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Objectives: To provide a foundational methodology for differentiating comorbidity patterns in subphenotypes through investigation of a multi-site dementia patient dataset. Materials and Methods: Employing the National Clinical Cohort Collaborative Tenant Pilot (N3C Clinical) dataset, our approach integrates machine learning algorithms-logistic regression and eXtreme Gradient Boosting (XGBoost)-with a diagnostic hierarchical model for nuanced classification of dementia subtypes based on comorbidities and gender. The methodology is enhanced by multi-site EHR data, implementing a hybrid sampling strategy combining 65% Synthetic Minority Over-sampling Technique (SMOTE), 35% Random Under-Sampling (RUS), and Tomek Links for class imbalance. The hierarchical model further refines the analysis, allowing for layered understanding of disease patterns. Results: The study identified significant comorbidity patterns associated with diagnosis of Alzheimer's, Vascular, and Lewy Body dementia subtypes. The classification models achieved accuracies up to 69% for Alzheimer's/Vascular dementia and highlighted challenges in distinguishing Dementia with Lewy Bodies. The hierarchical model elucidates the complexity of diagnosing Dementia with Lewy Bodies and reveals the potential impact of regional clinical practices on dementia classification. Conclusion: Our methodology underscores the importance of leveraging multi-site datasets and tailored sampling techniques for dementia research. This framework holds promise for extending to other disease subtypes, offering a pathway to more nuanced and generalizable insights into dementia and its complex interplay with comorbid conditions. Discussion: This study underscores the critical role of multi-site data analyzes in understanding the relationship between comorbidities and disease subtypes. By utilizing diverse healthcare data, we emphasize the need to consider site-specific differences in clinical practices and patient demographics. Despite challenges like class imbalance and variability in EHR data, our findings highlight the essential contribution of multi-site data to developing accurate and generalizable models for disease classification.
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Objective: Determine the incidence of vestibular disorders in patients with SARS-CoV-2 compared to the control population. Study Design: Retrospective. Setting: Clinical data in the National COVID Cohort Collaborative database (N3C). Methods: Deidentified patient data from the National COVID Cohort Collaborative database (N3C) were queried based on variant peak prevalence (untyped, alpha, delta, omicron 21K, and omicron 23A) from covariants.org to retrospectively analyze the incidence of vestibular disorders in patients with SARS-CoV-2 compared to control population, consisting of patients without documented evidence of COVID infection during the same period. Results: Patients testing positive for COVID-19 were significantly more likely to have a vestibular disorder compared to the control population. Compared to control patients, the odds ratio of vestibular disorders was significantly elevated in patients with untyped (odds ratio [OR], 2.39; confidence intervals [CI], 2.29-2.50; P < 0.001), alpha (OR, 3.63; CI, 3.48-3.78; P < 0.001), delta (OR, 3.03; CI, 2.94-3.12; P < 0.001), omicron 21K variant (OR, 2.97; CI, 2.90-3.04; P < 0.001), and omicron 23A variant (OR, 8.80; CI, 8.35-9.27; P < 0.001). Conclusions: The incidence of vestibular disorders differed between COVID-19 variants and was significantly elevated in COVID-19-positive patients compared to the control population. These findings have implications for patient counseling and further research is needed to discern the long-term effects of these findings.
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Natural patterns of physical activity in youth are characterized by brief periods of exercise of varying intensity interspersed with rest. To better understand systemic physiologic response mechanisms in children and adolescents, we examined five responses [heart rate (HR), respiratory rate (RR), oxygen uptake (VÌO2 ), carbon dioxide production (VÌCO2 ), and minute ventilation (VÌE), measured breath-by-breath] to multiple brief exercise bouts (MBEB). Two groups of healthy participants (early pubertal: 17 female, 20 male; late-pubertal: 23 female, 21 male) performed five consecutive 2-min bouts of constant work rate cycle-ergometer exercise interspersed with 1-min of rest during separate sessions of low- or high-intensity (~40% or 80% peak work, respectively). For each 2-min on-transient and 1-min off-transient we calculated the average value of each cardiopulmonary exercise testing (CPET) variable (YÌ ). There were significant MBEB changes in 67 of 80 on- and off-transients. YÌ increased bout-to-bout for all CPET variables, and the magnitude of increase was greater in the high-intensity exercise. We measured the metabolic cost of MBEB, scaled to work performed, for the entire 15 min and found significantly higher VÌO2 , VÌCO2 , and VÌE costs in the early-pubertal participants for both low- and high-intensity MBEB. To reduce breath-by-breath variability in estimation of CPET variable kinetics, we time-interpolated (second-by-second), superimposed, and averaged responses. Reasonable estimates of τ (<20% coefficient of variation) were found only for on-transients of HR and VÌO2 . There was a remarkable reduction in τHR following the first exercise bout in all groups. Natural patterns of physical activity shape cardiorespiratory responses in healthy children and adolescents. Protocols that measure the effect of a previous bout on the kinetics of subsequent bouts may aid in the clinical utility of CPET.
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Teste de Esforço , Exercício Físico , Adolescente , Criança , Ergometria , Exercício Físico/fisiologia , Teste de Esforço/métodos , Feminino , Frequência Cardíaca/fisiologia , Humanos , Masculino , Consumo de Oxigênio/fisiologiaRESUMO
OBJECTIVE: The integrated Translational Health Research Institute of Virginia (iTHRIV) aims to develop an information architecture to support data workflows throughout the research lifecycle for cross-state teams of translational researchers. MATERIALS AND METHODS: The iTHRIV Commons is a cross-state harmonized infrastructure supporting resource discovery, targeted consultations, and research data workflows. As the front end to the iTHRIV Commons, the iTHRIV Research Concierge Portal supports federated login, personalized views, and secure interactions with objects in the ITHRIV Commons federation. The canonical use-case for the iTHRIV Commons involves an authenticated user connected to their respective high-security institutional network, accessing the iTHRIV Research Concierge Portal web application on their browser, and interfacing with multi-component iTHRIV Commons Landing Services installed behind the firewall at each participating institution. RESULTS: The iTHRIV Commons provides a technical framework, including both hardware and software resources located in the cloud and across partner institutions, that establishes standard representation of research objects, and applies local data governance rules to enable access to resources from a variety of stakeholders, both contributing and consuming. DISCUSSION: The launch of the Commons API service at partner sites and the addition of a public view of nonrestricted objects will remove barriers to data access for cross-state research teams while supporting compliance and the secure use of data. CONCLUSIONS: The secure architecture, distributed APIs, and harmonized metadata of the iTHRIV Commons provide a methodology for compliant information and data sharing that can advance research productivity at Hub sites across the CTSA network.
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Software , Pesquisa Translacional Biomédica , Disseminação de Informação , Fluxo de TrabalhoRESUMO
Histologic diagnosis of Barrett's esophagus and esophageal malignancy via probe-based confocal laser endomicroscopy (pCLE) allows for real-time examination of epithelial architecture and targeted biopsy sampling. Although pCLE demonstrates high specificity, sensitivity remains low. This study employs deep learning architectures in order to improve the accuracy of pCLE in diagnosing esophageal cancer and its precursors. pCLE videos are curated and annotated as belonging to one of the three classes: squamous, Barrett's (intestinal metaplasia without dysplasia), or dysplasia. We introduce two novel video architectures, AttentionPooling and Multi-Module AttentionPooling deep networks, that outperform other models and demonstrate a high degree of explainability.
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AIM: Recurrent herpetic stromal keratitis (rHSK), due to an immune response to reactivation of herpes simplex virus (HSV-1), can cause corneal blindness. The development of therapeutic interventions such as drugs and vaccines to decrease rHSK have been hampered by the lack of a small and reliable animal model in which rHSK occurs at a high frequency during HSV-1 latency. The aim of this study is to develop a rabbit model of rHSK in which stress from elevated temperatures increases the frequency of HSV-1 reactivations and rHSK. MATERIALS AND METHODS: Rabbits latently infected with HSV-1 were subjected to elevated temperatures and the frequency of viral reactivations and rHSK were determined. RESULTS: In an experiment in which rabbits latently infected with HSV-1 were subjected to ill-defined stress as a result of failure of the vivarium air conditioning system, reactivation of HSV-1 occurred at over twice the normal frequency. In addition, 60% of eyes developed severe rHSK compared to <1% of eyes normally. All episodes of rHSK were preceded four to five days prior by an unusually large amount of reactivated virus in the tears of that eye and whenever this unusually large amount of reactivated virus was detected in tears, rHSK always appeared 4-5 days later. In subsequent experiments using well defined heat stress the reactivation frequency was similarly increased, but no eyes developed rHSK. CONCLUSIONS: The results reported here support the hypothesis that rHSK is associated not simply with elevated reactivation frequency, but rather with rare episodes of very high levels of reactivated virus in tears 4-5 days earlier.
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Substância Própria/virologia , Resposta ao Choque Térmico/fisiologia , Herpesvirus Humano 1/fisiologia , Ceratite Herpética/virologia , Lágrimas/virologia , Ativação Viral/fisiologia , Latência Viral/fisiologia , Animais , DNA Viral/análise , Modelos Animais de Doenças , Feminino , Coelhos , Recidiva , Eliminação de Partículas ViraisRESUMO
At least six microRNAs (miRNAs) appear to be encoded by the latency-associated transcript (LAT) of herpes simplex virus type 1 (HSV-1). The gene for ICP0, an important immediate early (IE) viral protein, is anti-sense to, and overlaps with, the region of LAT from which miRNA H2 (miR-H2) is derived. We recently reported that a mutant (McK-ΔH2) disrupted for miR-H2 on the wild-type HSV-1 strain McKrae genomic background has increased ICP0 expression, increased neurovirulence, and slightly more rapid reactivation. We report here that HSV-1 mutants deleted for the LAT promoter nonetheless make significant amounts of miR-H2 during lytic tissue culture infection, presumably via readthrough transcription from an upstream promoter. To determine if miR-H2 might also play a role in the HSV-1 latency/reactivation cycle of a LAT-negative mutant, we constructed dLAT-ΔH2, in which miR-H2 is disrupted in dLAT2903 without altering the predicted amino acid sequence of the overlapping ICP0 open reading frame. Similar to McK-ΔH2, dLAT-ΔH2 expressed more ICP0, was more neurovirulent, and had increased reactivation in the mouse TG explant-induced reactivation model of HSV-1 compared with its parental virus. Interestingly, although the increased reactivation of McK-ΔH2 compared with its parental wild-type (wt) virus was subtle and only detected at very early times after explant TG induced reactivation, the increased reactivation of dLAT-ΔH2 compared with its dLAT2903 parental virus appeared more robust and was significantly increased even at late times after induction. These results confirm that miR-H2 plays a role in modulating the HSV-1 reactivation phenotype.
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Herpesvirus Humano 1/genética , Herpesvirus Humano 1/patogenicidade , Proteínas Imediatamente Precoces/genética , MicroRNAs/genética , RNA Viral/genética , Ubiquitina-Proteína Ligases/genética , Animais , Linhagem Celular Tumoral , Modelos Animais de Doenças , Feminino , Regulação Viral da Expressão Gênica , Herpes Simples/patologia , Herpes Simples/virologia , Herpesvirus Humano 1/metabolismo , Humanos , Proteínas Imediatamente Precoces/metabolismo , Camundongos , MicroRNAs/metabolismo , Neurônios/patologia , Neurônios/virologia , Regiões Promotoras Genéticas , RNA Viral/metabolismo , Técnicas de Cultura de Tecidos , Gânglio Trigeminal/patologia , Gânglio Trigeminal/virologia , Ubiquitina-Proteína Ligases/metabolismo , Virulência , Ativação Viral/genética , Latência Viral/genéticaRESUMO
The herpes simplex virus type 1 (HSV-1) latency-associated transcript (LAT) encodes several microRNAs. One of these, miR-H2, overlaps and is antisense to the ICP0 gene and appears to decrease expression of the ICP0 protein. To determine if miR-H2 plays a role in the HSV-1 latency-reactivation cycle, we constructed a mutant, McK-ΔH2, in which this microRNA has been disrupted without altering the predicted amino acid sequence of ICP0. McK-ΔH2 produced increased amounts of ICP0. Although replication of McK-ΔH2 was similar to that of its wild-type (wt) McKrae parental virus in RS cells and mouse eyes, McK-ΔH2 was more neurovirulent in Swiss-Webster mice than McKrae based on the percent of mice that died from herpes encephalitis following ocular infection. In addition, using a mouse trigeminal ganglia (TG) explant model of induced reactivation, we show here for the first time that miR-H2 appears to play a role in modulating HSV-1 reactivation. Although the percent of TG from which virus reactivated by day 10 after explant was similar for McK-ΔH2, wt McKrae, and the marker-rescued virus McK-ΔH2Res, at earlier times, significantly more reactivation was seen with McK-ΔH2. Our results suggest that in the context of the virus, miR-H2 downregulates ICP0 and this moderates both HSV-1 neurovirulence and reactivation.
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Regulação Viral da Expressão Gênica/genética , Herpes Simples/genética , MicroRNAs/genética , RNA Viral/genética , Ativação Viral/genética , Animais , Modelos Animais de Doenças , Feminino , Herpesvirus Humano 1/patogenicidade , Herpesvirus Humano 1/fisiologia , Proteínas Imediatamente Precoces/biossíntese , Proteínas Imediatamente Precoces/genética , Immunoblotting , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Ubiquitina-Proteína Ligases/biossíntese , Ubiquitina-Proteína Ligases/genética , Virulência , Latência Viral/genéticaRESUMO
A multiresidue method for the analysis of 168 pesticides in dried powdered ginseng has been developed using acetonitrile or acetone mixture (acetone/cyclohexane/ethyl acetate, 2:1:1 v/v/v) extraction, solid-phase extraction (SPE) cleanup with octyl-bonded silica (C(8)), graphitized carbon black/primary-secondary amine (GCB/PSA) sorbents and toluene, and capillary gas chromatography-mass spectrometry/selective ion monitoring (GC-MS/SIM) or -tandem mass spectrometry (GC-MS/MS). The geometric mean limits of quantitation (LOQs) were 53 and 6 microg/kg for the acetonitrile extraction and 48 and 7 microg/kg for the acetone-based extraction for GC-MS/SIM and GC-MS/MS, respectively. Mean percent recoveries and standard deviations from the ginseng fortified at 25, 100, and 500 microg/kg using GC-MS/SIM were 87 +/- 10, 88 +/- 8, and 86 +/- 10% from acetonitrile extracts and 88 +/- 13, 88 +/- 12, and 88 +/- 14% from acetone mixture extracts, respectively. The mean percent recoveries from the ginseng at the 25, 100, and 500 microg/kg levels using GC-MS/MS were 83 +/- 19, 90 +/- 13, and 89 +/- 11% from acetonitrile extracts and 98 +/- 20, 91 +/- 13, and 88 +/- 14% from acetone extracts, respectively. Twelve dried ginseng products were found to contain one or more of the following pesticides and their metabolites: BHCs (benzene hexachlorides, alpha-, beta-, gamma-, and delta-), chlorothalonil, chlorpyrifos, DDT (dichlorodiphenyl trichloroethane), dacthal, diazinon, iprodione, quintozene, and procymidone ranging from <1 to >4000 microg/kg. No significant differences were found between the two extraction solvents, and GC-MS/MS was found to be more specific and sensitive than GC-MS/SIM. The procedures described were shown to be effective in screening, identifying, confirming, and quantitating pesticides in commercial ginseng products.
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Fracionamento Químico/métodos , Cromatografia Gasosa-Espectrometria de Massas/métodos , Panax/química , Resíduos de Praguicidas/análise , Extratos Vegetais/química , Espectrometria de Massas em Tandem/métodos , Acetona , Acetonitrilas , Indicadores e Reagentes , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Extração em Fase Sólida/métodosRESUMO
A multiresidue method for the analysis of pesticides in fresh produce has been developed using salt-out acetonitrile extraction, solid-phase dispersive cleanup with octadecyl-bonded silica (C(18)), and graphitized carbon black/primary-secondary amine (GCB/PSA) sorbents and toluene, followed by capillary gas chromatography-mass spectrometry in selected ion monitoring mode (GC-MS/SIM) or -tandem mass spectrometry (GC-MS/MS). Quantitation was determined from calibration curves using matrix-matched standards ranging from 3.3 to 6667 ng/mL with r(2) > 0.99, and geometric mean limits of quantitation were typically 8.4 and 3.4 microg/kg for GC-MS/SIM and GC-MS/MS, respectively. Identification was determined by using target and qualifier ions and qualifier-to-target ratios for GC-MS/SIM and two ion transitions for GC-MS/MS. Fortification studies (10, 25, 100, and 500 microg/kg) were performed on 167 organohalogen, organophosphorus, and pyrethroid pesticides in 10 different commodities (apple, broccoli, carrot, onion, orange, pea, peach, potato, spinach, and tomato). The mean percent recoveries were 90 +/- 14, 87 +/- 14, 89 +/- 14, and 92 +/- 14% for GC-MS/SIM and 95 +/- 22, 93 +/- 14, 93 +/- 13, and 97 +/- 13% for GC-MS/MS at 10, 25, 100, and 500 microg/kg, respectively. GC-MS/MS was shown to be more effective than GC-MS/SIM due to its specificity and sensitivity in detecting pesticides in fresh produce samples. The method, based on concepts from the multiresidue procedure used by the Canadian Food Inspection Agency and QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe), was shown to be efficient in screening, identifying, and quantitating pesticides in fresh produce samples.