bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving the suppressive power of homing gene drive by co-targeting a distant-site female fertility gene
Authors: Faber Nicky R. , Xu Xuejiao , Chen Jingheng , Hou Shibo , Du Jie , Pannebakker Bart A. , Zwaan Bas J. , van den Heuvel Joost , Champer Jackson
Published: December 2023

Gene drive technology has the potential to address major biological challenges, including the management of disease vectors, invasive species, and agricultural pests. After releasing individuals carrying the gene drive in the target population, suppression gene drives are designed to spread at a rapid rate and carry a recessive fitness cost, thus bringing about a decline in population size or even complete suppression. Well-studied homing suppression drives have been shown to be highly efficient inAnophelesmosquitoes and were successful in eliminating large cage populations. However, for other organisms, includingAedesmosquitoes, homing gene drives are so far too inefficient to achieve complete population suppression, mainly due to lower rates of drive conversion, which is the rate at which wild type alleles are converted into drive alleles. Low drive conversion is also a major issue in vertebrates, as indicated by experiments in mice. To tackle this issue, we propose a novel gene drive design that has two targets: a homing site where the drive is located and drive conversion takes place (with rescue for an essential gene), and a distant site for providing the fitness cost for population suppression (preferably a female fertility gene, for which no rescue is provided). We modeled this design and found that the two-target system allows suppression to occur over a much wider range of drive conversion efficiency. Specifically, in the new design, the suppressive power depends mostly on total gRNA cutting efficiency instead of just drive conversion efficiency, which is advantageous because cut rates are often substantially higher than drive conversion rates. We constructed a proof of concept inDrosophila melanogasterand show that both components of the gene drive function successfully. However, embryo drive activity from maternally deposited Cas9 as well as fitness costs for female drive heterozygotes both remain significant challenges for two-target and standard suppression drives. Overall, our improved gene drive design eases the development of strong homing suppression gene drives for many species where drive conversion is less efficient.
Unified Multi-caller Ensemble (UME) generates an unbiased maize haplotype map for variable coverage whole genome data
Authors: Vallebueno-Estrada Miguel , Swarts Kelly
Published: December 2023

We present a novel diversity-focused haplotype map (HapMap) that characterizes over 64.5 million maize (Zea maysssp. mays) single nucleotide polymorphisms (SNPs) genotyped across 818 individuals from diverse backgrounds. This HapMap aims to balance the variation obtained from domesticated landraces and inbred lines, outgroupZea spp.and more distantTripsacum spp.in order to minimize ascertainment bias for diversity studies. Included individuals derive from public data from various experimental setups and coverages, which is challenging for standard SNP callers to accommodate. We provide evidence of coverage biases associated with standard callers that influence resulting variation and introduce a novel approach called Unified Multi-Caller Ensemble (UME), which enhances variant calling accuracy in low-coverage and mixed-coverage genomic datasets. UME corrects for coverage bias resulting from inter-sample coverage heterogeneity by leveraging evidence from variant callers with orthogonal strategies, re-calibrating the error probabilities across callers to minimize the impact of error biases inherent to a given caller. It outperforms individual strategies and excels inde novovariant calling, taking advantage of instances of higher depth reads, even in low coverage individuals, while preserving biologically informative variant relationships across coverage levels. An important feature of UME is the independence from population allele frequencies in the discovery panel, thus avoiding ascertainment bias resulting from unbalanced input genetic diversity. Discovered variants are unbiased because no population filtering is used, and the full diversity of SNPs is retained in the final variant call set to maximize the utility of the dataset for production calling newly sequenced samples. We present a strategy for filtering the recalibrated error profiles that relies on maximizing demographic signals to retain genetic relationships within the population while reducing sequencing error. After the variant discovery phase, we employ the UME production stage, which enriches genotype calling across all coverage levels, benefiting low-coverage samples. Error introduced in this process is removed through subsequent filtering. Using this approach, we generated a coverage bias-controlled maize HapMap database, providing a comprehensive representation of maize accessions and emphasizing landrace diversity. This diverse panel of domesticated maize and outgroups from across the Americas enables accurate genotyping in low-coverage samples while offering crucial context for interpreting diversity, particularly for natural diversity and paleogenomic analyses.
Two distinct ferredoxins are essential for nitrogen fixation by the iron nitrogenase inRhodobacter capsulatus
Authors: Addison Holly , Glatter Timo , Hochberg Georg K. A. , Rebelein Johannes G.
Published: December 2023

Nitrogenases are the only enzymes able to fix gaseous nitrogen into bioavailable ammonia and, hence, are essential for sustaining life. Catalysis by nitrogenases requires both a large amount of ATP and electrons donated by strongly reducing ferredoxins or flavodoxins. Our knowledge about the mechanisms of electron transfer to nitrogenase enzymes is limited: The electron transport to the iron (Fe)-nitrogenase has hardly been investigated. Here, we characterised the electron transfer pathway to the Fe-nitrogenase inRhodobacter capsulatusvia proteome analyses, genetic deletions, complementation studies and phylogenetics. Proteome analyses revealed an upregulation of four ferredoxins under nitrogen-fixing conditions reliant on the Fe-nitrogenase in a molybdenum nitrogenase knockout strain, compared to non-nitrogen-fixing conditions. Based on these findings,R. capsulatusstrains with deletions of ferredoxin (fdx) and flavodoxin (fld, nifF) genes were constructed to investigate their roles in nitrogen fixation by the Fe-nitrogenase.R. capsulatusdeletion strains were characterised by monitoring diazotrophic growth and Fe-nitrogenase activityin vivo. Only deletions offdxCorfdxNresulted in slower growth and reduced Fe-nitrogenase activity, whereas the double-deletion of bothfdxCandfdxNabolished diazotrophic growth. Differences in the proteomes of ΔfdxCand ΔfdxNstrains, in conjunction with differing plasmid complementation behaviours offdxCandfdxN, indicate that the two Fds likely possess different roles and functions. These findings will guide future engineering of the electron transport systems to nitrogenase enzymes, with the aim of increased electron flux and product formation.

Importance

Nitrogenases are essential for biological nitrogen fixation, converting atmospheric nitrogen gas to bioavailable ammonia. Production of ammonia by diazotrophic organisms, harbouring nitrogenases, is essential for sustaining plant growth. Hence, there is a large scientific interest in understanding the cellular mechanisms for nitrogen fixation via nitrogenases. Nitrogenases rely on highly reduced electrons to power catalysis, though we lack knowledge as to which proteins shuttle the electrons to nitrogenases within cells. Here, we characterised the electron transport to the iron (Fe)-nitrogenase in the model diazotrophRhodobacter capsulatus, showing that two distinct ferredoxins are very important for nitrogen fixation despite having different redox centres. Additionally, our research expands upon the debate on whether ferredoxins have functional redundancy or perform distinct roles within cells. Here, we observe that both essential ferredoxins likely have distinct roles based on differential proteome shifts of deletion strains and different complementation behaviours.
Adhesome Receptor Clustering is Accompanied by the Co- localization of the Associated Genes in the Cell Nucleus
Authors: Cammarata Louis V. , Uhler Caroline , Shivashankar G. V.
Published: December 2023

Proteins on the cell membrane cluster to respond to extracellular signals; for example, adhesion proteins cluster to enhance extracellular matrix sensing; or T-cell receptors cluster to enhance antigen sensing. Importantly, the maturation of such receptor clusters requires transcriptional control to adapt and reinforce the extracellular signal sensing. However, it has been unclear how such efficient clustering mechanisms are encoded at the level of the genes that code for these receptor proteins. Using the adhesome as an example, we show that genes that code for adhesome receptor proteins are spatially co-localized and co-regulated within the cell nucleus. Towards this, we use Hi-C maps combined with RNA-seq data of adherent cells to map the correspondence between adhesome receptor proteins and their associated genes. Interestingly, we find that the transcription factors that regulate these genes are also co-localized with the adhesome gene loci, thereby potentially facilitating a transcriptional reinforcement of the extracellular matrix sensing machinery. Collectively, our results highlight an important layer of transcriptional control of cellular signal sensing.
Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
Authors: Maeng Ju Heon , Jang H. Josh , Du Alan Y. , Tzeng Shin-Cheng , Wang Ting
Published: December 2023

Recent studies have shown that the noncoding genome can produce unannotated proteins as antigens that induce immune response. One major source of this activity is the aberrant epigenetic reactivation of transposable elements (TEs). In tumors, TEs often provide cryptic or alternate promoters, which can generate transcripts that encode tumor-specific unannotated proteins. Thus, TE-derived transcripts (TE transcripts) have the potential to produce tumor-specific, but recurrent, antigens shared among many tumors. Identification of TE-derived tumor antigens holds the promise to improve cancer immunotherapy approaches; however, current genomics and computational tools are not optimized for their detection. Here we combined CAGE technology with full-length long-read transcriptome sequencing (long-read CAGE, or LRCAGE) and developed a suite of computational tools to significantly improve immunopeptidome detection by incorporating TE and other tumor transcripts into the proteome database. By applying our methods to human lung cancer cell line H1299 data, we show that long-read technology significantly improves mapping of promoters with low mappability scores and that LRCAGE guarantees accurate construction of uncharacterized 5′ transcript structure. Augmenting a reference proteome database with newly characterized transcripts enabled us to detect noncanonical antigens from HLA-pulldown LC-MS/MS data. Lastly, we show that epigenetic treatment increased the number of noncanonical antigens, particularly those encoded by TE transcripts, which might expand the pool of targetable antigens for cancers with low mutational burden.
BlackRock, Inc. (USA): An environmentally sustainable asset investor as it claims to be?
Authors: Glowik Mario , Bhatti Waheed Akbar , Chwialkowska Agnieszka
Published: December 2023

Purpose

Against the background of sustainable finance, this study aims to address whether global asset management firms started transforming toward more environmentally friendly investment policies according to the Agenda for Sustainable Development launched by the United Nations General Assembly in 2015.

Design/methodology/approach

The authors apply qualitative, explorative research methods through the development of the case study of BlackRock, Inc. (USA). Addressing sustainable finance, the authors compare the opposite to the editorial page (op-eds) communication strategy of BlackRock against real life for the period from 2015 until today.

Findings

The op-eds communication strategy by BlackRock is multi-faceted targeting to develop a leading sustainable reputation supported by fine-grained relationships to business and policy makers. This study empirically proves that there is a discrepancy between BlackRock’s op-eds communication contends concerning sustainable finance and the reality. Among others this study found that BlackRock still invests in fossils and increasingly launches passively managed funds with limited transparency standards in terms of sustainable finance.

Research limitations/implications

This study contributes to the corporate social responsibility literature focusing on fossil energy and sustainable finance. As BlackRock did not reply to the authors’ requests for conducting interviews, the authors rely on a broad range of secondary sources including material provided by non-governmental organizations. This study proposes that research should be amplified by further empirical studies among various sustainable finance stakeholders based on the research propositions the authors have developed as a result of this study.

Practical implications

This research provides empirical evidence for business executives and policy decision-makers involved in the energy industry, corporate ethics and global financial asset management.

Social implications

This study provides insights toward sustainable finance policies of BlackRock with corresponding outcomes related to global climate change and its impact on societies.

Originality/value

This study delivers empirical evidence on the energy transformation from fossils toward renewables against the background of sustainable finance strategies of large asset management enterprises such as BlackRock which is rare to find in the literature.
Ramping up the food park business: a case study of Urban Chowk
Authors: Shah Priyanka , Gupta Anu , Mitra Subhasish
Published: December 2023

Learning outcomes

After completion of the case study, students will be able to critically appraise the strategic growth opportunities of an “eating out” industry brand; evaluate the role of customer relationship and retention management in sustaining a brand; and analyse the importance of developing core competencies for long-term business viability.

Case overview/synopsis

Since its inception in 2017, Urban Chowk was one of the pioneer places that successfully managed to create a hospitality format called “food and lifestyle park” which combined multiple food brands with good ambience and entertainment, all under the same roof. Although Urban Chowk was one of the popular brands in the given format, its USP was not difficult to challenge or copy. The owner, Mr Kartikey Rajput, anticipated a deluge of similar establishments in the near future. Urban Chowk led the pack in terms of footfalls compared to similar establishments, with Rajput looking to expand his brand beyond Ahmedabad. The case took 2022 as the timeline and brought forth the challenge that Urban Chowk faced. The primary challenge was retaining the existing customer base along with adding newer ones. Second, with the industry being extremely dynamic, it was important to determine how marketing analytics could be used to collect customer data and convert them into repeat customers, thus building a loyal customer base.

Complexity academic level

This case is applicable for teaching at undergraduate and graduate levels for understanding the concepts of brand development and strategic growth as well as creating and maintaining customer relationships, also helping the students in assimilating these concepts as a part of brand building.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 11: Strategy.
Perfectly imperfect and muddling through for sustainable futures
Authors: Domegan Christine T. , Flaherty Tina , McNamara John , Murphy David , Derham Jonathan , McCorry Mark , Nally Suzanne , Eakin Maurice , Brychkov Dmitry , Doyle Rebecca , Devine Arthur , Greene Eva , McKenna Joseph , OMahony Finola , O'Mahony Tadgh
Published: December 2023

Purpose

To combat climate change, protect biodiversity, maintain water quality, facilitate a just transition for workers and engage citizens and communities, a diversity of stakeholders across multiple levels work together and collaborate to co-create mutually beneficial solutions. This paper aims to illustrate how a 7.5-year collaboration between local communities, researchers, academics, companies, state agencies and policymakers is contributing to the reframing of industrial harvested peatlands to regenerative ecosystems and carbon sinks with impacts on ecological, economic, social and cultural systems.

Design/methodology/approach

The European Union LIFE Integrated Project, Peatlands and People, responding to Ireland’s Climate Action Plan, represents Europe’s largest rehabilitation of industrially harvested peatlands. It makes extensive use of marketing research for reframing strategies and actions by partners, collaborators and communities in the evolving context of a just transition to a carbon-neutral future.

Findings

The results highlight the ecological, economic, social and cultural reframing of peatlands from fossil fuel and waste lands to regenerative ecosystems bursting with biodiversity and climate solution opportunities. Reframing impacts requires muddling through the ebbs and flows of planned, possible and unanticipated change that can deliver benefits for peatlands and people over time.

Research limitations/implications

At 3 of 7.5 years into a project, the authors are muddling through how ecological reframing impacts economic and social/cultural reframing. Further impacts, planned and unplanned, can be expected.

Practical implications

This paper shows how an impact planning canvas tool and impact taxonomy can be applied for social and systems change. The tools can be used throughout a project to understand, respond to and manage for unplanned events. There is constant learning, constantly going back to the impact planning canvas and checking where we are, what is needed. There is action and reaction to each other and to the diversity of stakeholders affected and being affected by the reframing work.

Originality/value

This paper considers how systemic change through ecological, economic, social and cultural reframing is a perfectly imperfect process of muddling through which holds the promise of environmental, economic, technological, political, social and educational impacts to benefit nature, individuals, communities, organisations and society.
Evaluation of UN SDG-related formal learning activities in a university common core curriculum
Authors: Lei Chi-Un , Chan Wincy , Wang Yuyue
Published: December 2023

Purpose

Higher education plays an essential role in achieving the United Nations sustainable development goals (SDGs). However, there are only scattered studies on monitoring how universities promote SDGs through their curriculum. The purpose of this study is to investigate the connection of existing common core courses in a university to SDG education. In particular, this study wanted to know how common core courses can be classified by machine-learning approach according to SDGs.

Design/methodology/approach

In this report, the authors used machine learning techniques to tag the 166 common core courses in a university with SDGs and then analyzed the results based on visualizations. The training data set comes from the OSDG public community data set which the community had verified. Meanwhile, key descriptions of common core courses had been used for the classification. The study used the multinomial logistic regression algorithm for the classification. Descriptive analysis at course-level, theme-level and curriculum-level had been included to illustrate the proposed approach’s functions.

Findings

The results indicate that the machine-learning classification approach can significantly accelerate the SDG classification of courses. However, currently, it cannot replace human classification due to the complexity of the problem and the lack of relevant training data.

Research limitations/implications

The study can achieve a more accurate model training through adopting advanced machine learning algorithms (e.g. deep learning, multioutput multiclass machine learning algorithms); developing a more effective test data set by extracting more relevant information from syllabus and learning materials; expanding the training data set of SDGs that currently have insufficient records (e.g. SDG 12); and replacing the existing training data set from OSDG by authentic education-related documents (such as course syllabus) with SDG classifications. The performance of the algorithm should also be compared to other computer-based and human-based SDG classification approaches for cross-checking the results, with a systematic evaluation framework. Furthermore, the study can be analyzed by circulating results to students and understanding how they would interpret and use the results for choosing courses for studying. Furthermore, the study mainly focused on the classification of topics that are taught in courses but cannot measure the effectiveness of adopted pedagogies, assessment strategies and competency development strategies in courses. The study can also conduct analysis based on assessment tasks and rubrics of courses to see whether the assessment tasks can help students understand and take action on SDGs.

Originality/value

The proposed approach explores the possibility of using machine learning for SDG classifications in scale.
Information needs and information-seeking behavior of visual artists: a systematic review of the literature
Authors: Kolyvas Spyros , Kostagiolas Petros
Published: December 2023

Purpose

Information makes an important contribution to the promotion of the creativity of visual artists. This work aims to explore relevant research through a systematic review of the literature and discuss the impact of information on visual artists' creativity.

Design/methodology/approach

A systematic literature review was conducted through Preferred Reporting Items for Systematic reviews and Meta-Analyses method. The authors searched and retrieved 1,320 papers from which, after evaluation, 41 papers have been analyzed.

Findings

Two thematic categories were identified for visual artists' information needs: (1) the need for professional development and (2) the need for creative techniques and materials. In terms of information sources visual artists employ, the authors have also identified seven broad categories: (1) conventional resources (galleries, museums, etc.), (2) professional scholar sources, (3) digital art websites, (4) informal information online and colleagues, (5) libraries, (6) personal collections and (7) professional scholar social networks. In addition, the study proceeded to classify the obstacles faced by visual artists in their search for visual information into two general categories: (1) environmental barriers and (2) digital literacy barriers.

Originality/value

Although the investigation of the information needs satisfaction of visual artists as well as the evaluation of their information behavior patterns and information literacy competences is essential, it is understudied. This paper summarizes the relevant literature in a concrete and systematic way providing evidences to be considered in a variety of situations, i.e. developing lifelong learning programs, managing visual art library collections, library services development for artists, etc.
Joint effects of resource supply and resource types on properties of population dynamic models
Authors: Xiao Junli , Li Yuanzhi , Meiners Scott J. , Chu Chengjin
Published: December 2023

The Lotka–Volterra competition model is the foundation of many ecological theories including competitive exclusion principle, limiting similarity and modern coexistence theory. However, competition between species is often modelled phenomenologically without explicitly considering the underlying mechanisms (e.g. resource competition with various resource supply forms and resource types). Deriving phenomenological models from the first principles and linking parameters in phenomenological models to the mechanisms of competition are critical to advance our understanding of population dynamics and community assembly.

Here, we used time‐scale separation to theoretically derive phenomenological competition models from mechanistic consumer‐resource models with different resource supply forms (logistic and chemostatic) and resource types (substitutable and essential). We then compared the performance of the resulting phenomenological models with simulation experiments and observational plant dynamic data during 50 years of succession. We further explored how the resource supply ratio such as nutrient imbalance induced by human activities affected the critical parameters, including species' intrinsic growth rate and interaction strength in phenomenological models and consequently the population dynamics.

We found that consumer population dynamics can be described by the Lotka–Volterra competition model when consumers are competing for substitutable or essential resources under logistic supply. In contrast, a novel reciprocal model was derived when consumers are competing for essential resources under chemostatic supply. Results from simulation experiments supported the model derivations. We also found that the reciprocal model outperformed the Lotka–Volterra model in explaining and predicting the population growth of 90 herbaceous plants during 50 years of succession. Moreover, the resource supply ratio affected species' intrinsic growth rates and competitive strengths differently under various resource supply forms and resource types and thus determined competitive outcomes.

Synthesis. Our study provides an alternative model (reciprocal model) when organisms compete for essential resources under chemostatic supply and sets up a basis for the selection of phenomenological competition models through the lens of ecological processes and contributes to a more accurate prediction of population dynamics, especially those driven by human‐induced nutrient imbalance.
The economic impacts of a hypothetical foot and mouth disease outbreak in Australia
Authors: Wittwer Glyn
Published: December 2023

This study uses a multicountry, dynamic, quarterly CGE model, GlobeTERM, to estimate the economic impacts of a hypothetical foot and mouth disease outbreak in Australia. The national welfare losses arising from the outbreak depend mostly on the duration of trade sanctions by importers of Australian animal products. If an outbreak is contained within several months, and trade sanctions are dropped within a year of the outbreak, the net present value of Australia's welfare losses may be around AUS$10 billion. If all importers restore Australian access within a year, other than China–Hong Kong, which delays by 5 years, welfare losses are around AUS$21 billion. In a less likely scenario, in which trade sanctions persist in all trading partners for 5 years after the disease has been eradicated, contrary to international guidelines, welfare losses may exceed AUS$85 billion. Trading partners also suffer welfare losses due to trade sanctions. These losses are large enough to imply, from a global perspective, that a shift towards vaccinate‐to‐live policies combined with global efforts to eradicate the disease may be cost‐effective.
Bayesian hybrid index and genomic cline estimation with the R package gghybrid
Authors: Bailey Richard Ian
Published: December 2023

Admixture, the interbreeding of individuals from differentiated source populations, is now known to be a widespread phenomenon. Genomic studies of natural hybridisation can help to answer many questions on the impacts of admixture on adaptive evolution, reproductive isolation, and speciation. When a large variety of admixture proportions between two source populations exist, both geographic and genomic cline analysis are suitable methods for inferring biased, restricted or excessive gene flow at individual loci into the foreign genomic background, providing evidence for reproductive isolation, selection across an environmental transition, balancing selection, and adaptive introgression. Genomic cline analysis replaces geographic location with genome‐wide hybrid index and is therefore useable in circumstances that violate geographic cline assumptions. Here, I introduce gghybrid, an R package for simple and flexible Bayesian estimation of Buerkle's hybrid index and Fitzpatrick's logit‐logistic genomic clines using bi‐allelic data, suitable for both small and large datasets. gghybrid allows any ploidy and uses Structure input file format. It has separate functions for hybrid index and cline estimation, treating each individual and locus respectively as an independent analysis, making it highly parallelisable. Admixture proportions from other software can alternatively be used in cline analysis, alongside parental allele frequencies. Parameters can be fixed and samples pooled for statistical model comparison with AIC or waic. Here, I describe the functions, pipeline, and statistical properties of gghybrid. Simulations reveal that model comparison with waic is preferred, and use of Bayesian posterior distributions and p values to select candidate non‐null loci is problematic and should be avoided.
Aggressive multi‐combination therapy for anti‐MDA5 antibody‐positive dermatomyositis‐rapidly progressive interstitial lung disease
Authors: Hata Kenichiro , Kotani Takuya , Matsuda Shogo , Fujiki Youhei , Suzuka Takayasu , Kiboshi Takao , Wada Yumiko , Shiba Hideyuki , Shoda Takeshi , Kagitani Maki , Takeuchi Tohru
Published: December 2023

Objectives

To elucidate the efficacy and safety of aggressive multi‐combination therapy with mycophenolate mofetil, rituximab, and plasma exchange or polymyxin B immobilized fiber column direct hemoperfusion followed by conventional therapy with corticosteroids, calcineurin inhibitors, and intravenous pulse cyclophosphamide in patients with rapidly progressive interstitial lung disease (RPILD) with anti‐melanoma differentiation‐associated gene 5 (MDA5)‐antibody‐positive dermatomyositis (DM).

Methods

A total of 23 patients with anti‐MDA5 antibody‐positive DM‐RPILD were enrolled, with nine patients in Group A (treated conventionally before March 2015) and 14 patients in Group B (received aggressive treatment after April 2015).

Results

Pretreatment severity of interstitial lung disease (ILD) did not differ between the two groups. However, Group B exhibited a higher cumulative survival rate at 48 weeks than Group A (64.3% vs. 33.3%). The corticosteroid dose, divided by the initial dose at 3 months and 12 months, was significantly lower in Group B than in Group A (p = .046 and .026, respectively). Among the ILD‐related deaths in Group B, there was a tendency toward a higher proportion of males and more severe ILD. The incidence of infection did not differ between the groups, but leukopenia was more common in Group B.

Conclusion

This aggressive multi‐combination therapy may improve the survival outcome of patients with anti‐MDA5 antibody‐positive DM‐RPILD. However, careful management of complications, such as opportunistic infections and leukopenia, is essential. Future refinement through longitudinal investigations tracking the long‐term efficacy, safety, and cost‐effectiveness of this treatment strategy is needed.
Microbial perspective of inhibited carbon turnover in Tangel humus of the Northern Limestone Alps
Authors: Rzehak Theresa , Praeg Nadine , Zink Harald , Simon Alois , Geitner Clemens , Illmer Paul
Published: December 2023

Tangel humus primarily occurs in montane and subalpine zones of the calcareous Alps that exhibit low temperatures and high precipitation sums. This humus form is characterized by inhibited carbon turnover and accumulated organic matter, leading to the typical thick organic layers. However, the reason for this accumulation of organic matter is still unclear, and knowledge about the microbial community within Tangel humus is lacking. Therefore, we investigated the prokaryotic and fungal communities along with the physical and chemical properties within a depth gradient (0–10, 10–20, 20–30, 30–40, 40–50 cm) of a Tangel humus located in the Northern Limestone Alps. We hypothesized that humus properties and microbial activity, biomass, and diversity differ along the depth gradient and that microbial key players refer to certain humus depths. Our results give the first comprehensive information about microbiota within the Tangel humus and establish a microbial zonation of the humus. Microbial activity, biomass, as well as microbial alpha diversity significantly decreased with increasing depths. We identified microbial biomarkers for both, the top and the deepest depth, indicating different, microbial habitats. The microbial characterization together with the established nutrient deficiencies in the deeper depths might explain reduced C‐turnover and Tangel humus formation.
Simulating animal space use from fitted integrated Step‐Selection Functions (iSSF)
Authors: Signer J. , Fieberg J. , Reineking B. , Schlägel U. , Smith B. , Balkenhol N. , Avgar T.
Published: December 2023

A standing challenge in the study of animal movement ecology is the capacity to predict where and when an individual animal might occur on the landscape, the so‐called, utilisation distribution (UD). Under certain assumptions, the steady‐state UD can be predicted from a fitted exponential habitat selection function. However, these assumptions are rarely met. Furthermore, there are many applications that require the estimation of transient dynamics rather than steady‐state UDs (e.g. when modelling migration or dispersal). Thus, there is a clear need for computational tools capable of predicting UDs based on observed animal movement data.

Integrated Step‐Selection Analyses (iSSAs), which integrates movement of the animal into habitat selection analyses, are widely used to study habitat selection and movement of wild animals, and result in a fully parametrised individual‐based model of animal movement, which we refer to as an integrated Step Selection Function (iSSF). An iSSF can be used to generate stochastic animal paths based on random draws from a series of Markovian redistribution kernels, each consisting of a selection‐free, but possibly habitat‐influenced, movement kernel and a movement‐free selection function. The UD can be approximated by a sufficiently large set of such stochastic paths.

Here, we present a set of functions in R to facilitate the simulation of animal space use from fitted iSSFs. Our goal is to provide a general purpose simulator that is easy to use and is part of an existing workflow for iSSAs (within the amt R package).

We demonstrate through a series of applications how the simulator can be used to address a variety of questions in applied movement ecology. By providing functions in amt and coded examples, we hope to encourage ecologists using iSSFs to explore their predictions and model goodness‐of‐fit using simulations, and to further explore mechanistic approaches to modelling landscape connectivity.
Intermittent supplementation with fisetin improves arterial function in old mice by decreasing cellular senescence
Authors: Mahoney Sophia A. , Venkatasubramanian Ravinandan , Darrah Mary A. , Ludwig Katelyn R. , VanDongen Nicholas S. , Greenberg Nathan T. , Longtine Abigail G. , Hutton David A. , Brunt Vienna E. , Campisi Judith , Melov Simon , Seals Douglas R. , Rossman Matthew J. , Clayton Zachary S.
Published: December 2023

Cellular senescence and the senescence‐associated secretory phenotype (SASP) contribute to age‐related arterial dysfunction, in part, by promoting oxidative stress and inflammation, which reduce the bioavailability of the vasodilatory molecule nitric oxide (NO). In the present study, we assessed the efficacy of fisetin, a natural compound, as a senolytic to reduce vascular cell senescence and SASP factors and improve arterial function in old mice. We found that fisetin decreased cellular senescence in human endothelial cell culture. In old mice, vascular cell senescence and SASP‐related inflammation were lower 1 week after the final dose of oral intermittent (1 week on—2 weeks off—1 weeks on dosing) fisetin supplementation. Old fisetin‐supplemented mice had higher endothelial function. Leveraging old p16‐3MR mice, a transgenic model allowing genetic clearance of p16INK4A‐positive senescent cells, we found that ex vivo removal of senescent cells from arteries isolated from vehicle‐ but not fisetin‐treated mice increased endothelium‐dependent dilation, demonstrating that fisetin improved endothelial function through senolysis. Enhanced endothelial function with fisetin was mediated by increased NO bioavailability and reduced cellular‐ and mitochondrial‐related oxidative stress. Arterial stiffness was lower in fisetin‐treated mice. Ex vivo genetic senolysis in aorta rings from p16‐3MR mice did not further reduce mechanical wall stiffness in fisetin‐treated mice, demonstrating lower arterial stiffness after fisetin was due to senolysis. Lower arterial stiffness with fisetin was accompanied by favorable arterial wall remodeling. The findings from this study identify fisetin as promising therapy for clinical translation to target excess cell senescence to treat age‐related arterial dysfunction.
Low screening rates and high prevalence of osteoporosis in cirrhosis: A real‐world retrospective analysis
Authors: Thomson Mary , Scott Adam , Trost Suzanne , Lake Jack , Lim Nicholas
Published: December 2023

Background

Patients with cirrhosis are at increased risk for osteoporosis, and those who suffer a fracture are at high risk for mortality. Despite this, osteoporosis is often overlooked and undertreated. This study aimed to evaluate osteoporosis screening, management, and adverse osteoporosis medication events in patients with cirrhosis.

Methods

We performed a retrospective chart review of adult outpatients with compensated and decompensated cirrhosis seen in single health system over a 6‐year period. Patient demographics, liver and bone health comorbidities, DEXA scan results, and medications were abstracted.

Results

In total, 5398 patients met criteria. The cohort was predominately white (79.1%) and older (age 59). 44.4% were female. 64.6% had decompensated cirrhosis. Median MELD‐Na score was 12.8. 23.5% had a DEXA scan ordered, approximately 50% completed this test. Patients who were older, female, white, with more severe liver disease, and other osteoporosis risk factors were more likely to have a DEXA scan ordered. 48.5% of patients had osteopenia and 30.2% had osteoporosis on DEXA scan. Only 22.6% of patients with osteoporosis received treatment, most commonly oral bisphosphonates. Oral bisphosphonate prescription was not associated with variceal bleeding (8.4% without vs. 4.8% with, p = 0.487).

Conclusion

A minority of patients with cirrhosis were screened for osteoporosis. The majority screened had osteopenia or osteoporosis on DEXA scan. Less than a quarter of patients with osteoporosis were started on treatment. Real‐world experience of oral bisphosphonate use did not reveal higher rates of gastrointestinal bleeding. There is room for improvement in all aspects of bone health care in cirrhosis.
Letter: Antibiotics prescription and new‐onset irritable bowel syndrome—Authors' reply
Authors: Staller Kyle , Ludvigsson Jonas F.
Published: December 2023

LINKED CONTENT

This article is linked to Staller et al papers. To view these articles, visit https://doi.org/10.1111/apt.17736 and https://doi.org/10.1111/apt.17820
Environmental, social, and governance (ESG) and idiosyncratic volatility: The COVID‐19 pandemic and its impact on ESG‐sensitive industries
Authors: Kim Jihun , Kang Jongho , Hyun Suk
Published: December 2023

This study provides an in‐depth examination of the relationship between environmental, social, and governance (ESG) performance and the idiosyncratic volatility of Korean companies. In line with the risk‐mitigation view, the study finds that strong ESG performance is associated with a reduction in a firm's idiosyncratic volatility. The impact of ESG performance on reducing firm volatility was particularly evident during the COVID‐19 pandemic, highlighting the role of ESG performance in risk mitigation during crisis periods. The study also shows that companies with strong ESG performance in industries that are highly sensitive to ESG factors are particularly adept at reducing idiosyncratic volatility. These findings underscore the importance of ESG enhancement for both firm managers and policymakers, particularly within ESG‐sensitive industries.
Canadian politicians' rhetoric on Twitter/X: Analysing prejudice and inclusion towards Muslims using structural topic modelling and rhetorical analysis
Authors: Shayegh John , Sumantry David , Jagayat Arvin , Choma Becky
Published: December 2023

We analysed tweets from five English‐speaking Canadian political parties in the year leading up to the 2019 federal election to explore both prejudicial and inclusive rhetoric in relation to Muslim identities on social media. We used structural topic modelling to understand what topics were discussed before moving to a rhetorical approach to analyse how topics were discussed. We identified 10 topics. Seven talked about Muslim groups in primarily inclusive ways, including depicting the positive contributions to Canadian society, creating ideological space for Muslim religious practices and invoking superordinate identities with victims of hate crimes to cultivate solidarity. However, the effectiveness of inclusive rhetoric was sometimes questioned due to omitting the subgroup‐specific prejudice faced by Muslims. Prejudicial rhetoric occurred in three of the topics due to the nativist populist PPC party depicting Muslims as a threat to Canadian values, as hostile to people from other religious faiths, and depicting ‘elites’ in society as concealing the ‘true’ information concerning Muslims. The study contributes to understanding how politicians attempt to cultivate minority inclusion/exclusion in multicultural contexts through social media, as well as understanding the rhetoric of nativist populism in Canada and its similarities to other Global North contexts.
Evaluation of MV140 in preventing recurrent urinary tract infections: a multicentre double‐blind randomized controlled trial protocol
Authors: Kovacic James , Canagasingham Ashan , Zhong Wenjie , Lockhart Kathleen , Dhar Ankur , Shepherd Andrew , Chung Amanda
Published: December 2023

Objectives

To determine, firstly, whether MV140 reduces rates of recurrent urinary tract infections (rUTIs) in patients older than 65 years, measured as the number of urinary tract infections (UTIs) detected over 12 months following the completion of a 3‐month treatment course and, additionally, to assess the number of re‐admissions to the emergency department, the rate of antibiotic use for UTIs, the safety profile of MV140, and quality of life.

Materials and Methods

This is a multicentre, double‐blind, randomized controlled trial with two arms. Patients will be randomized and allocated to receive either a 3‐month course of MV140 or placebo (two sublingual sprays daily). Participants will have 3‐monthly consultations with the investigator for 12 months to assess differences in rates of rUTIs between the two groups. Study candidates will be identified and recruited from inpatient and outpatient clinics across Sydney via referral to the investigation team. After obtaining consent, participants will undergo initial study consultations including urine microscopy and culture, uroflowmetry, and bladder scan to assess postvoid residual urine volume. Participants will be randomized and provided with a unique trial number. Electronic medical records will be reviewed to collect relevant information. Participants will be provided with a study diary to record relevant data.

Results

Follow‐up consultations will be conducted every 3 months for a 12‐month duration, during which the study diary will be reviewed. These follow‐up consultations will primarily occur via telephone review, however, there will be flexibility for in‐person reviews for participants who find telephone consultation prohibitively difficult.

Conclusion

This is a multicentre, double‐blinded, randomised control trial, the first in Australia to assess the safety and efficacy of MV140 Uromune vaccine in prevention of recurrent UTIs. Results have been promissing in the global literatures.
Gender‐affirming care in urology: emergency care of the gender‐affirming surgical patient—what the primary urologist needs to know
Authors: Krakowsky Yonah , Shah Gresha , Nguyen Anna‐Lisa V. , Kavanagh Alex G. , Potter Emery , Remondini Taylor , Goldsher Yulia Wilk , Millman Alexandra
Published: December 2023

Objective

To present a narrative review of fundamental information needed to manage postoperative complications in patients who have undergone genital gender‐affirming surgery (GAS).

Methods

A narrative review was performed using the following keywords: ‘gender‐affirming surgery’, ‘complications’, ‘emergency’, ‘postoperative’. Articles were included after being reviewed by two primary authors for relevance. Four clinicians with significant experience providing both primary and ongoing urological care to patients after GAS were involved in article selection and analysis.

Results

The most common feminising genital GAS performed is a vaginoplasty. The main post‐surgical complications seen by urologists include wound healing complications, voiding dysfunction, postoperative bleeding, vaginal stenosis, acute vaginal prolapse and graft loss, rectovaginal fistula, and urethrovaginal fistula. The most common masculinising genital GAS options include metoidioplasty and phalloplasty. Complications for these surgeries include urethral strictures, urethral fistulae, and urethral diverticula. Penile implants may also accompany phalloplasties and their complications include infection, erosion, migration, and mechanical failure.

Conclusion

Genital GAS is increasing, yet there are still many barriers that individuals face not only in accessing the surgeries, but in receiving follow‐up care critical for optimal outcomes. Improved education and training programmes would be helpful to identify and manage postoperative complications. Broader cultural level changes are also important to ensure a safe, gender‐inclusive environment for all patients.
To squeeze or not: Regulation of cell size by mechanical forces in development and human diseases
Authors: Claude‐Taupin Aurore , Dupont Nicolas
Published: December 2023

Physical constraints, such as compression, shear stress, stretching and tension play major roles during development and tissue homeostasis. Mechanics directly impact physiology, and their alteration is also recognized as having an active role in driving human diseases. Recently, growing evidence has accumulated on how mechanical forces are translated into a wide panel of biological responses, including metabolism and changes in cell morphology. The aim of this review is to summarize and discuss our knowledge on the impact of mechanical forces on cell size regulation. Other biological consequences of mechanical forces will not be covered by this review. Moreover, wherever possible, we also discuss mechanosensors and molecular and cellular signaling pathways upstream of cell size regulation. We finally highlight the relevance of mechanical forces acting on cell size in physiology and human diseases.