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Abstract Tuber size, shape, colorimetric characteristics, and defect susceptibility are all factors that influence the acceptance of new potato cultivars. Despite the importance of these characteristics, our understanding of their inheritance is substantially limited by our inability to precisely measure these features quantitatively on the scale needed to evaluate breeding populations. To alleviate this bottleneck, we developed a low‐cost, semiautomated workflow to capture data and measure each of these characteristics using machine vision. This workflow was applied to assess the phenotypic variation present within 189 F1 progeny of the A08241 breeding population. Machine vision was applied to estimate linear and volumetric tuber size, assess tuber shape characteristics using aspect ratio and biomass profiles, and quantify tuber skin and flesh color; additionally, a deep learning mode was developed to classify the presence of hollow‐heart defect. Our results provide an example of quantitative measurements acquired using machine vision methods that are reliable, heritable, and capable of being used to understand and select multiple traits simultaneously in structured potato breeding populations.

The gastrointestinal (GI) tract harbors a complex and remarkably diverse microbial ecosystem that profoundly impacts various aspects of health and pathophysiology. While bacteria overwhelmingly represent most of the GI microbiota, it is imperative to consider the presence and function of fungal constituents (i.e. mycobiota) within the GI ecosystem. The substantial incidence of GI disorders and associated manifestations in children diagnosed with autism spectrum disorder (ASD) suggests a plausible contributory role of the gut mycobiota. This work aimed to elucidate the gut mycobiota in a cohort of 38 typically developing children (TD) and 40 children with ASD. Fecal samples were collected from all participants, autism severity and GI symptoms were assessed to unravel the potential implications of mycobiota alterations in the gut. We performed fungal internal transcribed spacer (ITS) gene amplicon sequencing to analyze the fungal composition and investigate their relationship with GI and autism symptoms. Among gut mycobiota, Saccharomyces cerevisiae was significantly lower (relative abundance) in the ASD fecal samples compared to TD children. Candida and C. albicans demonstrated a bimodal distribution among children with ASD. The small subset of children with elevated C. albicans or decreased S. cerevisiae had increased Autism Treatment Evaluation Checklist (ATEC) scores. Our findings suggest that a deficit of S. cerevisiae, and an overgrowth of C. albicans in a subset of children is associated with worse autism severity. Future work employing shotgun metagenomics with a larger cohort is encouraged to advance understanding of the functional role of fungi, and their possible interplay with GI symptoms and autism severity in children with ASD.

Abstract Chronic kidney disease (CKD) impacts about 1 in 7 adults in the United States, but African Americans (AAs) carry a disproportionately higher burden of disease. Epigenetic modifications, such as DNA methylation at cytosine-phosphate-guanine (CpG) sites, have been linked to kidney function and may have clinical utility in predicting the risk of CKD. Given the dynamic relationship between the epigenome, environment, and disease, AAs may be especially sensitive to environment-driven methylation alterations. Moreover, risk models incorporating CpG methylation have been shown to predict disease across multiple racial groups. In this study, we developed a methylation risk score (MRS) for CKD in cohorts of AAs. We selected nine CpG sites that were previously reported to be associated with estimated glomerular filtration rate (eGFR) in epigenome-wide association studies to construct a MRS in the Hypertension Genetic Epidemiology Network (HyperGEN). In logistic mixed models, the MRS was significantly associated with prevalent CKD and was robust to multiple sensitivity analyses, including CKD risk factors. There was modest replication in validation cohorts. In summary, we demonstrated that an eGFR-based CpG score is an independent predictor of prevalent CKD, suggesting that MRS should be further investigated for clinical utility in evaluating CKD risk and progression.

Abstract This study investigates the desiccation process of soft-tissue in South Africa, analyzing its interaction with environmental parameters and its implications for estimating the post-mortem interval. Through the examination of four decomposing porcine bodies across two summer seasons and one winter season, the research quantifies desiccation patterns using custom-designed and constructed printed circuit boards to measure the moisture content of body tissue over time. Generalized additive models were used to determine the environmental forces driving desiccation. Tissue resistivity was tested against the environmental predictor variables to determine the amount of variation they account for, and predicted values of the region-specific tissue resistivity variables were measured for each decomposing body. Results reveal distinct desiccation trajectories between summer and winter, with summer conditions conducive to precocious natural mummification. Environmental factors, particularly temperature and solar radiation, emerge as significant drivers of desiccation. This study represents the first quantitative analysis of deep tissue desiccation internationally, but also the first quantitative assessment of desiccation and natural precocious mummification in the Western Cape, South Africa. The exploration of desiccation as a potential indicator for estimating PMI opens new avenues for research and the integration of innovative methodologies and technologies promises to revolutionize forensic taphonomy practices.

This research aims to: 1) determine the process of developing teaching module, 2) determine the validity of teaching modules, 3) determine the practicality of teaching modules, and 4) determine the effectiveness of teaching modules. In general, the development of this CLT-based teaching module is to find out whether the taching module can minimize students’ mathematical anxiety.The research follows a development model, specifically the Plomp development model which consists of 5 phase, 1) preliminary phase, 2) design phase, 3) realization phase, 4) test, evaluation and revision phase, 5) implementation phase. The developed teaching module focuses on trigonometry material for phase E students at MAN Se-Tulungagung. Data collection methods include validation, objective observation, and questionnaires. Practicality data were obtained from teacher questionnaires, while effectiveness data were derived from students’ mathematical anxiety questionnaires. Based on data analysis, the following results were obtained: 1.) The validation score for the teaching module was 3.754, categorizing it as valid. 2.) The practicality score for the teaching module was 4.02, indicating high practicality. 3.) The teaching module effectively minimized mathematical anxiety, as evidenced by anxiety levels in experimental classes compared to control classes. Control classes using conventional learning showed higher anxiety levels, with MAN 3 Tulungagung at 2,89 (‘anxious’), MAN 2 Tulungagung at 2.615 (‘anxious’), and MAN 1 Tulungagung at 2.204 (‘anxious’). Meanwhile, experimental classes, after using the teaching module, showed lower anxiety levels: MAN 3 Tulungagung at 1.98 (‘moderate anxiety’), MAN 2 Tulungagung at 1.96 (‘moderate anxiety’), and MAN 1 Tulungagung at 1.44 (‘moderate anxiety’)

Abstract Chronic wasting disease (CWD), a prion disease affecting cervids, has been known in North America (NA) since the 1960s and emerged in Norway in 2016. Surveillance and studies have revealed that there are different forms of CWD in Fennoscandia: contagious CWD in Norwegian reindeer and sporadic CWD in moose and red deer. Experimental studies have demonstrated that NA CWD prions can infect various species, but thus far, there have been no reports of natural transmission to non-cervid species. In vitro and laboratory animal studies of the Norwegian CWD strains suggest that these strains are different from the NA strains. In this work, we describe the intracerebral transmission of reindeer CWD to six scrapie-susceptible sheep. Detection methods included immunohistochemistry (IHC), western blot (WB), enzyme-linked immunosorbent assay (ELISA), real-time quaking-induced conversion (RT-QuIC) and protein misfolding cyclic amplification (PMCA). In the brain, grey matter vacuolation was limited, while all sheep exhibited vacuolation of the white matter. IHC and WB conventional detection techniques failed to detect prions; however, positive seeding activity with the RT-QuIC and PMCA amplification techniques was observed in the central nervous system of all but one sheep. Prions were robustly amplified in the lymph nodes of all animals, mainly by RT-QuIC. Additionally, two lymph nodes were positive by WB, and one was positive by ELISA. These findings suggest that sheep can propagate reindeer CWD prions after intracerebral inoculation, resulting in an unusual disease phenotype and prion distribution with a low amount of detectable prions.

Background: The rates of firearm injuries among pediatric patients have risen significantly in recent years. Extremity injuries resulting from gunshot wounds (GSWs) often require orthopaedic management. In addition to rare nationwide database studies, there are 2 regional studies examining this trend in the South only. Our state has notably high gun ownership and lenient gun protection laws. To examine the orthopaedic burden of gunshot injuries in our region, we reviewed the pediatric patients presenting with GSWs at a tertiary level-1 trauma center over a 7-year period. Methods: A retrospective chart review was conducted of pediatric patients

Abstract The gut microbiome (GM) modulates body weight/composition and gastrointestinal functioning; therefore, approaches targeting resident gut microbes have attracted considerable interest. Intermittent fasting (IF) and protein pacing (P) regimens are effective in facilitating weight loss (WL) and enhancing body composition. However, the interrelationships between IF- and P-induced WL and the GM are unknown. The current randomized controlled study describes distinct fecal microbial and plasma metabolomic signatures between combined IF-P (n = 21) versus a heart-healthy, calorie-restricted (CR, n = 20) diet matched for overall energy intake in free-living human participants (women = 27; men = 14) with overweight/obesity for 8 weeks. Gut symptomatology improves and abundance of Christensenellaceae microbes and circulating cytokines and amino acid metabolites favoring fat oxidation increase with IF-P (p

Mathematics is a branch of science whose object of study is abstract in the form of symbols and shapes. The perception that emerged among the public said that only smart students (high learning outcomes) could master mathematics. However, what happens in the field is that the majority of students will experience anxiety when learning mathematics in the low to high category. Anxiety when learning mathematics is commonly called mathematical anxiety. This study used a quantitative approach with experimental method. The purpose of this study was to investigate the effect of cooperative learning model type Student Facilitator and Eksplaining (SFE) with poster media on students' mathematical anxiety. The population in this study were all students of class X MAN 3 Tulungagung. Two samples were selected by drawing lots. Learning with conventional methods was carried out in the control class, while the cooperative learning model of the Student Facilitator and Explaining (SFE) type with poster media was carried out in the experimental class. The results of data analysis showed that: (1) the average test of students' mathematical representation abilities in the control class was 73.2 while in the experimental class was 78.6; (2) the mathematic anxiety of students who learn using the Student Facilitator and Explaining (SFE) cooperative learning model with poster media is lower than the ability of the mathematical representation of students who learn with conventional methods; and (3) there is an influence of the Student Facilitator and Explaining (SFE) cooperative learning model with poster media on students' mathematical anxiety

Environmental evaluations of metal nanoparticles (NP) rely on seperating the effects of the metal NP from its dissolution products. However, the coordinating or counter anion used in experimental controls may potentially influence biotic indicators used in ecotoxicology and soil health monitoring, thereby compromising the ability to detect real nanoparticle effects and potentially confounding interpretation of metal-NP impacts. Using the example of copper oxide (CuO) NP, we demonstrate for the first time that depending on the anion used in the metal ion control (CuCl2 versus CuSO4), different and even opposite conclusions may be drawn for CuO-NP effects. This include a key biological indicator such as enzyme activity in soil samples. Moreover, this effect was specific to environmental conditions and indicator type, raising important methodological and interpretive implications to assess the CuO-NP impacts on soils. Our findings imply that assessments of soil health impacts of metal-NP should consider multiple coordinating anion controls for a given metal, especially when the counterion is known to impact the biological indicator including nutrient ions.

Introduction: Optimal management of transverse sacral fractures (TSF) remains inconclusive. These injuries may present with neurological deficits including cauda equina syndrome. We present our series of laminectomy for acute TSF with cauda equina compression. Methods: This was a retrospective chart review of all patients that underwent sacral laminectomy for treatment of cauda equina compression in acute TSF at our institution between 2007 through 2023. Results: A total of 9 patients (5 male and 4 female) underwent sacral laminectomy to decompress the cauda equina in the setting of acute high impact trauma. Surgeries were done early within a mean time of 5.9 days. All but one patient had symptomatic cauda equina syndrome. In one instance surgery was applied due to significant canal stenosis present on imaging in a patient with diminished mental status not allowing proper neurological examination. Torn sacral nerve roots were repaired directly when possible. All patients regained their neurological function related to the sacral cauda equina on follow up. The rate of surgical site infection (SSI) was 33%. Conclusion: Acute early sacral laminectomy and nerve root repair as needed was effective in recovering bowel and bladder function in patients after high impact trauma and TSF with cauda equina compression. A high SSI rate may be reduced by delaying surgery past 1 week from trauma, but little data exists at this time for clear recommendations.

The decomposition of a body, and the associated gaseous and liquid discharges emanating from it, attract gravid female blow flies which lay their eggs in or on the body. After the eggs have hatched, the emerging larvae start feeding on the body. As decomposition progresses, the blow fly larvae often migrate away, typically in a random manner in search of favourable conditions for pupation. In this paper, we report on a rarely described phenomenon of unidirectional mass migration of blow fly larvae and postulate on the factors which may drive this process. A decomposition trial utilising a 60-kg pig carcass, deployed in the summer months in Table Mountain National Park, Cape Town, South Africa, was conducted in 2022. On the fifth day of the trial, simultaneous unidirectional mass dispersal of blow fly larvae was observed. The larvae moved downhill in a southeasterly direction, following the flow of decomposition fluids oozing out from the pig carcass. The ‘larval migration stream’ had a length of approximately 1.5 m with a width of 40 cm, tapering to 17 cm at the terminal point. The larval migration stream consisted of the larvae of Chrysomya albiceps and Chrysomya chloropyga. This study demonstrates the importance of understanding the timing and pattern of dispersal of post-feeding blow fly larvae in each geographical region. This is crucial as the minimum post-mortem interval can be miscalculated if older immature insects dispersing from the corpse are not considered and collected during crime scene investigations. Significance: • Understanding the timing and pattern of dispersal of blow fly larvae from decomposing vertebrate remains in each geographical region is important in time-since-death estimations when using entomological evidence. • In the summer season of the Western Cape Province, Chrysomya albiceps and Chrysomya chloropyga are among the blow fly species of forensic importance as they deposit their eggs on vertebrate remains. • When a decomposing body is found within the Table Mountain region, we suggest that crime scene investigators should examine the downhill area of the scene for larval/pupal entomological evidence that can assist in time and season of death estimations. Supplementary video 1: https://doi.org/10.6084/m9.figshare.26028766.v1 Supplementary video 2: https://doi.org/10.6084/m9.figshare.26028805.v2

Knowledge of the geographic distribution and connectivity of marine populations is essential for ecological understanding and informing management. Previous works have assessed spatial structure by quantifying exchange using Lagrangian particle-tracking simulations, but their scope of analysis is limited by their use of predefined subpopulations. To instead delineate subpopulations emerging naturally from marine population connectivity, we interpret this connectivity as a network, enabling the use of powerful analytic tools from the field of network theory. The modelling approach presented here uses particle-tracking to construct a transport network, and then applies the community detection algorithm Infomap to identify subpopulations that exhibit high internal connectivity and sparse connectivity with other subpopulations. An established quality metric, the coherence ratio, and a new metric we introduce indicating self-recruitment to subpopulations, dubbed the fortress ratio, are used to interpret community-level exchange. We use the Atlantic sea scallop (Placopecten magellanicus) in the northwest Atlantic as a case study. Results suggest that genetic lineages of P. magellanicus demonstrate spatial substructure that depends on horizontal transport, vertical motility, and suitable habitat. Our results support connectivity previously characterized on Georges Bank and Mid-Atlantic Bight. The Gulf of St. Lawrence genetic lineage is found to consist of five subpopulations that are classified as being a sink, source, permeable, or impermeable using quality metrics. This approach may be applied to other planktonic dispersers and prove useful to management.

Domestication of algae for food and renewable biofuels remains limited by the low photosynthetic efficiencies of processes that have evolved to be competitive for optimal light capture, incentivizing the development of large antennas in light-limiting conditions, thus decreasing efficient light utilization in cultivated ponds or photobioreactors. Reducing the pigment content to improve biomass productivity has been a strategy discussed for several decades and the ability to reduce pigment significantly is now fully at hand thanks to the widespread use of genome editing tools. Picochlorum celeri is one of the fastest growing marine algae identified and holds particular promise for outdoor cultivation, especially in saline water and warm climates. We show that while chlorophyll b is essential to sustain high biomass productivities under dense cultivation, removing Picochlorum celeri’s main carotenoid, lutein, leads to a decreased total chlorophyll content, higher a/b ratio, reduced functional LHCII cross section and higher maximum quantum efficiencies at lower light intensities, resulting in an incremental increase in biomass productivity and increased PAR-to-biomass conversion efficiency. These findings further strengthen the existing strategies to improve photosynthetic efficiency and biomass production in algae.

Abstract Northern root‐knot nematode (Meloidogyne hapla) and ring nematode (Mesocriconema xenoplax) are the most prevalent plant‐parasitic nematodes of wine grapes in the Pacific Northwest, but M. hapla is most important in eastern Washington and M. xenoplax in western Oregon. These regions differ edaphically where Washington soils are minimally weathered and alkaline while Oregon soils are highly weathered and acidic. To examine the effect of soil texture and pH on nematode reproduction, an alkaline, sandy loam soil (pH 7.9) from Washington and an acidic loam soil from Oregon (pH 5.4) were modified to the other pH extreme, and to a middle pH of 6.9. Tomatoes were planted into each soil/pH combination, and either 500 M. hapla second‐stage juveniles or M. xenoplax individuals were added to each pot. After 7 weeks, plants were harvested, three roots collected for analysis, remaining roots and leaves dried and weighed, and nematode population densities determined as eggs on roots (M. hapla) and nematodes in soil (M. xenoplax). Soil texture (sandy loam or loam) had no effect on either nematode, but M. hapla reproduction was greater in the lowest pH soil while M. xenoplax was unaffected by soil pH. Mesocriconema xenoplax parasitism reduced root length and root tip number, whereas M. hapla increased root mass in the highest pH Washington soil. Under these experimental conditions, it appears vineyard soil texture in the Pacific Northwest is not a determining factor in population growth of these nematodes, but M. hapla performed better at low pH.

We describe the successful detection of human, porcine and canine picornaviruses (CanPV) in sewage sludge (at each stage of treatment) from Louisville, Kentucky, USA, using Pan-enterovirus amplicon-based long-read Illumina sequencing. Based on publicly available sequence data in GenBank, this is the first detection of CanPV in the USA and the first detection globally using wastewater-based epidemiology. Our findings also suggest there might be clusters of endemic porcine enterovirus (which have been shown capable of causing systemic infection in porcine) circulation in the USA that have not been sampled for around two decades. Our findings highlight the value of WBE coupled with amplicon based long-read Illumina sequencing for virus surveillance and demonstrates this approach can provide an avenue that supports a “One Health” model to virus surveillance. Finally, we describe a new CanPV assay targeting the capsid protein gene region that can be used globally, especially in resource limited settings for its detection and molecular epidemiology.

It is important to understand species-habitat relationships to implement effective adaptive management for rare species. However, it can be challenging to assess habitat associations and their relationships to abiotic stressors in dynamic habitats without the insights that can be gained from long-term monitoring. We report results from the first six years of extensive track tube monitoring of the largest two of three remaining extant populations of federally endangered Pacific pocket mouse (Perognathus longimembris pacificus) in a coastal Mediterranean-type ecosystem on Marine Corps Base, Camp Pendleton in southern California, USA. We used dynamic occupancy and structural equation modeling to assess potential drivers of population trends that included habitat, fire history, rainfall, disturbance, and the presence of other small mammals. We found that the variables that best predicted mouse occupancy were moderate to high forb and perennial herb cover (40–80%), and moderate to high open ground (20–70%) and low non-native grass cover (20%) was also a strong predictor of lower PPM colonization and increased extinction probabilities, with the extent of non-native grass cover being strongly influenced by annual rainfall and recency of fire. Our study adds to the growing literature on effects of invasive annual grasses on native species in Mediterranean-type ecosystems. We suggest that habitat management could be based upon promotion of open forb and perennial herb dominated habitats with reduction of non-native grasses by prescribed fire and other methods. These types of spatial and temporal monitoring programs can support land managers by creating a monitoring and management feedback loop. They can reveal landscape and environmental variables associated with species persistence, inform habitat management goals, and help managers to assess the success of management actions on populations of conservation concern.

Understanding the difficult to predict interactive effects of anthropogenic stressors is recognized as one of the major challenges facing environmental scientists and ecosystem managers. Despite burgeoning research, predicting stressor interactions is still difficult, in part because the same two stressors can interact, or not, depending on their intensities. While laboratory experiments have provided useful insights about how organisms respond to serial doses of single stressors, we lack ‘response-surface’ field experiments in which naturally occurring assemblages are exposed to multiple types and concentrations of stressors. Here we used a field-based dosing system combined with a ‘response-surface’ design to test the individual and combined effects of two stressors (copper and chlorpyrifos) at five concentrations of each, for a total of 25 replicated treatments (n=4). After six weeks of dosing, chemical uptake and impacts at several levels of biological organization in mussel assemblages were measured. Stressor combinations produced interactive effects that would not have been revealed without using this replicated ‘response-surface approach’. Results show that non-additive effects of multiple stressors may be more complex and more common than previously thought. Additionally, our findings suggest that interactive effects of multiple stressors vary across levels of organization which has implications for monitoring and managing the chemical, biological and ecological impacts of priority pollutants in the real world.

Abstract High cellular pigment levels in dense microalgal cultures contribute to excess light absorption. To improve photosynthetic yields in the marine microalga Picochlorum celeri, CAS9 gene editing was used to target the molecular chaperone cpSRP43. Depigmented strains (>50% lower chlorophyll) were generated, with proteomics showing attenuated levels of most light harvesting complex (LHC) proteins. Gene editing generated two types of cpSRP43 transformants with distinct lower pigment phenotypes: (i) a transformant (Δsrp43) with both cpSRP43 diploid alleles modified to encode non‐functional polypeptides and (ii) a transformant (STR30309) with a 3 nt in‐frame insertion in one allele at the CAS9 cut site (non‐functional second allele), leading to expression of a modified cpSRP43. STR30309 has more chlorophyll than Δsrp43 but substantially less than wild type. To further decrease light absorption by photosystem I in STR30309, CAS9 editing was used to stack in disruptions of both LHCA6 and LHCA7 to generate STR30843, which has higher (5–24%) productivities relative to wild type in solar‐simulating bioreactors. Maximal productivities required frequent partial harvests throughout the day. For STR30843, exemplary diel bioreactor yields of ~50 g m−2 day−1 were attained. Our results demonstrate diel productivity gains in P. celeri by lowering pigment levels.

Abstract Information on diet breadth and preference can assist in understanding links between food resources and population growth and inform habitat restoration for rare herbivores. We assessed the diet of the endangered Pacific pocket mouse using metabarcoding of fecal samples and compared it to plant community composition in long‐term study plots in two populations on Marine Corps Base Camp Pendleton, San Diego County, CA. Fecal samples (n = 221) were collected between spring 2016 and fall 2017 during monthly live‐trap surveys. Concurrently, percent cover and plant phenology were measured in plots centered on trap locations. Fecal samples were sequenced with paired‐end reads of the internal transcribed spacer 2 region of the nuclear ribosomal gene, and the resulting amplicons were matched to a regionally specific database. Seventy‐three plant taxa were detected, which were mostly forbs and perennial herbs (70–90%). Diet composition differed between populations, years, seasons, and plots. Overall, diet and local habitat composition in plots were significantly correlated. However, we detected some differences in above‐ground seed availability and proportion in fecal samples that indicate diet preferences for some forbs, perennial herbs, and native bunch grasses over perennial shrubs and non‐native grasses. This is the first study of PPM to pair plant phenology surveys with diet metabarcoding to estimate resource selection, and results suggest that managing habitat for diverse native forb communities and reducing non‐native grass cover may be beneficial for this critically endangered species.

This study aims to develop a valid, practical, and effective teaching aid in learning mathematical logic material. The teaching aid developed is Logic Toll Board named PATOLOGI (Papan Tol Logika). The development model used in this study uses the ADDIE development model. The stages of ADDIE development include analysis, design, development, implementation, and evaluation. Data collection was obtained from observation and interviews, then analyzed descriptively. The results of the research that has been carried out indicate that the PATOLOGI teaching aids have been well developed, starting from the analysis stage to the evaluation stage. The tests carried out included testing the validity of teaching aids to experts, practicality tests and effectiveness tests through trial activities with students. The trial results show that students have no difficulty in using teaching aids, so that teaching aids are said to be practical. The trial results also show that the use of visual aids can arouse students' enthusiasm and interest in participating in learning activities, so that students more easily understand the concepts of mathematical logic material, especially compound statements. This shows that the PATOLOGI teaching aids can be categorized as effective. Thus, it is concluded that the PATOLOGI teaching aid is valid, practical, and effective.

Heart failure with preserved ejection fraction (HFpEF) is a complex clinical syndrome, but a predominant subset of HFpEF patients has metabolic syndrome (MetS). Mechanistically, systemic, nonresolving inflammation associated with MetS might drive HFpEF remodeling. Free fatty acid receptor 4 (Ffar4) is a GPCR for long-chain fatty acids that attenuates metabolic dysfunction and resolves inflammation. Therefore, we hypothesized that Ffar4 would attenuate remodeling in HFpEF secondary to MetS (HFpEF-MetS). To test this hypothesis, mice with systemic deletion of Ffar4 (Ffar4KO) were fed a high-fat/high-sucrose diet with L-NAME in their water to induce HFpEF-MetS. In male Ffar4KO mice, this HFpEF-MetS diet induced similar metabolic deficits but worsened diastolic function and microvascular rarefaction relative to WT mice. Conversely, in female Ffar4KO mice, the diet produced greater obesity but no worsened ventricular remodeling relative to WT mice. In Ffar4KO males, MetS altered the balance of inflammatory oxylipins systemically in HDL and in the heart, decreasing the eicosapentaenoic acid-derived, proresolving oxylipin 18-hydroxyeicosapentaenoic acid (18-HEPE), while increasing the arachidonic acid-derived, proinflammatory oxylipin 12-hydroxyeicosatetraenoic acid (12-HETE). This increased 12-HETE/18-HEPE ratio reflected a more proinflammatory state both systemically and in the heart in male Ffar4KO mice and was associated with increased macrophage numbers in the heart, which in turn correlated with worsened ventricular remodeling. In summary, our data suggest that Ffar4 controls the proinflammatory/proresolving oxylipin balance systemically and in the heart to resolve inflammation and attenuate HFpEF remodeling.

The detection of conserved motifs by pattern recognition receptors is a crucial component of the innate detection of pathogens and danger signals via conserved pattern recognition receptors. Here the authors define a pathway that transfers partially digested material from the phagolysosomal pathway of macrophages to release at the plasma membrane which is associated with enhanced inflammatory potential, by a process they introduce as eructophagy.

Here, Hiatt et al. report the knock-out of over 400 genes in primary CD4+ T cells to assess their functional role in HIV replication, finding 86 initial candidates of which 47 are validated as HIV host factors, including 23 with restrictive activity.

We describe a process of restitution of nine unethically acquired human skeletons to their families, together with attempts at redress. Between 1925-1927 C.E., the skeletonised remains of nine San or Khoekhoe people, eight of them known-in-life, were removed from their graves on the farm Kruisrivier, near Sutherland in the Northern Cape Province of South Africa. They were donated to the Anatomy Department at the University of Cape Town. This was done without the knowledge or permission of their families. The donor was a medical student who removed the remains from the labourers' cemetery on his family farm. Nearly 100 years later, the remains are being returned to their community, accompanied by a range of community-driven interdisciplinary historical, archaeological and analytical (osteobiographic, craniofacial, ancient DNA, stable isotope) studies to document, as far as possible, their lives and deaths. The restitution process began by contacting families living in the same area with the same surnames as the deceased. The restitution and redress process prioritises the descendant families' memories, wishes and desire to understand the situation, and learn more about their ancestors. The descendant families have described the process as helping them to reconnect with their ancestors. A richer appreciation of their ancestors' lives, gained in part from scientific analyses, culminating with reburial, is hoped to aid the descendant families and wider community in [re-]connecting with their heritage and culture, and contribute to restorative justice, reconciliation and healing while confronting a traumatic historical moment. While these nine individuals were exhumed as specimens, they will be reburied as people.

Signal Transducer and Activator of Transcription 3 (STAT3) plays a crucial role in cancer development and thus is a viable target for cancer treatment. STAT3 functions as a dimer mediated by phosphorylation of the SRC-homology 2 (SH2) domain, a key target for therapeutic drugs. While great efforts have been employed towards the development of compounds that directly target the SH2 domain, no compound has yet been approved by the FDA due to a lack of specificity and pharmacologic efficacy. Studies have shown that allosteric regulation of SH2 via the coiled-coil domain (CCD) is an alternative drug design strategy. Several CCD effectors have been shown to modulate SH2 binding and affinity, and at the time of writing at least one drug candidate has entered phase I clinical trials. However, the mechanism for SH2 regulation via CCD is poorly understood. Here, we investigate structural and dynamic features of STAT3 and compare the wild type to the reduced function variant D170A in order to delineate mechanistic differences and propose allosteric pathways. Molecular dynamics simulations were employed to explore conformational space of STAT3 and the variant, followed by structural, conformation, and dynamic analysis. The trajectories explored show distinctive conformational changes in the SH2 domain for the D170A variant, indicating long range allosteric effects. Multiple analyses provide evidence for long range communication pathways between the two STAT3 domains, which seem to be mediated by a rigid core which connects the CCD and SH2 domains via the linker domain (LD) and transmits conformational changes through a network of short-range interactions. The proposed allosteric mechanism provides new insight into the understanding of intramolecular signaling in STAT3 and potential pharmaceutical control of STAT3 specificity and activity.

Background: Transcutaneous auricular Vagus Nerve Stimulation (taVNS) applies low-intensity electrical current to the ear with the intention of activating the auricular branch of the Vagus nerve. The sensitivity and selectivity of stimulation applied to the ear depends on current flow pattern produced by a given electrode montage (size and placement). Objective: We compare different electrodes designs for taVNS considering both the predicted peak electric fields (sensitivity) and their spatial distribution (selectivity). Methods: Based on optimized high-resolution (0.47 mm) T1 and T2 weighted MRI, we developed an anatomical model of the left ear and the surrounding head tissues including brain, CSF/meninges, skull, muscle, blood vessels, fat, cartilage, and skin. The ear was further segmented into 6 regions of interest (ROI) based on various nerve densities: cavum concha, cymba concha, crus of helix, tragus, antitragus, and earlobe. A range of taVNS electrode montages were reproduced spanning varied electrodes sizes and placements over the tragus, cymba concha, earlobe, cavum concha, and crus of helix. Electric field across the ear (from superficial skin to cartilage) for each montage at 1 mA or 2 mA taVNS, assuming an activation threshold of 6.15 V/m, 12.3 V/m or 24.6 V/m was predicted using a Finite element method (FEM). Finally, considering every ROI, we calculated the sensitivity and selectivity of each montage. Results: Current flow patterns through the ear were highly specific to the electrode montage. Electric field was maximal at the ear regions directly under the electrodes, and for a given total current, increases with decreasing electrode size. Depending on the applied current and nerves threshold, activation may also occur in the regions between multiple anterior surface electrodes. Each considered montage was selective for one or two regions of interest. For example, electrodes across the tragus restricted significant electric field to the tragus. Stimulation across the earlobe restricted significant electric field to the earlobe and the antitragus. Because of this relative selectivity, use of control ear montages in experimental studies, support testing of targeting. Relative targeting was robust across assumptions of activation threshold and tissue properties. Discussion: Computational models provide additional insight on how details in electrode shape and placement impact sensitivity (how much current is needed) and selectivity (spatial distribution), thereby supporting analysis of existing approaches and optimization of new devices. Our result suggest taVNS current patterns and relative target are robust across individuals, though (variance in) axon morphology was not represented.

Abstract The evolution of evidence and availability of Clinical Pharmacogenetic Implementation Consortium (CPIC) guidelines have enabled assessment of pharmacogenetic (PGx) actionability and clinical implementation. However, population‐level actionability is not well‐characterized. We leveraged the Alabama Genomic Health Initiative (AGHI) to evaluate population‐level PGx actionability. Participants (>18 years), representing all 67 Alabama counties, were genotyped using the Illumina Global Screening array. Using CPIC guidelines, actionability was evaluated using (1) genotype data and genetic ancestry, (2) prescribing data, and (3) combined genotype and medication data. Of 6,331 participants, 4230 had genotype data and 3386 had genotype and prescription data (76% women; 76% White/18% Black [self‐reported]). Genetic ancestry was concordant with self‐reported race. For CPIC level A genes, 98.6% had an actionable genotype (99.4% Blacks/African; 98.5% White/European). With the exception of DPYD and CYP2C19, the prevalence of actionable genotypes by gene differed significantly by race. Based on prescribing, actionability was highest for CYP2D6 (70.9%), G6PD (54.1%), CYP2C19 (53.5%), and CYP2C9 (47.5%). Among participants prescribed atenolol, carvedilol, or metoprolol, ~ 50% had an actionable ADRB1 genotype, associated with decreased therapeutic response, with higher actionability among Blacks compared to Whites (62.5% vs. 47.4%; p

OBJECTIVES/GOALS: Supported by the State of Alabama, the Alabama Genomic Health Initiative (AGHI) is aimed at preventing and treating common conditions with a genetic basis. This joint UAB Medicine-HudsonAlpha Institute for Biotechnology effort provides genomic testing, interpretation, and counseling free of charge to residents in each of Alabama’s 67 counties. METHODS/STUDY POPULATION: Launched in 2017, as a state-wide population cohort, AGHI (1.0) enrolled 6,331 Alabamians and returned individual risk of disease(s) related to the ACMG SF v2.0 medically actionable genes. In 2021, the cohort was expanded to include a primary care cohort. AGHI (2.0) has enrolled 750 primary care patients, returning individual risk of disease(s) related to the ACMG SF v3.1 gene list and pre-emptive pharmacogenetics (PGx) to guide medication therapy. Genotyping is done on the Illumina Global Diversity Array with Sanger sequencing to confirm likely pathogenic / pathogenic variants in medically actionable genes and CYP2D6 copy number variants using Taqman assays, resulting in a CLIA-grade report. Disease risk results are returned by genetic counselors and Pharmacogenetics results are returned by Pharmacists. RESULTS/ANTICIPATED RESULTS: We have engaged a statewide community (>7000 participants), returning 94 disease risk genetic reports and 500 PGx reports. Disease risk reports include increased predisposition to cancers (n=38), cardiac diseases (n=33), metabolic (n=12), other (n=11). 100% of participants harbor an actionable PGx variant, 70% are on medication with PGx guidance, 48% harbor PGx variants and are taking medications affected. In 10% of participants, pharmacists sent an active alert to the provider to consider/ recommend alternative medication. Most commonly impacted medications included antidepressants, NSAIDS, proton-pump inhibitors and tramadol. To enable the EMR integration of genomic information, we have developed an automated transfer of reports into the EMR with Genetics Reports and PGx reports viewable in Cerner. DISCUSSION/SIGNIFICANCE: We share our experience on pre-emptive implementation of genetic risk and pharmacogenetic actionability at a population and clinic level. Both patients and providers are actively engaged, providing feedback to refine the return of results. Real time alerts with guidance at the time of prescription are needed to ensure future actionability and value.

Nutritional interventions are a promising therapeutic option for addressing obesity and cardiometabolic dysfunction. One such option, intermittent fasting (IF), has emerged as a viable alternative to daily caloric restriction and may beneficially modulate body weight regulation and alter the gut microbiome (GM) and plasma metabolome. This secondary analysis of a larger, registered trial (ClinicalTrials.gov ID: NCT04327141) examined the effect of a four-week intervention comparing one vs. two-consecutive days of IF in combination with protein pacing (IF-P; 4-5 meals/day, >30% protein/day) on the GM, the plasma metabolome, and associated clinical outcomes in overweight and obese adults. Participants (n = 20) were randomly assigned to either a diet consisting of one fasting day (total of 36 h) and six low-calorie P days per week (IF1-P, n = 10) or two fasting days (60 h total) and five low-calorie P days per week (IF2-P, n = 10). The fecal microbiome, clinical outcomes, and plasma metabolome were analyzed at baseline (week 0) and after four weeks. There were no significant time or interaction effects for alpha diversity; however, baseline alpha diversity was negatively correlated with percent body fat change after the four-week intervention (p = 0.030). In addition, beta-diversity for both IF groups was altered significantly by time (p = 0.001), with no significant differences between groups. The IF1-P group had a significant increase in abundance of Ruminococcaceae Incertae Sedis and Eubacterium fissicatena group (q ≤ 0.007), while the IF2-P group had a significant increase in abundance of Ruminococcaceae Incertae Sedis and a decrease in Eubacterium ventriosum group (q ≤ 0.005). The plasma metabolite profile of IF2-P participants displayed significant increases in serine, trimethylamine oxide (TMAO), levulinic acid, 3-aminobutyric acid, citrate, isocitrate, and glucuronic acid (q ≤ 0.049) compared to IF1-P. Fecal short-chain fatty acid concentrations did not differ significantly by time or between groups (p ≥ 0.126). Interestingly, gastrointestinal symptoms were significantly reduced for the IF2-P group but not for the IF1-P group. Our results demonstrate that short-term IF modestly influenced the GM community structure and the plasma metabolome, suggesting these protocols could be viable for certain nutritional intervention strategies.

Rift Valley fever (RVF) is a disease of animals and humans associated with abortions in ruminants and late-gestation miscarriages in women. Here, we use a rat model of congenital RVF to identify tropisms, pathologies, and immune responses in the placenta during vertical transmission. Infection of late-gestation pregnant rats resulted in vertical transmission to the placenta and widespread infection throughout the decidua, basal zone, and labyrinth zone. Some pups from infected dams appeared normal while others had gross signs of teratogenicity including death. Histopathological lesions were detected in placenta from pups regardless of teratogenicity, while teratogenic pups had widespread hemorrhage throughout multiple placenta layers. Teratogenic events were associated with significant increases in placental pro-inflammatory cytokines, type I interferons, and chemokines. RVFV displays a high degree of tropism for all placental tissue layers and the degree of hemorrhage and inflammatory mediator production is highest in placenta from pups with adverse outcomes. Given the potential for RVFV to emerge in new locations and the recent evidence of emerging viruses, like Zika and SARS-CoV-2, to undergo vertical transmission, this study provides essential understanding regarding the mechanisms by which RVFV crosses the placenta barrier.

X-ray micro-computed tomography (X-ray μCT) has enabled the characterization of the properties and processes that take place in plants and soils at the micron scale. Despite the widespread use of this advanced technique, major limitations in both hardware and software limit the speed and accuracy of image processing and data analysis. Recent advances in machine learning, specifically the application of convolutional neural networks to image analysis, have enabled rapid and accurate segmentation of image data. Yet, challenges remain in applying convolutional neural networks to the analysis of environmentally and agriculturally relevant images. Specifically, there is a disconnect between the computer scientists and engineers, who build these AI/ML tools, and the potential end users in agricultural research, who may be unsure of how to apply these tools in their work. Additionally, the computing resources required for training and applying deep learning models are unique, more common to computer gaming systems or graphics design work, than to traditional computational systems. To navigate these challenges, we developed a modular workflow for applying convolutional neural networks to X-ray μCT images, using low-cost resources in Google’s Colaboratory web application. Here we present the results of the workflow, illustrating how parameters can be optimized to achieve best results using example scans from walnut leaves, almond flower buds, and a soil aggregate. We expect that this framework will accelerate the adoption and use of emerging deep learning techniques within the plant and soil sciences.

The chemical composition and size distribution of particulate matter produced at broiler poultry houses is not well understood, so this is a novel study to understand the particulate size distributions at a poultry house as well as the ionic composition of the particulate matter using real-time methods. Two optical particle counters provided particle size distributions inside and outside the house. An ambient ion monitor and a particle-in-liquid sampler analyzed the ionic chemical composition of the particulate matter in the house while a scanning mobility particle sizer provided size information in the nanoparticle range. Ammonia concentrations in the house were measured using a chemical sensor. Ammonia concentrations in the house were consistently in the lower part of the per million range 2–20 ppm. The optical particle counter and ion chromatography measurements both showed a strong diurnal variation of particulate matter concentration in the house throughout the study, associated with the lights being on and animal activity. Particulate mass concentration inside the house was dominated by coarse mode particles as opposed to the outdoor sampler which showed much smaller sizes. A few new particle formation and growth events were observed in the house. Ionic constituents detected by chromatography made up a small fraction of the overall mass concentration. The composition of the ionic constituents was similar for most of the study with typical ions being ammonium, sodium, potassium, chloride, sulfate, nitrate, nitrite, phosphate, and several carboxylates (formate, acetate, propionate, and butyrate.) At the end of the study, bromide was also detected during the last several days. Overall, we determined that the ionic components of the particulate matter formed through secondary particle formation was small, but also that some ionic constituents can be associated with management practices.

The start of the COVID-19 pandemic altered the research landscape dramatically, but the need to understand impacts on communities through research was as great as ever. In this paper, we detail the adaptive processes we leveraged to bring a network of community and academic partners together virtually and collaboratively build a survey reaching diverse populations, the challenges we faced, and what ultimately facilitated our success. The largest driver of our work was our shared goal of gaining a better understanding of the psychosocial impacts of the pandemic on New Yorkers in order to address their needs more meaningfully. Pre-existing relationships with community partners and flexible working processes grounded in equity also supported the functioning of the team. While participant recruitment proved to be challenging, the team pivoted and employed several strategies to reach our intended audiences and increase participation. This paper includes community stakeholders’ reflections on facilitators and barriers to survey development and recruitment in the context of a pandemic, as well as considerations for moving forward with virtual community-engaged research under challenging circumstances. In addition to sharing the collaborative processes that we built, our research-to-action network’s outputs, and our reflections on successes and roadblocks we faced, this paper highlights lessons in the importance of flexibility, trust, and innovation when conducting collaborative research during rapidly evolving public health crises.

Venezuelan equine encephalitis virus (VEEV) is a positively-stranded RNA arbovirus of the genus Alphavirus that causes encephalitis in humans. Cynomolgus macaques are a relevant model of the human disease caused by VEEV and are useful in exploring pathogenic mechanisms and the host response to VEEV infection. Macaques were exposed to small-particle aerosols containing virus derived from an infectious clone of VEEV strain INH-9813, a subtype IC strain isolated from a human infection. VEEV-exposed macaques developed a biphasic fever after infection similar to that seen in humans. Maximum temperature deviation correlated with the inhaled dose, but fever duration did not. Neurological signs, suggestive of virus penetration into the central nervous system (CNS), were predominantly seen in the second febrile period. Electroencephalography data indicated a statistically significant decrease in all power bands and circadian index during the second febrile period that returned to normal after fever resolved. Intracranial pressure increased late in the second febrile period. On day 6 post-infection macaques had high levels of MCP-1 and IP-10 chemokines in the CNS, as well as a marked increase of T lymphocytes and activated microglia. More than four weeks after infection, VEEV genomic RNA was found in the brain, cerebrospinal fluid and cervical lymph nodes. Pro-inflammatory cytokines & chemokines, infiltrating leukocytes and pathological changes were seen in the CNS tissues of macaques euthanized at these times. These data are consistent with persistence of virus replication and/or genomic RNA and potentially, inflammatory sequelae in the central nervous system after resolution of acute VEEV disease.

Genomes of a Campylobacter coli OR12-like strain ChP2023 (1,713,995 bp) isolated from broiler chicken and Campylobacter jejuni subsp. jejuni NCTC 11168R-like strain KF2023 (1,729,995 bp) isolated from turkey, from poultry production facilities in Ukraine in 2023, were sequenced using Oxford Nanopore Technologies. Both genomes included antibiotic resistance genes and other virulence factors.

Interpretation of patient-reported outcome (PRO) scores has been supported by identifying score thresholds or ranges that indicate clinical importance. There has been a recent focus on the estimation of meaningful within patient change (MWPC). While much attention has been focused on anchor-based methods, some researchers prefer that a lower bound to these estimates should exceed a change score that could be observed due to measurement error alone as a safeguard against misclassifying individual patients as changed when they have not. The standard error of measurement (SEM) is often used as the lower bound of anchor estimates. Here, we argue that the SEM is not an the best lower bound for MWPCs. Instead, statistically significant individual change as calculated by the reliable change index (RCI) should be used as the lower bound. Our argument is based on two points. First, conceptually, the SEM does not provide specific enough information to serve as a lower bound for MWPCs, which should be based on the level of observed score change that is unlikely to be due to chance alone. Second, the SEM is not appropriate for direct application to observed scores, and requires a multiplier when examining observed change instead of true change. We conclude with recommendations for using the RCI with a thoughtful range of p-values in combination with anchor estimates.

X-linked lymphoproliferative disease (XLP1) results from SH2D1A gene mutations affecting the SLAM-associated protein (SAP). A regulated lentiviral vector (LV), XLP-SMART LV, designed to express SAP at therapeutic levels in T, NK, and NKT cells, is crucial for effective gene therapy. We experimentally identified 34 genomic regulatory elements of the SH2D1A gene and designed XLP-SMART LVs to emulate the lineage and stage-specific control of SAP. We screened them for their on-target enhancer activity in T, NK, and NKT cells and their off-target enhancer activity in B cell and myeloid populations. In combination, three enhancer elements increased SAP promoter expression up to 4-fold in on-target populations in vitro. NSG-Tg(Hu-IL15) xenograft studies with XLP-SMART LVs demonstrated up to 7-fold greater expression in on-target cells over a control EFS-LV, with no off-target expression. The XLP-SMART LVs exhibited stage-specific T and NK cell expression in peripheral blood, bone marrow, spleen, and thymic tissues (mimicking expression patterns of SAP). Transduction of XLP1 patient CD8+ T cells or BM CD34+ cells with XLP-SMART LVs restored restimulation-induced cell death and NK cytotoxicity to wild-type levels, respectively. These data demonstrate that it is feasible to create a lineage and stage-specific LV to restore the XLP1 phenotype by gene therapy.