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Abstract The Colorado River drains about 8% of the conterminous United States, provides water for 40 million people, and is one of the most overallocated rivers in the world. As the upper Colorado River Basin (UCOL) contributes an estimated 92% of the total basin natural streamflow, knowledge of the location and amount of surface water withdrawals in the UCOL is important for managing the Colorado River system. Since the UCOL encompasses portions of five states, water use data are dispersed among numerous federal and state agency databases, and there is no centralized dataset that documents surface water use within the entire UCOL at a fine spatial and temporal resolution. This article presents an inventory of 1,358 major structures that divert surface water from and within the UCOL with corresponding daily time series withdrawal records from 1980 through 2022. Data compilation efforts, processing methods, and contents of this diversion database are documented, and summary information is provided.

Abstract Collisions of the transcription and replication machineries on the same DNA strand can pose a significant threat to genomic stability. These collisions occur in part due to the formation of RNA-DNA hybrids termed R-loops, in which a newly transcribed RNA molecule hybridizes with the DNA template strand. This study investigated the role of RAD52, a known DNA repair factor, in preventing collisions by directing R-loop formation and resolution. We show that RAD52 deficiency increases R-loop accumulation, exacerbating collisions and resulting in elevated DNA damage. Furthermore, RAD52’s ability to interact with the transcription machinery, coupled with its capacity to facilitate R-loop dissolution, highlights its role in preventing collisions. Lastly, we provide evidence of an increased mutational burden from double-strand breaks at conserved R-loop sites in human tumor samples, which is increased in tumors with low RAD52 expression. In summary, this study underscores the importance of RAD52 in orchestrating the balance between replication and transcription processes to prevent collisions and maintain genome stability.

Abstract Nonrelativistic Quantum Chromodynamics (NRQCD) breaks down in the region of low transverse momentum, where the transverse momentum of the produced quarkonium state is sensitive to multiple scattering with the incoming hadron and to soft gluon radiation. In this kinematic regime, the transverse-momentum-dependent (TMD) factorization framework is required, promoting the long-distance matrix elements (LDMEs) of NRQCD to the so-called TMD shape functions (TMDShFs), which encode both the soft gluon radiation and the formation of the heavy-quark bound state. In this work, we apply an effective-field theory approach (combining NRQCD and SCET) to the photon-gluon fusion process in inclusive J/ψ leptoproduction. We derive a factorization theorem for the cross section in terms of TMDShFs, compute these quantities at next-to-leading order, establish their evolution, and study their matching onto the corresponding LDMEs in the high-transverse-momentum region. Our results are particularly relevant to the Electron-Ion Collider, where J/ψ leptoproduction can be used to probe gluon transverse-momentum-dependent parton distribution functions (gluon TMDPDFs).

Abstract Background Significant recent efforts have facilitated increased access to clinical genetics assessment and genomic sequencing for children with rare diseases in many centres, but there remains a service gap for adults. The Austin Health Adult Undiagnosed Disease Program (AHA-UDP) was designed to complement existing UDP programs that focus on paediatric rare diseases and address an area of unmet diagnostic need for adults with undiagnosed rare conditions in Victoria, Australia. It was conducted at a large Victorian hospital to demonstrate the benefits of bringing genomic techniques currently used predominantly in a research setting into hospital clinical practice, and identify the benefits of enrolling adults with undiagnosed rare diseases into a UDP program. The main objectives were to identify the causal mutation for a variety of diseases of individuals and families enrolled, and to discover novel disease genes. Methods Unsolved patients in whom standard genomic diagnostic techniques such as targeted gene panel, exome-wide next generation sequencing, and/or chromosomal microarray, had already been performed were recruited. Genome sequencing and enhanced genomic analysis from the research setting were applied to aid novel gene discovery. Results In total, 16/50 (32%) families/cases were solved. One or more candidate variants of uncertain significance were detected in 18/50 (36%) families. No candidate variants were identified in 16/50 (32%) families. Two novel disease genes (TOP3B, PRKACB) and two novel genotype–phenotype correlations (NARS, and KMT2C genes) were identified. Three out of eight patients with suspected mosaic tuberous sclerosis complex had their diagnosis confirmed which provided reproductive options for two patients. The utility of confirming diagnoses for patients with mosaic conditions (using high read depth sequencing and ddPCR) was not specifically envisaged at the onset of the project, but the flexibility to offer recruitment and analyses on an as-needed basis proved to be a strength of the AHA-UDP. Conclusion AHA-UDP demonstrates the utility of a UDP approach applying genome sequencing approaches in diagnosing adults with rare diseases who have had uninformative conventional genetic analysis, informing clinical management, recurrence risk, and recommendations for relatives.

Abstract Sequence-based genetic testing identifies causative variants in ~ 50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. We interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 582 individuals with genetically unsolved DEEs. We identify rare differentially methylated regions (DMRs) and explanatory episignatures to uncover causative and candidate genetic etiologies in 12 individuals. Using long-read sequencing, we identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and four copy number variants. We also identify pathogenic variants associated with episignatures. Finally, we refine the CHD2 episignature using an 850 K methylation array and bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate variants as 2% (12/582) for unsolved DEE cases.

Abstract Background The effects of environmental disturbances on livestock are often observed indirectly through the variability patterns of repeated performance records over time. Sheep are frequently exposed to diverse extensive environments but currently lack appropriate measures of resilience (or sensitivity) towards environmental disturbance. In this study, random regression models were used to analyse repeated records of the fibre diameter of wool taken along the wool staple (bundle of wool fibres) to investigate how the genetic and environmental variance of fibre diameter changes with different growing environments. Results A model containing a fifth, fourth and second-order Legendre polynomial applied to the fixed, additive and permanent environmental effects, respectively, was optimal for modelling fibre diameter along the wool staple. The additive genetic and permanent environmental variance both showed variability across the staple length trajectory. The ranking of sire estimated breeding values (EBV) for fibre diameter was shown to change along the staple and the genetic correlations decreased as the distance between measurements along the staple increased. This result suggests that some genotypes were potentially more resilient towards the changes in the growing environment compared to others. In addition, the eigenfunctions of the random regression model implied the ability to change the fibre diameter trajectory to reduce its variability along the wool staple. Conclusions These results show that genetic variation in fibre diameter measured along the wool staple exists and this could be used to provide greater insight into the ability to select for resilience in extensively raised sheep populations.

Abstract Overconsumption of dietary sugar can lead to many negative health effects including the development of Type 2 diabetes, metabolic syndrome, cardiovascular disease, and neurodegenerative disorders. Recently, the human intestinal microbiota, strongly associated with our overall health, has also been known to be affected by diet. However, mechanistic insight into the importance of the human intestinal microbiota and the effects of chronic sugar ingestion has not been possible largely due to the complexity of the human microbiome which contains hundreds of types of organisms. Here, we use an interspecies C. elegans/E. coli system, where E. coli are subjected to high sugar, then consumed by the bacterivore host C. elegans to become the microbiota. This glucose-fed microbiota results in a significant lifespan reduction accompanied by reduced healthspan (locomotion), reduced stress resistance, and changes in behavior and feeding. Lifespan reduction is also accompanied by two potential major contributors: increased intestinal bacterial density and increased concentration of reactive oxygen species. The glucose-fed microbiota accelerated the age-related development of intestinal cell permeability, intestinal distention, and dysregulation of immune effectors. Ultimately, the changes in the intestinal epithelium due to aging with the glucose-fed microbiota results in increased susceptibility to multiple bacterial pathogens. Taken together, our data reveal that chronic ingestion of sugar, such as a Western diet, has profound health effects on the host due to changes in the microbiota and may contribute to the current increased incidence of ailments including inflammatory bowel diseases as well as multiple age-related diseases.

Abstract Type II diabetes mellitus (T2DM) is a rising global health burden due to its rapidly increasing prevalence worldwide, and can result in serious complications. Therefore, it is of utmost importance to identify individuals at risk as early as possible to avoid long-term T2DM complications. In this study, we developed an interpretable machine learning model leveraging baseline levels of biomarkers of oxidative stress (OS), inflammation, and mitochondrial dysfunction (MD) for identifying individuals at risk of developing T2DM. In particular, Isolation Forest (iForest) was applied as an anomaly detection algorithm to address class imbalance. iForest was trained on the control group data to detect cases of high risk for T2DM development as outliers. Two iForest models were trained and evaluated through ten-fold cross-validation, the first on traditional biomarkers (BMI, blood glucose levels (BGL) and triglycerides) alone and the second including the additional aforementioned biomarkers. The second model outperformed the first across all evaluation metrics, particularly for F1 score and recall, which were increased from 0.61 ± 0.05 to 0.81 ± 0.05 and 0.57 ± 0.06 to 0.81 ± 0.08, respectively. The feature importance scores identified a novel combination of biomarkers, including interleukin-10 (IL-10), 8-isoprostane, humanin (HN), and oxidized glutathione (GSSG), which were revealed to be more influential than the traditional biomarkers in the outcome prediction. These results reveal a promising method for simultaneously predicting and understanding the risk of T2DM development and suggest possible pharmacological intervention to address inflammation and OS early in disease progression.

Summary: Background: Phenotypic variability within families with epilepsy is often observed, even when relatives share the same monogenic cause. We aimed to investigate whether common polygenic risk for epilepsy could explain the penetrance and phenotypic expression of rare pathogenic variants in familial epilepsies. Methods: We studied 58 clinically heterogeneous families with genetic epilepsy with febrile seizures plus (GEFS+). Relatives were coded as either unaffected or affected with epilepsy, and graded according to phenotype severity: no seizures, febrile seizures (FS) only, febrile seizures plus (FS+), generalised/focal epilepsy, or developmental and epileptic encephalopathy (DEE). Epilepsy polygenic risk scores (PRSs) were tested for association with epilepsy phenotype. Within families, the mean PRS difference was compared between pairs concordant versus discordant for phenotype severity. Statistical analyses were performed using mixed-effect regression models. Findings: 304 individuals segregating a known, or presumed, rare variant of large effect, were studied. Within families, higher epilepsy polygenic risk was associated with an epilepsy diagnosis (OR = 1.39, 95% CI 1.08, 1.80, padj = 0.040). Relatives with a more severe phenotype had a mean pairwise PRS difference of +0.19 higher than relatives with a milder phenotype (padj = 0.010). The difference increased with greater phenotype discordance between relatives. As the cohort included two rare variants with >30 relatives each, variant-specific genotype–phenotype associations could also be analysed. Whilst the epilepsy PRS effect was strong for relatives segregating the GABRG2 p.Arg82Gln pathogenic variant (padj = 0.0010), the effect was not significant for SCN1B p.Cys121Trp. Interpretation: We provide support for genetic background modifying the penetrance and phenotypic expression of rare variants associated with ‘monogenic’ epilepsies. In GEFS+ families, relatives with higher epilepsy PRSs were more likely to show penetrance (epilepsy diagnosis) and a more severe phenotype. Variant-specific analyses suggest that some rare variants may be more susceptible to PRS modification, carrying important genetic counselling and disease prognostication implications for patients. Funding: National Health and Medical Research Council of Australia, Medical Research Future Fund of Australia.

Nuclear envelope repair is a fundamental cellular response to stress, especially for cells experiencing frequent nuclear ruptures, such as cancer cells. Moreover, for chromosomally unstable cancer cells, characterized by the presence of micronuclei, the irreversible rupture of these structures constitutes a fundamental step toward cancer progression and therapy resistance. For these reasons, the study of nuclear envelope rupture and repair is of paramount importance. Nonetheless, due to the constraint imposed by the stochastic nature of rupture events, a precise characterization of the initial stage of nuclear repair remains elusive. In this study, we overcame this limitation by developing a new imaging pipeline that deterministically induces rupture while simultaneously imaging fluorescently tagged repair proteins. We provide a detailed step-by-step protocol to implement this method on any confocal microscope and applied it to study the major nuclear repair protein, barrier-to-autointegration factor (BAF). As a proof of principle, we demonstrated two different downstream analysis methods and showed how BAF is differentially recruited at sites of primary and micronuclear rupture. Additionally, we applied this method to study the recruitment at primary nuclei of the inner nuclear membrane protein LEM-domain 2 (LEMD2) and Charged Multivesicular Protein 7 (CHMP7), the scaffolding protein of the endosomal sorting complex required for transport III (ESCRT-III) membrane remodeling complex. The CHMP7-LEMD2 binding is the fundamental step allowing the recruitment of ESCRT-III, which represents the other major nuclear repair mechanism. This demonstrates the method’s applicability for investigating protein dynamics at sites of nuclear and micronuclear envelope rupture and paves the way to more time-resolved studies of nuclear envelope repair.

Abstract Increased left atrial volume and decreased left atrial function have long been associated with atrial fibrillation. The availability of large-scale cardiac magnetic resonance imaging data paired with genetic data provides a unique opportunity to assess the genetic contributions to left atrial structure and function, and understand their relationship with risk for atrial fibrillation. Here, we use deep learning and surface reconstruction models to measure left atrial minimum volume, maximum volume, stroke volume, and emptying fraction in 40,558 UK Biobank participants. In a genome-wide association study of 35,049 participants without pre-existing cardiovascular disease, we identify 20 common genetic loci associated with left atrial structure and function. We find that polygenic contributions to increased left atrial volume are associated with atrial fibrillation and its downstream consequences, including stroke. Through Mendelian randomization, we find evidence supporting a causal role for left atrial enlargement and dysfunction on atrial fibrillation risk.

Abstract Objective Lennox‐Gastaut syndrome (LGS) is an archetypal developmental and epileptic encephalopathy, for which novel treatments are emerging. Diagnostic criteria for LGS have recently been defined by the International League Against Epilepsy (ILAE). We aimed to apply these criteria in a real‐world setting. Methods We applied ILAE diagnostic criteria to a cohort of patients diagnosed with LGS by epileptologists following inpatient video‐EEG monitoring (VEM) at tertiary comprehensive epilepsy centers between 1995 and 2015. We also assessed mortality in this cohort. Results Sixty patients diagnosed with LGS and had complete records available for review were identified. Among them, 29 (48%) patients met ILAE diagnostic criteria for LGS (ILAE‐DC group). Thirty‐one did not meet criteria (non‐ILAE‐DC) due to the absence of documented tonic seizures (n = 7), EEG features (n = 12), or both tonic seizures and EEG features (n = 10), intellectual disability (n = 1), or drug resistance (n = 1). The ILAE‐DC group had a shorter duration of epilepsy at VEM than the non‐ILAE‐DC group (median = 12.0 years vs. 23.7 years, respectively; p = 0.015). The proportions of patients with multiple seizure types (100% vs. 96.7%), ≤2.5 Hz slow spike‐and‐wave EEG activity (100% vs. 90%), seizure‐related injuries (27.6% vs. 25.8%), and mortality (standardized mortality ratio 4.60 vs. 5.12) were similar between the groups. Significance Up to 52% of patients diagnosed with LGS following VEM may not meet recently accepted ILAE criteria for LGS diagnosis. This may reflect both the limitations of retrospective medical record review and a historical tendency of applying the LGS diagnosis to a broad spectrum of severe, early‐onset drug‐resistant epilepsies with drop attacks. The ILAE criteria allow the delineation of LGS based on distinct electroclinical features, potentiating accurate diagnosis, prognostication, and management formulation. Nonetheless, mortality outcomes between those who did and did not meet ILAE diagnostic criteria for LGS were similarly poor, and both groups suffered high rates of seizure‐related injury. Plain Language Summary More than half of patients diagnosed with Lennox‐Gastaut Syndrome (LGS) at three Australian epilepsy monitoring units between 1995 and 2015 did not meet the recently devised International League Against Epilepsy (ILAE) diagnostic criteria for LGS. Mortality was equally high in those who did and did not meet the ILAE diagnostic criteria, and seizure‐related injury was common. The ILAE diagnostic criteria will guide accurate diagnosis, management, prognostication, and research in patients with LGS, however may be limited in their practical application to patients with a longer duration of epilepsy, or to those for whom detailed assessment is difficult.

IntroductionAdvances in farming technologies and practices have helped farmers to increase crop yields, but continued production increases – while needed to feed a growing global population – are being hindered by climate change and other environmental challenges. Kansas, a globally important region for wheat production, is already experiencing threats to staple crop production. This study explores one possible alternative future for Kansas crop production in which farmers could, by crop switching, continue to grow nutrient-rich crops while responding to hotter temperatures and increasing water demand.MethodsWe used a combination of climate and crop modeling with simple water budgets to identify optimal crop mixes under anticipated climatic and water constraints. Interviews with Kansas farmers helped identify feasible crop switching options: sorghum instead of corn (maize), winter rye and winter oats instead of winter wheat, and millet instead of soybeans.ResultsOur analysis suggests that a sizeable proportion of current Kansas cropland would need to shift to these alternative crops by 2050 to meet anticipated water constraints and produce equivalent nutritional value under projected climate conditions. Alternative crops could increase from 16% of Kansas' crop area in 2021 to 43% of the area in 2050, resulting in a reduction in 2050 crop water demand of 12% relative to that of the current crop mix. This crop water demand reduction would be concentrated in parts of the state that will experience the greatest change in water needs between today and mid-century due to changing climate conditions.DiscussionOur analysis shows that, by changing (diversifying) the mix of crops grown, it is biophysically possible for crop production in Kansas to be both sustainable and resilient under future climate conditions. However, achieving a more climate-resilient crop mix on the ground, in Kansas and elsewhere, will require major shifts in the broader agricultural system. Food companies, agricultural lenders, and policymakers can play a key role in enabling farmers to adapt cropping systems in the face of climate and environmental challenges.

Background Black patients meeting indications for implantable cardioverter‐defibrillators (ICDs) have lower rates of implantation compared with White patients. There is little understanding of how mental health impacts the decision‐making process among Black patients considering ICDs. Our objective was to assess the association between depressive symptoms and ICD implantation among Black patients with heart failure. Methods and Results This is a secondary analysis of the VIVID (Videos to Address Racial Disparities in ICD Therapy via Innovative Designs) randomized trial, which enrolled self‐identified Black individuals with chronic systolic heart failure. Depressive symptoms were assessed by the Patient Health Questionnaire‐2 and the Mental Component Summary of the 12‐Item Short‐Form Health Survey. Decisional conflict was measured by an adapted Decisional Conflict Scale (DCS). ANCOVA was used to assess differences in Decisional Conflict Scale scores. Multivariable logistic regression was used to examine the association between depressive symptoms and ICD implantation. Among 306 participants, 60 (19.6%) reported depressed mood, and 142 (46.4%) reported anhedonia. Participants with the lowest Mental Component Summary of the 12‐Item Short‐Form Health Survey scores (poorer mental health and higher likelihood of depression) had greater decisional conflict regarding ICD implantation compared with those with the highest Mental Component Summary of the 12‐Item Short‐Form Health Survey scores (adjusted mean difference in Decisional Conflict Scale score, 3.2 [95% CI, 0.5–5.9]). By 90‐day follow‐up, 202 (66.0%) participants underwent ICD implantation. There was no association between either the Patient Health Questionnaire‐2 score or the Mental Component Summary of the 12‐Item Short‐Form Health Survey score and ICD implantation. Conclusions Depressed mood and anhedonia were prevalent among ambulatory Black patients with chronic systolic heart failure considering ICD implantation. The presence of depressive symptoms did not impact the likelihood of ICD implantation in this population.

This article explores the recent history of early warning systems in Kenya, determining key features of the entangled political, technical and conceptual processes that prefigure contemporary drought management there. In doing so, it draws out wider implications regarding drought and anticipatory action across Africa’s drylands, considering the friction between the dynamics of disaster risk management that structure formal early warning systems and those that shape pastoralist engagements with the volatile and uncertain worlds they inhabit. Surveying recent literature on pastoralism’s unique relationship with uncertainty, and associated forms of networked, relational resilience, it reflects on some of the inherent limitations of current approaches to “local knowledge” in the humanitarian sphere. In doing so, it emphasises the need for new, creative approaches to early warning and anticipatory action, which are not merely established via the external synthesis of data but are rather oriented around local pastoralist drought preparation and mitigation strategies and comprise enough flexibility to adapt to a fast-shifting terrain of challenges and possibilities.

Abstract Background There can be variation between animals in how stable their genetic merit is across different environments due to genotype-by-environment (G×E) interactions. This variation could be used in breeding programs to select robust genotypes that combine high overall performance with stable genetic ranking across environments. There have been few attempts to validate breeding values for robustness in livestock, although this is a necessary step towards their implementation in selection decisions. The objective of this study was to validate breeding values for the robustness of body weight across different growth environments that were estimated using reaction norm models in sheep data. Results Using threefold cross-validation for the progeny of 337 sires, the average correlation between single-step breeding values for the reaction norm slope and the realised robustness of progeny across different growth environments was 0.21. The correlation between breeding values for the reaction slope estimated independently in two different datasets linked by common sires was close to the expected correlation based on theory. Conclusions Slope estimated breeding values (EBV) obtained using reaction norm models were predictive of the phenotypic robustness of progeny across different environments and were consistent for sires with progeny in two different datasets. Selection based on reaction norm EBV could be used to increase the robustness of a population to environmental variation.

Abstract We compute the gluon transverse-momentum-dependent fragmentation function (TMDFF) at next-to-leading order (NLO) into heavy quarkonium in the color-octet S 1 8 3 $$ {}^3{S}_1^{\left[8\right]} $$ channel, based on the NRQCD factorization approach. The spurious rapidity divergences are explicitly shown to cancel in a well-defined TMDFF, which incorporates the needed soft factor. We also compute the integrated gluon FF at NLO in the same S 1 8 3 $$ {}^3{S}_1^{\left[8\right]} $$ channel, and show that the matching coefficient of the TMDFF onto the FF at large transverse momentum is the expected one. These results are relevant to perform precise and sensible phenomenological studies of transverse-momentum spectra of quarkonium production, for which the production mechanism through fragmentation plays a relevant role, like in the future Electron-Ion Collider.

Abstract Altered reactivity and responses to auditory input are core to the diagnosis of autism spectrum disorder (ASD). Preclinical models implicate ϒ-aminobutyric acid (GABA) in this process. However, the link between GABA and auditory processing in humans (with or without ASD) is largely correlational. As part of a study of potential biosignatures of GABA function in ASD to inform future clinical trials, we evaluated the role of GABA in auditory repetition suppression in 66 adults (n = 28 with ASD). Neurophysiological responses (temporal and frequency domains) to repetitive standard tones and novel deviants presented in an oddball paradigm were compared after double-blind, randomized administration of placebo, 15 or 30 mg of arbaclofen (STX209), a GABA type B (GABAB) receptor agonist. We first established that temporal mismatch negativity was comparable between participants with ASD and those with typical development (TD). Next, we showed that temporal and spectral responses to repetitive standards were suppressed relative to responses to deviants in the two groups, but suppression was significantly weaker in individuals with ASD at baseline. Arbaclofen reversed weaker suppression of spectral responses in ASD but disrupted suppression in TD. A post hoc analysis showed that arbaclofen-elicited shift in suppression was correlated with autistic symptomatology measured using the Autism Quotient across the entire group, though not in the smaller sample of the ASD and TD group when examined separately. Thus, our results confirm: GABAergic dysfunction contributes to the neurophysiology of auditory sensory processing alterations in ASD, and can be modulated by targeting GABAB activity. These GABA-dependent sensory differences may be upstream of more complex autistic phenotypes.

Scale measuring the construct of “health security in chronic illness” (HSCI) was piloted in Canadian cardiac device patients (N = 176) enrolled in a remote-monitoring study at 2 timepoints. Analysis revealed a 2-factor solution, labeled as “support” and ”certainty”. Patients reported receiving less support over time, but consistent health certainty. Patients with implantable cardioverter defibrillators felt less secure over time and reported lower levels of health security in chronic illness than pacemaker patients. Résumé: Une échelle mesurant le concept de la « sécurité en matière de santé en présence d’une maladie chronique » a fait l’objet d’un projet pilote auprès de patients canadiens porteurs de dispositifs cardiaques (N = 176) inscrits dans une étude de télésurveillance comportant deux évaluations. L’analyse a révélé une solution à deux facteurs, soit le soutien et la certitude. Les patients ont déclaré qu’ils recevaient moins de soutien au fil du temps, mais que la certitude quant à leur santé était constante. Les porteurs d’un défibrillateur cardioverteur implantable se sentaient moins en sécurité au fil du temps et signalaient de plus bas niveaux de sécurité en matière de santé, relativement à leur maladie chronique, que les porteurs d’un stimulateur cardiaque.

Tomato (Solanum lycopersicum) is an important vegetable crop and a valuable source of nutrients for the human diet. The southeast is the main fresh market tomato producer of the United States, with much of the production concentrated in Florida. However, production in this region is threatened by plant diseases such as target spot of tomato (TS) caused by Corynespora cassiicola, a multitrophic fungus widely distributed in tropical and subtropical areas. TS can infect foliage and fruit, often resulting in significant yield losses in conductive environments. There are no known TS-resistant cultivars, and control relies entirely on fungicidal sprays. However, several studies have demonstrated that the fungus is developing resistance to commonly used fungicides which further complicates disease management. The objective of this work was to identify sources of resistance to TS from wild Solanum accessions. Initial screens of 83 accessions informed the selection of 24 accessions for a more robust screening in which six diverse C. cassiicola isolates were used for single-isolate inoculation experiments. The results from a broad-sense mixed-model analysis including data from all six experiments demonstrated that all 24 accessions had significantly lower disease severities compared with the susceptible controls, suggesting that all accessions potentially harbor resistance quantitative trait loci (QTLs). Solanum cheesmaniae accession LA0524, S. galapagense accessions LA0483 and LA0532, and S. pimpinellifolium accession LA2093 were among the most resistant accessions tested and may be particularly useful for introgression of resistance into cultivated germplasm and for mapping of TS resistance QTLs.

Abstract Glasshouse plants are species that trap warmth via specialized morphology and physiology, mimicking a human glasshouse. In the Himalayan alpine region, the highly specialized glasshouse morphology has independently evolved in distinct lineages to adapt to intensive UV radiation and low temperature. Here we demonstrate that the glasshouse structure – specialized cauline leaves – is highly effective in absorbing UV light but transmitting visible and infrared light, creating an optimal microclimate for the development of reproductive organs. We reveal that this glasshouse syndrome has evolved at least three times independently in the rhubarb genus Rheum. We report the genome sequence of the flagship glasshouse plant Rheum nobile and identify key genetic network modules in association with the morphological transition to specialized glasshouse leaves, including active secondary cell wall biogenesis, upregulated cuticular cutin biosynthesis, and suppression of photosynthesis and terpenoid biosynthesis. The distinct cell wall organization and cuticle development might be important for the specialized optical property of glasshouse leaves. We also find that the expansion of LTRs has likely played an important role in noble rhubarb adaptation to high elevation environments. Our study will enable additional comparative analyses to identify the genetic basis underlying the convergent occurrence of glasshouse syndrome.

Abstract Objective In vitro data prompted U.S Food and Drug Administration warnings that lamotrigine, a common sodium channel modulating anti‐seizure medication (NaM‐ASM), could increase the risk of sudden death in patients with structural or ischaemic cardiac disease, however, its implications for Sudden Unexpected Death in Epilepsy (SUDEP) are unclear. Methods This retrospective, nested case–control study identified 101 sudden unexpected death in epilepsy (SUDEP) cases and 199 living epilepsy controls from Epilepsy Monitoring Units (EMUs) in Australia and the USA. Differences in proportions of lamotrigine and NaM‐ASM use were compared between cases and controls at the time of admission, and survival analyses from the time of admission up to 16 years were conducted. Multivariable logistic regression and survival analyses compared each ASM subgroup adjusting for SUDEP risk factors. Results Proportions of cases and controls prescribed lamotrigine (P = 0.166), one NaM‐ASM (P = 0.80), or ≥2NaM‐ASMs (P = 0.447) at EMU admission were not significantly different. Patients taking lamotrigine (adjusted hazard ratio [aHR] = 0.56; P = 0.054), one NaM‐ASM (aHR = 0.8; P = 0.588) or ≥2 NaM‐ASMs (aHR = 0.49; P = 0.139) at EMU admission were not at increased SUDEP risk up to 16 years following admission. Active tonic–clonic seizures at EMU admission associated with >2‐fold SUDEP risk, irrespective of lamotrigine (aHR = 2.24; P = 0.031) or NaM‐ASM use (aHR = 2.25; P = 0.029). Sensitivity analyses accounting for incomplete ASM data at follow‐up suggest undetected changes to ASM use are unlikely to alter our results. Significance This study provides additional evidence that lamotrigine and other NaM‐ASMs are unlikely to be associated with an increased long‐term risk of SUDEP, up to 16 years post‐EMU admission.

Tumour survival and growth are reliant on angiogenesis, the formation of new blood vessels, to facilitate nutrient and waste exchange and, importantly, provide a route for metastasis from a primary to a secondary site. Whilst current models can ensure the transport and exchange of nutrients and waste via diffusion over distances greater than 200 μm, many lack sufficient vasculature capable of recapitulating the tumour microenvironment and, thus, metastasis. In this study, we utilise gelatin-containing polymerised high internal phase emulsion (polyHIPE) templated polycaprolactone-methacrylate (PCL-M) scaffolds to fabricate a composite material to support the 3D culture of MDA-MB-231 breast cancer cells and vascular ingrowth. Firstly, we investigated the effect of gelatin within the scaffolds on the mechanical and chemical properties using compression testing and FTIR spectroscopy, respectively. Initial in vitro assessment of cell metabolic activity and vascular endothelial growth factor expression demonstrated that gelatin-containing PCL-M polyHIPEs are capable of supporting 3D breast cancer cell growth. We then utilised the chick chorioallantoic membrane (CAM) assay to assess the angiogenic potential of cell-seeded gelatin-containing PCL-M polyHIPEs, and vascular ingrowth within cell-seeded, surfactant and gelatin-containing scaffolds was investigated via histological staining. Overall, our study proposes a promising composite material to fabricate a substrate to support the 3D culture of cancer cells and vascular ingrowth.

Introduction: Autism spectrum disorder (ASD) is characterized by deficits in social communication, repetitive behaviors, and can be accompanied by a spectrum of psychiatric symptoms, such as schizophrenia and catatonia. Rarely, these symptoms, if left untreated, can result in spinal deformities. Research question and case description: This case report details the treatment of a 16-year-old male ASD patient with catatonic schizophrenia and mutism, presenting with neck pain, left-rotated torticollis, and fever. MRI revealed atlantoaxial rotational instability and spinal cord compression from a dislocated dens axis. After inconclusive biopsies, empirical antibiotics, hard collar and halo fixation treatment, persistent instability necessitated C1/2 fusion. The ongoing catatonia was addressed with electroconvulsive therapy. Concurrently, he developed severe subaxial hyperkyphosis. The report examines the decision-making between conservative and surgical management for an adolescent with significant psychiatric comorbidity and progressive spinal symptoms against a backdrop of uncertain etiology. Materials and methods: A case report and review of the literature. Results: Posterior C1-C7 stabilization was successfully executed, effectively restoring cervical sagittal alignment, which was maintained throughout a two-year follow-up. Concurrently, the catatonia resolved. Discussion and conclusion: To our knowledge, this is the third reported case of severe cervical deformity associated with fixed posture in a psychiatric patient. This case report emphasizes the critical importance of multidisciplinary collaboration in managing the interplay between neuropsychiatric disorders and severe spinal deformities. It showcases the practicality and efficacy of surgical intervention for persistent cervical deformity in pediatric schizophrenia patients, highlighting the necessity for a comprehensive risk-benefit analysis.

A genome-wide association study of cardiac magnetic resonance-derived left ventricular mass index including 43,000 UK Biobank participants reveals 12 associations (11 novel), implicating genes involved in cardiac contractility and cardiomyopathy.

In this work, the authors identify regulators of actin filament assembly involved in chiral organisation of the actin cytoskeleton in single cells and chiral alignment of cells in groups. This provides insights into how actin-driven chirality underlies tissue and organ asymmetry.

Abstract Objective The objectives of this study were to define the clinical and biochemical spectrum of spinal muscular atrophy with progressive myoclonic epilepsy (SMA‐PME) and to determine if aberrant cellular ceramide accumulation could be normalized by enzyme replacement. Methods Clinical features of 6 patients with SMA‐PME were assessed by retrospective chart review, and a literature review of 24 previously published cases was performed. Leukocyte enzyme activity of acid ceramidase was assessed with a fluorescence‐based assay. Skin fibroblast ceramide content and was assessed by high performance liquid chromatography, electrospray ionization tandem mass spectroscopy. Enzyme replacement was assessed using recombinant human acid ceramidase (rhAC) in vitro. Results The six new patients showed the hallmark features of SMA‐PME, with variable initial symptom and age of onset. Five of six patients carried at least one of the recurrent SMA‐PME variants observed in two specific codons of ASAH1. A review of 30 total cases revealed that patients who were homozygous for the most common c.125C > T variant presented in the first decade of life with limb‐girdle weakness as the initial symptom. Sensorineural hearing loss was associated with the c.456A > C variant. Leukocyte acid ceramidase activity varied from 4.1%–13.1% of controls. Ceramide species in fibroblasts were detected and total cellular ceramide content was elevated by 2 to 9‐fold compared to controls. Treatment with rhAC normalized ceramide profiles in cultured fibroblasts to control levels within 48 h. Interpretation This study details the genotype–phenotype correlations observed in SMA‐PME and shows the impact of rhAC to correct the abnormal cellular ceramide profile in cells.

Accidental releases of untreated sewage into the environment, known as sewage spills, may cause adverse gastrointestinal stress to exposed populations, especially in young, elderly, or immune-compromised individuals. In addition to human pathogens, untreated sewage contains high levels of micropollutants, organic matter, nitrogen, and phosphorus, potentially resulting in aquatic ecosystem impacts such as algal blooms, depleted oxygen, and fish kills in spill-impacted waterways. Our Geographic Information System (GIS) model, Spill Footprint Exposure Risk (SFER) integrates fine-scale elevation data (1/3 arc-second) with flowpath tracing methods to estimate the expected overland pathways of sewage spills and the locations where they are likely to pool. The SFER model can be integrated with secondary measures tailored to the unique needs of decision-makers so they can assess spatially potential exposure risk. To illustrate avenues to assess risk, we developed risk measures for land and population health. The land risk of sewage spills is calculated for subwatershed regions by computing the proportion of the subwatershed’s area that is affected by one modeled footprint. The population health risk is assessed by computing the estimated number of individuals who are within the modeled footprint using fine-scale (90 square meters) population estimates data from LandScan USA. In the results, with a focus on the Atlanta metropolitan region, potential strategies to combine these risk measures with the SFER model are outlined to identify specific areas for intervention.

Background Lifestyle and metabolic diseases influence the severity and pathogenesis of cardiovascular disease through numerous mechanisms, including regulation via posttranslational modifications. A specific posttranslational modification, the addition of O‐linked β‐N acetylglucosamine (O‐GlcNAcylation), has been implicated in molecular mechanisms of both physiological and pathologic adaptations. The current study aimed to test the hypothesis that in cardiomyocytes, sustained protein O‐GlcNAcylation contributes to cardiac adaptations, and its progression to pathophysiology. Methods and Results Using a naturally occurring dominant‐negative O‐GlcNAcase (dnOGA) inducible cardiomyocyte‐specific overexpression transgenic mouse model, we induced dnOGA in 8‐ to 10‐week‐old mouse hearts. We examined the effects of 2‐week and 24‐week dnOGA overexpression, which progressed to a 1.8‐fold increase in protein O‐GlcNAcylation. Two‐week increases in protein O‐GlcNAc levels did not alter heart weight or function; however, 24‐week increases in protein O‐GlcNAcylation led to cardiac hypertrophy, mitochondrial dysfunction, fibrosis, and diastolic dysfunction. Interestingly, systolic function was maintained in 24‐week dnOGA overexpression, despite several changes in gene expression associated with cardiovascular disease. Specifically, mRNA‐sequencing analysis revealed several gene signatures, including reduction of mitochondrial oxidative phosphorylation, fatty acid, and glucose metabolism pathways, and antioxidant response pathways after 24‐week dnOGA overexpression. Conclusions This study indicates that moderate increases in cardiomyocyte protein O‐GlcNAcylation leads to a differential response with an initial reduction of metabolic pathways (2‐week), which leads to cardiac remodeling (24‐week). Moreover, the mouse model showed evidence of diastolic dysfunction consistent with a heart failure with preserved ejection fraction. These findings provide insight into the adaptive versus maladaptive responses to increased O‐GlcNAcylation in heart.

Hypothalamic hamartoma (HH) is a rare benign developmental brain lesion commonly associated with a well characterized epilepsy phenotype. Most individuals with HH are non-syndromic without additional developmental anomalies nor a family history of disease. Nonetheless, HH is a feature of Pallister-Hall (PHS) and Oro-Facial-Digital Type VI (OFD VI) syndromes, both characterized by additional developmental anomalies. Initial genetic of analysis HH began with syndromic HH, where germline inherited or de novo variants in GLI3, encoding a central transcription factor in the sonic hedgehog (Shh) signalling pathway, were identified in most individuals with PHS. Following these discoveries in syndromic HH, the hypothesis that post-zygotic mosaicism in related genes may underly non-syndromic HH was tested. We discuss the identified mosaic variants within individuals with non-syndromic HH, review the analytical methodologies and diagnostic yields, and explore understanding of the functional role of the implicated genes with respect to Shh signalling, and cilia development and function. We also outline future challenges in studying non-syndromic HH and suggest potential novel strategies to interrogate brain mosaicism in HH.

This study examines the nexus between economic policy uncertainty and real exchange rates of ECOWAS countries to observe the countries’ responses to external shocks and explore the potential success of exchange rate mechanism (ERM) in the West African region. We explore several robustness in the analysis which include consideration of symmetric and asymmetric Autoregressive Distributed Lag model specifications, four alternative real exchange rates measures (US dollar-denominated, Euro-denominated, SDR-denominated, and real effective exchange rates), and three alternative economic policy uncertainty measures (global EPU, US-EPU, and EU-EPU). In line with theory, the findings suggest that the Meese–Rogoff puzzle is alive in West Africa given the widespread statistical insignificance of the estimates. Other dimension of the findings suggest that the countries respond asymmetrically to external shocks. The study highlights the importance of commitment to flexibility criteria in the region in place of devotion to macroeconomic convergence.

Scale insects are some of the most abundant and damaging pests of urban forests in North America. Despite their prevalence, scale insect emergence during the winter dormant season, which could contribute to their population growth and spread and thereby inform management, has not been thoroughly investigated. Crapemyrtle bark scale (CMBS), Acanthococcus lagerstroemiae (Kuwana) (Hemiptera: Eriococcidae), is a nonnative pest of a widely grown landscape tree, crapemyrtle (Lagerstroemia spp.). Now present throughout the Southeast and Mid-Atlantic regions of the United States, CMBS has spread rapidly since its initial detection in Plano, TX, USA, in 2004. The contributions of year-round activity to the insect’s widespread abundance and economic importance are unclear. Here, after infesting crapemyrtles with known numbers of CMBS in Summer 2021, we recorded the presence or absence of CMBS immatures on infested trees from Autumn 2021 to late Winter 2022. We found that active nymphs occurred throughout the entirety of these colder seasons. Additionally, average CMBS density drastically increased from October to March, growing from 28 ± 10 SE insects per plant to 554 ± 133 SE, respectively. Our results highlight previously unknown aspects of year-round crawler emergence by CMBS, which could provide opportunities for landscape managers to use targeted winter applications of less harmful pesticides such as horticultural oils.

Abstract Here we respond to Zhou (BMC Genomics 21:734, 2020) “Combined Transcriptome and Metabolome analysis of Pitaya fruit unveiled the mechanisms underlying peel and pulp color formation” published in BMC Genomics. Given the evolutionary conserved anthocyanin biosynthesis pathway in betalain-pigmented species, we are open to the idea that species with both anthocyanins and betalains might exist. However, in absence of LC-MS/MS spectra, apparent lack of biological replicates, and no comparison to authentic standards, the findings of Zhou (BMC Genomics 21:734, 2020) are not a strong basis to propose the presence of anthocyanins in betalain-pigmented pitaya. In addition, our re-analysis of the datasets indicates the misidentification of important genes and the omission of key flavonoid and anthocyanin synthesis genes ANS and DFR. Finally, our re-analysis of the RNA-Seq dataset reveals no correlation between anthocyanin biosynthesis gene expression and pigment status.

Heart failure (HF) is a leading cause of morbidity and mortality in the United States. While medical management and mechanical circulatory support have undergone significant advancement in recent years, orthotopic heart transplantation (OHT) remains the most definitive therapy for refractory HF. OHT has seen steady improvement in patient survival and quality of life (QoL) since its inception, with one-year mortality now under 8%. However, a significant number of HF patients are unable to receive OHT due to scarcity of donor hearts. The United Network for Organ Sharing has recently revised its organ allocation criteria in an effort to provide more equitable access to OHT. Despite these changes, there are many potential donor hearts that are inevitably rejected. Arbitrary regulations from the centers for Medicare and Medicaid services and fear of repercussions if one-year mortality falls below established values has led to a current state of excessive risk aversion for which organs are accepted for OHT. Furthermore, non-standardized utilization of extended criteria donors and donation after circulatory death, exacerbate the organ shortage. Data-driven systems can improve donor-recipient matching, better predict patient QoL post-OHT, and decrease needless organ waste through more uniform application of acceptance criteria. Thus, we propose a data-driven future for OHT and a move to patient-centric and holistic transplantation care processes.

Abstract Background Crescent cannula adhesion in the setting of COVID-19 respiratory failure requiring extracorporeal membrane oxygenation (ECMO) support is a novel complication. The objective of this case presentation is to highlight this rare complication and to explore potential predisposing factors and our management strategies. Case presentation We present the case of a 25 y.o. patient with COVID-19 respiratory failure requiring ECMO support for 16-days in which a 32 Fr crescent cannula became adherent to the SVC and proximal jugular vein. Attempts to remove the cannula at the bedside failed due to immobility of the cannula. Ultrasound of the right neck was unremarkable, so he was taken to the hybrid OR where both TEE and fluoroscopy were unrevealing. An upper sternotomy was performed, and the superior vena cava and proximal jugular vein were dissected revealing a 2 cm segment of the distal SVC and proximal jugular vein that was densely sclerosed and adherent to the cannula. The vessel was opened across the adherent area at the level of the innominate vein and the cannula was then able to be withdrawn. The patient suffered no ill effects and had an unremarkable recovery to discharge. Conclusions To date, there have been no reports of crescent cannula adhesion related complications. In patients with COVID-19 respiratory failure requiring ECMO, clinicians should be aware of widespread hypercoagulability and the potential of unprovoked, localized venous sclerosis and cannula adhesion. We report our technique of decannulation in the setting of cannula adhesion and hope that presentation will shed further light on this complication allowing clinicians to optimize patient care.

Neuropsychological symptoms associated with post-COVID-19 conditions may prevent patients from resuming normal activities at home or work. We report a retrospective, cross-sectional evaluation of neuropsychological and cardiopulmonary outcomes in 2 groups of patients: outpatients with mild enough infection to be spared from hospitalization and those who required inpatient admission. We hypothesized a dose-response model of post-COVID symptom severity in which persistent consequences would be more severe in those who experienced worse acute infections. In a dedicated COVID clinic, 321 patients were seen (33% outpatient, 67% inpatient). Outpatients skewed female, White, non-Hispanic, and younger. Outpatients had worse insomnia (measured with insomnia severity index) and were less able to resume their usual activities (EQ-5D-5L usual activities scale), despite inpatients experiencing worse cognition (Montreal Cognitive Assessment), having greater obesity (body mass index), decreased exercise tolerance (6-minute-walk distance), and more exertional oxygen desaturation. In both groups, insomnia worsened while cognition improved significantly with time from infection to testing while controlling for patient age; other variables did not. In logistic regression, female sex, higher MoCA score, EQ-5D-5L “usual activities” subscore, less oxygen desaturation with exertion, and longer time from infection remained as significant associations with outpatient status. Our study demonstrated that the functional sequelae of post-COVID-19 conditions in patients with mild acute disease have the potential to be as severe as that in patients who have recovered from severe illness.

Key Clinical Message Postcardiotomy RV dysfunction is an under‐recognized cause of acute kidney injury (AKI). Insertion of a percutaneous right ventricular assist device (RVAD) reduces central venous hypertension and congestive nephropathy by augmenting cardiac output. In selected patients, percutaneous RVAD insertion may improve renal function and obviate the need for long‐term dialysis.

IntroductionType II diabetes mellitus (T2DM) is a metabolic disorder that poses a serious health concern worldwide due to its rising prevalence. Hypertension (HT) is a frequent comorbidity of T2DM, with the co-occurrence of both conditions increasing the risk of diabetes-associated complications. Inflammation and oxidative stress (OS) have been identified as leading factors in the development and progression of both T2DM and HT. However, OS and inflammation processes associated with these two comorbidities are not fully understood. This study aimed to explore changes in the levels of plasma and urinary inflammatory and OS biomarkers, along with mitochondrial OS biomarkers connected to mitochondrial dysfunction (MitD). These markers may provide a more comprehensive perspective associated with disease progression from no diabetes, and prediabetes, to T2DM coexisting with HT in a cohort of patients attending a diabetes health clinic in Australia.MethodsThree-hundred and eighty-four participants were divided into four groups according to disease status: 210 healthy controls, 55 prediabetic patients, 32 T2DM, and 87 patients with T2DM and HT (T2DM+HT). Kruskal-Wallis and χ2 tests were conducted between the four groups to detect significant differences for numerical and categorical variables, respectively.Results and discussionFor the transition from prediabetes to T2DM, interleukin-10 (IL-10), C-reactive protein (CRP), 8-hydroxy-2’-deoxyguanosine (8-OHdG), humanin (HN), and p66Shc were the most discriminatory biomarkers, generally displaying elevated levels of inflammation and OS in T2DM, in addition to disrupted mitochondrial function as revealed by p66Shc and HN. Disease progression from T2DM to T2DM+HT indicated lower levels of inflammation and OS as revealed through IL-10, interleukin-6 (IL-6), interleukin-1β (IL-1β), 8-OHdG and oxidized glutathione (GSSG) levels, most likely due to antihypertensive medication use in the T2DM +HT patient group. The results also indicated better mitochondrial function in this group as shown through higher HN and lower p66Shc levels, which can also be attributed to medication use. However, monocyte chemoattractant protein-1 (MCP-1) levels appeared to be independent of medication, providing an effective biomarker even in the presence of medication use. The results of this study suggest that a more comprehensive review of inflammation and OS biomarkers is more effective in discriminating between the stages of T2DM progression in the presence or absence of HT. Our results further indicate the usefulness of medication use, especially with respect to the known involvement of inflammation and OS in disease progression, highlighting specific biomarkers during disease progression and therefore allowing a more targeted individualized treatment plan.

How rapidly the mutation rate responds evolutionarily to ecological and population-genetic factors over time is unclear. Here, the authors show that the evolution of mutation rates in E. coli proceeds rapidly in response to these factors with substantial bidirectional shifts.

A comprehensive biophysical analysis of disease-associated mutations in the voltage-gated sodium channel gene, SCN2A, suggests that dynamic action potential clamp may be a better predictor than voltage clamp of how these mutations alter neuronal excitability, though other approaches are needed to predict severity.

Abstract Despite substantial efforts to control locusts they remain periodically a major burden in Africa, causing severe yield loss and hence loss of food and income. Distribution maps indicating the value of the basic reproduction number R 0 was used to identify areas where an insect pest can be controlled by a natural enemy. A dynamic process-based mathematical model integrating essential features of a natural enemy and its interaction with the pest is used to generate R 0 risk maps for insect pest outbreaks, using desert locust and the entomopathogenic fungus Metarhizium acridum (Synn. Metarhizium anisoliae var. acridum) as a case study. This approach provides a tool for evaluating the impact of climatic variables such as temperature and relative humidity and mapping spatial variability on the efficacy of M. acridum as a biocontrol agent against desert locust invasion in Africa. Applications of M. acridum against desert locust in a few selected African countries including Morocco, Kenya, Mali, and Mauritania through monthly spatial projection of R 0 maps for the prevailing climatic condition are illustrated. By combining mathematical modeling with a geographic information system in a spatiotemporal projection as we do in this study, the field implementation of microbial control against locust in an integrated pest management system may be improved. Finally, the practical utility of this model provides insights that may improve the timing of pesticide application in a selected area where efficacy is highly expected.

It is thought that Atlantic style passive margins have experienced episodes of uplift and volcanism in response to changes in mantle circulation. The authors here employ U-Pb dating of calcite in faults and fractures along the eastern North American margin and find a 40 Myr long period of fracturing and faulting from 115 to 75 Ma.

Abstract Electronic health record (EHR) datasets are statistically powerful but are subject to ascertainment bias and missingness. Using the Mass General Brigham multi-institutional EHR, we approximated a community-based cohort by sampling patients receiving longitudinal primary care between 2001-2018 (Community Care Cohort Project [C3PO], n = 520,868). We utilized natural language processing (NLP) to recover vital signs from unstructured notes. We assessed the validity of C3PO by deploying established risk models for myocardial infarction/stroke and atrial fibrillation. We then compared C3PO to Convenience Samples including all individuals from the same EHR with complete data, but without a longitudinal primary care requirement. NLP reduced the missingness of vital signs by 31%. NLP-recovered vital signs were highly correlated with values derived from structured fields (Pearson r range 0.95–0.99). Atrial fibrillation and myocardial infarction/stroke incidence were lower and risk models were better calibrated in C3PO as opposed to the Convenience Samples (calibration error range for myocardial infarction/stroke: 0.012–0.030 in C3PO vs. 0.028–0.046 in Convenience Samples; calibration error for atrial fibrillation 0.028 in C3PO vs. 0.036 in Convenience Samples). Sampling patients receiving regular primary care and using NLP to recover missing data may reduce bias and maximize generalizability of EHR research.

Bacterial spot caused by Xanthomonas euvesicatoria is a major disease of pepper (Capsicum annuum L.) in warm and humid production environments. Use of genetically resistant cultivars is an effective approach to manage bacterial spot. Two recessive resistance genes, bs5 and bs6, confer non-race-specific resistance against bacterial spot. The objective of our study was to map these two loci in the pepper genome. We used a genotyping-by-sequencing approach to initially map the position of the two resistances. Segregating populations for bs5 and bs6 were developed by crossing susceptible Early CalWonder (ECW) with near-isogenic lines ECW50R (bs5 introgression) or ECW60R (bs6 introgression). Following fine-mapping, bs5 was delimited to a ~535 Kbp interval on chromosome 3, and bs6 to a ~666 Kbp interval in chromosome 6. We identified 14 and 8 candidate resistance genes for bs5 and bs6, respectively, based on predicted protein coding polymorphisms between ECW and the corresponding resistant parent. This research enhances marker-assisted selection of bs5 and bs6 in breeding programs and is a crucial step towards elucidating the molecular mechanisms underlying the resistances.

Abstract Analyses of spontaneous mutation have shown that total genome‐wide mutation rates are quantitatively similar for most prokaryotic organisms. However, this view is mainly based on organisms that grow best around neutral pH values (6.0–8.0). In particular, the whole‐genome mutation rate has not been determined for an acidophilic organism. Here, we have determined the genome‐wide rate of spontaneous mutation in the acidophilic Acidobacterium capsulatum using a direct and unbiased method: a mutation‐accumulation experiment followed by whole‐genome sequencing. Evaluation of 69 mutation accumulation lines of A. capsulatum after an average of ~2900 cell divisions yielded a base‐substitution mutation rate of 1.22 × 10−10 per site per generation or 4 × 10−4 per genome per generation, which is significantly lower than the consensus value (2.5−4.6 × 10−3) of mesothermophilic (~15–40°C) and neutrophilic (pH 6–8) prokaryotic organisms. However, the insertion‐deletion rate (0.43 × 10−10 per site per generation) is high relative to the base‐substitution mutation rate. Organisms with a similar effective population size and a similar expected effect of genetic drift should have similar mutation rates. Because selection operates on the total mutation rate, it is suggested that the relatively high insertion‐deletion rate may be balanced by a low base‐substitution rate in A. capsulatum, with selection operating on the total mutation rate.