bluuebunny/crossref_metadata_2025_split huggingface dataset:
fMRI-based spatio-temporal parcellations of the human brain
Authors: Ling Qinrui , Liu Aiping , Li Yu , McKeown Martin J. , Chen Xun 
Published: May 2024

Purpose of review
Human brain parcellation based on functional magnetic resonance imaging (fMRI) plays an essential role in neuroscience research. By segmenting vast and intricate fMRI data into functionally similar units, researchers can better decipher the brain's structure in both healthy and diseased states. This article reviews current methodologies and ideas in this field, while also outlining the obstacles and directions for future research.

Recent findings
Traditional brain parcellation techniques, which often rely on cytoarchitectonic criteria, overlook the functional and temporal information accessible through fMRI. The adoption of machine learning techniques, notably deep learning, offers the potential to harness both spatial and temporal information for more nuanced brain segmentation. However, the search for a one-size-fits-all solution to brain segmentation is impractical, with the choice between group-level or individual-level models and the intended downstream analysis influencing the optimal parcellation strategy. Additionally, evaluating these models is complicated by our incomplete understanding of brain function and the absence of a definitive “ground truth”.

Summary
While recent methodological advancements have significantly enhanced our grasp of the brain's spatial and temporal dynamics, challenges persist in advancing fMRI-based spatio-temporal representations. Future efforts will likely focus on refining model evaluation and selection as well as developing methods that offer clear interpretability for clinical usage, thereby facilitating further breakthroughs in our comprehension of the brain.
Genomic Hotspots: Localized chromosome gene expansions identify lineage-specific innovations as targets for functional biodiversity and predictions of stress resilience
Authors: Edsinger Eric , Moroz Leonid L. 
Published: May 2024

1AbstractFunctional and biodiversity genomics is essential for assessment and monitoring of planetary health and species-specific management in changing ecosystems. However, experimental knowledge of gene functions is limited to a few species, and dependencies on distantly related models. Combined with unrecognized degrees of lineage-specific gene family expansion, this means that traditional comparative methods are insufficient. Here, we clarify definitions of homology and genomic ‘dark matter’ and introduce the concept of a hotspot, defined as innovations underlying the evolution of lineage-specific biology. We illustrate hotspots using molluscs having chromosome-scale genome assemblies and focus on heat-sensing TRPM channels and species living in environments of extreme heat stress (e.g., high intertidal and hydrothermal vent gastropods and bivalves). Integrating gene family, orthogroup, and domain-based methods with genomic hotspots (local paralog expansions on chromosomes), we show that conventional approaches overlook substantial amounts of species-specific gene family diversity due to limitations of distant homology detection. In contrast, local segmental duplications are often recent, lineage-specific genetic innovations reflecting emerging adaptions and can be identified for any genome. Revealed TRPM gene family diversification highlights unique neural and behavioral mechanisms that could be beneficial in predicting species’ resilience to heat stress. In summary, the identification of hotspots and their integration with other types of analyses illuminate evolutionary (neuro)genomic strategies that do not depend on knowledge from model organisms and unbiasedly reveal evolutionarily recent lineage-specific adaptations. This strategy enables discoveries of biological innovations across species as prospective targets for modeling, management, and biodiversity conservation.
Plant hormone manipulation impacts salt spray tolerance, which preempts herbivory as a driver of local adaptation in the yellow monkeyflower,Mimulus guttatus
Authors: Toll Katherine , Blanchard Megan , Scharnagl Anna , Holeski Liza M. , Lowry David B. 
Published: May 2024

AbstractA major challenge in evolutionary biology is identifying the selective agents and phenotypes underlying local adaptation. Local adaptation along environmental gradients may be driven by trade-offs in allocation to reproduction, growth, and herbivore resistance. To identify environmental agents of selection and their phenotypic targets, we performed a manipulative field reciprocal transplant experiment with coastal perennial and inland annual ecotypes of the common yellow monkeyflower (Mimulus guttatus). We manipulated herbivory with exclosures built in the field and exogenously manipulated hormones to shift allocation of plant resources among growth, reproduction, and herbivore resistance. Our hormone treatments influenced allocation to reproduction and phytochemical defense, but this shift was small relative to ecotype differences in allocation. Herbivore exclosures reduced herbivory and increased fitness of plants at the coastal site. However, this reduction in herbivory did not decrease the homesite advantage of coastal perennials. Unexpectedly, we found that the application of exogenous gibberellin increased mortality due to salt spray at the coastal site for both ecotypes. Our results suggest that divergence in salt spray tolerance, potentially mediated by ecotype differences in gibberellin synthesis or bioactivity, is a strong driver of local adaptation and preempts any impacts of herbivory in coastal habitats that experience salt spray.
TSPDB: A curated resource of tailspike proteins with potential applications in phage research
Authors: Lawal Opeyemi U. , Goodridge Lawrence 
Published: May 2024

AbstractPhages are ubiquitous viruses that drive bacterial evolution through infection and replication within host bacteria. Phage tailspike proteins (TSPs) are key components of phage tail structures, exhibiting polysaccharide depolymerase activity and host specificity. Despite their potential as novel antimicrobials, few TSPs have been fully characterized due to laborious detection techniques. To address this, we present TSPDB, a curated resource for rapid detection of TSPs in genomics and metagenomics sequence data. We mined public databases, obtaining 17,211 TSP sequences, which were filtered to exclude duplicates and partial sequences, resulting in 8,099 unique TSP sequences. TSPDB contains TSPs from over 400 bacterial genera, with significant diversity among them as revealed by the phylogenetic analysis. The top 13 genera represented were Gram-positive, withBacillus, Streptococcus, andClostridiumbeing the most common. Of note, Phage TSPs in Gram-positive bacteria were on average 1 Kbp larger than those in Gram-negative bacteria. TSPDB has been applied in a recent study to screen phage genomes, demonstrating its potential for functional annotation. TSPDB serves as a comprehensive repository and a resource for researchers in phage biology, particularly in phage associated therapy and antimicrobial or biocontrol applications. TSPDB is compatible with bioinformatics tools forin silicodetection of TSPs in genomics and metagenomic data, and is freely accessible on GitHub and Figshare, providing a valuable resource for the scientific community.
Reorganization of innate immune cell lipid profiles by bioinspired meroterpenoids to limit inflammation
Authors: Waltl Lorenz , Speck Klaus , Wildermuth Raphael , Haut Franz-Lucas , Permann Stephan , D’Avino Danilo , Cerqua Ida , Siller Anita , Schennach Harald , Rossi Antonietta , Magauer Thomas , Koeberle Andreas 
Published: May 2024

AbstractLipidomics-guided screening of unexplored chemical space in natural products provides access to small molecules capable of modifying cellular lipid profiles on a global scale. Here, we show that the meroterpenoid cyclosmenospongine fromSpongia sp. shapes the lipid profile of immune cells, favoring anti-inflammatory and pro-resolving over pro-inflammatory lipid mediators. Structural variation revealed derivatives that inhibit leukotriene biosynthesis to varying extents while differentially upregulating pro-resolving lipid mediators, epoxyeicosatrienoic acids, endocannabinoids, and sphingosine-1-phosphate, along with other mediators, both in resting and activated innate immune cellsin vitroand in self-resolving murine peritonitisin vivo. Mechanistically, meroterpenoids target 5-lipoxygenase or 5-lipoxygenase-activating protein, promote the translocation of 15-lipoxygenase-1 to cytoplasmatic sites, and inhibit monoacylglycerol lipase. They also redirect arachidonic acid (AA) from neutral lipids to specific phospholipids, while increasing the total concentration of free AA. Furthermore, meroterpenoids reprogram lipid metabolism in immune cells, decreasing the levels of neutral lipids, triacylglycerols, and cholesteryl esters. This shift correlates with a reduced capacity for leukotriene biosynthesis and is mimicked by the inhibition of sterol-O-acyltransferase and diacylglycerol acyltransferase-1/2. In conclusion, specific meroterpenoids exert anti-inflammatory effects by intervening in lipid mediator biosynthesis, prompting structure-controlled switches in lipid mediator classes, among others, through an unexpected link between lipogenesis and inflammation.
Assessing avoidant/restrictive food intake disorder symptoms using the Nine Item ARFID Screen in >9,000 Swedish adults with and without eating disorders
Authors: Presseller Emily K , Cooper Gabriella E , Thornton Laura M , Birgegård Andreas , Abbaspour Afrouz , Bulik Cynthia M , Mantilla Emma Forsén , Dinkler Lisa 
Published: May 2024

AbstractObjectiveThe Nine Item ARFID Screen (NIAS) is a widely used measure assessing symptoms of avoidant/restrictive food intake disorder (ARFID). Previous studies suggest that individuals with eating disorders driven by shape/weight concerns also have elevated scores on the NIAS. To further clarify this issue, we characterized NIAS scores in a large sample of individuals with eating disorders and evaluated overlap in symptoms measured by the NIAS and the Eating Disorder Examination-Questionnaire (EDE-Q) version 6.0.MethodOur sample comprised 9,148 participants from the Eating Disorders Genetics Initiative Sweden (EDGI-SE), who completed surveys including NIAS and EDE-Q. NIAS scores were calculated and compared by eating disorder diagnostic group using descriptive statistics and linear models.ResultsParticipants with current anorexia nervosa demonstrated the highest mean NIAS scores and had the greatest proportion (57.0%) of individuals scoring above a clinical cutoff on at least one of the NIAS subscales. Individuals with bulimia nervosa, binge-eating disorder, and other specified feeding or eating disorder also demonstrated elevated NIAS scores compared to individuals with no lifetime history of an eating disorder (ps < .05). All subscales of the NIAS showed small to moderate correlations with all subscales of the EDE-Q (rs = 0.26-0.40).DiscussionOur results substantiate that individuals with eating disorders other than ARFID demonstrate elevated scores on the NIAS, suggesting that this tool is inadequate on its own for differentiating ARFID from shape/weight-motivated eating disorders. Further research is needed to inform clinical interventions addressing the co-occurrence of ARFID-related drivers and shape/weight-related motivation for dietary restriction.
Population scale whole genome sequencing provides novel insights into cardiometabolic health
Authors: Zhao Yajie , Lockhart Sam , Liu Jimmy , Li Xihao , Cortes Adrian , Hua Xing , Gardner Eugene J. , Kentistou Katherine A. , Lo Yancy , Davitte Jonathan , Savage David B. , Buser-Doepner Carolyn , Ong Ken K. , Zhang Haoyu , Scott Robert , O’Rahilly Stephen , Perry John R.B. 
Published: May 2024

AbstractIn addition to its coverage of the non-coding genome, whole genome sequencing (WGS) may better capture the coding genome than exome sequencing. We sought to exploit this and identify novel rare, protein-coding variants associated with metabolic health in newly released WGS data (N=708,956) from the UK Biobank and All of Us studies. Identified genes highlight novel biological mechanisms, including protein truncating variants (PTVs) in the DNA double-strand break repair geneRIF1that have a substantial effect on body mass index (BMI, 2.66 kg/m2, s.e. 0.43,P= 3.7×10-10).UBR3is an intriguing example where PTVs independently increase BMI and type 2 diabetes (T2D) risk. Furthermore, PTVs inIRS2have a substantial effect on T2D (OR 6.4 [3.7-11.3],P= 9.9×10-14, 34% case prevalence among carriers) and were unexpectedly also associated with chronic kidney disease independent of diabetes status, suggesting an important role for IRS-2 in maintaining renal health. We identified genetic evidence of functional heterogeneity inIRS1andIRS2, suggesting a greater role for IRS-1 in mediating the growth promoting effects of insulin and IGF-I, while IRS-2 has a greater impact on glucose homeostasis likely through its actions in the pancreatic islet and insulin target tissues. Our study demonstrates that large-scale WGS provides novel mechanistic insights into human metabolic phenotypes through improved capture of coding sequences.
The effect of playing career on chronic neurophysiological changes in retired male football players. An exploratory study using transcranial magnetic stimulation
Authors: Pearce Alan J , Tallent Jamie , Frazer Ashlyn K , Rist Billymo , Kidgell Dawson J 
Published: May 2024

AbstractAimRepetitive head impact exposure, from contact and collision sports, are increasingly being attributed to increased risk of neurodegenerative disease in aging athletes. This exploratory study investigated the association of playing career in retired professional contact sport athletes with cortical neurophysiology via transcranial magnetic stimulation (TMS).MethodsMale athletes between the ages of 28-68 years (n=113; mean age [SD] 48.8 [9.7]) who had been retired from professional sport for a minimum of five years were recruited. Cortical excitability was measured using single pulse TMS for motor evoked potentials and paired pulse transcranial magnetic stimulation short-interval intracortical inhibition and long-interval intracortical inhibition. Associations were assessed between transcranial magnetic stimulation measures and concussion history, clinical symptom scores, total career length (including junior to complete retirement), and professional career length (elite competition only).ResultsCorrelations showed significant associations between motor evoked potentials and clinical symptom reporting (rho: -0.21 – -0.38;P<0.01); and motor evoked potentials and short-interval intracortical inhibition with total career length (rho: 0.26 – -0.33;P<0.01). No significant correlations were observed between single and paired-pulse transcranial magnetic stimulation and professional career length (rho: 0.16 – -0.15), nor the number of concussions (rho: 0.17 – -0.17).ConclusionsThis study is the first to report pathophysiological outcomes in a cohort of retired professional athletes associated with total career exposure, rather than professional career exposure or concussion history. TMS assessment could be considered a viable biomarker in future studies of retired athletes suspected with traumatic encephalopathy syndrome.
Environmental disasters and the elusiveness of prevention
Authors: Mulvihill Peter Royston 
Published: May 2024

PurposeEnvironmental disasters are preventable, but this remains a complicated and elusive prospect. This article discusses factors that combine to limit and undermine environmental disaster prevention efforts and explores directions for improved theory and practice.Design/methodology/approachThe challenge of integrating root cause analysis of environmental disasters with interventions and preventive measures at later stages of disaster incubation is outlined. The prospect of learning and transferring lessons from past environmental disasters is discussed. Eighteen environmental disaster cases are summarized and analyzed.FindingsA range of factors, including complexity, lack of lesson transfer, perceived lack of incentives and inaction, limits advances in environmental disaster prevention. Theoretical challenges involve better bridging of root cause and incubation analyses, enhanced understanding of the nature and discipline of foresight and greater documentation of alternative approaches to prevention, including post–normal techniques. Although a transformative breakthrough in environmental disaster prevention is unlikely, substantial progress could be made through better lesson transfer and application of alternative approaches.Originality/valueThis article draws attention to problems and opportunities surrounding the challenge of environmental disaster prevention and proposes directions for improved theory and practice.
Deciphering volatility spillovers amidst crises: analyzing the interplay among commodities, equities and socially responsible investments during the COVID-19 shock and financial turbulence
Authors: Ben Amar Amine , Hasnaoui Amir , Boubrahimi Nabil , Dkhissi Ilham , Bellalah Makram 
Published: May 2024

PurposeThis study aims to elucidate the volatility spillovers among commodities, equities and socially responsible investments, underpinning their dynamic correlations during the economic instability wrought by the COVID-19 pandemic and associated financial crises.Design/methodology/approachThis research quantitatively analyzes volatility transmission across various financial assets from January 2005 to October 2020 by employing the Diebold and Yilmaz (2012) spillover index. The methodology incorporates a temporal examination to capture the evolution of volatility dependencies pre and post the emergence of COVID-19.FindingsThe findings indicate substantial volatility spillovers among the assets in question, aligning with the current financialisation of commodity markets and a rise in financial market integration. These spillovers also show variation over time. Notably, the interconnectedness among the assets intensifies during periods of stress. For instance, the total spillover index significantly surpassed 80% toward the end of January 2020, following the onset of the COVID-19 crisis. Furthermore, the results imply that financial markets appear to be segmented.Practical implicationsThe findings afford investors a more comprehensive insight into both the character and scale of the interdependencies across a broad array of financial markets. Indeed, grasping the extent to which financial markets are segmented or integrated during times of stress and stability is crucial for investors. Such understanding is key to more accurately evaluating risks, diversifying investment portfolios and devising more efficient hedging strategies.Originality/valueThis study contributes to financial literature by offering a comprehensive investigation into the spillover effects across a diverse set of asset classes during an unprecedented global health crisis, filling a gap in existing research on market behavior against the backdrop of a pandemic-induced financial crisis.
User and service provider assessment of technology readiness of library commons in selected universities in Ghana
Authors: Koteikor Baidoo Dinah , Nwagwu Williams E. 
Published: May 2024

PurposeThis study assessed the technology readiness of library commons in selected universities in Ghana from the perspectives of both clients and service providers.Design/methodology/approachA sample survey research design was used to carry out the study, and the study consisted of quantitative and qualitative approaches. The data were collected from 157 of the 430 commons’ users and six library directors/commons librarians, using a questionnaire and an interview schedule respectively. The quantitative data were analysed using descriptive statistics and inferential analysis with SPSS Ver. 22, and structural equation modelling with AMOS Ver. 23.FindingsThe study found significant relationships between the availability of learning resources and users' experience, use and satisfaction with the commons. Additionally, there were significant relationships between the readiness of the commons, users' perceptions and their satisfaction levels. The library/commons managers identified key preparedness issues, including inadequate planning and poor space allocation. Furthermore, the study revealed negative feelings among library/commons managers, such as insecurity, resistance and low confidence.Practical implicationsThe academic libraries in Ghana should evaluate their commons following the findings of this study, and use other readiness implementation tools to identify and address the gaps in their implementation of the commons.Originality/valueThis study was based on the opinions of the users and operators of the commons and focused primarily on technology-related factors. However, it is essential to evaluate other readiness factors, such as change and services, and institutional factors, using frameworks such as Hess and Ostrom’s (2005) Institutional Development Framework, to provide complementary results that can guide better implementation of the commons and improve the quality of services.
Skilful surfing: modelling the optimum method of online health information seeking during pregnancy
Authors: Rathbone Amy Leigh , Clarry Laura , Prescott Julie 
Published: May 2024

PurposeThe purpose of this study was to develop a model of skilful surfing to aid understanding of how best to seek health information, online and offline, during pregnancy.Design/methodology/approachThis study used an observational, descriptive design, using a purpose written questionnaire, factor analysis and structural equation modelling.FindingsAnalysis resulted in the factor loading of five components: online health information seeking behaviour, normalisation, offline support, trust and data saturation. These components were included as latent variables in an SEM to evaluate the credibility, and subsequently confirm the viability of the theory of skilful surfing.Originality/valueTo the authors' knowledge, this study is the first of its kind to successfully model and define what it is to skilfully surf health information online whilst pregnant, with empirical and theoretical underpinnings.
Improving value chain data lifecycle management utilising design for Lean Six Sigma methods
Authors: Trubetskaya Anna , McDermott Olivia , Durand Pierre , Powell Daryl John 
Published: May 2024

PurposeThis project aims to optimise a secondary agricultural company’s reporting and data lifecycle by providing self-help business intelligence at an optimal price point for all business users.Design/methodology/approachA design for Lean Six Sigma approach utilising the define, measure analyse, design and verify methodology was utilised to design a new reporting and data product lifecycle.FindingsThe study found that this approach allowed a very structured delivery of a complex program. The various tools used assisted greatly in delivering results while balancing the needs of the team.Practical implicationsThis study demonstrates how improving data analysis and enhanced intelligence reporting in agribusinesses enable better decision making and thus improves efficiencies so that the agribusiness can leverage the learnings.Social implicationsImproving data analysis increases efficiency and reduces agrifood food wastage thus improving sustainability and environmental impacts.Originality/valueThis paper proposes creating a standardised approach to deploying Six Sigma methodology to correct both the data provisioning lifecycle and the subsequent business intelligence reporting lifecycle. It is the first study to look at process optimisation across the agricultural industry’s entire data and business intelligence lifecycle.