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The WiDS Datathon 2025 requires participants to build a model to predict both an individual’s sex and their ADHD diagnosis using functional brain imaging data of children and adolescents and their socio-demographic, emotions, and parenting information. The task is to create a multi-outcome model to predict two target variables: 1) ADHD (1=yes or 0=no) and 2) female (1=yes or 0=no).
The project focused on validating the previously developed Greater Sage-Grouse Individual-based Model (GrSG IBM; LaGory et al. 2012, 2021). The objective was to transform this predictive, spatially and temporally explicit model into a portable resource to assist siting/resource managers in proactively assessing the cumulative impacts of wind energy development on the greater sage-grouse. Utilizing a bottom-up, individual-based approach, the GrSG IBM accounts for landscape context and species behavior, aiming to reduce uncertainty in estimating development impacts and support ecologically mindful land-based wind energy development. The validation effort covered approximately 6,540 km 2 near the Seven Mile Hill Wind Project in Wyoming. The GrSG IBM tool, built on the NetLogo platform (Tisue and Wilensky 2004), was executed over a 50-year period, with the analysis focusing on years following a 10-year initialization phase. Key results demonstrated the tool’s biological soundness across five key biological metrics: non-chick age class distribution (older than 10 weeks), adult sex ratio, life expectancy, population size, and overall population growth. For instance, the tool estimated that 58.6% of the non-chick population was reproductively immature, while the reference ranges from 51.4% to 57.8% (Patterson 1952, Rogers 1964). Experts confirmed the tool’s estimate was within a reasonable range for the species. The tool estimated average life expectancy of 1.43 years, while the reference ranges from 0.9 years to 1.1 years (Ammann 1957, Hamerstrom 1949). Experts also supported the model’s life-expectancy estimate as ecologically sound for the species in the study area. In terms of population change, the model estimated an annual shift between a 0.6% decline and a 1.0% increase over 50 years. While the reference suggests 2.9% annual decline in range-wide populations (Cortes et al. 2023), that includes many at-risk populations in South Dakota and Washington, for example. Our study area—in the northeastern part of Carbon County and western-edge of Albany County, Wyoming—is one of the remaining greater sage-grouse habitats supporting some of the most stable populations. Experts confirmed that the range of the annual population change spanning from a 0.6% decline to a 1.0% increase estimated by the tool was reasonable for our study area for this reason and confirmed that aligned with population estimates from existing studies on the greater sage-grouse and wind energy development in the study area (LeBeau et al. 2017a, Smith et al. 2024). Furthermore, the project showed that temporally explicit biological metrics generated by the GrSG IBM tool can complement the USGS’ Prioritizing Restoration of Sagebrush Ecosystems Tool (PReSET; Duchardt et al. 2021) by incorporating habitat restoration strategies into seasonal habitat suitability models to visualize population responses over time.
A total of 172 children from the DAISY study with multiple plasma samples collected over time, with up to 23 years of follow-up, were characterized via proteomics analysis. Of the children there were 40 controls and 132 cases. All 132 cases had measurements across time relative to IA. Sampling was not consistent for all children. There were 47 of the children who had samples taken and evaluated prior to IA (Pre-IA), and 131 children had measurements at or after IA, but prior to diagnosis of clinical T1D (Post-IA). The control children were frequency matched on HLA genotypes and age and sex with an observed lower frequency of first degree relatives within the control group versus the cases For machine learning the children that will develop islet autoantibodies the 40 control and 47 Pre-IA children were down-selected to a single sample time point. For the 40 control children this was the earliest sample collected and for the 47 Pre-IA children it was a random selection of the first or second time point prior to the detection of autoantibodies to assure the age distributions were not significantly different.
A total of 172 children from the DAISY study with multiple plasma samples collected over time, with up to 23 years of follow-up, were characterized via proteomics analysis. Of the children there were 40 controls and 132 cases. All 132 cases had measurements across time relative to IA. Sampling was not consistent for all children. There were 47 of the children who had samples taken and evaluated prior to IA (Pre-IA), and 131 children had measurements at or after IA, but prior to diagnosis of clinical T1D (Post-IA). The control children were frequency matched on HLA genotypes and age and sex with an observed lower frequency of first degree relatives within the control group versus the cases For machine learning the children that will develop islet autoantibodies the 40 control and 47 Pre-IA children were down-selected to a single sample time point. For the 40 control children this was the earliest sample collected and for the 47 Pre-IA children it was a random selection of the first or second time point prior to the detection of autoantibodies to assure the age distributions were not significantly different.
Gas chromatography-mass spectrometry-based metabolomics to identify molecular signatures of Type 1 Diabetes (T1D) in urine. We utilize three cohorts in different stages post-diagnosis: (1) new onset, (2) within one year of diagnosis and (3) after 6 years of diagnosis. There were 91 metabolites identified in all three datasets with complete data represented in each cohort dataset. Cohort 1 (CNMC): 32 T1D cases; 32 healthy controls siblings Cohort 2 (BDCD): 27 T1D cases; 27 healthy controls siblings Cohort 3 (IUSOM): 12 T1D cases; 20 healthy controls Cases and controls matched on sex and age
Background: Sweden reached the UNAIDS 90–90–90 target in 2015. It is important to reassess the HIV epi- demiological situation due to ever-changing migration patterns, the roll-out of PrEP and the impact of the COVID-19 pandemic. Aim: We aimed to assess the pro- gress towards the UNAIDS 95–95–95 targets in Sweden by estimating the proportion of undiagnosed people with HIV (PWHIV) and HIV incidence trends. Methods: We used routine laboratory data to inform a biomarker model of time since infection. When available, we used previous negative test dates, arrival dates for PWHIV from abroad and transmission modes to inform our incidence model. We also used data collected from the Swedish InfCareHIV register on antiretroviral therapy (ART). Results: The yearly incidence of HIV in Sweden decreased after 2014. In part, this was because the fraction of undiagnosed PWHIV had decreased almost twofold since 2006. After 2015, three of four PWHIV in Sweden were diagnosed within 1.9 and 3.2 years after infection among men who have sex with men and in heterosexual groups, respectively. While 80% of new PWHIV in Sweden acquired HIV before immigration, they make up 50% of the current PWHIV in Sweden. By 2022, 96% of all PWHIV in Sweden had been diag- nosed, and 99% of them were on ART, with 98% virally suppressed. Conclusions: By 2022, about half of all PWHIV in Sweden acquired HIV abroad. Using our new biomarker model, we assess that Sweden has reached the UNAIDS goal at 96–99–98.
The antiretroviral (ARV) drug combination of abacavir sulfate, dolutegravir, and lamivudine [ABC/DTG/3TC; Tri combination Anti-retroviral therapy (TC-ART)] has revolutionized HIV treatment by effectively targeting different stages of viral replication. Despite its therapeutic efficiency for maintaining low viremia in the mother during pregnancy, there are concerns for long-term liabilities in offspring that are indirectly exposed during vulnerable periods of development. The commensal microbiota plays a crucial role in maintaining overall gut health, and disruption of the microbiome is often linked to various extraintestinal effects such as immune dysregulation and inflammation. We recently reported the effects of this drug combination in altering fecal microbiome composition of aged rats perinatally exposed to ABC/DTG/3TC-ART. The fecal microbiome can provide only a snapshot of the composition of microbial community at the end of the digestive tract, which may not reflect the microbial population interacting with ileal mucosa. Thus, the current work reports the effects of this drug combination in the gut mucosa-associated microbiome of the same animals, which showed significant microbial diversity and species richness in high dose exposed female adult offspring, along with dose-dependent changes in Firmicutes/Bacteroidetes ratio. The high dose exposure also showed an increase in opportunistic bacterial species in male animals. Overall, we found that, similar to the fecal microbiome, perinatal exposure to TC-ART led to sex- and dose-dependent alterations in the gut mucosa-associated microbial population in aged rats, suggesting that early life exposure to these drugs may influence gut mucosa-associated immune responses and intestinal permeability.
While corn is considered to be a healthy food option, common agricultural practices, such as the application of soil amendments, might be introducing contaminants of concern (COC) into corn plants. The use of dredged material, which contain contaminants such as heavy metals, polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs), as a soil amendment is increasing. Contaminants from these amendments can accumulate in corn kernels harvested from plants grown on these sediments and potentially biomagnify in organisms that consume them. The extent to which secondary exposure to such contaminants in corn affect the mammalian central nervous system has been virtually unexplored. In this preliminary study, we examine the effects of exposure to corn grown in dredge amended soil or a commercially available feed corn on behavior and hippocampal volume in male and female rats. Perinatal exposure to dredge-amended corn altered behavior in the open-field and object recognition tasks in adulthood. Additionally, dredge-amended corn led to a reduction in hippocampal volume in male but not female adult rats. These results suggest the need for future studies examining how dredge-amended crops and/or commercially available feed corn may be exposing animals to COC that can alter neurodevelopment in a sex-specific manner. This future work will provide insight into the potential long-term consequences of soil amendment practices on the brain and behavior.
Background Numerous studies have already identified an association between excessive consumption of red meat and colorectal cancer (CRC). However, there has been a lack of detailed understanding regarding the disease burden linked to diet high in red meat and CRC. Objective We aim to offer evidence-based guidance for developing effective strategies that can mitigate the elevated CRC burden in certain countries. Methods We used the data from the Global Burden of Disease (GBD) Study 2019 to evaluate global, regional, and national mortality rates and disability-adjusted Life years (DALYs) related to diet high in red meat. We also considered factors such as sex, age, the socio-demographic index (SDI), and evaluated the cross-national inequalities. Furthermore, we utilized DALYs data from 204 countries and regions to measure cross-country inequalities of CRC by calculating the slope index of inequality and concentration index as standard indicators of absolute and relative inequalities. Discussion The results show that globally, the age-standardized mortality rate (ASMR) and age-standardized disability adjusted life year rate (ASDR) related to CRC due to diet high in red meat have decreased, with estimated annual percent change (EAPCs) of −0.32% (95% CI −0.37 to −0.28) and-0.18% (95% CI −0.25 to −0.11). Notably, the burden was higher among males and the elderly. The slope index of inequality rose from 22.0 (95% CI 18.1 to 25.9) in 1990 to 32.9 (95% CI 28.3 to 37.5) in 2019 and the concentration index fell from 59.5 (95% CI 46.4 to 72.6) in 1990 to 48.9 (95% CI 34.6 to 63.1) in 2019. Also, according to our projections, global ASDR and ASMR might tend to increase up to 2030. Conclusion ASMR and ASDR for CRC associated with high red meat diets declined globally from 1990 to 2019, but the absolute number of cases is still rising, with men and the elderly being more affected. CRC associated with diets high in red meat exhibits significant income inequality, placing a disproportionate burden on wealthier countries. Moreover, according to our projections, ASMR and ASDR are likely to increase globally by 2030. In order to address this intractable disease problem, understanding changes in global and regional epidemiologic trends is critical for policy makers and others.
Nitric oxide (NO), a bioactive molecule, is often involved in the regulation of physiological and biochemical processes in stressed plants. However, the effects of NO donors on dioecious plants remain unclear. Using a pot experiment, female and male Torreya grandis were used to study the role of sex and NO in salt stress tolerance. In the present study, female and male T. grandis seedlings pretreated with an NO donor (sodium nitroprusside, SNP) were exposed to salt stress, and then leaf relative water content (RWC), photosynthetic pigments, chlorophyll fluorescence parameters, NO and glutathione levels, oxidative damage, and antioxidant enzyme activities were investigated. Female T. grandis plants had better tolerance to salinity, as they were characterized by significantly higher RWC, pigment content, and photochemical activities of photosystem II (PSII) and fewer negative effects associated with higher nitrate reductase (NR) activity and NO content. Pretreatment with an NO donor further increased the endogenous NO content and NR activity of both female and male T. grandis plants compared with salt treatment. Moreover, pretreatment with an NO donor alleviated salt-induced oxidative damage of T. grandis , especially in male plants, as indicated by reduced lipid peroxidation, through an enhanced antioxidant system, including proline and glutathione accumulation, and increased antioxidant enzyme activities. However, the ameliorating effect of the NO donor was not effective in the presence of the NO scavenger (Nω-nitro-L-arginine methyl ester, L-name). In conclusion, enhanced salt tolerance in T. grandis plants is related to nitric oxide levels and the supply of NO donors is an interesting strategy for alleviating the negative effect of salt on T. grandis . Our data provide new evidence to contribute to the current understanding of NO-induced salt stress tolerance.
Nokuse Plantation, a 22,055 ha private conservation preserve in northwest Florida, is a recipient site for gopher tortoises translocated from development sites in Florida. Since 2006, Nokuse has received over 5,000 tortoises from multiple development sites. During 2013–2015, 52 tortoises were found sick (n = 14) or dead (n = 38) in multiple soft-release enclosures in which tortoises consistently exhibited clinical signs, with additional sick (n = 5) and dead (n = 5) tortoises presenting similarly during 2016–2017. When found alive, tortoises behaved abnormally (e.g., frequently out of burrows during cold weather, pacing along enclosure fencing), appeared emaciated, were lethargic, and had developed redness under plastron scutes. Similar numbers of male (n = 28) and female (n = 32) tortoises were recovered along with two of unidentified sex, including mainly adults (n = 59) and three subadults. Physical examination, blood analysis, and other diagnostics were indicative of starvation and dehydration. Most sick tortoises provided with supportive care recovered. Necropsy findings generally confirmed starvation, with no evidence of infectious pathogens or contaminants. There were no apparent differences in quality of habitat, plant community, or soil or water among affected and unaffected enclosures. Botanical surveys indicated adequate forage quality and quantity, with no poisonous exotic or native plants detected. No land management practices changed prior to this event. Analysis of epidemiological data and demographic factors from before and during this mortality event identified initial density of tortoises in the enclosures as exerting the strongest influence on detection of tortoise morbidity and mortality. We believe that the stress associated with mixing tortoises from different populations and at higher densities during translocation impacted an individual tortoise’s ability to obtain or absorb adequate nutrients from foraging, ultimately leading to a wasting condition consistent with starvation. Based on our findings, we recommend a maximum of 3 gopher tortoises per ha in soft-release enclosures for translocation, but further research is warranted to investigate the complexity of stress and social pressures associated with translocation.
Repetitive low-level blast exposure is one of the major occupational health concerns among US military service members and law enforcement. This study seeks to identify gene expression using microRNA and RNA sequencing in whole-blood samples from experienced breachers and unexposed controls. We performed experimental RNA sequencing using Illumina’s HiSeq 2500 Sequencing System, and microRNA analysis using NanoString Technology nCounter miRNA expression panel in whole-blood total RNA samples from 15 experienced breachers and 14 age-, sex-, and race-matched unexposed controls. We identified 10 significantly dysregulated genes between experienced breachers and unexposed controls, with FDR corrected <0.05: One upregulated gene, LINC00996 (long intergenic non-protein coding RNA 996); and nine downregulated genes, IGLV3-16 (immunoglobulin lambda variable 3-16), CD200 (CD200 molecule), LILRB5 (leukocyte immunoglobulin-like receptor B5), ZNF667-AS1 (ZNF667 antisense RNA 1), LMOD1 (leiomodin 1), CNTNAP2 (contactin-associated protein 2), EVPL (envoplakin), DPF3 (double PHD fingers 3), and IGHV4-34 (immunoglobulin heavy variable 4-34). The dysregulated gene expressions reported here have been associated with chronic inflammation and immune response, suggesting that these pathways may relate to the risk of lasting neurological symptoms following high exposures to blast over a career.
Environmental factors play an important role in obesity-related behaviors. Evidence indicates significant associations between weight and urban green spaces in adults, but it is not clear whether this relationship applies to adolescents. Therefore, our aim was to determine the associations between urban green spaces, greenness exposure and species richness in residential environments with physical activity and body mass index. Sixty-two adolescents between 12 and 18 years of age answered a self-administered questionnaire, providing information on height, weight, age, sex and home address. Data on socioeconomic deprivation were obtained from the European Index of Deprivation for Small Portuguese Areas. Physical activity levels were assessed using accelerometers. Urban green space counts and the normalized difference vegetation index values were measured using buffers along the roads with distances of 300, 500, 1000 and 1500 m from each participant’s residence. To quantify the species richness, the species richness index was used. Linear regression models were fitted to analyze whether urban green spaces, exposure to green spaces and species richness counts for each distance were associated with physical activity and self-reported body mass index. We did not find significant associations between the independent variables and the probability of overweight or obesity. The relationship between environmental variables, adolescents’ physical activity and body weight seems to be complex and further studies may contribute to better understanding of the topic.
Total mercury content (THg) in hair is an accepted biomarker for chronic dietary methylmercury (MeHg) exposure. In artisanal and small-scale gold mining (ASGM) communities, the validity of this biomarker is questioned because of the potential for contamination from inorganic mercury. As mining communities may have both inorganic and organic mercury exposures, the efficacy of the hair-THg biomarker needs to be evaluated, particularly as nations begin population exposure assessments under their commitments to the Minamata Convention. We sought to validate the efficacy of hair THg for public health monitoring of MeHg exposures for populations living in ASGM communities. We quantified both THg and MeHg contents in hair from a representative subset of participants (N = 287) in a large, population-level mercury exposure assessment in the ASGM region in Madre de Dios (MDD), Peru. We compared population MeHg-THg correlations and %MeHg values with demographic variables including community location, sex, occupation, and nativity. We observed that hair MeHg-THg correlations were high (r > 0.7) for all communities, regardless of location or nativity. Specifically, for individuals within ASGM communities, 81% (121 of 150 total) had hair THg predominantly in the form of MeHg (i.e., >66% of THg) and reflective of dietary exposure to mercury. Furthermore, for individuals with hair THg exceeding the U.S. EPA threshold (1.0 μg/g), 88 out of 106 (83%) had MeHg as the predominant form. As a result, had urine THg solely been used for mercury exposure monitoring, approximately 59% of the ASGM population would have been misclassified as having low mercury exposure. Our results support the use of hair THg for monitoring of MeHg exposure of populations in ASGM settings where alternative biomarkers of MeHg exposure are not feasible.
Cuticle coloration in insects is a consequence of the accumulation of pigments in a species-specific pattern. Numerous genes are involved in regulating the underlying processes of melanization and sclerotization, and their manipulation can be used to create externally visible markers of successful gene editing. To clarify the roles for many of these genes and examine their suitability as phenotypic markers in Lygus hesperus Knight (western tarnished plant bug), transcriptomic data were screened for sequences exhibiting homology with the Drosophila melanogaster proteins. Complete open reading frames encoding putative homologs for six genes (aaNAT, black, ebony, pale, tan, and yellow) were identified, with two variants for black. Sequence and phylogenetic analyses supported preliminary annotations as cuticle pigmentation genes. In accord with observable difference in color patterning, expression varied for each gene by developmental stage, adult age, body part, and sex. Knockdown by injection of dsRNA for each gene produced varied effects in adults, ranging from the non-detectable (black 1, yellow), to moderate decreases (pale, tan) and increases (black 2, ebony) in darkness, to extreme melanization (aaNAT). Based solely on its expression profile and highly visible phenotype, aaNAT appears to be the best marker for tracking transgenic L. hesperus.
The development of multiple chromosome-scale reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple genomes remains a significant challenge in nearly all eukaryotic systems. These challenges range from studying the evolution of chromosome structure, to finding candidate genes for quantitative trait loci, to testing hypotheses about speciation and adaptation. Here, we present GENESPACE, which addresses these challenges by integrating conserved gene order and orthology to define the expected physical position of all genes across multiple genomes. We demonstrate this utility by dissecting presence–absence, copy-number, and structural variation at three levels of biological organization: spanning 300 million years of vertebrate sex chromosome evolution, across the diversity of the Poaceae (grass) plant family, and among 26 maize cultivars. The methods to build and visualize syntenic orthology in the GENESPACE R package offer a significant addition to existing gene family and synteny programs, especially in polyploid, outbred, and other complex genomes.
Chagas disease, a significant public health concern in the Americas, is caused by a protozoan parasite, Trypanosoma cruzi. The life cycle of T. cruzi involves kissing bugs (Triatoma spp.) functioning as vectors and mammalian species serving as hosts. Raccoons (Procyon lotor) and opossums (Didelphis virginiana) have been identified as important reservoir species in the life cycle of T. cruzi, but prevalence in both species in the southeastern US is currently understudied. We quantified T. cruzi prevalence in these two key reservoir species across our study area in South Carolina, US, and identified factors that may influence parasite detection. We collected whole blood from 183 raccoons and 126 opossums and used PCR to detect the presence of T. cruzi. We then used generalized linear models with parasite detection status as a binary response variable and predictor variables of land cover, distance to water, sex, season, and species. Our analysis indicated that raccoons experienced significantly higher parasite detection rates than Virginia opossums, with T. cruzi prevalence found to be 26.5% (95% confidence interval [CI], 20.0–33.8) in raccoons and 10.5% (95% CI, 5.51–17.5) in opossums. Altogether, our results concur with previous studies, in that T. cruzi is established in reservoir host populations in natural areas of the southeastern US.
Ophidiomycosis, also known as snake fungal disease, is caused by Ophidiomyces ophidiicola and is a threat to snake conservation worldwide. Ophidiomycosis has been reported throughout much of the eastern US, and outbreaks have been associated with local population declines of already strained populations. Previous studies report significant variability in ophidiomycosis among species sampled, with higher prevalence typically observed in Nerodia spp. Although ophidiomycosis can lead to morbidity and mortality in affected individuals, little is known about disease dynamics in free-ranging populations. Herein, we examine how individual-specific factors (e.g., life stage [immature, mature], contaminant status, sex, hemograms) may be associated with ophidiomycosis status in the brown watersnake (Nerodia taxispilota). During 2018–19, we sampled 97 N. taxispilota from five locations along the Savannah River in South Carolina and Georgia, US. Ophidiomyces ophidiicola DNA was detected in 66 snakes for a prevalence of 68% (95% confidence interval, 59–77). Mature snakes had a significantly higher risk of apparent ophidiomycosis (skin lesions present and quantitative PCR [qPCR], positive) relative to immature snakes. Snakes classified as having possible (skin lesions present, but qPCR negative) or apparent ophidiomycosis exhibited a relative azurophilia and heterophilia compared with individuals classified as negative (P≤0.037). Nerodia taxispilota in this region appear to have a high prevalence of apparent ophidiomycosis (22%; 95% CI, 14–31), similar to previous reports from the southeastern US. Furthermore, additional epidemiologic investigations are warranted to further elucidate other individual-specific and environmental factors that may dictate disease risk and outcomes in affected populations.