bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial heterogeneity influences phage-host co-existence dynamics and phage resistance development inVibrio anguillarum
Authors: Chen Ling , Middelboe Mathias , Svenningsen Sine Lo 
Published: December 2024

AbstractExposure of bacterial populations to phage infection pressure is a significant driver of phage-host co-evolution and diversification. However, the impact of the spatial organization of bacterial population ‘co-existence and co-evolution dynamics remains poorly understood. Here, we investigated how the spatial structure of the host population affects phage-host interactions by co-cultivating aVibrio anguillarumstrain with the lytic T4-like vibriophage KVP40 under conditions that resulted in either a homogenous, well-mixed population or a heterogeneous population with bacterial aggregates. We observed markedly different temporal dynamics associated with the two population structures over a 30-day adaptive laboratory evolution experiment. Phage and host dynamics suggested that phage-sensitive subpopulations retained in the aggregates substantially prolonged the coexistence of phages and bacteria, relative to the homogenous environment. However, the limited phage propagation on the sensitive subpopulations was insufficient for host range expansion to occur. In contrast, daily supplementation of sensitive host bacteria in parallel experiments readily led to the emergence of phage mutants with enhanced infective capability and an expanded host range. These results underscore the importance of bacterial spatial organization in determining the outcome of phage attacks and highlight the complex interplay between genomic processes and ecological conditions in driving evolutionary innovations.
Interaction between native and prosthetic visual responses in optogenetic visual restoration
Authors: Carpentiero Eleonora , Hughes Steven , Rodgers Jessica , Xhaferri Nermina , Biswas Sumit , Gilhooley Michael J , Hankins Mark W , Lindner Moritz 
Published: December 2024

ABSTRACTDegenerative retinal disorders leading to irreversible photoreceptor death are a common cause of blindness. Optogenetic gene therapy aims to restore vision in affected individuals by introducing light sensitive opsins into the surviving neurons of inner retina. While up until now the main focus of optogenetic therapy has been on terminally blind individuals, treating at stages where residual native vision is present could have several advantages. Yet, it is still unknown how residual native and optogenetic vision would interact if present at the same time.Using transgenic mice expressing the optogenetic tool ReaChR in ON-bipolar cells, we herein examine this interaction through electroretinography (ERG) and visually evoked potentials (VEP). We find that optogenetic responses show a peculiar ERG signature and are enhanced in retinas without photoreceptor loss. Conversely, native responses are dampened in the presence of ReaChR. Moreover, in VEP recordings we find that optogenetic responses reach the cortex asynchronous to the native response.These findings should be taken into consideration when planning future clinical trials and may direct future preclinical research to optimize optogenetic approaches for visual restoration. The identified ERG signatures moreover may serve to track treatment efficiency in clinical trials.
Inferring fine-scale mutation and recombination rate maps in aye-ayes (Daubentonia madagascariensis)
Authors: Soni Vivak , Versoza Cyril J. , Terbot John W. , Jensen Jeffrey D. , Pfeifer Susanne P. 
Published: December 2024

AbstractThe rate of input of new genetic mutations, and the rate at which that variation is reshuffled, are key evolutionary processes shaping genomic diversity. Importantly, these rates vary not just across populations and species, but also across individual genomes. Despite previous studies having demonstrated that failing to account for rate heterogeneity across the genome can bias the inference of both selective and neutral population genetic processes, mutation and recombination rate maps have to date only been generated for a relatively small number of organisms. Here, we infer such fine-scale maps for the aye-aye (Daubentonia madagascariensis) – a highly endangered strepsirrhine that represents one of the earliest splits in the primate clade, and thus stands as an important outgroup to the more commonly-studied haplorrhines – utilizing a recently released fully-annotated genome combined with high-quality population sequencing data. We compare our indirectly inferred rates to previous pedigree-based estimates, finding further evidence of relatively low mutation and recombination rates in aye-ayes compared to other primates.
A new metoposaurid (Temnospondyli) bonebed from the lower Popo Agie Formation (Carnian, Triassic) and an assessment of skeletal sorting in temnospondyls
Authors: Kufner Aaron M. , Deckman Max E. , Miller Hannah R. , So Calvin , Price Brandon R. , Lovelace David M. 
Published: December 2024

AbstractMetoposaurid-dominated bonebeds are relatively commonplace in Upper Triassic continental deposits with at least ten monodominant, densely populated bonebeds globally. The biostratinomy of several classic localities in India, North America, and Poland have been explored in detail, however, variability in methods and resultant conclusions point to the need for a more nuanced approach to understanding both the taphonomic and the ecological origins of metoposaurid-dominated bonebeds. Here we present the first monodominant metoposaurid mass mortality assemblage from the Late Triassic Popo Agie Formation and the stratigraphically lowest known record of several fauna from the Popo Agie Fm including the first occurrence of theBuettnererpeton bakeriin Wyoming. We employ previously used binning methods based on perceived hydrodynamic equivalence (“Voorhies groups”) to assess pre-burial skeletal sorting. We suggest a simple counting and normalization method that avoids the inherent bias introduced by the interpretation of hydrodynamic equivalence of skeletal elements in taxa that lack actualistic experimental data. In contrast to other North American metoposaurid bonebeds, the sedimentology and skeletal sorting analyses of the Nobby Knob quarry support an autochthonous origin of this assemblage in a fluvio-lacustrine system with relatively little pre-burial sorting. Despite differences in underlying assumptions regarding the dispersal potential of specific skeletal elements, binning methods tend to follow similar trends regardless of framework used to assess different assemblages.
Apolipoprotein-L1 G1 variant contributes to hydrocephalus but not to atherosclerosis in apolipoprotein-E knock-out mice
Authors: Yoshida Teruhiko , Yang Zhi-Hong , Ashida Shinji , Xi Yu Zu , Shrivastav Shashi , Rojulpote Krishna Vamsi , Bahar Piroz , Nguyen David , Springer Danielle A. , Munasinghe Jeeva , Starost Matthew F. , Hoffmann Victoria J. , Rosenberg Avi Z. , Bielekova Bibi , Wen Han , Remaley Alan T. , Kopp Jeffrey B. 
Published: December 2024

AbstractIntroductionIn USA, six million individuals with Sub-Saharan ancestry carry twoAPOL1high-risk variants, which increase the risk for kidney diseases. Whether APOL1 high-risk variants are independent risk factors for cardiovascular diseases is unclear and requires further investigation.MethodsWe characterized a mouse model to investigate the role of APOL1 in dyslipidemia and cardiovascular diseases. Transgenic mice carrying APOL1 (G0 and G1 variants) on bacterial artificial chromosomes (BAC/APOL1 mice) were crossed with the ApoE knock-out (ApoE-KO) atherosclerosis mouse model. The compound transgenic mice were evaluated for the impact of APOL1 on systemic phenotypes.ResultsApoE-KO mice carrying APOL1-G0 and APOL1-G1 did not show differences in the extent of atherosclerotic lesions or aortic calcification, as evaluated by Sudan IV staining and radiographic examination, respectively. However, ∼20% of ApoE-KO; BAC/APOL1-G1 mice developed hydrocephalus and required euthanasia. The hydrocephalus was communicating and likely was due to excess cerebrospinal fluid produced by the choroid plexus, where epithelial cells expressed APOL1. Single-nuclear RNA-seq of choroid plexus identified solute transporter upregulation and mTORC2 pathway activation in APOL1-G1-expressing epithelial cells. Further, in the All of Us cohort, we found higher hydrocephalus prevalence among individuals with theAPOL1-G1variant in both recessive and dominant models, supporting the mouse findings.ConclusionWhile APOL1-G1 expression in ApoE-KO mice did not worsen cardiovascular disease phenotypes, we uncovered hydrocephalus as a novel APOL1 risk allele-mediated phenotype. These findings extend the spectrum of APOL1-associated pathologies.
Bovine Formative Embryonic Stem Cell Plasticity in Embryonic and Extraembryonic Differentiation
Authors: Su Yue , Zhao Ruifeng , Fang Yifei , Li Guangsheng , Jin Liangliang , Liu Jiaxi , Yang Zhen , Li Ningxiao , Zhu Jiaqi , Mishra Neha , Kaback Deborah , Yee Siu Pok , Lei Chuzhao , Duan Jingyue (Ellie) , Tian Xiuchun (Cindy) , Tang Young 
Published: December 2024

SummaryBovine embryonic stem cells (bESCs) can greatly enhance understanding of bovine embryonic development and applications for disease-resistance, biomedical and zoonotic pre-clinical models. However, formative bESCs with distinct morphology and complete differentiation capacity are still unreported. We document here the generation of bESCs which are pluripotent bothin vitroandin vivo,and efficiently converted into neural progenitor cells (NPCs) and primordial germ cell-like cells (PGCLCs) by direct differentiation. These cells exhibited distinct metabolic features from human and mouse ESCs and early embryos. Formative bESCs contributed to a wide range of cell types in both embryonic and extraembryonic tissues after aggregating with mouse and bovine embryos. The establishment of bovine formative ESCs with dual developmental plasticity represents a milestone for agricultural biotechnology and decoding the underlying mechanism ofbona fidebovine pluripotency.
Leveraging machine learning and accelerometry to classify animal behaviours with uncertainty
Authors: Agarwal Medha , Rafiq Kasim , Mehta Ronak , Abrahms Briana , Harchaoui Zaid 
Published: December 2024

AbstractAnimal-worn sensors have revolutionised the study of animal behaviour and ecology. Accelerometers, which measure changes in acceleration across planes of movement, are increasingly being used in conjunction with machine learning models to classify animal behaviours across taxa and research questions. However, the widespread adoption of these methods faces challenges from imbalanced training data, unquantified uncertainties in model outputs, shifts in model performance across contexts, and noisy classifications.To address these challenges, we introduce an open-source approach for classifying animal behaviour from raw acceleration data. Our approach integrates machine learning and statistical inference techniques to evaluate and mitigate class imbalances, changes in model performance across ecological settings, and noisy classifications. Importantly, we extend predictions from single behaviour classifications to prediction sets –collections of probable behaviours with a user-specified likelihood of containing the true behaviour – in a framework analogous to the use of confidence intervals in statistical analyses.We highlight the utility of our approach using data collected from a free-ranging large carnivore, African wild dogs (Lycaon pictus),in the Okavango Delta, Botswana. We demonstrate significantly improved predictions along with associated uncertainty metrics in African wild dog behaviour classification, particularly for rare and ecologically important behaviours such as feeding, where correct classifications more than doubled following quality checks and data rebalancing introduced in our pipeline.Our approach is applicable across taxa and represents a key step towards advancing the burgeoning use of machine learning to remotely observe around-the-clock behaviours of free-ranging animals. Future work could include the integration of multiple data streams, such as accelerometer, audio, and GPS data, for model training and could be incorporated directly into our pipeline.
Aniline Dioxygenase inRhodococcus ruberR1: Insights into Skatole Degradation
Authors: Galaz S.J. , Saavedra B. , Zúñiga A. , González-Toro F. , Donoso R. 
Published: December 2024

ABSTRACTSkatole is an aromatic heterocyclic compound with a strong offensive odor, produced by microorganisms during the anaerobic breakdown of tryptophan. Skatole accumulation is linked to environmental and health issues. Despite its persistence and harmful effects, skatole’s biodegradation by microorganisms is poorly understood. We have recently isolated a gram-positive bacterium,Rhodococcus ruberR1, which uses skatole as its sole carbon and energy source. Here we report an operon consisting of 14 genes encoding aromatic oxygenase systems involved in skatole degradation inRhodococcus ruberR1. Cells growing on skatole accumulate aniline transiently, indicating its role as an intermediate in the degradation pathway. We characterize six genes in this cluster that encode for an aniline dioxygenase, which converts aniline to catechol and is only activated in the presence of skatole. This gene cluster was successfully introduced into a heterologous strain enabling the full degradation of aniline and its derivatives. Phylogenetic analysis of aniline dioxygenase present in R1 strain reveals a widespread distribution of this system among bacteria, in contrast to the full skatole cluster, which is restricted to a few genera. These findings advance our understanding of the skatole degradation pathway and highlight R1’s potential for bioremediation of skatole, aniline, and related contaminants.
QC4Metabolomics: Real-time and Retrospective Quality Control of Metabolomics Data
Authors: Stanstrup Jan , Dragsted Lars Ove 
Published: December 2024

AbstractMotivationThe ability to answer complex biological questions in metabolomics relies on the acquisition of high-quality data. However, due to the complex nature of liquid chromatography–mass spectrometry acquisition, data quality checks are often not done comprehensively and only at the post-processing step. This can be too late to mitigate analytical problems such as loss ofm/zcalibration, retention time drift and severe ion suppression. It is often not practically or economically feasible to reanalyze samples, and interpretation of the acquired compromised data, if at all possible, is limited, despite the considerable expenses incurred to obtain them.ResultsWe therefore introduceQC4Metabolomics, a real-time quality control monitoring software for untargeted metabolomics data.QC4Metabolomicsmonitors files as they are acquired or retrospectively by tracking any user-defined compound(s) and extracting diagnostic information such as observedm/z, retention time, intensity and peak shape, and presents the results on a web dashboard.QC4Metabolomicsalso monitors the levels of common or user-defined contaminants. We report herein real-world examples whereQC4Metabolomicseasily reveals analytical problems retrospectively that could have been immediately addressed with real-time monitoring, so that the samples would have been analyzed without any quality control issues.Availability and ImplementationQC4Metabolomicsis available as code athttps://github.com/stanstrup/QC4Metabolomics. ADockerimage, adocker-composesetup file and demo data are also provided for easy deployment.
Barcoding-inferred biodiversity of shallow-water Indo-Pacific demosponges
Authors: Erpenbeck Dirk , Galitz Adrian , Berumen Michael L. , Büttner Gabriele , Debitus Cécile , Dirnberger Moritz , Ekins Merrick , Hall Kathryn , Namuth Leonard , Petek Sylvain , Rahnamae Neda , Reddy Maggie M. , Rettenberger Daniela , Ries Stefanie R. , Schätzle Simone , Schönberg Christine H.L. , Setiawan Edwin , van der Sprong Joëlle , Thomas Olivier P. , Tirumalasetty Vani , de Voogd Nicole J. , Voigt Oliver , Hooper John N.A. , Wörheide Gert 
Published: December 2024

AbstractAimThe Indo-Pacific is the world’s largest marine biogeographic region. It is characterised by different degrees of connectivity among its subregions, and harbours the majority of demosponge species currently known to science. Comparisons between several regional sponge faunas have been undertaken in the past, mostly based on identifying the sponge species morphologically. The Sponge Barcoding Project, in tandem with other regional DNA taxonomy campaigns, provides one of the largest DNA-based taxonomic data collections from sponges of the Indo-Pacific. Here, we utilise the sponge barcoding data in the largest molecular biodiversity study of sponges to date, which reveals patterns of shallow-water demosponge faunal connectivity, endemism, and distribution in the Indo-Pacific with a level of resolution unavailable in prior morphology-based studies.LocationDemosponge specimens in this study cover 13 marine provinces of the Indo-Pacific, from the Red Sea to South East Polynesia.MethodsWe classified demosponge barcodes using the ribosomal subunit (28S rDNA) of 1,910 sponge samples into molecular operational taxonomic units (MOTUs). MOTU composition of the 13 marine provinces was compared based on Jaccard and Sørenson dissimilarities, and other biodiversity indices.ResultsOur data corroborated high levels of endemism among demosponges. Faunal overlaps were revealed between the Red Sea and the Gulf, which displayed relatively small connectivity with other marine provinces of the Western Indian Ocean. In the Western Indian Ocean, we observed a strong faunistic boundary to the Central Indo-Pacific. The Polynesian sponge faunas were comparatively isolated marine provinces of the Central Indo-Pacific.Main conclusionsOur data corroborate case studies on sponges that generally reject the presence of cosmopolitan or otherwise widespread sponge species, instead revealing high levels of regional endemism. This is consistent with similar observations and hypotheses in other marine invertebrates. Connectivity among Indo-Pacific marine provinces differs for demosponges in many aspects from that of other marine taxa, such as corals and fishes, probably due to their shorter pelagic larval phase.
Leveraging digital transformation to develop a data-driven culture for supply chain resilience: an empirical investigation
Authors: Kokkinou Alinda , Mitas Ondrej , Mandemakers Albert 
Published: January 2025

PurposeCompanies rely on supply chain robustness and resilience to maintain their competitive advantage despite disruptions. The study examines how organizations can orchestrate employee empowerment, digital transformation technologies, and trust to develop supply chain robustness and resilience capabilities.Design/methodology/approachA cross-sectional survey design is used to test the study hypotheses. Data are collected from international and domestic organizations operating in the Netherlands, Belgium, and Luxemburg using an online survey, and analyzed using Partial Least Squares-Structural Equation Modeling (PLS-SEM).FindingsDigital transformation tools contribute to supply chain robustness and resilience in different ways. Digital transformation tools and employee empowerment contribute to the development of a data-driven culture and thereby to supply chain robustness. Digital transformation tools also contribute to increased supply chain visibility. This in turns strengthens trust relationships with suppliers, contributing to supply chain resilience.Originality/valueThe study extends dynamic capability theory and organization information processing theory by demonstrating how investments in assets such as digital technologies can contribute to increasing an organization’s information processing capability directly, by building vertical information systems, but also indirectly, by contributing to the development of lateral relations.
Environmental, social and governance investing: systematic literature review using ADO model
Authors: Aggarwal Shalini , Dsouza Suzan , Joshi Mahesh , Antoun Roger , Phan Duc Hong Thi 
Published: January 2025

PurposeThis paper systematically analyzes the literature on environmental, social and governance (ESG). It explores the antecedents, decisions and outcomes (ADO) influencing ESG investments; theories used in the literature; publication years, geographical locations and journals of publication of ESG-related articles; notable gaps in research on ESG investments; theoretical and managerial implications and prospective research avenues within the ESG field. All ESG components are interconnected with the United Nations’ Sustainable Development Goals (SDGs).Design/methodology/approachThe PRISMA framework was employed to screen articles from the Scopus database. A total of 386 articles spanning 2011–2024 were included. The search terms used to screen the articles for inclusion were “sustainable finance,” “ESG,” “environment, social, corporate governance,” “green finance,” “green bond,” “social bond,” “blue bond,” “social finance” and “corporate social responsibility.”FindingsThe findings indicate that organizations utilize green bonds, blue bonds and green loans to mitigate environmental concerns. To address social issues, companies issue social bonds and sustainable bonds and engage in socially responsible investing. To address concerns about corporate governance, companies emphasize corporate social responsibility and intellectual capital.Practical implicationsThe findings can be used to inform policymakers on the implementation of comprehensive regulatory frameworks in the realm of ESG. Tax benefits and subsidies should be extended to firms fostering ESG practices.Originality/valueThis study offers a comprehensive synthesis of the ESG literature by examining the ADO framework, which has not been systematically applied to ESG investments before. It integrates diverse components of ESG investments with the United Nations’ SDGs, providing a unique perspective on how these investments align with global sustainability objectives.