bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating a Cassava Crop Growth Model by Optimizing Genotypic-Specific Parameters Using Multi-environment Trial Breeding Data
Authors: Okoma Pamelas M. , Kayondo Siraj S. , Rabbi Ismail Y. , Moreno-Cadena Patricia L. , Hoogenboom Gerrit , Jannink Jean-Luc 
Published: November 2024

AbstractCassava (Manihot esculentaCrantz) is a critical food security crop for sub-Saharan Africa. Efforts to improve cassava through breeding have expanded over the past decade. At the same time, crop growth models (CGM) are becoming common place in breeding efforts to expand the inference of evaluations of breeding germplasm to environments that have not been tested and to prepare for breeding for adaptation to future climates. We parameterized a CGM, the CROPGRO-MANIHOT-Cassava model in the DSSAT family of models, using data on 67 clones from the International Institute of Tropical Agriculture cassava breeding program evaluated from 2017 to 2020 and over eight locations in Nigeria using trial and error parameter adjustments and the General Likelihood Uncertainty Estimation method. Our objectives were to assess the feasibility of this large-scale calibration in the context of a cassava breeding program and to identify systematic biases of the model. For each cultivar we calculated the Pearson correlation between model prediction and observation across the environments, as well as root mean squared error and d statistics. As a result of calibration, the correlation coefficient increased from −0.03 to +0.08, the RMSE dropped from 21 t ha-1to 5 t ha-1while d increased from 0.23 to 0.44. We found that the model underestimated root yield in dry environments (low precipitation and high temperature) and overestimated root yield in wet environments (high precipitation and low temperature). Our experience suggests both that CGM calibration could become a routine component of the cassava breeding data analysis cycle and that there are opportunities for model improvement.
How reliably can species co-occurrence be inferred from occupancy models?
Authors: Louvrier Julie , Fidino Mason , Stuardo Josefa Vergara , Gimenez Olivier 
Published: November 2024

AbstractInterspecific interactions, such as predation, competition, and mutualism, are fundamental to the structure and function of any biotic community. Understanding these interactions provides valuable insights into community dynamics and informs conservation efforts. One common approach to studying these interactions is through co-occurrence patterns, which remain essential for understanding species relationships. Occupancy models have emerged as powerful tools to investigate these patterns, offering a flexible framework for ecological questions. Among these models, the co-occurrence framework developed by Rota et al. (2016) has seen widespread applications across various species and habitats.In this study, we used simulations to evaluate the performance of the Rota et al. (2016) co-occurrence model under different study designs and species interaction scenarios. Specifically, we examined how the bias and precision of species occupancy estimates are influenced by the presence or absence of another species, varying the number of sampling units surveyed and the number of temporal replicates per unit. Additionally, we compared the co-occurrence model’s performance with a simpler model that does not account for species interactions to determine when statistically significant co-occurrence patterns emerge.We observed that occupancy parameters become more precise as the intensity of species avoidance increased, and while the number of sampling sites significantly influenced precision, the number of temporal replicates did not. Notably, the co-occurrence model outperformed the non-interaction model only when species avoidance was strong and at least 150 sites were sampled. Based on these results, we recommend a minimum of 150 sampling sites when applying the Rota et al. (2016) model to evaluate co-occurrence between two potentially interacting species. Our study emphasizes the need for further development of methods capable of detecting interaction signals, even at low to moderate interaction levels, and in studies with fewer sampling sites.
Single-Cell Atlas of AML Reveals Age-Related Gene Regulatory Networks in t(8;21) AML
Authors: Whittle Jessica , Meyer Stefan , Lacaud Georges , Baker Syed Murtuza , Iqbal Mudassar 
Published: November 2024

AbstractBackgroundAcute myeloid leukemia (AML) is characterized by cellular and genetic heterogeneity, which correlates with clinical course. Although single-cell RNA sequencing (scRNA-seq) reflect this diversity to some extent, the low sample numbers in individual studies limit the analytic potential of comparisons of specific patient groups.ResultsWe performed large scale integration of published scRNA-seq datasets to create a unique single-cell transcriptomic atlas for AML (AML scAtlas), totaling 748,679 cells, from 159 AML patients and 44 healthy donors from 20 different studies. This is the largest single-cell data resource for AML to our knowledge, publicly available athttps://cellxgene.bmh.manchester.ac.uk/AML/. This AML scAtlas, allowed exploration of the clinical importance of age in t(8;21) AML to an unprecedented level, given thein-uteroorigin of pediatric disease. We uncovered age-associated gene regulatory network (GRN) signatures, which we validated using bulk RNA sequencing data to delineate distinct groups with divergent biological characteristics. Furthermore, using an additional multiomic dataset (scRNA-seq and scATAC-seq), we created a de-noised GRN reflecting the previously defined age-related signatures.ConclusionsApplying integrated data analysis of the AML scAtlas, we reveal age-dependent gene regulation in t(8;21), perhaps reflecting immature/fetal HSC origin in prenatal origin disease vs postnatal origin. Our analysis revealed that BCLAF1, which is particularly enriched in t(8;21) pediatric AML of inferredin-uteroorigin, is a promising prognostic indicator. The AML scAtlas provides a powerful resource to investigate molecular mechanisms underlying different AML subtypes.
Tools for intersectional optical and chemical tagging on cell surfaces
Authors: Innes-Gold Sarah , Cheng Hanzeng , Liu Luping , Cohen Adam E. 
Published: November 2024

AbstractWe present versatile tools for intersectional optical and chemical tagging of live cells. Photocaged tetrazines serve as “photo-click” adapters between recognition groups on the cell surface and diverse chemical payloads. We describe two new functionalized photocaged tetrazine structures which add a light-gating step to three common cell-targeting chemical methods: HaloTag/chloroalkane labeling, nonspecific primary amine labeling, and antibody labeling. We demonstrate light-gated versions of these three techniques in live cultured cells. We then explore two applications: monitoring tissue flows on the surface of developing zebrafish embryos, and combinatorial multicolor labeling and sorting of optically defined groups of cells. Photo-click adapters add optical control to cell tagging schemes, with modularity in both tag and cell attachment chemistry.
Isotonic medium treatment limits burn wound microbial colonization and improves tissue repair
Authors: Horn Adam , Wagner Andrew S. , Hou Yiran , Zajac Jocelyn C. , Fister Alexandra M. , Chen Zhili , Pashaj Joana , Junak Mary , Mercado Soto Nayanna M. , Gibson Angela , Huttenlocher Anna 
Published: November 2024

AbstractBurn injuries undergo a complex healing process in which progressive spreading of epithelial damage can lead to secondary complications such as wound infection, which is a major driver of mortality among burn patients. We recently reported that burning larval zebrafish triggers dysregulated keratinocyte dynamics compared to mechanical injury. Here, we investigate keratinocyte behavior following burn injury and the subsequent potential for microbial colonization of burn wounds over time. Real-time imaging, coupled with tracking of photoconverted cells, revealed that early keratinocyte motility contributes to the spread of epithelial damage beyond the initial site of burn injury and that increased epithelial damage was associated with wound colonization by the fungal pathogenCandida albicans. Modulating osmotic balance by treating larval zebrafish with isotonic medium limited the spread of epithelial damage and reduced microbial colonization of burn wounds. Using cultured human skin, we found that topical treatment with isotonic solution (saline) similarly prevented the spread of epithelial damage over time. These findings indicate that keratinocyte behavior contribute to burn wound progression in larval zebrafish and link keratinocyte dynamics to microbial colonization of burn wounded tissue.
Exogenous ephrin-A3 administration restores vaginal epithelial barrier function in progestin-treated mice
Authors: Liu Mohan , Miguel Rodolfo D Vicetti , Aceves Kristen , Cherpes Thomas L 
Published: November 2024

ABSTRACTDesmosomes are junctional complexes that confer mechanical strength and enhance epithelial barrier function at mucosal surfaces by anchoring intermediate filaments to plasma membrane. While these roles are less explored in vaginal vs. cutaneous epithelium, we previously reported that treating mice with the progestin depot medroxyprogesterone acetate (DMPA) reduces vaginal epithelial levels of the desmosomal cadherins desmoglein-1 (DSG1) and desmocollin-1 (DSC1) and weakens vaginal epithelial barrier function. We also showed these effects were avoided by treating mice with DMPA and a conjugated equine estrogen vaginal cream. The current investigation further explored the effects of sex steroids on vaginal epithelial integrity, identifying ephrin-A3 (EFNA3) as a key regulator of desmosomal cadherin gene expression. We observed topical administration of recombinant EFNA3 (rEFNA3) promotes vaginal DSG1 expression in a biphasic dose-dependent manner and partially reverses the loss of vaginal epithelial barrier function induced by DMPA treatment. Consistent with this effect, morbidity and mortality elicited by genital herpes simplex virus type 2 infection were delayed, but not prevented, in mice administered DMPA and rEFNA3 vs. DMPA and vehicle. Together, these studies identify EFNA3 as an important regulator of desmosomal function in vaginal epithelium and improve current understanding of sex steroid-mediated mechanisms that control vaginal epithelial barrier function.
Golden eagles regularly use gravity waves to soar in the Alps: new insights from high-resolution weather data
Authors: Carrard Tom , Nourani Elham , Jansing Lukas , Zimmermann Tim , Sumasgutner Petra , Tschumi Matthias , Jenny David , Wikelski Martin , Safi Kamran , Sprenger Michael , Scacco Martina 
Published: November 2024

1AbstractSoaring flight developed as a result of behavioural and morphological adaptations that allow birds to reduce the metabolic cost of flight by harnessing the energy available in the atmosphere. Despite an increased attention given in the last decades to the physics and ecology that allow soaring flight, its study has been limited by the generally low spatio-temporal resolution of available atmospheric data. This constrained our ability to quantify the atmospheric conditions that allow soaring, and limited our understanding of its flexibility in different uplift conditions. While the use of updraughts such as thermals and orographic lifting are well described in the literature (albeit only quantified through atmospheric proxies), the use of others, such as gravity waves, was hypothesised but largely undocumented. Recent advancements in high-resolution atmospheric modelling, with hourly output available at the kilometer-scale grid spacing, offer new opportunities to investigate the flexibility of soaring flight in response to complex atmospheric dynamics. In this study, we used a combination of a high-resolution atmospheric analysis and high-resolution GPS tracking data to characterise the updraught sources used by golden eagles,Aquila chrysaetos, in the European Alps. We document that golden eagles in this region repeatedly use gravity waves, and that while thermals were still the main updraught source used for soaring, gravity waves were involved in at least 19% of the inspected soaring segments. In winter, when thermals were more scarce, the quasi-totality of soaring events were powered by gravity waves or orographic lifting, largely expanding the environmental energy available to soaring birds and therefore the landscape connectivity in topographically complex regions. Our results also emphasise the difficulty to distinguish between convective (thermals) and dynamic updraught sources, as these co-occur within the boundary layer over complex terrain.
Do short-term responses to product manipulation health warnings predict subsequent quitting-related behaviours? Findings from an Australian cohort study
Authors: Brennan Emily , Gascoyne Claudia , Dunstone Kimberley , Thrasher James F , Hoek Janet , Wakefield Melanie , Durkin Sarah 
Published: November 2024

ABSTRACTBackgroundPictorial health warnings on tobacco packs can stimulate short-term cognitive and emotional responses that lead to quit attempts. We tested novel product attribute health warnings (PAHWs) that corrected misperceptions about harm created by the use of filter-venting, menthol and roll-your-own tobacco. PAHWs uniquely influenced outcomes assessing knowledge of industry manipulation of cigarettes, industry-centric negative emotional responses, and product-specific smoking dissonance. In this study, we examined if these unique short-term responses predicted subsequent quitting-related behaviours.MethodWe analysed follow-up data from a between-subjects online experiment that assessed effects of new PAHWs. Participants were randomised to view PAHWs alone (PAHW condition) or with a complementary video (PAHW+Video), and exposure occurred during a baseline session and then repeatedly each day for 7 days. Short-term PAHW responses were measured at 8-day follow-up (N=712). Quitting-related behaviours were measured at 4-week follow-up (N=301). Covariate-adjusted logistic regression models examined associations between short-term PAHW responses and subsequent quitting-related behaviours.ResultsTwo of the short-term responses – knowledge of industry manipulation of cigarettes, and product-specific smoking dissonance – significantly and positively predicted all three quitting-related outcomes: smoke-limiting micro-behaviours (e.g., foregoing cigarettes), quit attempts, and 7-day sustained abstinence. Additionally, industry-centric negative emotional responses significantly and positively predicted smoke-limiting micro-behaviours and 7-day sustained abstinence, but not quit attempts.ConclusionPAHWs featuring corrective information about the tobacco industry’s manipulation of tobacco products elicited short-term responses that predicted subsequent engagement in smoke-limiting micro-behaviours, quit attempts, and sustained quit attempts. PAHWs can complement other health warnings featuring the health risks of smoking and may help motivate people who smoke to quit and stay quit.
Sperm sequencing reveals extensive positive selection in the male germline
Authors: Neville Matthew DC , Lawson Andrew RJ , Sanghvi Rashesh , Abascal Federico , Pham My H , Cagan Alex , Nicola Pantelis A , Bayzetinova Tetyana , Baez-Ortega Adrian , Roberts Kirsty , Lensing Stefanie V. , Widaa Sara , Alcantara Raul E , García María Paz , Wadge Sam , Stratton Michael R , Campbell Peter J , Small Kerrin , Martincorena Iñigo , Hurles Matthew E , Rahbari Raheleh 
Published: November 2024

AbstractMutations that occur in the cell lineages of sperm or eggs can be transmitted to offspring. In humans, positive selection of driver mutations during spermatogenesis is known to increase the birth prevalence of certain developmental disorders. Until recently, characterising the extent of this selection in sperm has been limited by the error rates of sequencing technologies. Using the duplex sequencing method NanoSeq, we sequenced 81 bulk sperm samples from individuals aged 24 to 75 years. Our findings revealed a linear accumulation of 1.67 (95% CI = 1.41-1.92) mutations per year per haploid genome, driven by two mutational signatures associated with human ageing. Deep targeted and exome NanoSeq of sperm samples identified over 35,000 germline coding mutations. We detected 40 genes (31 novel) under significant positive selection in the male germline, implicating both activating and loss-of-function mechanisms and diverse cellular pathways. Most positively selected genes are associated with developmental or cancer predisposition disorders in children, while four genes that exhibit elevated frequencies of protein-truncating variants in healthy populations. We find that positive selection during spermatogenesis drives a 2-3 fold elevated risk of known disease-causing mutations in sperm, resulting in 3-5% of sperm from middle-aged to elderly individuals carrying a pathogenic mutation across the exome. These findings shed light on the dynamics of germline mutations and highlight a broader increased disease risk for children born to fathers of advanced age than previously appreciated.
Device-measured moderate-to-vigorous physical activity and prognosis of inflammatory bowel disease
Authors: He Zixuan , Sun Yuhao , Huang Hanyi , Liu Yilong , Dan Lintao , Ruan Xixian , Fu Tian , Li Zhaoshen , Wang Xiaoyan , Chen Jie , Bai Yu 
Published: November 2024

AbstractImportanceEvidence on physical activity recommendations for inflammatory bowel disease (IBD) patients is limited, with concerns about high-intensity activity.ObjectiveTo investigate the associations of accelerometer-measured moderate-to-vigorous physical activity (MVPA) with bowel resection risk and mortality among individuals with IBD.Design, setting, and participantsThis longitudinal cohort study collected data from 1,303 UK Biobank participants with IBD diagnosis and device-measured physical activity from 2013 to 2015, with follow-up data examined until 2022.ExposuresMVPA was classified based on data measured by wrist-worn accelerometers over a 7-day period. MVPA patterns were defined as inactive (< 150 minutes/week), active weekend warrior (≥ 150 minutes/week, ≥50% of total MVPA achieved in 1-2 days), and regularly active (≥ 150 minutes/week, not active weekend warrior).Main Outcomes and MeasuresThe bowel resection was identified through operational records from hospital inpatient data of the National Health Service. Deaths were documented through linkage to the national death register. Associations were estimated using multivariable Cox regression models and nonlinearity was assessed by restricted cubic spline.ResultsDuring a median follow-up of 7.8 years, 56 incident bowel resection cases and 86 deaths were documented. After multivariable adjustment, participants in the highest tertile of MVPA duration had lower risks of bowel resection (HR, 0.44; 95% CI, 0.22-0.86) and mortality (HR, 0.49; 95% CI, 0.27-0.89) compared to those in the lowest tertile. MVPA duration is linearly associated with bowel resection (Pnon-linear= 0.13) while its dose-response relationship with mortality plateaus at approximately 58 min/day (Pnon-linear= 0.02). Regarding MVPA patterns, the active weekend warrior pattern was inversely associated with bowel resection risk (HR, 0.28; 95% CI, 0.12-0.65), the regularly active pattern was inversely associated with both bowel resection risk (HR, 0.37; 95% CI, 0.19-0.69) and mortality (HR, 0.53; 95% CI, 0.31-0.91) compared to the inactive.Conclusion and relevanceLonger accelerometer-measured MVPA was associated with reduced bowel resection risk and mortality. The regularly active pattern may be the optimal choice for individuals with IBD, while the active weekend warrior pattern still provides health benefits compared to being inactive.
Clinical Characteristics Associated with Functional Seizures in Individuals with Psychosis
Authors: Lake Allison M. , Reddy India A. , Havranek Robert , Davis Lea K. , Fox Jonah 
Published: November 2024

AbstractBackground and HypothesisFunctional seizures (FS) are episodes characterized by seizure-like events that are not caused by hypersynchronous neuronal activity. Prior studies have suggested an increased prevalence of psychotic disorders among patients with FS, but results have been inconsistent. We hypothesize that FS are associated with psychosis and that among patients with psychosis, the presence of FS may influence patient clinical characteristics, mortality, and medical resource utilization.Study DesignThe association between FS and psychosis was assessed using electronic health records data from a total of 752,883 individuals receiving care at Vanderbilt University Medical Center between 1989 and 2023. Analyses of the association between FS and psychiatric outcomes, sexual trauma, healthcare utilization, and other clinical comorbidities were conducted in a subset of 5,239 patients with psychosis.Study ResultsOdds of FS were elevated among patients with psychosis compared to controls (OR=10.17, 95% CI=8.55-12.08, p<0.001). Among patients with psychosis, those with FS exhibited higher rates of suicidality (OR=1.98, 95% CI=1.40-2.8, p<0.001), catatonia (OR=1.95, 95% CI=1.23-3.09, p=0.03), sexual trauma history (OR=2.98, 95% CI=2.08-4.26, p<0.001) and had a greater numbers of antipsychotic trials (4.56 versus 3.37, beta=1.16, SE=0.16, p<0.001) than those without FS. Furthermore, patients with comorbid FS had a greater numbers of hospital presentations at one, three, five, and ten years after receiving a psychosis diagnosis (p<0.001).ConclusionsFS are more common among patients with psychosis and are associated with increased healthcare utilization as well as an increased prevalence of suicidality, catatonia, and certain psychiatric and medical comorbidities.
Contrasting dissemination patterns of diploid cultivated cotton speciesGossypium herbaceumL. andG. arboreumL. in Antiquity
Authors: Viot Christopher R. 
Published: November 2024

AbstractThe textile use of cotton fibers from sister speciesGossypium arboreumL. (Tree Cotton) andG. herbaceumL. (Levant Cotton) began, respectively, in Asia in the eighth millennium BP and in Africa in the third millennium BP and probably earlier. Archaeological data show that cotton cultivation spread in the Antiquity over most tropical and subtropical regions suitable for agriculture in Afroeurasia. The geographical expansions of the two Old World cotton species appear very contrasted, in terms of their chronologies, in terms of the areas conquered, and as for their speed of diffusion.G. arboreumspread over humid or sub-humid regions of southern, western and eastern Asia atca. 0.8 to 1.7 km/yr, a rate close to that estimated for wheat from the Fertile Crescent to northwestern Europe during Antiquity, whileG. herbaceumspread over arid to sub-arid regions of Africa and western and central Asia, much later and more than five times faster thanG. arboreum. The very high speed of diffusion ofG. herbaceumcan be explained by the context and by the agricultural adaptations of this species but also leads to revisit the history of its domestication and beginning of cultivation.