bluuebunny/crossref_metadata_2025 huggingface dataset:
CNN3 in glioma
Authors: Xu Hao , Chai Song-shan , Lv Peng , Wang Jia-jing
Published: November 2021

Background:

Gliomas are the most intrinsic type of primary intracranial tumors. The protein encoded by The calponin 3 (CNN3) has been proven to be a member of the calponin family. Its relationships with cervical cancer, colorectal cancer, gastric cancer, and colon cancer have been emphasized by several studies. Our research aims to explore the prognosis value and immunotherapeutic targetability of CNN3 in glioma patients using bioinformatics approach.

Methods:

CNN3 expression in glioma was analyzed based on GEO and TCGA datasets. Gene expression profiling with clinical information was employed to investigate the correlation between clinicopathological features of glioma patients and relative CNN3 expression levels. Survival analysis was conducted using Kaplan-Meier analysis and the Cox proportional-hazards regression model. Gene set enrichment analysis was conducted to select the pathways significantly enriched for CNN3 associations. Correlations between inflammatory activities, immune checkpoint molecules and CNN3 were probed by gene set variation analysis, correlograms, and correlation analysis.

Results:

CNN3 was enriched in gliomas, and high expression of CNN3 correlated with worse clinicopathological features and prognosis. Associations between CNN3 and several immune-related pathways were confirmed using a bioinformatics approach. Correlation analysis revealed that CNN3 was associated with inflammatory and immune activities, tumor microenvironment, and immune checkpoint molecules.

Conclusion:

Our results indicate that high CNN3 expression levels predict poor prognosis, and CNN3 may be a promising immunotherapy target.
Usefulness of Jackson mask ventilation during bronchoscopy in patients with acute respiratory failure
Authors: Takumida Hiroshi , Suzuki Manabu , Suzuki Tomoyuki , Sakamoto Keita , Hashimoto Masao , Ishii Satoru , Naka Go , Iikura Motoyasu , Izumi Shinyu , Takeda Yuichiro , Hojo Masayuki , Sugiyama Haruhito
Published: November 2021

Bronchoscopy is a procedure for diagnosis and treatment decision-making in patients with lung disease, especially those with acute respiratory failure. However, the optimal bronchoscopic method for patients with acute respiratory failure is not known. Therefore, in the real world, we sometimes hesitate to perform bronchoscopy in such patients because of safety and have experienced treating patients without bronchoscopy. To address this problem, we evaluated the usefulness and safety of Jackson mask ventilation, a novel noninvasive method of bronchoscopy performed under mask ventilation using the Jackson Rees circuit, in patients with acute respiratory failure.

We retrospectively reviewed patients with acute respiratory failure who underwent bronchoscopy at our institution between January 2015 and May 2018. We compared patients who received Jackson mask ventilation (Jackson group) and those who received conventional oxygen administration (conventional group). Mean percutaneous oxygen saturation (SpO2) and mean oxygen flow rate were compared between the groups by the Wilcoxon signed-rank test. We excluded patients who were intubated and those without acute respiratory failure who received Jackson mask ventilation preventively.

Of 1262 patients who underwent bronchoscopy, 12 were classified into the Jackson group and 13 into the conventional group. Proper oxygenation was maintained in the Jackson group, with SpO2 increasing after Jackson mask ventilation (89.4% to 96.8%, P = .03). Mean SpO2 was significantly higher in the Jackson group than in the conventional group (96.8% vs 95.2%, P = .03). Mean oxygen flow rate was significantly lower in the Jackson group (4.0 L/min vs 7.9 L/min, P < .001). There was no significant difference in safety.

Our findings suggest that Jackson mask ventilation is safe and effective when performing bronchoscopy in patients with acute respiratory failure. Jackson mask ventilation maintained proper oxygenation and decreased the oxygen flow rate compared with the conventional method. Using Jackson mask ventilation, we could perform bronchoscopy safely and effectively in patients with acute respiratory failure, including some who had unstable respiratory status. (UMIN000038481).
The long-term success of mandatory vaccination laws at implementing the first vaccination campaign in 19thcentury rural Finland
Authors: Ukonaho Susanna , Lummaa Virpi , Briga Michael
Published: November 2021

In high income countries, childhood infections are on the rise, a phenomenon in part attributed to persistent hesitancy towards vaccines. To combat vaccine hesitancy, several countries recently made vaccinating children mandatory, but the effect of such vaccination laws on vaccination coverage remains debated and the long-term consequences are unknown. Here we quantified the consequences of vaccination laws on the vaccination coverage monitoring for a period of 63 years rural Finland’s first vaccination campaign against the highly lethal childhood infection smallpox. We found that annual vaccination campaigns were focussed on children up to 1 year old, but that their vaccination coverage was low and declined with time until the start of the vaccination law, which stopped the declining trend and was associated with an abrupt coverage increase of 20 % to cover >80 % of all children. Our results indicate that vaccination laws had a long-term beneficial effect at increasing the vaccination coverage and will help public health practitioners to make informed decisions on how to act against vaccine hesitancy and optimise the impact of vaccination programmes.
WebSeq: A Genomic Data Analytics Platform for Monogenic Disease Discovery
Authors: Agarwal Milind , Ghimire Kshitiz , Cogan Joy D. ,   Undiagnosed Disease Network, Markle Janet
Published: November 2021

Whole exome sequencing (WES) is commonly used to study monogenic diseases. The application of this sequencing technology has gained in popularity amongst clinicians and researchers as WES pricing has declined. The accumulation of WES data creates a need for a robust, flexible, scalable and easy-to-use analytics platform to allow researchers to gain biological insight from this genomic data. We present WebSeq, a self-contained server and web interface to facilitate intuitive analysis of WES data. WebSeq provides access to sophisticated tools and pipelines through a user-friendly and modern web interface. WebSeq has modules that support i) FASTQ to VCF conversion, ii) VCF to ANNOVAR1 CSV conversion, iii) family-based analyses for Mendelian disease gene discovery, iv) cohort-wide gene enrichment analyses, (v) an automated IGV2 browser, and (vi) a ‘virtual gene panel’ analysis module. WebSeq Pro, our expanded pipeline, also supports SNP genotype analyses such as ancestry inference and kinship testing. WebSeq Lite, our minimal pipeline, supports family-based analyses, cohort-wide gene enrichment analyses, and a virtual gene panel along with the IGV2 browser module. We anticipate that the rigorous use of our web application will allow researchers to expedite discoveries from human genomic data3. WebSeq Lite, WebSeq, and WebSeq Pro are fully containerized using Docker4, run on all major operating systems, and are freely available for personal, academic, and non-profit use at http://bitly.ws/g6cn
Aging and interferon gamma response drive the phenotype of neutrophils in the inflamed joint
Authors: Grieshaber-Bouyer Ricardo , Exner Tarik , Hackert Nicolaj S. , Radtke Felix A. , Jelinsky Scott A. , Halyabar Olha , Wactor Alexandra , Karimizadeh Elham , Schettini Jorge , Jonsson A. Helena , Rao Deepak A. , Henderson Lauren A. , Müller-Tidow Carsten , Lorenz Hanns-Martin , Wabnitz Guido , Lederer James A. , Hadjipanayis Angela , Nigrovic Peter A.
Published: November 2021

Objectives

Neutrophils are typically the most abundant leukocyte in arthritic synovial fluid. We sought to understand changes that occur in neutrophils as they migrate from blood to joint.

Methods

We performed RNA sequencing of neutrophils from healthy human blood, arthritic blood, and arthritic synovial fluid, comparing transcriptional signatures with those from murine K/BxN serum transfer arthritis. We employed mass cytometry to quantify protein expression and sought to reproduce the synovial fluid phenotypeex vivoin cultured healthy blood neutrophils.

Results

Blood neutrophils from healthy donors and patients with active arthritis exhibited largely similar transcriptional signatures. By contrast, synovial fluid neutrophils exhibited more than 1,600 differentially expressed genes. Gene signatures identified a prominent response to interferon gamma (IFNγ), as well as to tumor necrosis factor, interleukin 6, and hypoxia, in both humans and mice. Mass cytometry also found healthy and arthritic donor blood neutrophils largely indistinguishable but revealed a range of neutrophil phenotypes in synovial fluid defined by downregulation of CXCR1 and upregulation of FcγRI, HLA-DR, PD-L1, ICAM-1 and CXCR4. Reproduction of key elements of this signature in cultured blood neutrophils required both IFNγ and prolonged culture.

Conclusions

Circulating neutrophils from arthritis patients resemble those from healthy controls, but joint fluid cells exhibit a network of changes, conserved across species, that implicate IFNγ response and aging as complementary drivers of the synovial neutrophil phenotype.

KEY MESSAGES

What is already known about this subject?

Neutrophils are central in the effector phase of inflammatory arthritis but their phenotypic heterogeneity in inflamed synovial fluid is poorly understood.

What does this study add?

RNA-seq and mass cytometry identify a hallmark phenotype of neutrophils in synovial fluid consisting of upregulated ICAM-1, HLA-DR, PD-L1, Fc receptors and CXCR4.

Transcriptomics highlight an IFNγ response signature conserved across humans and mice.

In vitro experiments implicate aging and IFNγ as complementary factors orchestrating the synovial fluid neutrophil phenotype.

How might this impact on clinical practice or future developments?

Understanding the specific features of neutrophils in the arthritic joint may disclose opportunities for safe therapeutic targeting of this lineage.
The Flip-flop neuron – A memory efficient alternative for solving challenging sequence processing and decision making problems
Authors: Kumari Sweta , Vigneswaran C , Chakravarthy V. Srinivasa
Published: November 2021

Sequential decision making tasks that require information integration over extended durations of time are challenging for several reasons including the problem of vanishing gradients, long training times and significant memory requirements. To this end we propose a neuron model fashioned after the JK flip-flops in digital systems. A flip-flop is a sequential device that can store state information of the previous history. We incorporate the JK flip-flop neuron into several deep network architectures and apply the networks to difficult sequence processing problems. The proposed architectures include flip-flop neural networks (FFNNs), bidirectional flip-flop neural networks (BiFFNNs), convolutional flip-flop neural networks (ConvFFNNs), and bidirectional convolutional flip-flop neural networks (BiConvFFNNs). Learning rules of proposed architectures have also been derived. We have considered the most popular benchmark sequential tasks like signal generation, sentiment analysis, handwriting generation, text generation, video frame prediction, lung volume prediction, and action recognition to evaluate the proposed networks. Finally, we compare the results of our networks with the results from analogous networks with Long Short-Term Memory (LSTM) neurons on the same sequential tasks. Our results show that the JK flip-flop networks outperform the LSTM networks significantly or marginally on all the tasks, with only half of the trainable parameters.
Mitochondrial OPA1 deficiency causes reversible defects in adult neurogenesis-associated spatial memory in mice
Authors: Andraini Trinovita , Moulédous Lionel , Petsophonsakul Petnoi , Florian Cédrick , Lopez Sébastien , Botella-Daloyau Marlène , Arrázola Macarena , Nikolla Kamela , Philip Adam , Leydier Alice , Marque Manon , Arnauné-Pelloquin Laetitia , Belenguer Pascale , Rampon Claire , Miquel Marie-Christine
Published: November 2021

Mitochondria are integrative hubs central to cellular adaptive pathways. Such pathways are critical in highly differentiated post-mitotic neurons, the plasticity of which sustains brain function. Consequently, defects in mitochondrial dynamics and quality control appear instrumental in neurodegenerative diseases and may also participate in cognitive impairments. To directly test this hypothesis, we analyzed cognitive performances in a mouse mitochondria-based disease model, due to haploinsufficiency in the mitochondrial optic-atrophy-type-1 (OPA1) protein. While in Dominant Optic Atrophy (DOA) models, the known main symptoms are late onset visual deficits, we discovered early impairments in hippocampus-dependent spatial memory attributable to defects in adult neurogenesis. Moreover, less connected hippocampal adult-born neurons showed a decrease in mitochondrial content. Remarkably, modulating mitochondrial function through voluntary exercise or pharmacological treatment restored spatial memory.

Altogether, our study identifies a crucial role for OPA1-dependent mitochondrial functions in adult neurogenesis, and thus in hippocampal-dependent cognitive functions. More generally, our findings show that adult neurogenesis is highly sensitive to mild mitochondrial defects, generating impairments in spatial memory that can be detected at an early stage and counterbalanced by physical exercise and pharmacological targeting of mitochondrial dynamics. Thus, early amplification of mitochondrial function appears beneficial for late-onset neurodegenerative diseases.
Rapid adaptation often occurs through mutations to the most highly conserved positions of the RNA polymerase core enzyme
Authors: Cohen Yasmin , Hershberg Ruth
Published: November 2021

Mutations to the genes encoding the RNA polymerase core enzyme (RNAPC) and additional housekeeping regulatory genes were found to be involved in rapid adaptation, in the context of numerous evolutionary experiments, in which bacteria were exposed to diverse selective pressures. This provides a conundrum, as the housekeeping genes that were so often mutated in response to these diverse selective pressures tend to be among the genes that are most conserved in their sequences across the bacterial phylogeny. In order to further examine this apparent discrepancy, we characterized the precise positions of the RNAPC involved in adaptation to a large variety of selective pressures. We found that different positions of the RNAPC are involved in adaptation to various stresses, with very little overlap found between stresses. We further found that RNAPC positions involved in adaptation tended to be more evolutionary conserved, were more likely to occur within defined protein domains, and tended to be closer to the complex’s active site, compared to all other RNAPC positions. Finally, we could show that this observed trend of higher conservation of positions involved in rapid adaptation extends beyond the RNAPC to additional housekeeping genes. Combined, our results demonstrate that the positions that change most readily in response to well defined selective pressures exerted in lab environments are also those that evolve most slowly in nature. This suggests that such adaptations may not readily occur in nature, due to their antagonistically pleiotropic effects, or that if they do occur in nature, they are highly transient.
A neural mechanism for detecting object motion during self-motion
Authors: Kim HyungGoo R. , Angelaki Dora E. , DeAngelis Gregory C.
Published: November 2021

Detecting objects that move in a scene is a fundamental computation performed by the visual system. This computation is greatly complicated by observer motion, which causes most objects to move across the retinal image. How the visual system detects scene-relative object motion during self-motion is poorly understood. Human behavioral studies suggest that the visual system may identify local conflicts between motion parallax and binocular disparity cues to depth, and may use these signals to detect moving objects. We describe a novel mechanism for performing this computation based on neurons in macaque area MT with incongruent depth tuning for binocular disparity and motion parallax cues. Neurons with incongruent tuning respond selectively to scene-relative object motion and their responses are predictive of perceptual decisions when animals are trained to detect a moving object during self-motion. This finding establishes a novel functional role for neurons with incongruent tuning for multiple depth cues.
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

Fundamental 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 Summary

Identifying 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

Missense 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

The 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

Spodoptera 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

Defining 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.

Importance

Genetically 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

Bacteria 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

Background

Antimicrobial 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.

Results

We 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.

Conclusions

Our 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

Background

Random 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 methods

This 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.

Results

Participants 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.

Conclusions

This 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

Previously, 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.
As cheap as humanly possible: why consumers care less about worker welfare
Authors: Stringer Tara , Payne Alice Ruth , Mortimer Gary
Published: November 2021

Purpose

Worker welfare and modern slavery within the fashion industry remain a key supply chain challenge for many retailers, consumers, governments and advocacy groups. Yet, despite publicised worker-welfare violations, many fashion retailers continue to post record sales and profits, indicating that consumer concern does not always translate at the cash register. Research has shown that worker welfare is a less salient area of concern for fashion consumers, and the aim of this research is to investigate the reasons why this may be the case.

Design/methodology/approach

Due to the exploratory nature of the research, a qualitative methodology was deemed the most appropriate. Twenty-one semi-structured interviews were conducted with Australian fast-fashion consumers to investigate the underlying reasons worker-welfare violations are less likely to elicit pro-social consumer behavioural change and are a less salient area of concern.

Findings

This study found that consumers perceive worker-welfare concerns at both a proximal and cultural distance to themselves, and therefore struggle to connect with the issues associated with modern slavery. Additionally, there was an underlying social consensus that exploitative practices are an accepted part of the fast-fashion supply chain to ensure the continuation of low-cost clothing. Despite an underlying awareness of exploitative practices and acknowledgement that modern slavery is ethically wrong, other consumer values often influenced purchase behaviour and the level of concern expressed towards garment workers.

Originality/value

This is the first study to apply psychological distance in a fast-fashion context to better understand consumer perceptions towards modern slavery. Responding to calls for further research into ethical consumption of apparel, this study develops an in-depth understanding of the reasons why worker welfare is a less salient area of concern for fast-fashion consumers. Extending on current literature, this study qualitatively investigates consumer sentiment towards worker welfare, identifying the greatest barriers to consumers' levels of concern. In addition to a theoretical contribution to the fashion, ethics and business literature, this article provides key insight to guide practice.
Understanding destination evangelism: a social media viewpoint
Authors: Sharma Purvendu
Published: November 2021

Purpose

The present research aims to introduce and understand the promising nature of destination evangelism in the context of social media-based tourism communities (SMTCs). Further, factors that influence evangelism and information-seeking behaviors on SMTCs are examined.

Design/methodology/approach

A conceptual model is developed that features an interplay of destination distinctiveness, destination evangelism, travel commitment and information-seeking engagement. Data were collected from 215 active users of SMTCs and analyzed using structural equation models.

Findings

The research findings indicate that destination distinctiveness and information-seeking positively lead to destination evangelism. Information-seeking is found to mediate the relationship between (1) destination evangelism and travel commitment and (2) destination evangelism and distinctiveness.

Research limitations/implications

The research offers meaningful insights into exploring constituents of destination evangelism. The research also understands and highlights the critical role of information-seeking engagement about distinct destinations.

Practical implications

This research highlights key areas to build, improve and inspire destination evangelism on SMTCs.

Originality/value

This study offers a fresh contribution to tourism literature by investigating destination evangelism and its drivers. This is explained by closely uniting vital research streams of evangelism, tourism and engagement. It further highlights the dual mediating role of information seeking, suggesting that these engagements are critical to evangelizing destinations.
Impact of college education on incorporated and unincorporated self-employment: variations among African Americans and Hispanics
Authors: Guo Xuguang , Chen Wei , Iurchenko Denis
Published: November 2021

Purpose

This study examines the impact of college education on incorporated and unincorporated self-employments. It specifically compares the effects on African Americans and Hispanics with the effects on Whites.

Design/methodology/approach

The study sample was drawn from the US Current Population Survey between 1989 and 2018. Based on a sample size of 1,657,043 individuals, this study employed logit regression models to test the hypotheses. Racial variations were examined using African Americans and Hispanics as moderators.

Findings

The results suggest that college education increases incorporated self-employment and reduces unincorporated self-employment. The impact of college education on incorporated self-employment is stronger for African Americans and Hispanics than for Whites. In contrast, its effect on unincorporated self-employment is stronger for Whites than for African Americans and Hispanics.

Research limitations/implications

The findings provide empirical evidence of how college experience changes the motivation of starting an incorporated or unincorporated business. The results suggest that college education impacts African Americans and Hispanics differently than Whites in pursuing their career path of entrepreneurship.

Originality/value

It is the first study that examines the relationship between college education and incorporated/unincorporated self-employment. It also sheds light on radical variations.