bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harnessing light heterogeneity to optimise controlled environment agriculture
Authors: Claydon Will , Redmond Ethan J. , Vong Gina YW , Kluczkovski Alana , Thomas Alice , Sutton Phoebe , Denby Katherine , Ezer Daphne 
Published: August 2024

AbstractYield is impacted by the environmental conditions that plants are exposed to. Controlled environmental agriculture provides growers with an opportunity to fine-tune environmental conditions for optimising yield and crop quality. However, space and time constraints will limit the number of experimental conditions that can be tested, which will in turn limit the resolution to which environmental conditions can be optimised. Here we present an innovative experimental approach that utilises the existing heterogeneity in light quantity and quality across a vertical farm to evaluate hundreds of environmental conditions concurrently. It proposes a three-phase workflow for identifying critical light variables, which can guide targeted improvements in yield and energy use. Using an observational study design, we identify features in light quality that are most predictive of biomass in different microgreens crops (kale, radish and sunflower) that may inform future iterations of lighting technology development for vertical farms. The findings suggest that light quality, rather than just light intensity, plays a crucial role in uniform crop yields and that light sensitivities are variety-specific, highlighting the importance of tailored light recipes for different crops.
Live-tracking of replisomes reveals nutrient-dependent regulation of replication elongation rates inCaulobacter crescentus
Authors: Adhikashreni Inchara S , Joseph Asha Mary , Phadke Sneha , Badrinarayanan Anjana 
Published: August 2024

AbstractIn bacteria, commitment to genome replication (initiation) is intricately linked to nutrient availability. Whether growth conditions affect other stages of replication beyond initiation, remains to be systematically studied. To address this, we assess the replication dynamics ofCaulobacter crescentus, a bacterium that undergoes only single round of replication per cell cycle, by tracking the replisome across various growth phases and nutrient conditions. We find that the replication elongation rates slowdown as cells transition from exponential (high-nutrient) to stationary (low-nutrient) phase, and this contributes significantly to the overall cell cycle delay. While elongation rates are correlated with growth rates, both properties appear to be differentially influenced by nutrient status. This slowdown in replication progression is not associated with increased mutagenesis or upregulation of the DNA damage responses. We conclude that the growth conditions not only dictate the commitment to replication but also the rates of genome duplication. Such regulation appears to be distinct from stress-induced replication slowdown and likely serves as an adaptive mechanism to cope with fluctuations in nutrient availability in the environment.
Analysis of the effects of mating systems on lineage diversification across multiple genera
Authors: Xu Kuangyi 
Published: August 2024

SummaryThe transition from outcrossing to self-fertilization is a major evolutionary trend in plants, with selfing long hypothesized an evolutionary dead end. Recent theories suggest that elevated extinction rates may be restricted to highly selfing rather than mixed-mating populations. Previous analyses of the effects of mating systems on diversification found mixed results, varying by focal clades and potentially suffering from several limitations.We collected data on three mating-system-related characters. We also collected life form data to indirectly distinguish between mixed mating and highly selfing. We estimated speciation and extinction rates for character states, and state transition rates in 27 genera.We find that outcrossing lineages diversify at higher rates than selfing lineages, while the impact of mating systems on speciation is not consistent across genera. Among self-compatible lineages, annuals/short-lived exhibit significantly lower diversification rates than perennials. Models incorporating hidden states often provide a better fit than those without.The results suggest that selfing lineages overall have lower diversification rates. This may be primarily contributed by elevated extinction rates in highly selfing lineages, which may also explain the prevalence of mixed-mating systems. However, the influences of mating systems on diversification may be often driven by other factors correlated with mating system transitions.
Description of Bacterial RNA Transcripts Detected inMycobacterium tuberculosis– Infected Cells from Peripheral Human Granulomas using Single Cell RNA Sequencing
Authors: Moos Philip J. , Carey Allison F. , Joseph Jacklyn , Kialo Stephanie , Norrie Joe , Moyarelce Julie M. , Amof Anthony , Nogua Hans , Lim Albebson L. , Barrows Louis R. 
Published: August 2024

AbstractMycobacterium tuberculosis(Mtb) remains a global human health threat and a significant cause of human morbidity and mortality. We document here the capture of Mtb transcripts in libraries designed to amplify eukaryotic mRNA. These reads are often considered spurious or nuisance and are rarely investigated. Because of early literature suggesting the possible presence of polyadenylated transcripts in Mtb RNA, we included the H37Rv Mtb reference genome when assembling scRNA seq libraries from fine needle aspirate samples from patients presenting at the TB clinic, Port Moresby General Hospital, Papua New Guinea. We used 10X Genomics single-cell RNA sequencing transcriptomics pipeline, which initiates mRNA amplification with poly-T primers on ∼30-micron beads designed to capture, in this case, human mRNA associated with individual cells in the clinical samples. Utilizing the 10X Genomics Cell Ranger tool to align sequencing reads, we consistently detected bacterial small and large ribosomal subunit RNA sequences (rrs and rrl, respectively) and other bacterial gene transcripts in the cell culture and patient samples. We interpret Mtb reads associated with the host cell’s unique molecular identifier (UMI) and transcriptome to indicate infection of that individual host cell. The Mtb transcripts detected showed frequent sequence variation from the reference genome, with greater than 90% of the rrs or rrl reads from many clinical samples having at least 1 sequence difference compared to the H37Rv reference genome. The data presented includes only bacterial sequences from patients with TB infections that were confirmed by the hospital pathology lab using acid-fast microscopy and/or GeneXpert analysis. The repeated, non-random nature of the sequence variations detected in Mtb rrs and rrl transcripts from multiple patients, suggests that, even though this appears to be a stochastic process, there is possibly some selective pressure that limits the types and locations of sequence variation allowed. The variation does not appear to be entirely artefactual, and it is hypothesized that it could represent an additional mechanism of adaptation to enhance bacterial fitness against host defenses or chemotherapy.
Stabilizing selection generates selection against introgressed DNA
Authors: Veller Carl , Simons Yuval 
Published: August 2024

AbstractDNA introgressed from one population into another is often deleterious to the recipient population if the two populations have diverged genetically from one another. Previous explanations of this phenomenon have posited negative interactions between donor-population alleles and the recipient population’s genome or environment, or higher genetic load in the donor population. Here, we show that stabilizing selection on quantitative traits—even around the same optimal trait values in the two populations and when the populations are demographically identical—generates selection against the minor-parent ancestry in a population formed via unequal admixture of the two populations. We calculate the rate at which minor-parent ancestry is purged under this mechanism, both in the early generations after admixture and in the long term, and we verify these calculations with whole-genome simulations. Because of its ubiquity, stabilizing selection offers a general mechanism for the deleterious effect of introgressed ancestry.
Unveiling Genetic Associations: InvestigatingCLDN16, GRID2, NRG3,andCACNG4Gene Polymorphisms with Insulin Resistance Risk Among Normal BMI Individuals in the Indian Population
Authors: Thummala Sabitha , Khan Ghori Junaid Ahmed , Fathima Sarah , Saikia Katherine , Kruthi Nithya , Duraimani Shanti Lakshmi , Balamurali AR , Ranganathan Rahul 
Published: August 2024

AbstractStudies estimate that India has about 65+ million diabetic patients with a substantial impending increase, making it the international ‘diabetes capital’. Diabetes Mellitus is a metabolic disorder which is signified by elevated blood sugar levels due to defects in insulin action, secretion or both. Insulin resistance (IR) or insulin resistance-linked obesity is also known to be a causing factor of Metabolic syndrome which is a combination of cardiovascular risk factors that include raised fasting plasma glucose, central obesity, hypertension, raised triglycerides, and reduced High-Density Lipoprotein (HDL) cholesterol. This study investigated the association between four single nucleotide polymorphisms (SNPs) in the selected genes - rs6801387 (CLDN16), rs72872727 (GRID2), rs1414756 (NRG3), and rs8065294 (CACNG4) and (IR) among a normal BMI Indian population. Through Chi-Square tests, we detected significant associations between SNP genotypes and (IR). Allele frequency analysis revealed higher frequencies of allele G (rs6801387) and T (rs72872727) among individuals with HOMA2-IR >2, while allele T (rs8065294) indicated decreased risk, emphasizing the relevance of genetic factors in metabolic disorders. The differences in clinical parameters such as fat mass, serum triglycerides and HbA1c between the cases and controls highlights the multifactorial nature of the condition. Inheritance model suggested the dominant inheritance for rs6801387 and rs72872727 and codominant inheritance for rs1414756 and rs806529, offering insights into genetic associations with IR. Despite the study’s moderate sample size,these genetic biomarkers exhibit strong susceptibility to the studied condition, showing the importance of exploring their functional significance and underlying biological mechanisms in future research endeavours.
Parent attitudes and behaviors associated with household food security among rural lower income families
Authors: Moore Amy M. , Savage Jennifer S. , Poulsen Melissa N. , Hosterman Jennifer Franceschelli , McCabe Carolyn F. , Bailey-Davis Lisa 
Published: August 2024

ABSTRACTObjectiveTo examine associations between Theory of Planned Behavior constructs related to parent engagement in health-promoting behaviors and food resource management with household food security status.MethodsA cross-sectional secondary analysis of baseline data from 1622 parents enrolled in the ENCIRCLE study, a pragmatic cluster-randomized controlled trial to prevent obesity among preschool-aged children from rural lower-income families. Logistic regression models examined associations between parent engagement in health-promoting behaviors (attitude, subjective norm, perceived behavioral control) and food resource management (self-confidence, behaviors) with household food security status.ResultsParents with greater perceived behavioral control (OR=1.44, CI:1.14-1.82) and food resource management self-confidence (OR=2.08, CI:1.80-2.41) had significantly higher odds of experiencing household food security in adjusted models.Conclusions and ImplicationsFindings suggest that perceived behavioral control and food resource management self-confidence may help safeguard lower-income families. Health promotion efforts should target these factors to help parents engage in health-promoting behaviors during times of economic hardship.
Australian medical research that considered sex as a biological variable: a meta-analysis
Authors: Ryan Janelle , Landen Shanie , Harley Vincent 
Published: August 2024

AbstractSubjects in medical research have predominantly been male (1). Women experience 50-75% more adverse drug responses (2) resulting in withdrawn medications (3). While sex differences in metabolism, disease and treatment response are increasingly recognised, sex-informed medicine is lagging. In 2016, USAs National Institutes of Health (NIH) formulated the Sex as a Biological Variable policy (4), stating that grant recipients must consider sex in experimental design, planning, analysis and reporting of their findings. Australian data is lacking on the inclusion of both males and females as well as appropriate analysis of sex differences.We analysed the 219 Medical Journal of Australia (MJA) research articles over 2019-2023 (Box 1). We tallied when; i) both males and females were included in the study, ii) sex differences were reported and/or considered, and iii) the analysis was appropriate to support sex-related claims.We found that articles published in MJA are including males and females, however testing of sex differences is uncommon and appropriate statistical analysis is lacking. We hope that this article will bring attention to this fundamental issue and improve future efforts to investigate sex differences.
Health Data Nexus: An Open Data Platform for AI Research and Education in Medicine
Authors: Adams January , Cymerys Rafal , Szuster Karol , Hekman Daniel , Salo Zoryana , Solanki Rutvik , Mamdani Muhammad , Johnson Alistair , Ryniak Katarzyna , Pollard Tom , Rotenberg David , Haibe-Kains Benjamin 
Published: August 2024

ABSTRACTWe outline the development of the Health Data Nexus, a data platform which enables data storage and access management with a cloud-based computational environment. We describe the importance of this secure platform in an evolving public sector research landscape that utilizes significant quantities of data, particularly clinical data acquired from health systems, as well as the importance of providing meaningful benefits for three targeted user groups: data providers, researchers, and educators. We then describe the implementation of governance practices, technical standards, and data security and privacy protections needed to build this platform, as well as example use-cases highlighting the strengths of the platform in facilitating dataset acquisition, novel research, and hosting educational courses, workshops, and datathons. Finally, we discuss the key principles that informed the platform’s development, highlighting the importance of flexible uses, collaborative development, and open-source science.
Benchmarking Vision Encoders for Survival Analysis using Histopathological Images
Authors: Nizami Asad , Halder Arita 
Published: August 2024

AbstractCancer is a complex disease characterized by the uncontrolled growth of abnormal cells in the body but can be prevented and even cured when detected early. Advanced medical imaging has introduced Whole Slide Images (WSIs). When combined with deep learning techniques, it can be used to extract meaningful features. These features are useful for various tasks such as classification and segmentation. There have been numerous studies involving the use of WSIs for survival analysis. Hence, it is crucial to determine their effectiveness for specific use cases. In this paper, we compared three publicly available vision encoders-UNI, Phikon and ResNet18 which are trained on millions of histopathological images, to generate feature embedding for survival analysis. WSIs cannot be fed directly to a network due to their size. We have divided them into 256 × 256 pixels patches and used a vision encoder to get feature embeddings. These embeddings were passed into an aggregator function to get representation at the WSI level which was then passed to a Long Short Term Memory (LSTM) based risk prediction head for survival analysis. Using breast cancer data from The Cancer Genome Atlas Program (TCGA) and k-fold cross-validation, we demonstrated that transformer-based models are more effective in survival analysis and achieved better C-index on average than ResNet-based architecture. The code1for this study will be made available.
Treatment Efficacy of Theophylline in ADYC5 Dyskinesia: A Retrospective Case Series Study
Authors: Taenzler Dirk , Hause Frank , Merkenschlager Andreas , Sinz Andrea 
Published: August 2024

AbstractBackgroundADCY5-related dyskinesia is a rare disorder caused by mutations in the ADCY5 gene resulting in abnormal involuntary movements. Currently, there are no standardized guidelines to treat this condition.ObjectivesThe aim of this study is to evaluate the efficacy of theophylline administration in improving symptoms and quality of life in patients with ADCY5-related dyskinesia.MethodsA retrospective study was conducted involving 12 patients (aged 2-34 years) with ADCY5-related dyskinesia. Participants completed a questionnaire about theophylline administration, including dosage, improvement of symptoms, adverse effects, and changes in quality of life. Data were analyzed for reported efficacy and side effects.ResultsTheophylline administration demonstrated substantial efficacy, with 92% (11 out of 12) of patients reporting significant improvements in their movement disorders. The average improvement score was 7.0 (± 1.9) on a 10-point scale. Notable improvements included reductions in severity and frequency of episodes, improved gait, more independent mobility, psycho-social well-being, and quality of sleep. Adverse effects were reported by 6 patients, including dystonia, speech worsening, headaches, nausea, impaired sleep, and agitation.ConclusionsTheophylline shows substantial promise as a treatment option for ADCY5-related dyskinesia, improving various aspects of patients’ quality of life and movement disorder symptoms. Further research is needed to optimize dosing, to understand long-term effects, and to explore combinational drug therapies. Despite the small cohort size and the retrospective nature of this study, the results support theophylline administration to decrease dyskinetic movements and enhance overall quality of life in patients.
‘We need to feel that the Government value our lives’: Examining Irish women’s experience of cervical screening services
Authors: McGregor Royanne , Foley Sarah 
Published: August 2024

AbstractCervical cancer is one of the top three cancers diagnosed in women globally. When women have access to a testing programme, abnormal cells can be detected to prevent the development of cancer. Research to date indicates that social and cultural barriers are the top two barriers in accessing cervical screening. In Ireland there may be a lack of trust in the National Cervical Screening programme due to previous mishandling of tests, and media coverage of the impacts of inaccurate screening results in Ireland. To understand impact of the health scandal on women’s trust in cervical screening in Ireland, nine Irish women ages between 25-65 were interviewed. Data was thematically analysed using a feminist perspective to centre the women’s voices in making sense of their appraisal and engagement with services. The data analysis resulted in four themes: Personal Reflections on Systemic Failure; Collective Concern and Blame; Decision Making Influencers and Rebuilding Knowledge and Trust. This analysis conveys distrust in the Irish Cervical Screening programme, feelings of anger, and a sense of neglect from the services. Irish women now place their trust in each other, the experience of their friends, families, their local GP. We discuss these finding to explore how Irish women have reinterpreted the narrative over the screening test in Ireland, and the potential to decrease concern around the topic by incorporating this experience into official narratives. This scandal heightened existing distrust and concern for the quality of women’s screening services, and therefore has global relevance which can be applied to screening services more generally.
Remarkable similarity in oxygen tolerance among taxonomically diverse marine taxa revealed through hierarchical analysis
Authors: Essington Timothy E. , Thorson James T. , Deutsch Curtis 
Published: August 2024

AbstractSpecies’ ranges are shifting in response to increasing temperature and decreasing oxygen in coastal oceans. Forecasting these shifts is limited by information on physiological oxygen thresholds and how they depend on temperature. Here, we adopt an ecophysiological metric, the metabolic index, and estimate its parameters from data collected on marine taxa using phylogenetic trait imputation. The metabolic index is the ratio of temperature-dependent rates of oxygen supply to basal oxygen demands. By applying a hierarchical phylogenetic model to a data set of 74 marine taxa that accounts for both taxonomic distance (from Linnean classification) and biases related to lab methods, we find that the critical oxygen pressure at a reference body size and temperature is remarkably consistent across taxa, ranging 2.9 to 4.9 kPa. In comparison, the estimated effect of temperature on the critical oxygen pressure was more variable among taxa. These findings suggest that species-level differences in oxygen tolerance might be primarily related to differences in body size and preferred temperature. Further, this work provides data-informed distributions of parameters for species that lack experimental data to aid species distribution forecasting.
Modeling statin-induced myopathy with human iPSCs reveals that impaired proteostasis underlies the myotoxicity and is targetable for the prevention
Authors: Zhao Xiaolin , Ni Liyang , Kubo Miharu , Matsuto Mariko , Sakurai Hidetoshi , Shimizu Makoto , Takahashi Yu , Sato Ryuichiro , Yamauchi Yoshio 
Published: August 2024

AbstractStatins, HMG-CoA reductase inhibitors, have been widely prescribed to lower circulating low-density lipoprotein cholesterol levels and reduce the risk of cardiovascular disease. Although statins are well tolerated, statin-associated muscle symptoms (SAMS) are the major adverse effect and cause statin intolerance. Therefore, understanding the molecular mechanisms of SAMS and identifying effective strategies for its prevention are of significant clinical importance; however, both remain unclear. Here we establish a model of statin-induced myopathy (SIM) with human induced pluripotent stem cell (hiPSC)-derived myocytes (iPSC-MCs) and investigate the effect of statins on protein homeostasis (proteostasis) that affects skeletal muscle wasting and myotoxicity. We show that treating hiPSC-MCs with statins induces atrophic phenotype and myotoxicity, establishing a hiPSC-based SIM model. We then examine whether statins impair the balance between protein synthesis and degradation. The results show that statins not only suppress protein synthesis but also promote protein degradation by upregulating the expression of the muscle-specific E3 ubiquitin ligase Atrogin-1 in a mevalonate pathway-dependent manner. Mechanistically, blocking the mevalonate pathway inactivates the protein kinase Akt, leading to the inhibition of mTORC1 and GSK3β but the activation of FOXO1. These changes explain the statin-induced impairment in proteostasis. Finally, we show that pharmacological blockage of FOXO1 prevents SIM in hiPSC-MCs, implicating FOXO1 as a key mediator of SIM. Taken together, this study suggests that the mevalonate pathway is critical for maintaining skeletal muscle proteostasis and identifies FOXO1 as a potential target for preventing SIM.