data from 999 liana-infested canopies, and coarse-scale satellite reflectance data covering hectares of liana-infested forest stands. To unravel the mechanisms of the liana spectral signal, we applied mechanistic radiative transfer models across scales, corroborated by field data on liana leaf chemistry and canopy structure. We find a consistent liana spectral signature at canopy and stand scales across sites. This signature mainly arises at the canopy level due to direct effects of leaf angles, resulting in a larger apparent leaf area, and indirect effects from increased light scattering in the NIR and SWIR regions, linked to lianas’ less costly leaf construction compared to trees. The existence of a consistent global spectral signal for lianas suggests that large-scale quantification of liana infestation is feasible. However, because the traits identified are not exclusive to lianas, accurate large-scale detection requires rigorously validated remote sensing methods. Our models highlight challenges in automated detection, such as potential misidentification due to leaf phenology, tree life-history, topography, and climate, especially where the scale of liana infestation is less than a single remote sensing pixel. The observed cross-site patterns also prompt ecological questions about lianas’ adaptive similarities across environments, indicating possible convergent evolution due to shared constraints on leaf biochemical and structural traits.Open data statementOf the 17 datasets used, 10 are published and publicly accessible, with links provided in this submission (Appendix S1: Section S1). Upon acceptance, remaining seven datasets will be provided via Smithsonian’s Dspace. The open-source model code is available as R-package ccrtm (https://cran.r-project.org/web/packages/ccrtm/index.html) and on github (https://github.com/MarcoDVisser/ccrtm). Code will be archived in Zenodo should the manuscript be accepted for publication
S. pombe wtf genes use dual transcriptional regulation and selective protein exclusion from spores to cause meiotic drive
Authors: Nuckolls Nicole L. , Srinivasa Ananya Nidamangala , Mok Anthony C. , Bravo Núñez María Angélica , Lange Jeffrey J. , Gallagher Todd J. , Seidel Chris W. , Zanders Sarah E. 
Published: October 2021

AbstractMeiotic drivers bias gametogenesis to ensure their transmission into more than half the offspring of a heterozygote. In Schizosaccharomyces pombe, wtf meiotic drivers destroy the meiotic products (spores) that do not inherit the driver from a heterozygote, thereby reducing fertility. wtf drivers encode both a Wtfpoison protein and a Wtfantidote protein using alternative transcriptional start sites. Here, we analyze how the expression and localization of the Wtf proteins are regulated to achieve drive. We show that transcriptional timing and selective protein exclusion from developing spores ensure that all spores are exposed to Wtf4poison, but only the spores that inherit wtf4 receive a dose of Wtf4antidote sufficient for survival. In addition, we show that the Mei4 transcription factor, a master regulator of meiosis, controls the expression of the wtf4poison transcript. This dual transcriptional regulation, which includes the use of a critical meiotic transcription factor, likely complicates the universal suppression of wtf genes without concomitantly disrupting spore viability. We propose that these features contribute to the evolutionary success of the wtf drivers.Author SummaryKiller meiotic drivers are one type of selfish DNA sequence. When only one copy of a killer meiotic driver is found in a genome, the driver is expected to be transmitted to only half of the gametes (e.g. eggs or sperm). Killer meiotic drivers, however, kill developing gametes that do not inherit them, giving the driver a transmission advantage into the next generation. The molecular mechanisms used by these killers are not well understood. In this work, we analyzed how one killer meiotic driver, wtf4 from fission yeast, ensures targeted gamete (spore) killing. Previous work showed that wtf meiotic drivers encode a poison protein that is transmitted to all spores and an antidote protein that rescues only spores that inherit the locus. Here, we show that different timing of the expression of the two proteins, combined with differential inclusion of the proteins in developing spores, both contribute to targeted spore killing. We also demonstrate that wtf4 exploits an essential gene expression pathway, making it difficult for the genome to prevent this locus from being expressed and killing. This extends our knowledge both of how these genetic parasites act and how they are equipped to evade host suppression mechanisms.
Strain and rupture of HIV-1 capsids during uncoating
Authors: Yu Alvin , Lee Elizabeth M.Y. , Briggs John A.G. , Ganser-Pornillos Barbie K. , Pornillos Owen , Voth Gregory A. 
Published: October 2021

AbstractViral replication in HIV-1 relies on a fullerene-shaped capsid to transport genetic material deep into the nucleus of an infected cell. Capsid stability is linked to the presence of cofactors, including inositol hexakisphosphate (IP6) that bind to pores found in the capsid. Using extensive all-atom molecular dynamics simulations of HIV-1 cores imaged from cryo-electron tomography (cryo-ET) in intact virions, which contain IP6 and a ribonucleoprotein complex, we find markedly striated patterns of strain on capsid lattices. The presence of these cofactors also increases rigidity of the capsid. Conformational analysis of capsid (CA) proteins show CA accommodates strain by locally flexing away from structures resolved using x-ray crystallography and cryo-electron microscopy. Then, cryo-ET of HIV-1 cores undergoing endogenous reverse transcription demonstrate that lattice strain increases in the capsid prior to mechanical failure and that the capsid ruptures by crack propagation along regions of high strain. These results uncover HIV-1 capsid properties involved in their critical disassembly process.Significance statementThe mature capsids of HIV-1 are transiently stable complexes that self-assemble around the viral genome during maturation, and uncoat to release preintegration complexes that archive a double-stranded DNA copy of the virus in the host cell genome. However, a detailed view of how HIV cores rupture remains lacking. Here, we elucidate the physical properties involved in capsid rupture using a combination of large-scale all-atom molecular dynamics simulations and cryo-electron tomography. We find that intrinsic strain on the capsid forms highly correlated patterns along the capsid surface, along which cracks propagate. Capsid rigidity also increases with high strain. Our findings provide fundamental insight into viral capsid uncoating.
Anisotropy of plasmalemmal sterols and cell mating require StARkin domain proteins Ysp2 and Lam4
Authors: Chauhan Neha , Fairn Gregory D. 
Published: October 2021

AbstractIn the budding yeast S. cerevisiae Cdc42 is required for polarized growth and the formation of mating projections (shmoos). Negatively charged lipids including phosphatidylserine and phosphatidylinositol 4,5-bisphosphate support a positive feedback loop that recruits Cdc42 effectors and MAP kinase scaffolds, many of which contain polybasic patches that directly interact with the membrane. Here, using genetically encoded sterol sensor ALOD4 we find that ergosterol is accumulated in the cytosolic leaflet of buds and shmoos. The accumulation of ergosterol in the plasma membrane requires both Osh and Lam proteins however cells lacking Ysp2/Lam2 and Lam4 displayed a reversal in the polarity of ergosterol. The redistribution of ergosterol impairs the polarization of phosphatidylserine and phosphatidylinositol 4,5-bisphophate which further impacts shmoo formation, MAPK signaling and mating efficiency. Our observations demonstrate that the ability of Lam proteins to deliver ergosterol from the plasma membrane to the ER helps maintain a gradient of ergosterol which in turn supports robust cell polarity.SummaryThe sterol sensor ALOD4 is enriched at sites of polarized growth. Elimination of the Osh proteins solubilized the ALOD4 whereas elimination of Ysp2 and Lam4 reversed ALOD4 polarization. Cells lacking Ysp2 and Lam4 have defects in mating and MAP kinase signaling.
A Role for Cell Polarity in Lifespan and Mitochondrial Quality Control in the Budding Yeast Saccharomyces cerevisiae
Authors: Yang Emily J. , Pernice Wolfgang M , Pon Liza A. 
Published: October 2021

SummaryBabies are born young, largely independent of the age of their mothers. Mother-daughter age asymmetry in yeast is achieved, in part, by inheritance of higher-functioning mitochondria by daughter cells and retention of some high-functioning mitochondria in mother cells. The mitochondrial F-box protein, Mfb1p, tethers mitochondria at both poles in a cell cycle-regulated manner: it localizes to and anchors mitochondria to the mother cell tip throughout the cell cycle, and to the bud tip prior to cytokinesis. Here, we report that cell polarity and polarized localization of Mfb1p decline with age in S. cerevisiae. Moreover, deletion of BUD1/RSR1, a Ras protein required for cytoskeletal polarization during asymmetric yeast cell division, results in depolarized Mfb1p localization, defects in mitochondrial distribution and quality control, and reduced replicative lifespan. Our results demonstrate a role for the polarity machinery in lifespan through modulating Mfb1 function in asymmetric inheritance of mitochondria during yeast cell division.
Competitive evolution of H1N1 and H3N2 influenza viruses in the United States: A mathematical modeling study
Authors: Wilasang Chaiwat , Suttirat Pikkanet , Chadsuthi Sudarat , Wiratsudakul Anuwat , Modchang Charin 
Published: October 2021

AbstractSeasonal influenza causes vast public health and economic impact globally. The prevention and control of the annual epidemics remain a challenge due to the antigenic evolution of the viruses. Here, we presented a novel modeling framework based on changes in amino acid sequences and relevant epidemiological data to retrospectively investigate the competitive evolution and transmission of H1N1 and H3N2 influenza viruses in the United States during October 2002 and April 2019. To do so, we estimated the time-varying disease transmission rate from the reported influenza cases and the time-varying antigenic change rate of the viruses from the changes in amino acid sequences. By incorporating the time-varying antigenic change rate into the transmission models, we found that the models could capture the evolutionary transmission dynamics of influenza viruses in the United States. Our modeling results also showed that the antigenic change of the virus plays an essential role in seasonal influenza dynamics.
Regulation of the Evolutionarily Conserved Muscle Myofibrillar Matrix by Cell Type Dependent and Independent Mechanisms
Authors: Ajayi Peter T. , Katti Prasanna , Willingham T. Bradley , Sun Ye , Bleck Christopher K.E. , Glancy Brian 
Published: October 2021

AbstractSkeletal muscles play a central role in human movement through forces transmitted by contraction of the sarcomere. We recently showed that mammalian sarcomeres are connected through frequent branches forming a singular, mesh-like myofibrillar matrix. However, the extent to which myofibrillar connectivity is evolutionarily conserved as well as mechanisms which regulate the specific architecture of sarcomere branching remain unclear. Here, we demonstrate the presence of a myofibrillar matrix in the tubular, but not indirect flight (IF) muscles within Drosophila melanogaster. Moreover, we find that loss of transcription factor H15 increases sarcomere branching frequency in the tubular jump muscles, and we show that sarcomere branching can be turned on in IF muscles by salm-mediated conversion to tubular muscles. Finally, we demonstrate that neurochondrin knockdown results in myofibrillar connectivity in IF muscles without conversion to tubular muscles. These data indicate an evolutionarily conserved myofibrillar matrix regulated by both cell-type dependent and independent mechanisms.
Analysis of the interaction between safety measures and workers' safety awareness from the construction workers' perspective
Authors: Yılmaz Fatih 
Published: October 2021

PurposeThe research was carried out to statistically evaluate the relationship between the safety measures at the construction sites and the actual and perceived knowledge levels of the employees about these measures.Design/methodology/approachFace-to-face surveys were conducted with the workers. The survey included some perception-based questions about preventive measures at the construction site, as well as determining the level of awareness of employees on occupational health and safety (OHS) practices. The data were analyzed with descriptive statistical methods and bivariate correlation analysis.FindingsThe actual knowledge levels of workers on OHS measures in the workplace is significantly lower than their perceived knowledge levels. However, there is a positive, linear and strong relationship between the actual knowledge levels of the employees about some OHS rules applied in the workplace and the general level of knowledge they perceive about themselves. Some protective measures such as occupational safety expert, OHS board, employee representatives, training and information activities at construction sites positively affect the safety awareness of employees. However, low-frequency and documentation-intensive activities such as risk assessment, emergency activities and periodic controls have no or weak correlations.Originality/valuePerception-based opinions of construction site workers on occupational safety issues are transformed into numerical data and analyzed with a quantitative method.
OCTO SCM: assessment of determinants of seaport logistics for the export supply chain of agricultural products
Authors: Amonkar Raj V. , Sengupta Tuhin , Patnaik Debasis 
Published: October 2021

Learning outcomes
The learning outcomes of this paper are as follows: to understand the context of seaport logistics and supply chain design structure, to apply Monte Carlo simulation in the interface of the supply chain and to analyze the Monte Carlo simulation algorithm and statistical techniques for identifying the key seaport logistics factors.

Case overview/synopsis
It was 9:00 p.m. on November 10, 2020, and Nishadh Amonkar, the CEO of OCTO supply chain management (SCM) was glued to the television watching the final cricket match of the Indian Premier League, 2020. Amonkar’s mobile phone rang and it was a call from Vinod Nair, a member Logistics Panel of Ranji Industries Federation. Nair informed Amonkar that it was related to the rejection of several export consignments of agricultural products from Ranji (in the western part of India). The rejection was due to the deterioration in the quality of the exported agricultural products during transit from Ranji to various locations in Europe.

Complexity academic level
This course is suitable at the MBA level for the following courses: Operations research (Focus/Session: Applications on Monte Carlo Simulation). SCM (Focus/Session: Global SCM, Logistics Planning, Distribution Network). Logistics management (Focus/Session: Transportation Planning). Business statistics (Focus/Session: Application of Hypothesis Testing).

Supplementary materials
Teaching Notes are available for educators only.

Subject code
CSS 9: Operations and logistics.
Can gamification and interface design aesthetics lead to MOOCs' success?
Authors: Cheng Yung-Ming 
Published: October 2021

PurposeThe purpose of this study is to propose an integrated post-adoption model based on expectation-confirmation model (ECM) and flow theory to examine whether gamification and interface design aesthetics as antecedents to students' beliefs can affect their continuance intention of massive open online courses (MOOCs) and perceived impact on learning.Design/methodology/approachSample data for this study were collected from students enrolled in a comprehensive university in Taiwan. A total of 600 questionnaires were distributed in the campus, and 318 (53.0%) useable questionnaires were analyzed using structural equation modeling in this study.FindingsThis study's results verified that students' perceived gamification and interface design aesthetics of MOOCs positively affected their perceived usefulness, confirmation and flow experience elicited by MOOCs, and these in turn directly or indirectly led to their satisfaction, continuance intention of MOOCs and perceived impact on learning. Essentially, the results strongly support the research model with all hypothesized links being significant.Originality/valueIt should be particularly noticed that this study contributes to the application of capturing both ECM and flow experience (i.e. an intrinsic motivator) for completely explaining students' perceived gamification and interface design aesthetics as external variables to their continuance intention of MOOCs and perceived impact on learning, and this study's empirical evidence can further shed light on the possible formulation of MOOCs success.
“Ubuntu” I am because we are: COVID-19 and the legal framework for addressing communicable disease in the South African prison system
Authors: Van Hout Marie Claire , Wessels Jakkie 
Published: October 2021

Purpose
The purpose of the paper was to conduct a legal-realist assessment of the South African prison system response to COVID-19. Severely congested and ill-resourced prison systems in Africa face unprecedented challenges amplified by COVID-19. South Africa has recorded the highest COVID-19 positivity rate in Africa and, on March 15th 2020, declared a national state of disaster. The first prison system case was notified on April 6th 2020.

Design/methodology/approach
A legal-realist assessment of the South African prison system response to COVID-19 in the 12 months following initial case notification focused on the minimum State obligations to comply with human rights norms, and the extent to which human, health and occupational health rights of prisoners and staff were upheld during disaster measures.

Findings
A legal-realist account was developed, which revealed the indeterminate nature of application of South African COVID-19 government directives, ill-resourced COVID-19 mitigation measures, alarming occupational health and prison conditions and inadequate standards of health care in prisons when evaluated against the rule of law during State declaration of disaster.

Originality/value
This legal-realist assessment is original by virtue of its unique evaluation of the South African prison system approach to tackling COVID-19. It acknowledged State efforts, policymaking processes and outcomes and how these operated within the prison system itself. By moving beyond the deleterious impacts of the COVID-19 pandemic on the already precarious South African prison system, the authors argue for rights assurance for those who live and work in its prisons, improved infrastructure and greater substantive equality of all deprived of their liberty in South Africa.
Comparative analysis of ranking the lean supply chain enablers: An AHP, BWM and fuzzy SWARA based approach
Authors: Sharma Hemant , Sohani Nagendra , Yadav Ashish 
Published: October 2021

PurposeIn the recent scenario, there has been an increasing trend toward lean practices and implementation in production systems for the improvement of an organization’s performance as its basic nature is to eliminate the wastes. The increasing interest of customers in customized products and the fulfillment of customers’ demand with good productivity and efficiency within time are the challenges for the manufacturing organization; that is why adopting lean manufacturing concept is very crucial in the current scenario.Design/methodology/approachIn this paper, the authors considered three different methodologies for fulfilling the objective of our research. The analytical hierarchy process, best–worst method and fuzzy step-wise weight assessment ratio analysis are the three methods employed for weighting all the enablers and finding the priority among them and their final rankings.FindingsFurther, the best results among these methodologies could be used to analyze their interrelationships for successful lean supply chain management implementation in an organization. In this paper, 35 key enablers were identified after the rigorous analysis of literature review and the opinion of a group of experts consisting of academicians, practitioners and consultants. Thereafter, the brainstorming sessions were conducted to finalize 28 lean supply chain enablers (LSCEs).Practical implicationsFor lean manufacturing practitioners, the result of this study can be beneficial where the manufacturer is required to increase efficiency and reduce cost and wastage of resources in the lean manufacturing process.Originality/valueThis paper is the first of the research papers that considered deep literature review of identified LSCEs as the initial step, followed by finding the best priority weightage and developing the ranking of various lean enablers of supply chain with the help of various methodologies.