bluuebunny/crossref_metadata_2025 huggingface dataset:
Distinct chikungunya virus polymerase palm subdomains contribute to virus replication and virion assembly
Authors: Martin Marie-France , Bonaventure Boris , McCray Nia E. , Peersen Olve B. , Rozen-Gagnon Kathryn , Stapleford Kenneth A.
Published: January 2024

Alphaviruses encode an error-prone RNA-dependent RNA polymerase (RdRp), nsP4, required for genome synthesis, yet how the RdRp functions in the complete alphavirus life cycle is not well-defined. Previous work using chikungunya virus (CHIKV) has established the importance of the nsP4 residue cysteine 483 in maintaining viral genetic fidelity. Given the location of residue C483 in the nsP4 palm domain, we hypothesized that other residues within this domain and surrounding subdomains would also contribute to polymerase function. To test this hypothesis, we designed a panel of nsP4 variants via homology modeling based on the Coxsackievirus B3 3 polymerase. We rescued each variant in both mammalian and mosquito cells and discovered that the palm domain and ring finger subdomain contribute to polymerase host-specific replication and genetic stability. Surprisingly, in mosquito cells, these variants in the ring finger and palm domain were replication competent and produced viral structural proteins, but they were unable to produce infectious progeny, indicating a yet uncharacterized role for the polymerase in viral assembly. Finally, we have identified additional residues in the nsP4 palm domain that influence the genetic diversity of the viral progeny, potentially via an alteration in NTP binding and/or discrimination by the polymerase. Taken together, these studies highlight that distinct nsP4 subdomains regulate multiple processes of the alphavirus life cycle, placing nsP4 in a central role during the switch from RNA synthesis to packaging and assembly.

Author Summary

Chikungunya virus (CHIKV) is a re-emerging alphavirus transmitted to humans by mosquitoes and causing frequent explosive outbreaks. Its replication relies on a polymerase that incorporates a significant number of errors in the new genomes, making it a good candidate to develop vaccines or antiviral strategies. However, little is known on alphavirus polymerase function in alternate hosts. To begin to understand how the CHIKV polymerase nsP4 functions, we designed a panel of nsP4 variants taking advantage of the conservation of polymerase structure across positive strand RNA viruses. We discovered that the palm domain and ring finger of the polymerase were involved in host-specific RNA replication, genetic stability, and virus assembly. In addition, we demonstrated that the palm domain directly impacted the generation of viral genetic diversity. Taken together, these findings add further evidence to the crucial impact of the core palm domain of CHIKV polymerase not only on the replication of the RNA itself, but also on the genetic stability of the protein, as well as its involvement in viral assembly.
Pre-Columbian treponemes clarify worldwide spread of treponematosis
Authors: Mattéo Gueyrard , Pierre Pontarotti , Michel Drancourt , Laurent Abi-Rached
Published: January 2024

Syphilis dramatically hit Europe at the end of the fifteen century before spreading to other continents. Yet the origin of the sudden pandemic in the Old World remains debated, in particular because the leading Columbus hypothesis of a New World origin of historical syphilis in Europe lacks paleomicrobiological confirmation. Here we screened a worldwide set of >1,700 ancient humans and identified ancientTreponema pallidumstrains in two pre-Columbian child sacrifices from Tlatelolco, Mexico. Over 12,000Treponema-specific reads were recovered to define a novelTreponema pallidumancient population:Treponema pallidumstr.tlatelolcoensis. Phylogenetics show that this population displays ancestral features but also bears the genetic building blocks of disease-causing modernTreponema pallidumsubspecies, hence demonstrating how pre-Colombian Americas were the source of worldwide spread of treponematosis.
High-throughput analysis of membrane fluidity unveils a hidden dimension in immune cell states
Authors: Andronico Luca A. , Jiang Yidan , Carannante Valentina , Iskrak Sofia , Sandoz Patrick A. , Mikes Jaromir , Klymchenko Andrey , Buggert Marcus , Österborg Anders , Önfelt Björn , Brodin Petter , Sezgin Erdinc
Published: January 2024

Cell membranes undergo biophysical remodelling as an adaptation to the surroundings and to perform specific biological functions. However, the extent and relevance of such changes in human immune systems remain unknown, largely due to the lack of high throughput and multidimensional methodologies. Here, we describe a cytometry-based method with single-cell resolution which fills this technological gap by combining biophysical profiling with conventional biomarker analysis. This platform allows to reveal notable cell type-dependent remodelling of membrane fluidity during immune stimulations and in diseases. Using immune cells exposed to tumour microenvironment as well as from long COVID and chronic lymphocyte leukaemia patients, we demonstrate that membrane fluidity is orthogonal to surface marker expression. Moreover, this biophysical parameter identifies new functional and pathological states of immune cells previously undetectedviasurface marker profiling alone. Our findings will contribute to a more precise definition of immune cell states based on their biophysical properties and will pave the way for a better understanding of the functional heterogeneity of immune cells.
Self-supervised learning to predict intrahepatic cholangiocarcinoma transcriptomic classes on routine histology
Authors: Beaufrère Aurélie , Lazard Tristan , Nicolle Rémy , Lubuela Gwladys , Augustin Jérémy , Albuquerque Miguel , Pichon Baptiste , Pignolet Camille , Priori Victoria , Théou-Anton Nathalie , Lesurtel Mickael , Bouattour Mohamed , Mondet Kévin , Cros Jérôme , Calderaro Julien , Walter Thomas , Paradis Valérie
Published: January 2024

Objective

The transcriptomic classification of intrahepatic cholangiocarcinomas (iCCA) has been recently refined from two to five classes, associated with pathological features, targetable genetic alterations and survival. Despite its prognostic and therapeutic value, the classification is not routinely used in the clinic because of technical limitations, including insufficient tissue material or the cost of molecular analyses. Here, we assessed a self-supervised learning (SSL) model for predicting iCCA transcriptomic classes on whole-slide digital histological images (WSIs)

Design

Transcriptomic classes defined from RNAseq data were available for all samples. The SSL method, called Giga-SSL, was used to train our model on a discovery set of 766 biopsy slides (n=137 cases) and surgical samples (n=109 cases) from 246 patients in a five-fold cross-validation scheme. The model was validated in The Cancer Genome Atlas (TCGA) (n= 29) and a French external validation set (n=32).

Results

Our model showed good to very good performance in predicting the four most frequent transcriptomic class in the discovery set (area under the curve [AUC]: 0.63-0.84), especially for the hepatic stem-like class (37% of cases, AUC 0.84). The model performed equally well in predicting these four transcriptomic classes in the two validation sets, with AUCs ranging from 0.76 to 0.80 in the TCGA set and 0.62 to 0.92 in the French external set.

Conclusion

We developed and validated an SSL-based model for predicting iCCA transcriptomic classes on routine histological slides of biopsy and surgical samples, which may impact iCCA management by predicting prognosis and guiding the treatment strategy.
Transcriptome Analysis Identifies An ASD-Like Phenotype In Oligodendrocytes And Microglia From C58/J Amygdala That Is Dependent On Sex and Sociability
Authors: Dalton George D. , Siecinski Stephen K. , Nikolova Viktoriya D. , Cofer Gary P. , Hornburg Kathryn , Qi Yi , Johnson G. Allan , Jiang Yong-Hui , Moy Sheryl S. , Gregory Simon G.
Published: January 2024

Background

Autism Spectrum Disorder (ASD) is a group of neurodevelopmental disorders with higher incidence in males and is characterized by atypical verbal/nonverbal communication, restricted interests that can be accompanied by repetitive behavior, and disturbances in social behavior. This study investigated brain mechanisms that contribute to sociability deficits and sex differences in an ASD animal model.

Methods

Sociability was measured in C58/J and C57BL/6J mice using the 3-chamber social choice test. Bulk RNA-Seq and snRNA-Seq identified transcriptional changes in C58/J and C57BL/6J amygdala within which DMRseq was used to measure differentially methylated regions in amygdala.

Results

C58/J mice displayed divergent social strata in the 3-chamber test. Transcriptional and pathway signatures revealed immune-related biological processes differ between C58/J and C57BL/6J amygdala. Hypermethylated and hypomethylated genes were identified in C58/J versus C57BL/6J amygdala. snRNA-Seq data in C58/J amygdala identified differential transcriptional signatures within oligodendrocytes and microglia characterized by increased ASD risk gene expression and predicted impaired myelination that was dependent on sex and sociability. RNA velocity, gene regulatory network, and cell communication analysis showed diminished oligodendrocyte/microglia differentiation. Findings were verified using bulk RNA-Seq and demonstrated oxytocin’s beneficial effects on myelin gene expression.

Limitations

Our findings are significant. However, limitations can be noted. The cellular mechanisms linking reduced oligodendrocyte differentiation and reduced myelination to an ASD phenotype in C58/J mice need further investigation. Additional snRNA-Seq and spatial studies would determine if effects in oligodendrocytes/microglia are unique to amygdala or if this occurs in other brain regions. Oxytocin’s effects need further examination to understand its potential as an ASD therapeutic.

Conclusions

Our work demonstrates the C58/J mouse model’s utility in evaluating the influence of sex and sociability on the transcriptome in concomitant brain regions involved in ASD. Our single-nucleus transcriptome analysis elucidates potential pathological roles of oligodendrocytes and microglia in ASD. This investigation provides details regarding regulatory features disrupted in these cell types, including transcriptional gene dysregulation, aberrant cell differentiation, altered gene regulatory networks, and changes to key pathways that promote microglia/oligodendrocyte differentiation. Our studies provide insight into interactions between genetic risk and epigenetic processes associated with divergent affiliative behavior and lack of positive sociability.
Level of independence, anxiety and relevant challenges among persons with disabilities towards their use of facilities in public buildings
Authors: Okezue Obinna Chinedu , Uzoigwe Madonna , Ugwu Livinus Ekene , John Jeneviv Nene , John Davidson Okwudili , Mgbeojedo Ukamaka Gloria
Published: January 2024

Purpose

This study aims to explore the level of independence among persons with disabilities (PWDs) towards their use of public buildings’ facilities, as well as assess the anxiety and relevant challenges regarding such use.

Design/methodology/approach

In a cross-sectional survey design, 91 consenting PWDs were recruited via purposive sampling at diverse locations and invited to complete self-report questionnaires on their use of public buildings’ facilities.

Findings

Only 19 PWDs (20.9%) were able to independently use such facilities. The participants’ level of anxiety, observed to be mostly severe (41.7%), was significantly associated with sex and affected body region (p < 0.05). Most PWDs identified “lack of amenities” (85.7%), “inconvenience” (78%) and “safety issues” (59.4%) as relevant challenges towards the use of public buildings’ facilities.

Research limitations/implications

This research emphasises the urgent need to universally improve PWDs’ level of independence towards the use of public buildings’ facilities alongside eradicating anxiety and challenges experienced towards such use. Accessibility ought to be promoted among PWDs, with specific attention given to women and those affected in multiple body regions; as such populations are prone to experiencing substantial anxiety. This approach should entail the provision of barrier-free facilities as well as ensuring their safe and convenient use by PWDs.

Originality/value

This study sought and provided key feedback from PWDs on the current built environment, which ought to be considered by relevant stakeholders to improve accessibility, promote well-being and contribute towards meeting the global goals of reducing inequality and making cities/communities inclusive, safe, resilient and sustainable.
Parental financial support for housing: the importance of investment homes and family size
Authors: Wang Xueqi , Squires Graham , Dyason David
Published: January 2024

Purpose

Homeownership for younger generations is exacerbated by the deterioration in affordability worldwide. As a result, the role of parental support in facilitating homeownership requires attention. This study aims to assess the influence of parental wealth and housing tenure as support mechanisms to facilitate homeownership for their children.

Design/methodology/approach

This study uses data from a representative survey of the New Zealand population.

Findings

Parents who are homeowners tend to offer more financial support to their children than those who rent. Additionally, the financial support increases when parents have investment housing as well. The results further reveal differences in financial support when considering one-child and multi-child families. The intergenerational transmission of wealth inequality appears to be more noticeable in multi-child families, where parental housing tenure plays a dominant role in determining the level of financial support provided to offspring.

Originality/value

The insights gained serve as a basis for refining housing policies to better account for these family transfers and promote equitable access to homeownership.
Cardiovascular risk assessment of people living in prison in the Northern region of Ghana
Authors: Abukari Mohammed Hashim , Appiah Collins Afriyie , Kwarteng Alexander , Iddrisu Sherifa
Published: January 2024

Purpose

The health of people living in prisons (PLP) frequently remains marginalised in national development discourse, particularly in resource-constrained settings like Ghana. This study aims to determine the prevalence of cardiovascular disease (CVD) risk factors among PLP at a prison facility in the Northern Region of Ghana.

Design/methodology/approach

A cross-sectional study involving 134 male persons in prison, aged 18–79 years, was conducted to assess their dietary habits, tobacco use, alcohol consumption, sleep behaviour and physical activity practices. Serum lipid profile, fasting blood glucose (FBG), blood pressure (BP) and body mass indices of participants were also measured.

Findings

Almost half (48.1%) of the participants had abnormal lipid levels. Those with FBG in the diabetes range (= 7.0 mmol/l) constituted 3.9%, while 16.7% were in the impaired FBG range (6.1–6.9 mmol/l). Participants with BP within the pre-hypertension range were 54.5%. The majority of participants (92%) had a low daily intake of fruits and vegetables. Few participants were active smokers (5%) and alcohol users (2%). The average sleep duration at night among the participants was 5.54 ± 2.07 h. The majority (74%) of the participants were sedentary. About a quarter of the participants (24.6%) had overweight/obesity.

Originality/value

This study highlights the CVD risks among PLP. Findings suggest the need for targeted interventions, such as dietary and lifestyle modification strategies, regular physical activity and routine screening for diabetes, dyslipidaemia and hypertension. These interventions within the prison space could significantly improve the cardiovascular health of PLP in resource-limited settings.
What are the root causes of material delivery schedule inaccuracy in supply chains?
Authors: Jonsson Patrik , Öhlin Johan , Shurrab Hafez , Bystedt Johan , Sheikh Muhammad Azam , Verendel Vilhelm
Published: January 2024

Purpose

This study aims to explore and empirically test variables influencing material delivery schedule inaccuracies?

Design/methodology/approach

A mixed-method case approach is applied. Explanatory variables are identified from the literature and explored in a qualitative analysis at an automotive original equipment manufacturer. Using logistic regression and random forest classification models, quantitative data (historical schedule transactions and internal data) enables the testing of the predictive difference of variables under various planning horizons and inaccuracy levels.

Findings

The effects on delivery schedule inaccuracies are contingent on a decoupling point, and a variable may have a combined amplifying (complexity generating) and stabilizing (complexity absorbing) moderating effect. Product complexity variables are significant regardless of the time horizon, and the item’s order life cycle is a significant variable with predictive differences that vary. Decoupling management is identified as a mechanism for generating complexity absorption capabilities contributing to delivery schedule accuracy.

Practical implications

The findings provide guidelines for exploring and finding patterns in specific variables to improve material delivery schedule inaccuracies and input into predictive forecasting models.

Originality/value

The findings contribute to explaining material delivery schedule variations, identifying potential root causes and moderators, empirically testing and validating effects and conceptualizing features that cause and moderate inaccuracies in relation to decoupling management and complexity theory literature?
Environmental and sustainability education in teacher education research: an international scoping review of the literature
Authors: Blom Rob , Karrow Douglas D.
Published: January 2024

Purpose

Halfway into the United Nations (UN) sustainable development goals (SDGs) timeline, we deemed fruitful an injunction into current teacher education (TE) practices at higher educational institutes (HEIs). The scoping literature review used all known English nomenclature interrelating to environment, sustainability, development, and education as regards TE. We explicated and modelled the data through timelines favourable to UN initiatives within a spatiotemporal metric. Thematic research topics and research methodologies strictly pertaining to TE were rigorously researched and delineated. Our study aims to elucidate a grander picture of the trends-as-patterns of environmental and sustainability education in teacher education (ESE-TE) research in HEI and potential contributions to come.

Design/methodology/approach

The spatiotemporal study adopts a scoping review as an investigative tool to probe current research trends on ESE-TE in the academic literature with respect to thematic research topics and research methodologies midway through the SDGs.

Findings

A total of 2,142 research papers spanning five decades, 152 journals and 96 countries were screened equally by two researchers. Of the 788 papers deemed eligible (i.e. English-language, peer-reviewed, pre-service/in-service TE that explicitly mentioned ESE-TE research), data from 638 studies have been included in the authors’ study.

Originality/value

Comprehensive trends in the international literature of all known environmental and sustainable education nomenclature specific to international ESE-TE research throughout the time period (1974 – 2021) were identified. Value is accrued by illuminating international trends in research topics and methodologies, exposing gaps in the history of the subfield, and predicting future trends for Agenda 2030 (e.g. SDG 4 – education) to mature the field.
Digital transformation: strategy comes first to lay the groundwork
Authors: Kringelum Louise B. , Holm Casper Gamborg , Holmgren Jens , Friis Ole , Jensen Katrine Freja
Published: January 2024

Purpose

The purpose of this paper is to contribute to the successful implementation of digitalization by exploring what characterizes strategy work undertaken by companies that have achieved digital transformation. Based on empirical data, the authors delineate five essential strategic actions that are prerequisites for digital transformation: discuss and communicate the vision and strategy; align resources and activities with the strategy; ensure a continuous focus on operational improvements and efficiency; create an orientation toward customer or user needs and expectations; and develop the competencies of top managers, middle managers and employees.

Design/methodology/approach

Between January 2021 and February 2022, the authors conducted a survey on strategy work in Danish organizations with 2,251 respondents. The respondents encompass top managers, middle managers and employees representing 1,164 organizations.

Findings

The authors identify five strategic actions that positively influence whether organizations incorporate digitalization into their strategy work. These strategic actions can support organizations in their strategy work regarding digital transformation and offer valuable insights and inspiration for leaders currently undertaking the journey of digital transformation.

Research limitations/implications

Based on the empirical data, it is not possible to deem one action as more important than another in the context of digital transformation, as each action contributes significantly to facilitating the process. Given the nature of empirical data, the strategic actions reflect correlation rather than causation.

Originality/value

The empirical insights provide valuable practical guidance for leaders in managing digital transformation as a part of strategy work, which is typically discussed in a more conceptual manner. In addition, the authors identify new areas for further in-depth exploration in practice.
Evaluation of strategic orientation-led competitive advantage: the role of knowledge integration and service innovation
Authors: Sondhi Sundeep Singh , Salwan Prashant , Behl Abhishek , Niranjan Suman , Hawkins Tim
Published: January 2024

Purpose

This paper aims to derive a model that explores how the interplay between knowledge integration capability and innovation impacts strategic orientation, leading to the attainment of sustainable competitive advantage. The study considers the constituents of strategic orientation, namely, customer orientation, competitor orientation and technology orientation, as the basis for achieving sustainable competitive advantage. The study suggests that the firm’s capacity for integrating external and internal knowledge shapes how strategic orientation influences sustainable competitive advantage through service innovation.

Design/methodology/approach

This empirical research relies on qualitative and quantitative data gathered from telecom professionals to assess how knowledge integration and service innovation influence sustained competitive advantage. Structured equation modeling is used to examine the model and its interrelationships.

Findings

The research establishes significant relationships between strategic orientations, knowledge integration capability, service innovation and sustainable competitive advantage. Knowledge integration capability and service innovation are found to mediate the relationship between strategic orientations and the achievement of sustainable competitive advantage.

Practical implications

The study highlights the significant contribution of a firm’s knowledge integration capability in driving service innovation, especially in technology-intensive service industries facing hypercompetition. It also advocates prioritizing technology orientation and integrating knowledge from internal and external sources for competitive advantage.

Originality/value

To the best of the authors’ knowledge, this study is the first to model the effect of knowledge integration capability and service innovation on strategic orientation-led sustainable competitive advantage.
The impact of excessive dieting on eating disorders in adolescent women: a literature review
Authors: Son Eunhye , Kwon Ki Han
Published: January 2024

Purpose

This paper aims to in the modern world, possessing an attractive appearance is often considered a highly valued attribute. As such, the perceptions and satisfaction with one’s body are shaped by dominant cultural norms. Adolescents, women in particular, who are heavily influenced by media representations, may tend to have a distorted body image (BI), including adopting extreme dieting methods. This study reviews the adverse effects of excessive weight loss associated with this.

Design/methodology/approach

The authors searched journals and the internet for relevant literature using the keywords “eating disorders”, “body image” and “weight stigma”. In the case study field, they added papers that considered “nutrition” to identify the link between dieting behaviour and nutrition. From these reviews, the authors ultimately selected 190 articles that appeared to meet their research objectives. The papers cover a range of studies published between 1995 and 2023.

Findings

Among adolescent girls and young women in their early 20s, there is a social media-driven culture of being extremely thin and petite. Weight stigma puts more pressure on them and makes strange behaviours like pro-ana syndrome a part of the culture. The authors have seen that modern BI standards leave young women vulnerable to eating disorders caused by excessive dieting.

Originality/value

Adolescence is a time of continuous growth, so balanced nutrition is essential. However, biased societal standards of beauty can push adolescent girls who are sensitive to external gaze into excessive dieting and make eating disorders a culture. This review provides a perspective on the behaviours that should be pursued for a healthy BI.
Mechanical behavior investigation of fused deposition modeling joints by using different bonding geometry with variable adhesive thickness
Authors: Kemiklioğlu Uğur , Demir Sermet , Yüksel Caner
Published: January 2024

Purpose

Adhesively bonded joints are used in many fields, especially in the automotive, marine, aviation, defense and outdoor industries. Adhesive bonding offers advantages over traditional mechanical methods, including the ability to join diverse materials, even load distribution and efficient thermal-electrical insulation. This study aims to investigate the mechanical properties of adhesively bonded joints, focusing on adherends produced with auxetic and flat surfaces adhered with varying adhesive thicknesses.

Design/methodology/approach

The research uses three-dimensional (3D)-printed materials, polyethylene terephthalate glycol and polylactic acid, and two adhesive types with ductile and brittle properties for single lap joints, analyzing their mechanical performance through tensile testing. The adhesion region of one of these adherends was formed with a flat surface and the other with an auxetic surface. Adhesively bonded joints were produced with 0.2, 0.3 and 0.4 mm bonding thickness.

Findings

Results reveal that auxetic adherends exhibit higher strength compared to flat surfaces. Interestingly, the strength of ductile adhesives in auxetic bonded joints increases with adhesive thickness, while brittle adhesive strength decreases with thicker auxetic bonds. Moreover, the auxetic structure displays reduced elongation under comparable force.

Originality/value

The findings emphasize the intricate interplay between adhesive type, bonded surface configuration of adherend and bonding thickness, crucial for understanding the mechanical behavior of adhesively bonded joints in the context of 3D-printed materials.
The clip cage conundrum: Assessing the interplay of confinement method and aphid genotype in fitness studies
Authors: Martinez‐Chavez Laura Marcela , Roberts Joe M. , Karley Alison J. , Shaw Bethan , Pope Tom W.
Published: January 2024

Behavior and fitness are important ecological traits frequently measured in insect bioassays. A common method to measure them in soft‐bodied herbivorous insects involves confining individuals to plant leaves using clip cages. Although studies have previously highlighted the negative effects of clip cages on leaf physiology, little is known about the impact that using this confinement method has on insect fitness. The responses of different aphid genotypes/clones to different containment methods have not previously been investigated. Here we measured key fitness traits (intrinsic rate of natural increase, mean relative growth rate, time to reach reproductive adulthood and population doubling time) in the potato aphid, Macrosiphum euphorbiae Thomas (Hemiptera: Aphididae), when confined to plants using two methods: (1) clip cages to confine aphids to individual strawberry leaves and (2) a mesh bag to confine aphids to whole strawberry plants. Our study identified a strong negative impact on all the measured aphid fitness traits when using clip cages instead of mesh bags. We also identified genotype‐specific differences in response to confinement method, where clip cage confinement differentially affected the fitness of a given aphid genotype compared to the same genotype on whole plants. These results suggest that clip cage use should be carefully considered when experiments seek to quantify insect fitness and that whole plants should be used wherever possible. Given the prevalence of clip cage use in insect bioassays, our results highlight the need for caution when interpreting the existing literature as confinement method significantly impacts aphid fitness depending on their genotype.
Dealing with sampling bias and inferring absence data to improve distribution models of a widely distributed vulnerable marsupial
Authors: Brizuela‐Torres Diego , Elith Jane , Guillera‐Arroita Gurutzeta , Briscoe Natalie J.
Published: January 2024

Species distribution models are widely used to identify potential and high‐quality habitat of endangered species to inform conservation decisions. However, their usefulness is constrained by the amount and quality of biodiversity data and the approaches for dealing with data deficiencies. Presence‐only data, used in presence/background modelling methods, are widely available but are often affected by sampling bias. Presence/absence modelling methods are less affected by biases, but data are less common. We modelled the distribution of a widely distributed, endangered species from Australia – the greater glider – and tested how predictions were influenced by data treatment and modelling framework. We collated available species data and fitted generalized linear models and boosted regression trees using presence/absence data, as well as using an augmented dataset that included additional presences alongside absences inferred from survey data. We also fitted presence/background models, adopting three common strategies for bias correction. We compared model performance quantitatively through evaluation metrics calculated internally and on held out data, and qualitatively by identifying areas of agreement of spatial predictions. We found that presence/background models with bias correction performed better than not corrected, though evaluation metrics did not favour a single strategy. Presence/absence models outperformed presence/background models in comparable metrics and delivered different spatial predictions. Importantly, differences in spatial predictions between models had the potential to substantially alter decisions about where to protect high‐quality habitat. The approach to inferring absences proved useful, as models fitted with these outperformed all other models. Dealing with sampling bias requires additional time and data management strategies, but we found that the time invested allowed improvement of models and more reliable predictions. Our results suggest that ancillary occurrence data and careful data handling can improve both presence/background and presence/absence models.
Impact of sexual function domains on sexual satisfaction and quality of life: Importance across the age spectrum
Authors: Cabo Jackson J. , Kaufman Melissa R. , Johnsen Niels V.
Published: January 2024

Background

Sexual satisfaction is an important component of global quality life for many adult men. Substantial gaps exist in our appreciation of how age mediates sexual satisfaction in the context of functional sexual measures. We sought to evaluate modifiable factors associated with overall sexual satisfaction and health‐related quality of life (HRQoL) in a large, age‐stratified community‐based sample of adult men.

Methods

A sample of adult males registered with the online research service ResearchMatch completed a 75‐item online questionnaire in this cross‐sectional study. Queries included demographics, general health data, and validated sexual health measures including International Index of Erectile Function‐5 (IIEF‐5) and Premature Ejaculation Diagnostic Tool (PEDT). Multivariable regression was performed to assess associations with self‐reported sexual satisfaction (defined by “moderately satisfied” or “very satisfied” on the 5‐level Likert scale) and overall HRQoL (as measured by the EQ‐5D‐visual analog scale (VAS) stratified by age.

Results

One thousand thirty‐three men completed the survey and were stratified by age cohorts. IIEF‐5 and PEDT scores were higher in younger cohorts. On multivariable regression analysis, higher IIEF‐5, lower PEDT, better overall health‐related quality of life, and the presence of a sexual partner within the last month were associated with an increased likelihood of overall sexual satisfaction. When stratified by age cohort, higher IIEF‐5 scores were consistently positively associated with sexual satisfaction (Odds Ratio (OR) 1.18, 95% CI 1.15–1.22, P < 0.001), as well as independently associated with improved overall HRQoL by EQ‐5D‐VAS (β = 0.71, Standard Error (SE) = 0.08, P < 0.001).

Conclusions

The erectile function was independently associated with sexual satisfaction and quality of life across all age strata and predictive of both sexual satisfaction and global HRQoL. Low overall rates of sexual satisfaction across cohorts highlight the critical importance of evaluation and treatment of sexual health, regardless of age.
The development and evaluation of a homemade laparoscopic endotrainer using the IDEAL framework and MISTELS scoring system: a pilot study
Authors: Malik Muhammad Usman , Connelly Tara M. , Awan Naila Akhtar , Bhatti Fatima Rizwan , Hayat Rana Saddaqat , Awan Hafiz Riaz Hussain
Published: January 2024

Background

A prospective IDEAL stage 2a pilot study was carried out at a tertiary care center to evaluate the reliability of a homemade laparoscopic endotrainer, following the MISTEL and IDEAL framework guidelines.

Methods

The validated modified (MISTELS) score was used to test the reliability of a low‐cost laparoscopic trainer with commonly found components built by surgeons. Basic household materials including a cellular phone (camera source), wifi (linking source) and freely available webcam apps were used for construction. Five basic laparoscopic skills were performed by general surgery resident volunteers with minimal (1–6 months') laparoscopic surgery experience and tested and retested based on efficiency and precision. To determine interrater reliability, two trained observers scored all subjects. The Cronbach alpha test was used to test for internal consistency between tasks. The Interclass correlation coefficient is used for test and retest reliability.

Results

15 (80% male, mean age 28 ± 5 years) residents were included. The interrater and test–retest reliabilities for the total scores of the basic laparoscopic skills tests were 0.952 (95% CI, 0.895–0.981) and 0.64 (95% CI, 0.35–0.77), respectively. The Cronbach Alpha for the first assessment test and retest was 0.83. The MISTELS metrics had excellent reliability, exceeding the threshold level of 0.8.

Conclusion

It is possible to assemble a low‐cost, reliable trainer at home to enhance laparoscopic skills during residency.
Forest structure and heterogeneity increase diversity and alter composition of host–parasitoid networks
Authors: Rappa Nolan J. , Staab Michael , Ruppert Laura‐Sophia , Frey Julian , Mello Marco A. R. , Klein Alexandra‐Maria
Published: January 2024

Antagonistic host–parasitoid interactions can be quantified using bipartite and metanetworks, which have the potential to reveal how habitat structural elements relate to this important ecosystem function.

Here, we analysed the host–parasitoid interactions of cavity‐nesting bees and wasps, as well as their abundance, diversity and species richness with forest structural elements from 127 forest research plots in southwestern Germany.

We found that parasitoid abundance, diversity and species richness all increase with host abundance, a potential mediator between parasitoids and forest structure. Both parasitoid abundance and diversity increased with stand structural complexity, possibly mediated by the abundance of hosts. In addition, parasitoid abundance increased with increasing standing deadwood and herb cover.

The bipartite networks of host–parasitoid interactions showed higher connectance with increasing standing deadwood, herb cover and host abundance. Analyses of interactions within the host–parasitoid metanetwork revealed that increasing host abundance and decreasing canopy cover diversify the suites of interactions present at the plot level.

These results demonstrate that forest structural elements can improve the stability and resilience of host–parasitoid networks by promoting parasitoids and diversifying interactions in ecological networks.
Chestnut blight (Cryphonectria parasitica (Murr.) Barr) disease incidence and its effect on the morphological and anatomical features of Castanea sativa trees
Authors: Keleş Seray Özden , Ünal Sabri , Akan Sefer , Karadeniz Mertcan
Published: January 2024

Sweet chestnut (Castanea sativa) is an ecologically and economically valuable tree species worldwide. Various pathogens, both endemic or introduced, cause severe damage or death to chestnut trees. Chestnut blight, caused by the fungus Cryphonectria parasitica, is one of the most devastating plant diseases known which influences chestnut trees in all major cultivation regions. The work presented here aimed to investigate how the incidence of chestnut blight varied between trees growing at two altitudes (200–400 m vs. 400–600 m) and to determine the impact of chestnut blight on tree‐ring width, morphology and anatomy of C. sativa trees. The incidence of C. parasitica infections was greater at 200–400 m than at 400–600 m. Greater stem diameters were found at 200–400 m than at 400–600 m. There were no differences in stem diameters and heights, however, between healthy and C. parasitica infected chestnut trees. The anatomical characteristics of wood were also compared between healthy and C. parasitica‐infected chestnut trees. Fibre cell traits (length/width, lumen width, lumen area) were higher in healthy trees than in C. parasitica‐diseased trees. Vessel diameters were greater in infected compared with healthy trees. Tree ring widths and wood anatomical characteristics therefore were significantly influenced by C. parasitica infections.
Financial debt contracting and managerial agency problems
Authors: Imbierowicz Björn , Streitz Daniel
Published: January 2024

This paper analyzes if lenders resolve managerial agency problems in loan contracts using sweep covenants. Sweeps require a (partial) prepayment when triggered and are included in many contracts. Exploiting exogenous reductions in analyst coverage due to brokerage house mergers and closures, we find that increased borrower opacity significantly increases sweep use. The effect is strongest for borrowers with higher levels of managerial entrenchment and if lenders hold both debt and equity in the firm. Overall, our results suggest that lenders implement sweep covenants to mitigate managerial agency problems by limiting contingencies of wealth expropriation.
Opportunities and challenges with transitioning to non‐lethal sampling of wild fish for microbiome research
Authors: Kelly Lisa A. , Yost Christopher K. , Cooke Steven J.
Published: January 2024

The microbial communities of fish are considered an integral part of maintaining the overall health and fitness of their host. Research has shown that resident microbes reside on various mucosal surfaces, such as the gills, skin, and gastrointestinal tract, and play a key role in various host functions, including digestion, immunity, and disease resistance. A second, more transient group of microbes reside in the digesta, or feces, and are primarily influenced by environmental factors such as the host diet. The vast majority of fish microbiome research currently uses lethal sampling to analyse any one of these mucosal and/or digesta microbial communities. The present paper discusses the various opportunities that non‐lethal microbiome sampling offers, as well as some inherent challenges, with the ultimate goal of creating a sound argument for future researchers to transition to non‐lethal sampling of wild fish in microbiome research. Doing so will reduce animal welfare and population impacts on fish while creating novel opportunities to link host microbial communities to an individual's behavior and survival across space and time (e.g., life‐stages, seasons). Current lethal sampling efforts constrain our ability to understand the mechanistic ecological consequences of variation in microbiome communities in the wild. Transitioning to non‐lethal sampling will open new frontiers in ecological and microbial research.
MRI‐defined T3, clear mesorectal fascia mid–low rectal cancer: is neoadjuvant treatment necessary?
Authors: Zeng Ziwei , Li Ze , Luo Shuangling , Huang Liang , Liang Zhenxing , Zheng Xiaobin , Li Wenxin , Xiong Li , Liu Huashan , Kang Liang
Published: January 2024

Aim

Neoadjuvant treatments (nCRT) are becoming the standard treatment for patients with stage II or III mid‐low rectal cancer. Recently, some studies have shown that surgery alone may be sufficient for patients with T3 rectal cancer. This raises the question of whether nCRT is necessary for all patients with T3 rectal cancer. Therefore, this study compared the clinical outcomes of patients with MRI‐defined T3, clear MRF mid–low rectal cancer treated with surgery alone (TME group) or nCRT followed by surgery (nCRT + TME group).

Methods

A total of 1509 patients were enrolled in this study. After a 1:1 propensity score matching analysis, 480 patients were included in each group. The primary endpoint was 3‐year disease‐free survival (DFS). The secondary endpoints included the perioperative outcomes, histopathologic outcomes, and other follow‐up outcomes.

Results

nCRT had advantages in rates of sphincter‐preserving surgery and tumor downstaging, but it was accompanied by a higher rate of enterostomies. At 3 years after surgery, local recurrence occurred in 3.3% of patients in the TME group and in 3.5% of patients in the nCRT + TME group (P = 0.914), the DFS rates were 78.3% in the TME group and 75.3% in the nCRT + TME group (P = 0.188), and the overall survival rates were 90.3% in the TME group and 89.9% in the nCRT + TME group (P = 0.776).

Conclusions

Surgery alone versus nCRT followed by surgery may provide similar long‐term oncological outcomes for patients with MRI‐defined T3, clear MRF, and mid–low rectal cancer. nCRT may cause overtreatment in some patients.
Two‐stage deep‐learning‐based colonoscopy polyp detection incorporating fisheye and reflection correction
Authors: Hsu Chen‐Ming , Chen Tsung‐Hsing , Hsu Chien‐Chang , Wu Che‐Hao , Lin Chun‐Jung , Le Puo‐Hsien , Lin Cheng‐Yu , Kuo Tony
Published: January 2024

Background and Aim

Colonoscopy is a useful method for the diagnosis and management of colorectal diseases. Many computer‐aided systems have been developed to assist clinicians in detecting colorectal lesions by analyzing colonoscopy images. However, fisheye‐lens distortion and light reflection in colonoscopy images can substantially affect the clarity of these images and their utility in detecting polyps. This study proposed a two‐stage deep‐learning model to correct distortion and reflections in colonoscopy images and thus facilitate polyp detection.

Methods

Images were collected from the PolypSet dataset, the Kvasir‐SEG dataset, and one medical center's patient archiving and communication system. The training, validation, and testing datasets comprised 808, 202, and 1100 images, respectively. The first stage involved the correction of fisheye‐related distortion in colonoscopy images and polyp detection, which was performed using a convolutional neural network. The second stage involved the use of generative and adversarial networks for correcting reflective colonoscopy images before the convolutional neural network was used for polyp detection.

Results

The model had higher accuracy when it was validated using corrected images than when it was validated using uncorrected images (96.8%vs90.8%,P < 0.001). The model's accuracy in detecting polyps in the Kvasir‐SEG dataset reached 96%, and the area under the receiver operating characteristic curve was 0.94.

Conclusion

The proposed model can facilitate the clinical diagnosis of colorectal polyps and improve the quality of colonoscopy.
Escherichia coli NF73‐1 disrupts the gut–vascular barrier and aggravates high‐fat diet‐induced fatty liver disease via inhibiting Wnt/β‐catenin signalling pathway
Authors: Ke Ziliang , Huang Yibo , Xu Jun , Liu Yun , Zhang Yu , Wang Yang , Zhang Yifan , Liu Yulan
Published: January 2024

Background & Aims

Gut–vascular barrier (GVB) dysfunction has been shown to be a prerequisite for nonalcoholic fatty liver disease (NAFLD) development. However, the causes of GVB disruption and the underlying mechanisms are still elusive. Here, we explored whether and how Escherichia coli (E. coli) NF73‐1, a pathogenic E. coli strain isolated from nonalcoholic steatohepatitis patients, contributes to NAFLD by modulating the GVB.

Methods

C57BL/6J mice were fed with high‐fat diet (HFD) or normal diet in the presence or absence of E. coli NF73‐1 for the indicated time periods. Intestinal barrier function and infiltration of immune cells were evaluated in these mice. Endothelial cells were exposed to E. coli NF73‐1 for barrier integrity analysis.

Results

HFD‐induced GVB disruption preceded the damage of intestinal epithelial barrier (IEB) as well as intestinal and hepatic inflammatory changes and can be reversed by vascular endothelial growth factor A blockade. Antibiotic treatment prevented mice from HFD‐induced liver steatosis by restoration of the GVB. Notably, E. coli NF73‐1 caused a more conspicuous damage of GVB than that of the IEB and contributed to NAFLD development. Mechanistically, E. coli NF73‐1 dismantled the GVB by inhibiting the Wnt/β‐catenin signalling pathway. Activation of Wnt/β‐catenin improved the GVB and impeded the translocation of E. coli NF73‐1 into the liver in vitro and in vivo.

Conclusions

E. coli NF73‐1 disrupts GVB and aggravates NAFLD via inhibiting the Wnt/β‐catenin signalling pathway. Targeting E. coli NF73‐1 or selectively enhancing the GVB may act as potential avenues for the prevention and treatment of NAFLD.