bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial scale of transmission explains how acute infections circulate at low prevalence
Authors: Mancy Rebecca , Rajeev Malavika , Lugelo Ahmed , Brunker Kirstyn , Cleaveland Sarah , Ferguson Elaine A. , Hotopp Karen , Kazwala Rudovick , Magoto Matthias , Rysava Kristyna , Haydon Daniel T. , Hampson Katie 
Published: November 2021

AbstractFundamental questions remain about the regulation of acute pathogens in the absence of acquired immunity. This is especially true for canine rabies, a universally fatal zoonosis. From tracing rabies transmission in a population of 50,000 dogs in Tanzania between 2002-2016 we unravel the processes through which rabies is regulated and persists, fitting individual-based models to spatially-resolved data to investigate the mechanisms modulating transmission and the scale over which they operate. We find that while prevalence never exceeds 0.15%, we detect significant susceptible depletion at local scales commensurate with rabid dog movement, reducing transmission through clustering of rabies deaths and individuals incubating infection. Individual variation in rabid dog behaviour facilitates virus dispersal and co-circulation of lineages, enabling metapopulation persistence. These mechanisms likely operate in many pathogens circulating in spatially structured populations, with important implications for prediction and control, yet are unobservable unless the scale of host interactions is identified.One-Sentence SummaryIdentifying the spatial scale of contact reveals the mechanisms that limit the size of rabies outbreaks and that are critical for predicting transmission dynamics.
Missense variants reveal functional insights into the human ARID family of gene regulators
Authors: Deák Gauri , Cook Atlanta G. 
Published: November 2021

AbstractMissense variants are alterations to protein coding sequences that result in amino acid substitutions. They can be deleterious if the amino acid is required for maintaining structure or/and function, but are likely to be tolerated at other sites. Consequently, missense variation within a healthy population can mirror the effects of negative selection on protein structure and function, such that functional sites on proteins are often depleted of missense variants. Advances in high-throughput sequencing have dramatically increased the sample size of available human variation data, allowing for population-wide analysis of selective pressures. In this study, we developed a convenient set of tools, called 1D-to-3D, for visualizing the positions of missense variants on protein sequences and structures. We used these tools to characterize human homologues of the ARID family of gene regulators. ARID family members are implicated in multiple cancer types, developmental disorders, and immunological diseases but current understanding of their mechanistic roles is incomplete. Combined with phylogenetic and structural analyses, our approach allowed us to characterise sites important for protein-protein interactions, histone modification recognition, and DNA binding by the ARID proteins. We find that comparing missense depletion patterns among paralogs can reveal sub-functionalization at the level of domains. We propose that visualizing missense variants and their depletion on structures can serve as a valuable tool for complementing evolutionary and experimental findings.
Variability of in vivo sarcomere length measures in the upper limb obtained with second harmonic generation microendoscopy
Authors: Adkins Amy N , Fong Ryan , Dewald Julius P A , Murray Wendy M 
Published: November 2021

AbstractThe lengths of a muscle’s sarcomeres are a primary determinant of its ability to contract and produce force. In addition, sarcomere length is a critical parameter that is required to make meaningful comparisons of both the force-generating and excursion capacities of different muscles. Until recently, in vivo sarcomere length data have been limited to invasive or intraoperative measurement techniques. With the advent of second harmonic generation microendosopy, minimally invasive measures of sarcomere length can be made for the first time. This imaging technique expands our ability to study muscle adaptation due to changes in stimulus, use, or disease. However, due to the inability to measure sarcomeres outside of surgery or biopsy, little is known about the natural, anatomical variability in sarcomere length in living human subjects. To develop robust experimental protocols that ensure data provide accurate representations of a muscle’s sarcomere lengths, we sought to quantify experimental uncertainty associated with in vivo measures of sarcomere lengths. Specifically, we assessed the variability in sarcomere length measured 1) within a single image, along a muscle fiber, 2) across images captured within a single trial, across trials, and across days, as well as 3) across locations in the muscle using second harmonic generation in two upper limb muscles with different muscle architectures, functions, and sizes. Across all of our measures of variability we estimate that the magnitude of the uncertainty in in vivo sarcomere length are on the order of ~0.25μm. In the two upper limb muscles studied we found larger variability in sarcomere length within a single insertion than across locations. We also developed custom code to make measures of sarcomere length variability across a single fiber and determined that this codes’ accuracy is an order of magnitude smaller than our measurement uncertainty due to sarcomere variability. Together, our findings provide guidance for the development of robust experimental design and analysis of in vivo sarcomere lengths in the upper limb.
Susceptibility monitoring and the molecular characterization of resistance of Spodoptera frugiperda (Lepidoptera: Noctuidae) to lambda-cyhalothrin and chlorpyrifos
Authors: Nascimento Antonio Rogério Bezerra do , Rodrigues Juliana Gonzales , Kanno Rubens H. , Amaral Fernando S.A. , Malaquias José Bruno , Silva-Brandão Karina Lucas , Cônsoli Fernando Luís , Omoto Celso 
Published: November 2021

AbstractSpodoptera frugiperda (J. E. Smith) is a serious and widespread agricultural pest with several records of resistance to different insecticides and Bt proteins, including the neurotoxic insecticides chlorpyrifos (organophosphate) and lambda-cyhalothrin (pyrethroid). In this study, we (i) characterized and monitored the susceptibility of field populations of S. frugiperda to chlorpyrifos (194 populations) and lambda-cyhalothrin (197 populations) collected from major maize-growing regions of Brazil from 2003 to 2016, and (ii) compared gene expression levels of chlorpyrifos- and lambda-cyhalothrin-resistant strains to a susceptible reference strain (Sf-ss) of S. frugiperda. Laboratory-guided assays to monitor larval susceptibility detected average survival ranging from 29.3% to 36.0% to chlorpyrifos, and 23.1% to 68.0% to lambda-cyhalothrin at diagnostic concentration, based on LC99 of the susceptible reference strain of each insecticide. The resistance ratio of the chlorpyrifos-resistant strain (Clo-rr) was 25.4-fold and of the lambda-cyhalothrin-resistant strain (Lam-rr) was 217-fold. Differential gene expression analyses between resistant vs susceptible strains identified 1,098 differentially expressed genes (DEGs) between Clo-rr and Sf-ss, and 303 DEGs between Lam-rr and Sf-ss. Functional analyses of the DEGs revealed the up-regulation of several detoxification enzymes, mainly cytochrome P450 belonging to the CYP3 and CYP6 clans. Genes associated with regulatory processes, such as the forkhead box O (FoxO) were also up-regulated. Our data points that the resistance mechanisms of Clo-rr and Lam-rr strains of S. frugiperda to chlorpyrifos and lambda-cyhalothrin are mainly mediated by enzyme detoxification.
Genetic and antigenic characterization of an expanding H3 influenza A virus clade in US swine visualized by Nextstrain
Authors: Neveau Megan N. , Zeller Michael A. , Kaplan Bryan S. , Souza Carine K. , Gauger Phillip C. , Vincent Amy L. , Anderson Tavis K. 
Published: November 2021

AbstractDefining factors that influence spatial and temporal patterns of influenza A virus (IAV) is essential to inform vaccine strain selection and strategies to reduce the spread of potentially zoonotic swine-origin IAV. The relative frequency of detection of the H3 phylogenetic clade 1990.4.a (colloquially known as C-IVA) in US swine declined to 7% in 2017, but increased to 32% in 2019. We conducted phylogenetic and phenotypic analyses to determine putative mechanisms associated with increased detection. We created an implementation of Nextstrain to visualize the emergence, spatial spread, and genetic evolution of H3 IAV-S, identifying two C-IVA clades that emerged in 2017 and cocirculated in multiple US states. Phylodynamic analysis of the HA gene documented low relative genetic diversity from 2017 to 2019, suggesting clonal expansion. The major H3 C-IVA clade contained an N156H amino acid substitution, but HI assays demonstrated no significant antigenic drift. The minor HA clade was paired with the NA clade N2-2002B prior to 2016, but acquired and maintained N2-2002A in 2016, resulting in a loss in antigenic cross-reactivity between N2-2002B and −2002A containing H3N2 strains. The major C-IVA clade viruses acquired a nucleoprotein (NP) of the H1N1pdm09 lineage through reassortment in replacement of the North American swine lineage NP. Instead of genetic or antigenic diversity within the C-IVA HA, our data suggest that population immunity to H3 2010.1, along with antigenic diversity of the NA and acquisition of the H1N1pdm09 NP gene likely explain the re-emergence and transmission of C-IVA H3N2 in swine.ImportanceGenetically distinct clades of influenza A virus (IAV) in swine undermines efforts to control the disease. Swine producers commonly use vaccines, and vaccine strains are selected by identifying the most common hemagglutinin (HA) gene from viruses detected in a farm or a region. In 2019, we identified an increase in detection frequency of an H3 phylogenetic clade, C-IVA, which was previously circulating at much lower levels in U.S. swine. Our study identified genetic and antigenic factors contributing to its resurgence by linking comprehensive phylodynamic analyses with empirical wet-lab experiments and visualized these evolutionary analyses in a Nextstrain implementation. The contemporary C-IVA HA genes did not demonstrate an increase in genetic diversity nor significant antigenic changes. N2 genes did demonstrate antigenic diversity, and the expanding C-IVA clade acquired a nucleoprotein (NP) gene segment via reassortment. Virus phenotype and vaccination targeting prior dominant HA clades likely contributed to the clade’s success.
Edaphic controls on genome size and GC content of bacteria in soil microbial communities
Authors: Chuckran Peter F. , Flagg Cody , Propster Jeffrey , Rutherford William A. , Sieradzki Ella , Blazewicz Steven J. , Hungate Bruce , Pett-Ridge Jennifer , Schwartz Egbert , Dijkstra Paul 
Published: November 2021

ABSTRACTBacteria in soil microbial communities are crucial to terrestrial ecosystem function, yet our understanding of the fundamental characteristics of their genomes, such as GC content and genome size, is not complete. Much of our understanding of the mechanisms which shape their genomic traits is derived from other systems or from isolated bacteria. Here we determined average genome size, GC content, codon usage, and amino acid content from 398 soil metagenomes across a broad geographic range and used machine-learning to determine which environmental parameters most strongly explain the distribution of these traits. We found that genomic trait averages were most related to pH, which we suggest is primarily due to the correlation of pH with several environmental parameters, especially soil carbon content. Low pH soils had higher carbon to nitrogen ratios (C:N) and tended to have communities with lower GC content and larger genomes, potentially a response to increased physiological stress and a requirement for metabolic diversity. Conversely, smaller genomes with high GC content were associated with high pH and low soil C:N, indicating potential resource driven selection against AT base pairs. As soil bacteria tend to be more carbon limited, smaller genomes with higher GC content may reduce the cost of reproduction in carbon-limited soils. Similarly, we found that nutrient conservation also applied to amino acid stoichiometry, where bacteria in soils with low C:N ratios tended to code for amino acids with lower C:N. Together, these relationships point towards fundamental mechanisms that underpin nucleotide and amino acid selection in soil bacterial communities.
Glacier-fed stream biofilms harbour diverse resistomes and biosynthetic gene clusters
Authors: Busi Susheel Bhanu , de Nies Laura , Pramateftaki Paraskevi , Bourquin Massimo , Ezzat Leïla , Kohler Tyler J. , Fodelianakis Stilianos , Michoud Grégoire , Peter Hannes , Styllas Michail , Tolosano Matteo , De Staercke Vincent , Schön Martina , Galata Valentina , Battin Tom , Wilmes Paul 
Published: November 2021

AbstractBackgroundAntimicrobial resistance (AMR) is a universal phenomenon whose origins lay in natural ecological interactions such as competition within niches, within and between micro- to higher-order organisms. However, the ecological and evolutionary processes shaping AMR need to be better understood in view of better antimicrobial stewardship. Resolving antibiotic biosynthetic pathways, including biosynthetic gene clusters (BGCs), and corresponding antimicrobial resistance genes (ARGs) may therefore help in understanding the inherent mechanisms. However, to study these phenomena, it is crucial to examine the origins of AMR in pristine environments with limited anthropogenic influences. In this context, epilithic biofilms residing in glacier-fed streams (GFSs) are an excellent model system to study diverse, intra- and inter-domain, ecological crosstalk.ResultsWe assessed the resistomes of epilithic biofilms from GFSs across the Southern Alps (New Zealand) and the Caucasus (Russia) and observed that both bacteria and eukaryotes encoded twenty-nine distinct AMR categories. Of these, beta-lactam, aminoglycoside, and multidrug resistance were both abundant and taxonomically distributed in most of the bacterial and eukaryotic phyla. AMR-encoding phyla included Bacteroidota and Proteobacteria among the bacteria, alongside Ochrophyta (algae) among the eukaryotes. Additionally, BGCs involved in the production of antibacterial compounds were identified across all phyla in the epilithic biofilms. Furthermore, we found that several bacterial genera (Flavobacterium, Polaromonas, etc.) including representatives of the superphylum Patescibacteria encode both ARGs and BGCs within close proximity of each other, thereby demonstrating their capacity to simultaneously influence and compete within the microbial community.ConclusionsOur findings highlight the presence and abundance of AMR in epilithic biofilms within GFSs. Additionally, we identify their role in the complex intra- and inter-domain competition and the underlying mechanisms influencing microbial survival in GFS epilithic biofilms. We demonstrate that eukaryotes may serve as AMR reservoirs owing to their potential for encoding ARGs. We also find that the taxonomic affiliation of the AMR and the BGCs are congruent. Importantly, our findings allow for understanding how naturally occurring BGCs and AMR contribute to the epilithic biofilms mode of life in GFSs. Importantly, these observations may be generalizable and potentially extended to other environments which may be more or less impacted by human activity.
‘Kindness By Post’: A Mixed-Methods Evaluation of A Participatory Public Mental Health Project
Authors: Wang Congxiyu , Pearce Eiluned , Jones Rebecca , Lloyd-Evans Brynmor 
Published: November 2021

AbstractBackgroundRandom acts of kindness can improve wellbeing. However, less is known about the impacts of giving and receiving acts of kindness with strangers on wellbeing and loneliness. Therefore, this study’s objectives were to evaluate a participatory public mental health project involving sending and receiving a card with goodwill messages, to understand how such acts of kindness influence wellbeing and loneliness, and to investigate the potential mechanisms underlying the project’s impacts.Materials and methodsThis study was a secondary analysis of anonymised service evaluation data collected in the ‘Kindness by Post’ (KBP) project in 2020. It used a mixed-methods single-group design and data from 289 participants. Changes in wellbeing, loneliness, sense of belonging and hope from baseline to follow-up were analysed using linear or multinomial logistic regression. Regression models also examined the associations between changes in wellbeing and baseline loneliness or participation level. Free text responses about experiences and suggestions for the project were analysed using thematic analysis.ResultsParticipants had a small, but statistically significant improvement, in wellbeing equating to 0.21 standard deviations (SD) (95% CI: 0.12 to 0.30) after taking part in the project, as well as improvements in loneliness, sense of belonging and hope. How lonely a participant was at baseline and whether participants both sent and received a kindness card were not associated with improvements in wellbeing. In the qualitative analysis, a desire to help others emerged as the main motivator to take part in the card exchange. Participants reported enhanced personal fulfilment, leading to improvements in wellbeing. Receiving a card could make people feel special and cherished, which was reported to establish a sense of connection with others, with potential benefits for reducing loneliness.ConclusionsThis study provided preliminary evidence that the KBP project might improve wellbeing, loneliness, sense of belonging and hope. Sending a kindness card in this project played a predominant role in wellbeing enhancement, and receiving a kindness card could reduce loneliness. This study suggests that the KBP project can be replicated in more contexts in the future, and might improve wellbeing and loneliness in large communities.
Cortical microtubule pulling forces contribute to the union of the parental genomes in the C. elegans zygote
Authors: Velez-Aguilera G. , Ossareh-Nazari B. , Van Hove L. , Joly N. , Pintard L. 
Published: November 2021

AbstractPreviously, we reported that the Polo-like kinase PLK-1 phosphorylates the single C. elegans lamin (LMN-1) to trigger lamina depolymerization during mitosis. We showed that this event is required for the formation of a pronuclear envelopes scission event that removes membranes on the juxtaposed oocyte and sperm pronuclear envelopes in the zygote, allowing the parental chromosomes to merge in a single nucleus after segregation (Velez-Aguilera, 2020). Here we show that cortical microtubule pulling forces contribute to pronuclear envelopes scission by promoting mitotic spindle elongation. We also demonstrate that weakening of the pronuclear envelopes, via PLK-1-mediated lamina depolymerization, is a prerequisite for the astral microtubule pulling forces to trigger pronuclear membranes scission. Finally, we provide evidence that PLK-1 mainly acts via lamina depolymerization in this process. These observations thus indicate that temporal coordination between lamina depolymerization and mitotic spindle elongation facilitates pronuclear envelopes scission and parental genomes unification.
Transportation performance improvement through lean thinking implementation
Authors: Argiyantari Berty , Simatupang Togar Mangihut , Basri Mursyid Hasan 
Published: November 2021

Purpose
The application of lean thinking in the transportation industry provides opportunities to streamline operations with a value-added orientation. Prior literature shows evidence of limited application of lean thinking in the transportation operations of the pharmaceutical industry. This study aims to close this research gap by investigating the application of lean thinking for improving pharmaceutical transportation performance.

Design/methodology/approach
This study conducted an action research approach at an Indonesian pharmaceutical distribution company. One cycle in one year was analyzed; empirical data were collected and analyzed through direct observations, interviews and the study of company data and documentation.

Findings
The application of lean thinking in waste elimination allowed the delivered project to achieve a remarkable 40% reduction in overall transportation costs, 75% reduction in total lead time, 200% improvement in truck productivity and 100% improvement in truckload capacity utilization.

Practical implications
This study can guide the pharmaceutical industry toward achieving excellence in transportation operations through lean thinking implementation.

Originality/value
There has been limited research on this topic, and this study is the first attempt to generate new and significant evidence of a real-life application of lean thinking within the field of pharmaceutical transportation.
Archive access robot for smart archive repositories
Authors: Cui Jianwei , Cui Linwei , Jiang Huice 
Published: November 2021

Purpose
Managing archives using robots rather than people can considerably enhance efficiency, while need to modify the structure of archive shelves or installation tracks. This paper aims to develop a fully automated archive access robot without modification.

Design/methodology/approach
First, a mobile navigation chassis and a motion algorithm based on laser ranging and map matching are created for autonomous movement to any of the archives’ locations. Second, because the existing archives are stacked vertically, the bionic manipulator is made to mimic the movement of manual access to the archives, and it is attached to the robot arm’s end to access different layers of archives. In addition, an industrial camera is used to complete barcode identification of the archives and acquire data on their location and thickness. Finally, the archive bin is created to store archives.

Findings
The robot can move, identify and access multiple archival copies placed on floors 1–6 and 2–5 cm thick autonomously without modifying the archival repository or using auxiliary devices.

Research limitations/implications
The robot is currently able to navigate, identify and access files placed on different levels. In the future, the speed of the robot’s navigation and the movement of the robot arm could be even faster, while the level of visualization of the robot could be further improved and made more intelligent.

Practical implications
The archive access robot developed by the authors makes it possible for robots to manage archives instead of human, while being cheaper and easier to deploy than existing robots, and has already been tested in the archive storage room of the State Grid maintenance branch in Jiangsu, China, with better results.

Social implications
The all-in-one archive access robot can replace existing robotic access solutions, promote intelligent management of the archive industry and the construction of unmanned archive repositories and provide ideas for the development of robots for accessing book-like materials.

Originality/value
This study explores the use of robots to identify and access archives without changing archive shelves or installing auxiliary devices. In this way, the robot can be quickly applied to the storage room to improve the efficiency of archive management.