bluuebunny/crossref_metadata_2025 huggingface dataset:
Use and Product Characteristics of “Tobacco Free Nicotine” E-Cigarettes Among Young Adults
Authors: Davis Danielle R , Bold Krysten W , Camenga Deepa , Kong Grace , Jackson Asti , Lee Juhan , Rajesh-Kumar Lavanya , Krishnan-Sarin Suchitra , Morean Meghan E
Published: August 2022

Introduction

E-cigarettes are increasingly being marketed as containing tobacco-free nicotine (TFN). There is no data examining use of TFN e-cigarettes by young adults and how use may differ from non-TFN e-cigarettes. The current study aims to characterize young adult TFN e-cigarette use and examine differences between those who report using TFN and non-TFN e-cigarettes.

Method

U.S. young adults (18–25) with lifetime e-cigarette use (n = 927) were recruited via online panels in Fall 2021 and answered questions about TFN and non-TFN e-cigarettes. Participants were categorized by lifetime TFN e-cigarette use status (yes vs. no; 34% yes). Bivariate comparisons examined differences in e-cigarette characteristics (device type, flavors, nicotine concentration) between the TFN and non-TFN groups. Binary logistic regression models examined associations between lifetime frequency of vaping (<100 vs. ≥100 times), and other tobacco product, cannabis, and/or alcohol use and lifetime TFN e-cigarette use (yes vs. no). Adjusted models include age, race/ethnicity, vaping onset age, and sex.

Results

In multivariable adjusted models, lifetime TFN e-cigarette use was associated with younger age, greater lifetime vaping, and nicotine pouch use. Young adults who used TFN e-cigarettes were more likely to report fruit, mint, menthol, and beverage flavors and know their e-liquid nicotine concentration compared with those who used non-TFN e-cigarettes.

Conclusion

Among young adults who have used e-cigarettes, more frequent e-cigarette use and use of nicotine pouches, which can also contain TFN, were associated with TFN e-cigarette use. Understanding behaviors and characteristics of those using TFN e-cigarettes is critical to regulation of TFN containing products.

Implications

This study characterizes young adults who report experience with tobacco free nicotine (TFN) e-cigarettes and compares them to those who have not used TFN e-cigarettes. Young adults with more frequent e-cigarette use and use of nicotine pouches are more likely to report TFN e-cigarette use.
A Nonrestrictive Approach to Fluoroquinolone Stewardship at Two Community Hospitals
Authors: Truong William R , Robinson Philip A , Beuttler Richard C , Yamaki Jason
Published: August 2022

Background

Fluoroquinolones are one of the most prescribed antimicrobials in the United States and have been increasingly used in inpatient and outpatient settings to treat various infectious diseases syndromes. Due to the unwanted collateral effects on antibiotic resistance, poor susceptibility rates among Gram-negative pathogens, and adverse effects, fluoroquinolones are often targeted by hospital antimicrobial stewardship programs to prevent overutilization. This study describes the association of nonrestrictive antimicrobial stewardship interventions at 2 nonacademic community hospitals on levofloxacin utilization, prescribing patterns on alternative antibiotics, and Pseudomonas aeruginosa nonsusceptibility rates to levofloxacin.

Methods

Nonrestrictive antimicrobial stewardship interventions included monitoring and reporting of fluoroquinolone susceptibility trends to physician groups, performing medication use evaluations of levofloxacin accompanied with prescriber detailing, daily prospective audit and feedback, implementation of beta-lactam-based institutional guidelines for empiric therapy in various infectious disease syndromes, review and adjustment of electronic medical record order sets containing fluoroquinolones, and intensive prescriber education. No preauthorization of levofloxacin was used during this study period. Antibiotic utilization data were collected for the time periods of August 2015 through January 2021. Correlation between levofloxacin and other broad-spectrum antibiotc use was investigated as well as the impact on Pseudomonas aeruginosa levofloxacin nonsusceptibility rates.

Results

Both hospitals showed an overall downward trend in the prescribing of levofloxacin during the time period of August 2015 to January 2021. There was a significant negative correlation between monthly ceftriaxone and levofloxacin days of therapy for both hospitals (P < .0001). There was a positive correlation between levofloxacin days of therapy and P aeruginosa nonsusceptibility (P < .02 at both hospitals).

Conclusions

Our results demonstrate that a nonrestrictive approach to fluoroquinolone stewardship interventions had a significant impact on reducing levofloxacin utilization, increasing ceftriaxone utilization, and improving P aeruginosa levofloxacin susceptibility.
Conservation officer perceptions of stress associated with traditional policing duties
Authors: Ledford Logan , Osborne Dustin , Edwards Bradley , Stickle Ben
Published: August 2022

Though a limited amount of research has focused on conservation officers’ work, few studies have explored the levels of stress that they perceive to be associated with the work. Furthermore, no study has addressed the levels of stress that these officers associate with traditional policing duties. This is problematic since many are now being tasked with these duties in addition to their conservation-specific roles. This study seeks to address this knowledge gap by utilizing data from 346 conservation officers in six US states. It addresses the role that individual characteristics (for example tenure, education, age) and duty frequency play in influencing the levels of stress that officers associate with traditional policing duties. The analyses suggest that officers with higher education levels, those who have longer tenures in the field, and those who more frequently perform traditional policing duties tend to feature higher levels of perceived stress. Conversely, those with prior policing experience (before becoming a conservation officer) appear to be somewhat insulated from the negative impacts of performing traditional duties. The implications of these findings are discussed in relation to potential alterations in conservation officer recruitment and training.
A Systematic Review of the Efficacy and Availability of Targeted Treatments for Central Sensitization in Women With Endometriosis
Authors: Simpson Grace , Philip Moira , Lucky Tarana , Ang Catarina , Kathurusinghe Shamitha
Published: August 2022

Objectives:

Central sensitization (CS) contributes to patient variability when treating pain in endometriosis. Targeting this process may alleviate hyperalgesia and allodynia in women refractory to current treatments. Currently, there has been no review of targeted treatments for central sensitization in women with endometriosis. Therefore, this review aims to identify and summarize the findings of studies regarding the availability and efficacy of targeted treatments for CS in women with endometriosis.

Materials and Methods:

A systematic review was conducted searching MEDLINE, Embase and CINAHL. Inclusion criteria: primary research articles, women with endometriosis and CS features, and description of treatments for CS, or its effects on hyperalgesia and allodynia. Exclusion criteria: review articles, letters to the editor, commentaries, editorials, protocols, or women with endometriosis infiltrating nerves. Risk of bias analysis was conducted. Data was reviewed and summarized by treatment method.

Results:

Eight studies met inclusion criteria, demonstrating limited research in this area. Four treatment options were addressed: surgical approaches, nerve stimulation approaches, injection-based therapies, and hormonal therapies. Surgery and nerve stimulation appear the most promising treatments for CS. Injections have limited and mixed evidence of efficacy. Limited evidence suggests hormonal therapies may be ineffective.

Discussion:

Given the lack of evidence for any treatment, all require further research to determine treatment efficacy before options will be available clinically. There is a clear need for consistency in defining and identifying CS in study populations. This review identifies areas of interest, particularly surgery and nerve stimulation, from which future research must stem.
Illness stigma, body image dissatisfaction, thwarted belongingness and depressive symptoms in youth with inflammatory bowel disease
Authors: Roberts Caroline M. , Gamwell Kaitlyn L. , Baudino Marissa N. , Edwards Clayton S. , Jacobs Noel J. , Tung Jeanne , Grunow John E. , Mullins Larry L. , Chaney John M.
Published: August 2022

Background

Elevated depressive symptoms are observed in a significant number of youth with inflammatory bowel disease (IBD) and have been linked to illness stigma and social isolation. Body image dissatisfaction is an understudied variable in the pediatric IBD literature that may be related to both stigma and social difficulties. It is suspected that, due to the stigmatizing nature of IBD, some youth may feel self-conscious about their body image, which contributes to decreased feelings of social belongingness and ultimately depressive symptoms. The current study tested an illness stigma→ body image dissatisfaction→ thwarted belongingness→ depressive symptoms serial mediation model, in which IBD stigma was hypothesized to indirectly influence youth depressive symptoms through the sequential effects of stigma on body image dissatisfaction and thwarted social belongingness.

Methods

Youth with IBD (N = 75) between 10 and 18 years old were recruited from a pediatric gastroenterology clinic and completed psychosocial measures. Disease severity was assessed by a physician global assessment. Current medications and BMI data were collected.

Results

Analyses revealed significant direct effects among the modeled variables and a significant serial indirect path for illness stigma→ body image dissatisfaction→ thwarted belongingness→ depressive symptoms, controlling for sex, BMI and prednisone medication.

Conclusions:

Youth who perceive greater IBD stigma are more likely to experience increased body image dissatisfaction due to their IBD, which may engender feelings of social estrangement and ultimately elevated depressive symptoms. Depressive symptoms and the psychosocial challenges faced by youth should be routinely monitored as part of comprehensive IBD management.
A modified multibond model for nanoscale static friction
Authors: Milne Zachary B. , Hasz Kathryn , McClimon J. B. , Castro Juan , Carpick Robert W.
Published: August 2022

Several key features of nanoscale friction phenomena observed in experiments, including the stick-slip to smooth sliding transition and the velocity and temperature dependence of friction, are often described by reduced-order models. The most notable of these are the thermal Prandtl–Tomlinson model and the multibond model. Here we present a modified multibond (mMB) model whereby a physically-based criterion—a critical bond stretch length—is used to describe interfacial bond breaking. The model explicitly incorporates damping in both the cantilever and the contacting materials. Comparison to the Fokker–Planck formalism supports the results of this new model, confirming its ability to capture the relevant physics. Furthermore, the mMB model replicates the near-logarithmic trend of increasing friction with lateral scanning speed seen in many experiments. The model can also be used to probe both correlated and uncorrelated stick slip. Through greater understanding of the effects of damping and noise in the system and the ability to more accurately simulate a system with multiple interaction sites, this model extends the range of frictional systems and phenomena that can be investigated.

This article is part of the theme issue ‘Nanocracks in nature and industry’.
New theory explaining Griffith strength results on nano-cracked glass fibres
Authors: Kendall Kevin
Published: August 2022

The purpose of this paper is to propose a mechanism and theory that can explain the extraordinary increase in measured strength that Griffith observed for glass fibres containing nano-cracks. His 1921 theory (Griffith 1921Phil. Trans. R. Soc. Lond. A221, 163–198. (doi:10.1098/rsta.1921.0006)) predicted that the strength of a cracked sample should be independent of sample size, yet his results on stretched glass fibres gave strength increasing almost as the inverse of fibre diameter. He proposed a ‘flaw statistics’ argument in an attempt to explain these bizarre results, suggesting strength increased because large defects were less likely in the smaller volumes. But this ‘flaw statistics’ concept is unnecessary because the Griffith energy criterion of cracking must give a size effect, as demonstrated in many different crack-testing configurations. In general, the Griffith energy criterion for crack equilibrium predicts strength rising for smaller samples because such samples contain less volume energy to create new crack surface energy. The problem is that this ‘size effect’ idea has not until now been properly defined for the simple tension crack test. The new idea proposed is that many nano-cracks are likely to exist in an experimental glass sample, so these must also obey the thermodynamic analysis. A problem then arises because, as the main crack propagates, other cracks may close, but healing is not reversible in glass so thermodynamics does not apply completely to these secondary cracks. Crack healing is in the Griffith theory, which is perfectly reversible mathematically, though not explicitly stated.

This article is part of the theme issue 'Nanocracks in nature and industry'.
Genome-based reclassification of Azospirillum brasilense Az39 as the type strain of Azospirillum argentinense sp. nov.
Authors: dos Santos Ferreira Natália , Coniglio Anahí , Puente Mariana , Sant’Anna Fernando Hayashi , Maroniche Guillermo , García Julia , Molina Romina , Nievas Sofia , Volpiano Camila Gazolla , Ambrosini Adriana , Passaglia Luciane M. P. , Pedraza Raul O. , Reis Verônica Massena , Zilli Jerri Édson , Cassan Fabricio
Published: August 2022

Strain Az39T of

Azospirillum

is a diazotrophic plant growth-promoting bacterium isolated in 1982 from the roots of wheat plants growing in Marcos Juárez, Córdoba, Argentina. It produces indole-3-acetic acid in the presence of l-tryptophan as a precursor, grows at 20–38 °C (optimal 38 °C), and the cells are curved or spiral-shaped, with diameters ranging from 0.5–0.9 to 1.8–2.2 µm. They contain C16 : 0, C18 : 0 and C18 : 1
 ω7c/ω6c as the main fatty acids. Phylogenetic analysis of its 16S rRNA gene sequence confirmed that this strain belongs to the genus

Azospirillum

, showing a close relationship with

Azospirillum baldaniorum

Sp245T,

Azospirillum brasilense

Sp7T and

Azospirillum formosense

CC-Nfb-7T. Housekeeping gene analysis revealed that Az39T, together with five strains of the genus (Az19, REC3, BR 11975, MTCC4035 and MTCC4036), form a cluster apart from

A. baldaniorum

Sp245T,

A. brasilense

Sp7T and

A. formosense

CC-Nfb-7T. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) between Az39T and the aforementioned type strains revealed values below 96 %, the circumscription limit for the species delineation (ANI: 95.3, 94.1 and 94.0 %; dDDH: 62.9, 56.3 and 55.6 %). Furthermore, a phylogeny evaluation of the core proteome, including 809 common shared proteins, showed an independent grouping of Az39T, Az19, REC3, BR 11975, MTCC4035 and MTCC4036. The G+C content in the genomic DNA of these six strains varied from 68.3 to 68.5 %. Based on the combined phylogenetic, genomic and phenotypic characterization presented here, we consider that strain Az39T, along with strains Az19, REC3, BR 11975, MTCC4035 and MTCC4036, are members of a new

Azospirillum

species, for which the name Azospirillum argentinense sp. nov. is proposed. The type strain is Az39T (=LBPCV39T=BR 148428T=CCCT 22.01T).
Alizarin Red fluorescence imaging for nano calcification
Authors: Coralli Caterina Vanelli , Xue Jing , Chester Adrian H , Bertazzo Sergio
Published: August 2022

The formation of calcium phosphate (calcification) has been observed in a variety of healthy and diseased tissues and contributes to a wide range of pathologies. In physiological and pathological mechanisms, calcification begins at the nano scale and then develops into structures that range from a few micrometres to several centimetres. Fluorescence microscopy can be an efficient way to visualise such early calcification and its interaction with cells and proteins. The limited shelf life and high cost of commercial dyes for staining calcification, however, can be problematic when using this imaging method. Here, we aim to evaluate the effectiveness and stability of Alizarin Red (AR) as a fluorescent staining agent for nano and micro calcified structures. Our results show that AR staining for nano and micro calcified structures is a simple, reliable, effective, and quite inexpensive method to visualize calcification at the nano and micro scale in biological samples.
Eya-controlled affinity between cell lineages drives tissue self-organization during Drosophila oogenesis
Authors: Weichselberger Vanessa , Dondl Patrick , Classen Anne-Kathrin
Published: August 2022

The cooperative morphogenesis of cell lineages underlies the development of functional units and organs. To study mechanisms driving the coordination of lineages, we investigated soma-germline interactions during oogenesis. From invertebrates to vertebrates, oocytes develop as part of a germline cyst that consists of the oocyte itself and so-called nurse cells, which feed the oocyte and are eventually removed. The enveloping somatic cells specialize to either facilitate oocyte maturation or nurse cell removal, which makes it essential to establish the right match between germline and somatic cells. We uncover that the transcriptional regulator Eya, expressed in the somatic lineage, controls bilateral cell-cell affinity between germline and somatic cells in Drosophila oogenesis. Employing functional studies and mathematical modelling, we show that differential affinity proportional to Eya expression and the resulting forces drive somatic cell redistribution over the germline surface and control oocyte growth to match oocyte and nurse cells with their respective somatic cells. Thus, our data demonstrate that differential affinity between cell lineages is sufficient to drive the complex assembly of inter-lineage functional units and underlies tissue self-organization during Drosophila oogenesis.
Rethinking Population Bottlenecks: Intrinsic Fluctuations, Mutation and Dynamical Demographic Phases
Authors: Crosato Emanuele , Philippson Jeffrey N. , Thutupalli Shashi , Morris Richard G.
Published: August 2022

By abruptly changing the size and composition of a population, bottlenecks can dramatically alter evolutionary trajectories. In the traditional picture, the faster a population recovers from a bottleneck, the more rapidly finite-size intrinsic fluctuations are suppressed and therefore the greater the likelihood of fixation to the attractor within whose basin the bottleneck constrained the population, initially. We now argue that this intuition is misleading; demonstrating that precisely the opposite behaviour is also possible. Depending critically on the rate of mutation, increased population growth can drive fixation to attractors that are different to that from whose basin it started. These findings are explained in terms of statistically distinct regimes of demographic behaviour, drawing parallels with the notion of non-equilibrium phase transitions. Such dynamical demographic phases are delimited by sharp transitions in time, as a population grows, and ultimately result from a time-dependent antagonism between mutation and the stochastically-induced effects of frequency-dependent birth.
Investigating manta ray collective movements via drone surveys
Authors: Perryman Robert J. Y. , Brown Culum , Pasian Nicolò , Ward Ashley J. W. , Kent M. I. A.
Published: August 2022

Detailed observational research on free-ranging species of marine megafauna is required to understand their behavioural ecology, including how groups respond to environmental and anthropogenic pressures. New technologies are opening up potential for research on these species in the wild, especially on group-based and collective behaviours. Reef manta rays (Mobula alfredi) are socially interactive elasmobranchs that form groups in coastal reef habitats. Collective behaviours are likely important to their fitness, but may be disturbed by humans. Using small, remotely-piloted drones, we performed aerial observations of manta ray groups in Raja Ampat, West Papua. We empirically quantified patterns of collective movement including relative spatial positions, alignment, speed and leadership positions of conspecifics. We found unique patterns of spatial positioning, alignment and leadership, including differences between sexes, and high levels of local attraction, which were suggestive of distinct collective behaviour states. We suggest that ‘rules of interaction’ in manta rays vary at the individual level and can shift depending on local environmental and social conditions. Leader-follower behaviour likely has broad importance to cohesive movement and social behaviour inM. alfredi. We suggest that further studies on manta ray movement should consider utilising models of collective motion that capture group-level behavioural processes.
A Gene Expression Atlas of Lohmann White Chickens
Authors: Zhang Jiannan , Wang Xinglong , Lv Can , Wan Yiping , Zhang Xiao , Li Juan , Wang Yajun
Published: August 2022

Chicken (Gallus gallus domesticus) as one of the most economically important farm animals plays a major role in human food production and has been widely used as a key animal model that is presumed to be typical of avian and generally applicable to mammals in studies of developmental biology, virology, oncogenesis, and immunology. To get a better understanding of avian biology, global analysis of gene expression across multiple tissues is needed, which will aid genome annotation and support functional annotation of avian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult Lohmann White domesticus chickens. An open-access chicken tissue gene expression atlas (TGEA) (chickenatlas.avianscu.com) is presented based on the expression of 224 samples across 38 well-defined chicken tissues. Network-based cluster analysis of this dataset grouped genes according to dimensionality reduction and whole-body co-expression patterns, which were used to infer the function of uncharacterized genes from their co-expression with genes of known function. We describe the distribution and tissue specificity of 21,430 genes present in the chicken gene expression atlas and assign those signatures, where possible, to specific tissue populations or pathways. To better understand the functions of GPCRs in avian, we quantified the transcript levels of 254 nonodorant GPCRs in all tissues. Cluster analysis placed many GPCRs into expected anatomical and functional groups and predicted previously unidentified roles for less-studied receptors. We also produced this atlas to analyze male and female mRNA expression profiles in chicken somatic and gonad tissues. Our analyses uncovered numerous cases of somatic sex-biased mRNA expression, with the largest proportion found in the chicken pineal body, pituitary, and liver. This high-resolution gene expression atlas for chickens is, to our knowledge, the largest transcriptomic dataset of any avian to date. It provides a resource to improve the annotation of the current reference genome for chicken, presenting a model transcriptome for avian, and can be used as a resource for predicting roles for incompletely characterized GPCRs, exploring sex-biased specific gene expression, and for other purposes.
Physiological responses to drought stress and recovery reflect differences in leaf function and anatomy among grass lineages
Authors: Bachle Seton , Zaricor Marissa , Griffith Daniel , Qui Fan , Still Christopher J , Ungerer Mark C , Nippert Jesse B
Published: August 2022

Grasses are cosmopolitan, existing in many biome and climate types from xeric to tropical. Traits that control physiological responses to drought vary strongly among grass lineages, suggesting that tolerance strategies may differ with evolutionary history. Here, we withheld water from 12 species representing six tribes of grasses to compare how species respond to drought in different grass lineages. We measured physiological, morphological, and anatomical traits. Dominant lineages from tropical savannas, like Andropogoneae, tolerated drought due to above and belowground morphological traits (specific leaf area and root length, SLA and SRL), while temperate grasses in this study utilized conservative leaf physiology (gas exchange) and anatomy traits. Increased intrinsic water-use efficiency coincided with a larger number of stomata, resulting in greater water loss (with inherently greater carbon gain) and increased drought sensitivity. Inherent leaf and root economic strategies impacting drought response were observed in all species, resulting in either high SLA or SRL, but not both. Our results indicate that grasses subjected to severe drought were influenced by anatomical traits (e.g., number of stomata and xylem area) and similar within lineages. In addition, grasses recovered at least 50% of physiological functioning across all lineages and 92% within Andropogoneae species, illustrating how drought can influence functional responses across diverse grass lineages.
SpliceAI-10k calculator for the prediction of pseudoexonization, intron retention, and exon deletion
Authors: Canson Daffodil M. , Davidson Aimee L. , de la Hoya Miguel , Parsons Michael T. , Glubb Dylan M. , Kondrashova Olga , Spurdle Amanda B.
Published: August 2022

SpliceAI is a widely used splicing prediction tool and its most common application relies on the maximum delta score to assign variant impact on splicing. We developed the SpliceAI-10k calculator (SAI-10k-calc) to extend use of this tool to predict: the splicing aberration type including pseudoexonization, intron retention, partial exon deletion, and (multi)exon skipping using a 10 kb analysis window; the size of inserted or deleted sequence; the effect on reading frame; and the altered amino acid sequence.

SAI-10k-calc has 95% sensitivity and 96% specificity for predicting variants that impact splicing, computed from a control dataset of 1,212 single nucleotide variants (SNVs) with curated splicing assay results. Notably, it has high performance (≥84% accuracy) for predicting pseudoexon and partial intron retention. The automated amino acid sequence prediction allows for efficient identification of variants that are expected to result in mRNA nonsense-mediated decay or translation of truncated proteins.

Availability and implementation

SAI-10k-calc is implemented in R (https://github.com/adavi4/SAI-10k-calc) and also available as a Microsoft Excel spreadsheet. Users can adjust the default thresholds to suit their target performance values.

Supplementary information

Supplementary data are available online.
Risk of Myocarditis after Covid-19 mRNA Vaccination: Impact of Booster Dose and Dosing Interval
Authors: Le Vu Stéphane , Bertrand Marion , Jabagi Marie-Joëlle , Botton Jérémie , Weill Alain , Dray-Spira Rosemary , Zureik Mahmoud
Published: August 2022

Covid-19 mRNA vaccines have been shown to be associated with a short-term increased risk of myocarditis, with the highest risk observed after the second dose compared to the first. The extent of the risk associated with more distant booster doses is less clear. Here, we aimed to assess the relation between dosing interval and the risk of myocarditis, for both the two-dose primary series and the third dose (first booster). Extending our previous matched case-control study, we included 4 890 cases of myocarditis aged 12 or more and 48 900 controls up to January 31, 2022. We found that the risk of myocarditis remained elevated after the booster dose and that longer intervals between each consecutive dose (including booster doses) may decrease the occurrence of vaccine-associated myocarditis.
Hypergraph factorisation for multi-tissue gene expression imputation
Authors: Viñas Ramon , Joshi Chaitanya K. , Georgiev Dobrik , Dumitrascu Bianca , Gamazon Eric R. , Liò Pietro
Published: August 2022

Abstract

Integrating gene expression across scales and tissues is crucial for understanding the biological mechanisms that drive disease and characterise homeostasis. However, traditional multi-tissue integration methods cannot handle uncollected tissues or rely on genotype information, which is subject to privacy concerns and often unavailable. To address these challenges, we present HYFA (HypergraphFactorisation), a novel method for joint imputation of multi-tissue and cell-type gene expression. HYFA imputes tissue-specific gene expression via a specialised graph neural network operating on a hypergraph of individuals, metagenes, and tissues. HYFA is genotype- agnostic, supports a variable number of collected tissues per individual, and imposes strong inductive biases to leverage the shared regulatory architecture of tissues. In performance comparison on data from the Genotype Tissue Expression project, HYFA achieves superior performance over existing transcriptome imputation methods, especially when multiple reference tissues are available. Through transfer learning on a paired single-nucleus RNA-seq (snRNA-seq) dataset, we further show that HYFA can accurately resolve cell-type signatures from bulk gene expression, highlighting the method’s ability to leverage gene expression programs underlying cell-type identity, even in tissues that were never observed in the training set. Using Gene Set Enrichment Analysis, we find that the metagenes learned by HYFA capture information about known biological pathways. Notably, the HYFA-imputed dataset can be used to identify regulatory genetic variations (eQTLs), with substantial gains over the original incomplete dataset. Our framework can accelerate effective and scalable integration of tissue and cell-type gene expression biorepositories.
Streptococcus suis infection on European farms is associated with an altered tonsil microbiome and resistome
Authors: Fredriksen Simen , Neila-Ibáñez Carlos , Hennig-Pauka Isabel , Guan Xiaonan , Dunkelberger Jenelle , de Oliveira Isabela Fernandes , Ferrando Maria Laura , Correa-Fiz Florencia , Aragon Virginia , Boekhorst Jos , van Baarlen Peter , Wells Jerry M.
Published: August 2022

Streptococcus suisis a Gram-positive opportunistic pathogen causing systemic disease in piglets around weaning age. The factors predisposing to disease are not known. We hypothesised that the tonsillar microbiota might influence disease risk via colonisation resistance and/or co-infections. We conducted a cross-sectional case-control study within outbreak farms complemented by selective longitudinal sampling and comparison with control farms without disease occurrence. We found a small but significant difference in tonsil microbiota composition between case and control piglets (n=45+45). Variants of putative commensal taxa, includingRothia nasimurium, were reduced in abundance in case piglets compared to asymptomatic controls. Case piglets had higher relative abundances ofFusobacterium gastrosuis, Bacteroides heparinolyticus, and unculturedPrevotellaandAlloprevotellaspecies. Despite case-control pairs receiving equal antimicrobial treatment, case piglets had higher abundance of antimicrobial resistance genes (ARGs) conferring resistance to antimicrobial classes used to treatS. suis. This might be an adaption of disease-associated strains to frequent antimicrobial treatment.
Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic
Authors: Metheringham Carey L. , Plumb William J. , Flynn William R. M. , Stocks Jonathan J. , Kelly Laura J. , Gorriz Miguel Nemesio , Grieve Stuart W. D. , Moat Justin , Lines Emily R. , Buggs Richard J. A. , Nichols Richard A.
Published: August 2022

Rapid evolution via small shifts in allele frequencies at thousands of loci are a long- standing neo-Darwinian prediction but are hard to characterize in the wild. European ash tree (Fraxinus excelsior) populations have recently come under strong selection by the invasive fungal pathogenHymenoscyphus fraxineus. Using genomic prediction models based on field trial phenotypes and 7,985 loci, we show a shift in genomically estimated breeding values in an ancient woodland, between adult trees established before the epidemic started and juvenile trees established since. Using simulations, we estimate that natural selection has eliminated 31% of the juvenile population. Thus, we document a highly polygenic heritable micro-evolutionary adaptive change over a single generation in the wild.

One-Sentence Summary

Subtle changes at thousands of genomic locations in one generation allow woodland trees to respond to a new selective pressure
DNA Repair Strategy Sets Transposon Mobilization Rates in Caenorhabditis elegans
Authors: Chang Cindy , Pagano Daniel J. , Lowe David D. , Kennedy Scott
Published: August 2022

Transposons are parasitic nucleic acids that threaten genome integrity in all cells. In the metazoan model organism Caenorhabditis elegans, DNA transposons are active in the soma where they are reported to exhibit mobilization rates ≅1000 fold higher than in germ cells. How and why DNA transposons might be so highly active in the C. elegans soma is a mystery. To better understand this question, we constructed reporter genes that label cells in which Tc1 has mobilized with fluorescent protein. The reporters recapitulate the known properties of DNA transposons in C. elegans and allow transposon activity to be monitored in intact, living animals. Using these reporters, we identify cytoplasmic and nuclear factors that limit transposition in the germline. Interestingly, none of these factors limit transposition in the soma. Rather, we identify a gene (nhj-1/scb-1), which we show is required for 99.9% of Tc1 mobilization events in somatic tissues, but does not influence mobilization in the germline. nhj-1/scb-1 encodes a nematode-specific component of the non-homologous end joining (NHEJ) DNA repair machinery. Mutations in the other components of the NHEJ machinery (cku-70, cku-80, and lig-4) also suppress Tc1 mobilization in the C. elegans soma by ≅1000 fold. The data show that the use of NHEJ to repair transposon-induced DNA breaks in the soma dramatically increases the rate of transposon mobilization in this tissue. And because C. elegans germ cells use homology-based repair, and not NHEJ, to fix transposon-induced breaks, we propose that the 1000-fold difference in transposon mobility reported for the C. elegans soma and germline can, in large part, be explained by tissue-specific differences in DNA repair strategy.

Author Summary

Transposons are common parasitic genetic elements that threaten all genomes. For example, half of the human genome is made up of transposons. Transposon mobilization can disrupt gene function, causing disease, so transposon activity needs to be tightly regulated to prevent harm to the host. Transposons are typically less active in the soma than in the germline, because somatic transposition benefits neither host or transposon. Surprisingly, in the nematode model organism Caenorhabditis elegans, transposons are reported to be 1000-fold more active in the soma than the germline. Here, we develop a system to investigate transposon regulation in an intact live animal, and show that, in large part, tissue-specific differences in transposon activity in C. elegans is due to the use of different DNA repair pathways by these tissues, highlighting the importance of DNA repair strategy in determining outcomes of transposon excision events. Given that DNA repair factors have been linked to transposon regulation in other eukaryotes, we propose that DNA repair choice likely contributes to transposon mobilization in all eukaryotes.
ObiWan-Microbi: OMERO-based integrated workflow for annotating microbes in the cloud
Authors: Seiffarth Johannes , Scherr Tim , Wollenhaupt Bastian , Neumann Oliver , Scharr Hanno , Kohlheyer Dietrich , Mikut Ralf , Nöh Katharina
Published: August 2022

Reliable deep learning segmentation for microfluidic live-cell imaging requires comprehensive ground truth data. ObiWan-Microbi is a microservice platform combining the strength of state-of-the-art technologies into a unique integrated workflow for data management and efficient ground truth generation for instance segmentation, empowering collaborative semi-automated image annotation in the cloud.

Availability and Implementation

ObiWan-Microbi is open-source and available under the MIT license at https://github.com/hip-satomi/ObiWan-Microbi, along documentation and usage examples.

Contact

k.noeh@fz-juelich.de

Supplementary information

Supplementary data are available online.
Preparation of Pipettes and Pipette-Filling Devices for Patch-Clamping Drosophila Neurons
Authors: Fernandez-Chiappe Florencia , Muraro Nara I.
Published: August 2022

An essential requirement of every laboratory procedure is to have all materials ready when they are needed, so that the experimental flow is not disrupted. This is particularly true for patch clamping; therefore, effort must be devoted in advance to produce materials such as patch pipettes. This can be a fiddly business; hence, this protocol provides step-by-step advice on how to pull and polish patch-clamp pipettes. It also includes a brief description on how to prepare homemade filling devices to deliver saline efficiently and inexpensively into the pipettes. The protocol ends with guidelines on how to change the filament of a Sutter horizontal puller, a dreaded yet necessary activity that should be learned by anyone who wishes to become an expert patch clamper.
How to organize for open innovation from the ground up: a microfoundations approach in a foodservice firm
Authors: Annosi Maria Carmela , Martini Antonella , Marzi Giacomo , Vignoli Matteo , Parra Héctor
Published: August 2022

Purpose

This study aims to analyze what promotes the adoption of open innovation (OI) in the foodservice sector. Specifically, it seeks to shed light on the bottom-up mechanisms (the microfoundations) that allow a foodservice firm to organize for OI.

Design/methodology/approach

The research design is an in-depth exploratory case study with 18 semi-structured interviews. The findings have been triangulated with documentation available on the corporate website, the project reports and direct observation. Data were analyzed using an inductive approach, coding individual interview transcripts.

Findings

This study identifies three categories of capabilities that have to be spread to different organizational levels: the capability to sense organizational triggers to change, to develop external collaborations and knowledge exchanges with different parties and the management's ability to be aware of organizational imperatives and the need to proceed with process adjustment. Results highlight the importance of sensing organizational triggers, allowing a quick switch between new strategies in implementing an OI approach. It was crucial for the company to co-develop new products and services with a large audience of stakeholders, not only limited to customers. The case remarks on the required ability of the organization and management team to activate mechanisms aimed at reconfiguring the competencies within each business unit, keeping an alignment with the needs of the stakeholders.

Originality/value

The study emphasizes the multi-level characteristics of OI and provides a framework for microfoundations on how to organize for OI. Results contribute to the recent debate on the skills and routines an organization should design and promote within their employees.
Do bankrupt firms recognize publicly available bad news in a timely fashion?
Authors: Khalifa Mariem , Trabelsi Samir
Published: August 2022

Purpose

The purpose of this paper is to examine whether managers of bankrupt firms are more or less conditionally conservative in their financial reporting relative to non-bankrupt firms. The study further examines the cross-sectional differences in conditional conservatism among bankrupt and non-bankrupt firms.

Design/methodology/approach

The study employs a sample of US firms to investigate conditional conservatism in firms that experience financial distress and go bankrupt relative to non-stressed non-bankrupt firms. The study also uses switching regression models to identify the drivers of the cross-sectional difference in conditional conservatism among bankrupt and non-bankrupt firms.

Findings

Empirical results show that bankrupt firms are timelier in recognizing bad news than good news when compared to non-bankrupt firms. The higher level of conditional conservatism in bankrupt firms is mainly driven by their higher levels of leverage and tax-reduction incentives. The cross-sectional analyses show that these results largely hold for more leveraged firms and firms with higher tax costs. Taken together, these results suggest that the conservative tendency of managers of bankrupt firms can stem from the agency problem between lenders and managers and from tax-decreasing motivations.

Originality/value

The novelty of the authors’ research stands in studying the drivers of the cross-sectional differences in conditional conservatism between bankrupt and non-bankrupt firms and specifically, the demonstration that taxation also induces conditional conservatism in the setting of ex post bankrupt firms.
A theoretical model and empirical analysis of university library readers' spatial cognition
Authors: Jiang Yiping , Chen Yanhua , Chi Xiaobo
Published: August 2022

Purpose

The practice of renovation and construction of university libraries is flourishing, but how to attract readers to use the library is an issue that urgently needs to be explored. Spatial cognition is a subjective judgment of a person's tendency to take action in the future and implies behavioral intention. Based on the sensory–image–cognition relationship, a theoretical model of university library readers' spatial cognition is conducted, and the influencing factors and mechanisms of spatial cognition are explored based on empirical data to provide theoretical references for spatial practices in university libraries.

Design/methodology/approach

A visual and art-based mental map approach is introduced based on a questionnaire survey. The questionnaire is mainly used for the specific evaluation of spatial use and the breakdown of the detailed elements, while the mental map method is mainly used for the evaluation of readers' spatial cognition. Relevant empirical data are collected from the library of the Zhejiang University of Technology.

Findings

The results indicate that readers' spatial sensory experience and mental imagery have positive effects on readers' behavior via the mediator spatial cognition, readers' spatial sensory experience and mental imagery have a positive effect on readers' spatial cognition and spatial cognition has a significant effect on readers' behavior.

Originality/value

The main contribution of this study is to construct a theoretical model of readers' spatial cognition and to explore the factors that have an impact on spatial cognition and the influence of cognition on behavior. This provides a more rational and in-depth thinking paradigm for the study of university library space and provides theoretical references for library practice.
Doing the handfailure: At the margins of global capitalism
Authors: Baann Cecilie
Published: August 2022

What can an account of manual labour in an increasingly precarious environment tell us about how humans build meaningful lives? Using an ethnographic example from the working relations on a fishing boat based out of the fishing community Tombo in Sierra Leone, I argue that shared bodily work entails possibilities of individual economic gain while simultaneously laying the foundations for solidarity and care. We find a playful competition between working mates at the core of this seeming contradiction. This article explores how people make a living and make a life, not simply despite their continued marginalization in political and economic terms, but through it. In the physically demanding shared labour of hauling a fishing net and learning how to compete for the fish by doing the handfailure, crew members forge relations of care and solidarity that stimulate individual aspirations while asserting the right to life by the sea.
Striking health workers: Precarity and healthcare in neoliberal Kenya
Authors: Ameso Edwin Ambani , Prince Ruth Jane
Published: August 2022

Precarity is increasingly a condition of life for Kenyan health workers as even professionals face costs of living and forms of debt that exceed their (unstable) salaries. Years of austerity and chronic scarcity have eroded healthcare infrastructures and rendered crises part of everyday work. Based on ethnographic fieldwork in Kenya from 2018 to 2020, we explore health workers’ experiences and concerns about the precarity of their working conditions, livelihoods, health and futures amidst the government's attempts to experiment with ‘universal health coverage’ (UHC) and improve access to healthcare. While UHC appears to call for greater state responsibility for healthcare futures, healthcare provision is being further outsourced and privatized, underlining that seemingly progressive health policies like UHC are sustaining and replicating neoliberal trends.
Productivity Debacle in the UK: Do Post‐crisis Firm Cohorts Explain the Performance Puzzle?
Authors: Douch Mustapha , Edwards Huw , Mallick Sushanta
Published: August 2022

This paper investigates how the aftermath of the 2008 crisis affected firm productivity in the UK, focusing particularly on the cohort effect of firms established after 2008 – a previously overlooked aspect of the crisis – as well as the interaction with access to credit, which we test using firm‐specific and time‐varying credit scores. For identification, a matched sample is used based on credit score, firm age, size and ownership status, combining propensity score matching with difference‐in‐differences. While we find evidence that smaller firm size and changes in credit conditions affect productivity, about half of the difference in productivity remains unexplained. When we extend the matching analysis to examine across sectors and cohorts, we find that the low productivity performance during the years 2011–2016 is driven primarily by newer firms in the services sector, rather than in manufacturing. Within services, the underlying productivity puzzle is driven by a cessation of output growth in high‐productivity financial services, while abundant labour supply has led to a ‘levelling down’ of performance of newer firms in other services, converging towards the relatively low‐productivity manufacturing.