The GeoTox Package: Open-source software for connecting spatiotemporal exposure to individual and population-level risk.

Background: Comprehensive environmental risk characterization, encompassing physical, chemical, social, ecological, and lifestyle stressors, necessitates innovative approaches to handle the escalating complexity. This is especially true when considering individual and population-level diversity, where the myriad combinations of real-world exposures magnify the combinatoric challenges. The GeoTox framework offers a tractable solution by integrating geospatial exposure data from source-to-outcome in a series of modular, interconnected steps. Results: Here, we introduce the GeoTox open-source R software package for characterizing the risk of perturbing molecular targets involved in adverse human health outcomes based on exposure to spatially-referenced stressor mixtures. We demonstrate its usage in building computational workflows that incorporate individual and population-level diversity. Our results demonstrate the applicability of GeoTox for individual and population-level risk assessment, highlighting its capacity to capture the complex interplay of environmental stressors on human health. Conclusions: The GeoTox package represents a significant advancement in environmental risk characterization, providing modular software to facilitate the application and further development of the GeoTox framework for quantifying the relationship between environmental exposures and health outcomes. By integrating geospatial methods with cutting-edge exposure and toxicological frameworks, GeoTox offers a robust tool for assessing individual and population-level risks from environmental stressors. GeoTox is freely available at https://niehs.github.io/GeoTox/ .

Obstetric Anal Sphincter Injury Care Bundle: A Quality Improvement Initiative.

INTRODUCTION AND HYPOTHESIS: The objective was to implement an evidence-based peri-partum care bundle for women sustaining obstetric anal sphincter injuries and to evaluate compliance with recommendations for antibiotics use, repair in the operating room, and follow-up before and after implementation. METHODS: This project was reviewed by the Institutional Review Board and determined to be exempt. A clinical care bundle containing education and standardized orders in the electronic medical record was implemented. Characteristics of pre- (October 2017 to September 2019) and post-intervention (October 2019 to August 2021) cohorts were compared and compliance with recommendations for antibiotics use, surgical repair location, and follow-up were evaluated. Chi-squared, Fisher's exact, ANOVA F, and Kruskal-Wallis tests were performed, as indicated. Significance level was p < 0.05. RESULTS: A total of 185 cases were identified. Seventy-five percent of women were nulliparous. Mean gestational age was 39 weeks. Pre- and post-intervention groups did not differ in age, BMI, race, parity, gestational age, comorbidities, birthweight, or delivery type. Ninety-eight cases were identified pre-implementation. Eighty-six (88%) had third-degree lacerations. Post-implementation, 87 cases were identified. Seventy (80%) had third-degree lacerations (p = 0.17). Recommended antibiotic-type use improved from 35% pre-implementation to 93% post-implementation (p < 0.001). Repair in the operating room was similar pre-implementation and post-implementation (16.0% vs 12.6%, p = 0.48). Post-partum follow-up within 2 weeks improved from 16.3% pre-implementation to 52.8% post-implementation and mean time to follow-up was shorter post-implementation than pre-implementation (18 vs 33 days; both p < 0.001). CONCLUSIONS: Implementation of an evidence-based peri-partum care bundle resulted in standardization of care in accordance with established recommendations. Compliance with recommendations for surgical repair in the operating room remained unchanged.

Biallelic variation in the choline and ethanolamine transporter FLVCR1 underlies a severe developmental disorder spectrum.

PURPOSE: FLVCR1 encodes a solute carrier (SLC) protein implicated in heme, choline, and ethanolamine transport. While Flvcr1-/- mice exhibit skeletal malformations and defective erythropoiesis reminiscent of Diamond-Blackfan anemia (DBA), biallelic FLVCR1 variants in humans have previously only been linked to childhood or adult-onset ataxia, sensory neuropathy, and retinitis pigmentosa. METHODS: We identified individuals with undiagnosed neurodevelopmental disorders and biallelic FLVCR1 variants through international data sharing and characterized the functional consequences of their FLVCR1 variants. RESULTS: We ascertained 30 patients from 23 unrelated families with biallelic FLVCR1 variants and characterized a novel FLVCR1-related phenotype: severe developmental disorders with profound developmental delay, microcephaly (Z-score -2.5 to -10.5), brain malformations, epilepsy, spasticity, and premature death. Brain malformations ranged from mild brain volume reduction to hydranencephaly. Severely affected patients share traits including macrocytic anemia and skeletal malformations with Flvcr1-/- mice and DBA. FLVCR1 variants significantly reduce choline and ethanolamine transport and/or disrupt mRNA splicing. CONCLUSION: These data demonstrate a broad FLVCR1-related phenotypic spectrum ranging from severe multiorgan developmental disorders resembling DBA to adult-onset neurodegeneration. Our study expands our understanding of Mendelian choline and ethanolamine disorders and illustrates the importance of anticipating a wide phenotypic spectrum for known disease genes and incorporating model organism data into genome analysis to maximize genetic testing yield.

POPULATION PHARMACOKINETICS OF CEFPODOXIME IN BOTTLENOSE DOLPHINS (TURSIOPS TRUNCATUS).

Cefpodoxime proxetil is commonly used to treat cetacean patients with suspected or confirmed bacterial infections; however, pharmacokinetic data are needed to guide proper dosing in these species. Cefpodoxime proxetil is a time-dependent, semisynthetic, third-generation cephalosporin, appropriate for once-daily dosing and U.S. Food and Drug Administration-approved for use in dogs with a broad spectrum of activity including gram-positive and gram-negative species. The objective of this study was to evaluate the population pharmacokinetics of cefpodoxime in bottlenose dolphins (Tursiops truncatus). A sparse-sampling design was used, with serum from dolphins receiving cefpodoxime proxetil at 10 mg/kg orally every 24 h to treat suspected or confirmed bacterial infections. Serum samples (n = 57) from 24 dolphins were analyzed at 12 time points from 0 to 96 h postdose. Serum samples were analyzed using liquid chromatography-mass spectrometry. Population pharmacokinetic analysis was performed using nonlinear mixed-effects modeling. One- and two-compartment linear models with first order absorption were tested. Covariates including weight, age, and sex were considered for inclusion in the model, and between-subject variability was incorporated. A two-compartment model performed best, where following an oral dose of 10 mg/kg, serum concentration reached a mean maximum concentration of 23.0 µg/ml, mean time to maximum concentration of 5.0 h, and mean half-life of 11.4 h. With daily dosing, accumulation was approximately 18% and steady state was reached by the second dose. Serum protein binding was 82.8% as determined by equilibrium dialysis, similar to plasma protein binding reported in dogs. Based on the population pharmacokinetic model, once-daily oral dosing was systemically absorbed and quickly reached maximum concentrations. The half-life in dolphins appears to be longer than other species studied to date. Given the paucity of antimicrobial pharmacokinetic studies in dolphins, and limited once-daily oral antibiotic options for this species, these data are helpful for clinicians to make informed antimicrobial choices.

Osteopontin deletion attenuates cyst growth but exacerbates fibrosis in mice with cystic kidney disease.

Osteopontin (OPN) is a multi-functional glycoprotein that coordinates the innate immune response, prevents nanocrystal formation in renal tubule fluid, and is a biomarker for kidney injury. OPN expression is markedly increased in cystic epithelial cells of polycystic kidney disease (PKD) kidneys; however, its role in PKD progression remains unclear. We investigated the in vitro effects of recombinant OPN on the proliferation of tubular epithelial cells from PKD and normal human kidneys and in vivo effects of OPN deletion on kidney cyst formation, fibrosis, and mineral metabolism in pcy/pcy mice, a non-orthologous model of autosomal-dominant PKD. In vitro studies revealed that OPN enhanced the proliferation of PKD cells but had no effect on normal kidney cells. Deletion of OPN in pcy/pcy mice significantly reduced kidney cyst burden; however, this was accompanied by increased fibrosis and no change in kidney function. The loss of OPN had no effect on kidney macrophage numbers, cyst epithelial cell proliferation, or apoptosis. Furthermore, there was no difference in kidney mineral deposition or mineral metabolism parameters between pcy/pcy mice with and without OPN expression. Global deletion of OPN reduced kidney cyst burden, while paradoxically exacerbating kidney fibrosis in mice with cystic kidney disease.

COVID-19-Associated Hospitalizations and Maternal Vaccination Among Infants Aged <6 Months - COVID-NET, 12 States, October 2022-April 2024.

Infants aged <6 months are at increased risk for severe COVID-19 disease but are not yet eligible for COVID-19 vaccination; these children depend upon transplacental transfer of maternal antibody, either from vaccination or infection, for protection. COVID-19-Associated Hospitalization Surveillance Network (COVID-NET) data were analyzed to estimate COVID-19-associated hospitalization rates and identify demographic and clinical characteristics and maternal vaccination status of infants aged <6 months hospitalized with laboratory-confirmed COVID-19. During October 2022-April 2024, COVID-NET identified 1,470 COVID-19-associated hospitalizations among infants aged <6 months. COVID-19-associated hospitalization rates among young infants were higher than rates among any other age group, except adults aged ≥75 years, and are comparable to rates among adults aged 65-74 years. The percentage of hospitalized infants whose mothers had been vaccinated during pregnancy was 18% during October 2022-September 2023 and decreased to <5% during October 2023-April 2024. Severe outcomes among infants hospitalized with COVID-19 occurred frequently: excluding newborns hospitalized at birth, approximately one in five young infants hospitalized with COVID-19 required admission to an intensive care unit, nearly one in 20 required mechanical ventilation, and nine infants died during their COVID-19-associated hospitalization. To help protect pregnant persons and infants too young to be vaccinated, prevention for these groups should focus on ensuring that pregnant persons receive recommended COVID-19 vaccines.

On-demand nanoengineering of in-plane ferroelectric topologies.

Hierarchical assemblies of ferroelectric nanodomains, so-called super-domains, can exhibit exotic morphologies that lead to distinct behaviours. Controlling these super-domains reliably is critical for realizing states with desired functional properties. Here we reveal the super-switching mechanism by using a biased atomic force microscopy tip, that is, the switching of the in-plane super-domains, of a model ferroelectric Pb0.6Sr0.4TiO3. We demonstrate that the writing process is dominated by a super-domain nucleation and stabilization process. A complex scanning-probe trajectory enables on-demand formation of intricate centre-divergent, centre-convergent and flux-closure polar structures. Correlative piezoresponse force microscopy and optical spectroscopy confirm the topological nature and tunability of the emergent structures. The precise and versatile nanolithography in a ferroic material and the stability of the generated structures, also validated by phase-field modelling, suggests potential for reliable multi-state nanodevice architectures and, thereby, an alternative route for the creation of tunable topological structures for applications in neuromorphic circuits.

A review of geospatial exposure models and approaches for health data integration.

BACKGROUND: Geospatial methods are common in environmental exposure assessments and increasingly integrated with health data to generate comprehensive models of environmental impacts on public health. OBJECTIVE: Our objective is to review geospatial exposure models and approaches for health data integration in environmental health applications. METHODS: We conduct a literature review and synthesis. RESULTS: First, we discuss key concepts and terminology for geospatial exposure data and models. Second, we provide an overview of workflows in geospatial exposure model development and health data integration. Third, we review modeling approaches, including proximity-based, statistical, and mechanistic approaches, across diverse exposure types, such as air quality, water quality, climate, and socioeconomic factors. For each model type, we provide descriptions, general equations, and example applications for environmental exposure assessment. Fourth, we discuss the approaches used to integrate geospatial exposure data and health data, such as methods to link data sources with disparate spatial and temporal scales. Fifth, we describe the landscape of open-source tools supporting these workflows.

Timing of influenza antiviral therapy and risk of death in adults hospitalized with influenza-associated pneumonia, FluSurv-NET, 2012-2019.

BACKGROUND: Pneumonia is common in adults hospitalized with laboratory-confirmed influenza, but the association between timeliness of influenza antiviral treatment and severe clinical outcomes in patients with influenza-associated pneumonia is not well characterized. METHODS: We included adults aged ≥18 years hospitalized with laboratory-confirmed influenza and a discharge diagnosis of pneumonia over 7 influenza seasons (2012-2019) sampled from a multi-state population-based surveillance network. We evaluated 3 treatment groups based on timing of influenza antiviral initiation relative to admission date (day 0, day 1, days 2-5). Baseline characteristics and clinical outcomes were compared across groups using unweighted counts and weighted percentages accounting for the complex survey design. Logistic regression models were generated to evaluate the association between delayed treatment and 30-day all-cause mortality. RESULTS: 26,233 adults were sampled in the analysis. Median age was 71 years and most (92.2%) had ≥1 non-immunocompromising condition. Overall, 60.9% started antiviral treatment on day 0, 29.5% on day 1, and 9.7% on days 2-5 (median 2 days). Baseline characteristics were similar across groups. Thirty-day mortality occurred in 7.5%, 8.5%, and 10.2% of patients who started treatment on day 0, day 1, and days 2-5, respectively. Compared to those treated on day 0, adjusted OR for death was 1.14 (95%CI: 1.01-1.27) in those starting treatment on day 1 and 1.40 (95%CI: 1.17-1.66) in those starting on days 2-5. DISCUSSION: Delayed initiation of antiviral treatment in patients hospitalized with influenza-associated pneumonia was associated with higher risk of death, highlighting the importance of timely initiation of antiviral treatment at admission.

Outcomes of a Single Transverse Chest Roll for Prone Positioning Technique During Percutaneous Nephrolithotomy.

OBJECTIVE: To compare anesthetic parameters using a novel prone single transverse chest roll technique (STR) to the standard thoraco-pelvic dual transverse roll technique (DTR). METHODS: A retrospective review of 441 patients who underwent PCNL between 2018 and 2022 was performed. A total of 4 surgeons were included-surgeon 1 utilized the STR technique while surgeons 2, 3, and 4 used the DTR technique. Anesthetic parameters including end-tidal CO2 (ETCO2), mean arterial pressure (MAP), peak airway pressure (Ppeak), plateau airway pressure (Pplat), positive end-expiratory pressure (PEEP), oxygen saturation (SpO2), and tidal volume (TV) were compared between both groups at 0 (supine), 15-, 30-, and 60-minute post-intubation intervals. Mixed effects regression models with interaction and pairwise comparisons were made between both groups (P <.05). RESULTS: A total of 581 PCNLs were performed with 199 using STR and 382 using DTR. Surgery duration, ASA class, and age were similar amongst the STR and DTR groups. Estimated blood loss (59cc vs 83cc, P = .007) and length of stay (77 hrs vs 163 hrs, P = <.001) was significantly lower in the STR group. There was a significantly lower Ppeak, Pplat and TV in the STR compared to DTR group at 0, 15, 30, and 60 minutes (P <.001). CONCLUSION: Usage of a single transverse chest roll during prone PCNL appears to be a safe positioning method. STR patients had lower Ppeak and Pplat at all time points, which has been shown to be predictive of lower blood loss.

Unmet patient needs in monocarboxylate transporter 8 (MCT8) deficiency: a review.

Monocarboxylate transporter 8 (MCT8) deficiency is a rare, X-linked disorder arising from mutations in the SLC16A2 gene and resulting from dysfunctional thyroid hormone transport. This disorder is characterized by profound neurodevelopmental delay and motor disability due to a lack of thyroid hormone in the brain, and coexisting endocrinological symptoms, due to chronic thyrotoxicosis, resulting from elevated thyroid hormone outside the central nervous system (CNS). In February 2024, we reviewed the published literature to identify relevant articles reporting on the current unmet needs of patients with MCT8 deficiency. There are several main challenges in the diagnosis and treatment of MCT8 deficiency, with decreased awareness and recognition of MCT8 deficiency among healthcare professionals (HCPs) associated with misdiagnosis and delays in diagnosis. Diagnostic delay may also be attributed to other factors, including the complex symptomology of MCT8 deficiency only becoming apparent several months after birth and pathognomonic serum triiodothyronine (T3) testing not being routinely performed. For patients with MCT8 deficiency, multidisciplinary team care is vital to optimize the support provided to patients and their caregivers. Although there are currently no approved treatments specifically for MCT8 deficiency, earlier identification and diagnosis of this disorder enables earlier access to supportive care and developing treatments focused on improving outcomes and quality of life for both patients and caregivers.

Epididymal Cyst Lesions Are Not Associated With Impaired Semen Parameters Among Men Presenting for Fertility Evaluation.

PURPOSE: Epididymal cyst lesions (ECLs) include both spermatoceles and epididymal cysts and are often incidentally found on physical exam or scrotal US (SUS). We aimed to determine the association of ECLs and semen parameters among men presenting for fertility evaluation. MATERIALS AND METHODS: We reviewed men at our institution who had at least 1 semen analysis and SUS available for review between 2002 and 2022. SUS data included testicular measurements, presence or absence of subclinical varicocele, and size and laterality of ECL, if present. Demographic and clinical information including serum testosterone and follicle-stimulating hormone and semen parameters were compared between men with and without ECLs. RESULTS: Among 861 men, 164 (19%) had unilateral right ECL (median 4 mm, interquartile range 3-8 mm), 189 (22%) had unilateral left ECL (median 4 mm, interquartile range 3-9 mm), and 113 (13%) had bilateral ECL. Patients with ECLs were significantly older than men without ECLs at the time of evaluation but had no statistically significant difference in semen volume, sperm concentration, sperm motility, sperm morphology, total motile sperm count, or serum hormonal values. Analysis of men with unilateral and bilateral ECLs showed that ECL size and laterality did not significantly correlate with any semen parameter evaluated. CONCLUSIONS: We found no association between ECLs and semen parameters. Patients should be counseled toward conservative management with observation for asymptomatic ECLs in the setting of fertility evaluation.

Repair of facial dog bite wound utilizing cryopreserved umbilical cord allograft.

BACKGROUND: In the United States, craniofacial injuries are the most frequently observed traumas in the pediatric population. Human birth tissue products contain growth factors, cytokines, and signaling molecules that can be potentially harnessed for tissue regeneration and wound healing. PURPOSE: A cryopreserved ultra-thick amniotic membrane (AM) allograft wound dressing was used in a patient with significant facial soft tissue loss due to a dog bite injury. METHODS: This is a single case report of a pediatric patient. After obtaining IRB exemption, operative and postoperative clinic notes were reviewed. RESULTS: A 10-year-old female presented to the emergency department after suffering a dog bite to her left cheek and upper lip, resulting in tissue loss. A cryopreserved ultra-thick AM allograft was used to cover the area of tissue loss as part of surgical reconstruction. The patient was followed up at 1 week, 3 weeks, 4 months, and 1 year after the graft was placed, and rapid healing and full epithelialization were achieved in addition to scar contracture due to wound location. CONCLUSION: In the setting of acute trauma and tissue loss, human birth tissue was found to promote epithelialization and regenerative healing of facial tissues.

Identifying and training deep learning neural networks on biomedical-related datasets.

This manuscript describes the development of a resources module that is part of a learning platform named 'NIGMS Sandbox for Cloud-based Learning' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox at the beginning of this Supplement. This module delivers learning materials on implementing deep learning algorithms for biomedical image data in an interactive format that uses appropriate cloud resources for data access and analyses. Biomedical-related datasets are widely used in both research and clinical settings, but the ability for professionally trained clinicians and researchers to interpret datasets becomes difficult as the size and breadth of these datasets increases. Artificial intelligence, and specifically deep learning neural networks, have recently become an important tool in novel biomedical research. However, use is limited due to their computational requirements and confusion regarding different neural network architectures. The goal of this learning module is to introduce types of deep learning neural networks and cover practices that are commonly used in biomedical research. This module is subdivided into four submodules that cover classification, augmentation, segmentation and regression. Each complementary submodule was written on the Google Cloud Platform and contains detailed code and explanations, as well as quizzes and challenges to facilitate user training. Overall, the goal of this learning module is to enable users to identify and integrate the correct type of neural network with their data while highlighting the ease-of-use of cloud computing for implementing neural networks. This manuscript describes the development of a resource module that is part of a learning platform named ``NIGMS Sandbox for Cloud-based Learning'' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.

The effect of histopathologic analysis and tissue cultures on inpatient management of cellulitis: a randomized control trial.

BACKGROUND: In the absence of a gold-standard diagnostic modality for cellulitis, sterile inflammatory disorders may be misdiagnosed as cellulitis. OBJECTIVE: To determine the utility of skin biopsy and tissue culture for the diagnosis and management of patients admitted with a diagnosis of presumed cellulitis. DESIGN: Pilot single-blind parallel group randomized controlled clinical trial in 56 patients with a primary diagnosis of presumed cellulitis. In the intervention group only, skin biopsy and tissue culture results were made available to the primary care team to guide diagnosis and management. Length of hospital stay and antibiotic use were evaluated as outcome measures. RESULTS: Length of stay showed the greatest opportunity for further study as a primary outcome (intervention: 4, IQR (2-6) vs. control: 5 IQR (3-8) days; p = 0.124). LIMITATIONS: The COVID-19 pandemic placed limitations on participant enrollment and study duration; in addition, data was collected from a single medical center. CONCLUSION: This study demonstrates that length of stay and anti-pseudomonal antibiotic de-escalation are endpoints that may be influenced by biopsy and tissue culture results in presumed cellulitis patients; these outcomes warrant further study.

A novel missense variant in the ATPase domain of ATP8A2 and review of phenotypic variability of ATP8A2-related disorders caused by missense changes.

ATPase, class 1, type 8 A, member 2 (ATP8A2) is a P4-ATPase with a critical role in phospholipid translocation across the plasma membrane. Pathogenic variants in ATP8A2 are known to cause cerebellar ataxia, impaired intellectual development, and disequilibrium syndrome 4 (CAMRQ4) which is often associated with encephalopathy, global developmental delay, and severe motor deficits. Here, we present a family with two siblings born from a consanguineous, first-cousin union from Sudan presenting with global developmental delay, intellectual disability, spasticity, ataxia, nystagmus, and thin corpus callosum. Whole exome sequencing revealed a homozygous missense variant in the nucleotide binding domain of ATP8A2 (p.Leu538Pro) that results in near complete loss of protein expression. This is in line with other missense variants in the same domain leading to protein misfolding and loss of ATPase function. In addition, by performing diffusion-weighted imaging, we identified bilateral hyperintensities in the posterior limbs of the internal capsule suggesting possible microstructural changes in axon tracts that had not been appreciated before and could contribute to the sensorimotor deficits in these individuals.

Histopathologic Features of Mucosal Head and Neck Cancer Cachexia.

Objective: Determine the histopathologic features that correlate with head and neck cancer (HNC) cachexia. Methods: A single-institution, retrospective study was performed on adults with HPV-negative, mucosal squamous cell carcinoma of the aerodigestive tract undergoing resection and free flap reconstruction from 2014 to 2019. Patients with distant metastases were excluded. Demographics, comorbidities, preoperative nutrition, and surgical pathology reports were collected. Comparisons of histopathologic features and cachexia severity were made. Results: The study included 222 predominantly male (64.9%) patients aged 61.3 ± 11.8 years. Cachexia was identified in 57.2% patients, and 18.5% were severe (≥15% weight loss). No differences in demographics were identified between the groups. Compared to control, patients with severe cachexia had lower serum hemoglobin (p=0.048) and albumin (p < 0.001), larger tumor diameter (p < 0.001), greater depth of invasion (p < 0.001), and elevated proportions of pT4 disease (p < 0.001), pN2-N3 disease (p=0.001), lymphovascular invasion (p=0.009), and extranodal extension (p=0.014). Multivariate logistic regression identified tumor size (OR [95% CI] = 1.36 [1.08-1.73]), oral cavity tumor (OR [95% CI] = 0.30 [0.11-0.84]), and nodal burden (OR [95% CI] = 1.16 [0.98-1.38]) as significant histopathologic contributors of cancer cachexia. Conclusions: Larger, more invasive tumors with nodal metastases and aggressive histologic features are associated with greater cachexia severity in mucosal HNC.