A5061602393- HIV Research and Treatment
- Fault Detection and Control Systems
- Biomedical Text Mining and Ontologies
- RNA Research and Splicing
- Gene expression and cancer classification
- Advanced Statistical Process Monitoring
- Bayesian Modeling and Causal Inference
- Bioinformatics and Genomic Networks
- COVID-19 Clinical Research Studies
- Autophagy in Disease and Therapy
- Risk and Safety Analysis
- Neuroinflammation and Neurodegeneration Mechanisms
- Nuclear Structure and Function
- Electrochemical Analysis and Applications
- Kawasaki Disease and Coronary Complications
- Thermal Regulation in Medicine
- Advanced Statistical Methods and Models
- Extracellular vesicles in disease
- HIV-related health complications and treatments
- Paraquat toxicity studies and treatments
- Tryptophan and brain disorders
- Long-Term Effects of COVID-19
- Electrochemical sensors and biosensors
- Bone Tissue Engineering Materials
- Spectroscopy and Chemometric Analyses
Children's Hospital of Philadelphia
2022-2025
University of Pennsylvania
2023
Temple University
2017-2021
Drexel University
2013-2016
Abstract Elimination of HIV-1 requires clearance and removal integrated proviral DNA from infected cells tissues. Here, sequential long-acting slow-effective release antiviral therapy (LASER ART) CRISPR-Cas9 demonstrate viral in latent infectious reservoirs humanized mice. subgenomic fragments, spanning the long terminal repeats Gag gene, are excised vivo, resulting elimination DNA; virus is not detected blood, lymphoid tissue, bone marrow brain by nested digital-droplet PCR as well RNAscope...
Abstract Human immunodeficiency virus-associated neurological disorders (HANDs) affect the majority of AIDS patients and are a significant problem among HIV-1-infected individuals who live longer because combined anti-retroviral therapies. HIV-1 utilizes number viral proteins subsequent cytokine inductions to unleash its toxicity on neurons. Among proteins, Nef is small protein expressed abundantly in astrocytes brains has been suggested have role pathogenesis HAND. In order explore effect...
Multisystem inflammatory syndrome in children (MIS-C) is a severe complication of SARS-CoV-2 infection. It remains unclear how MIS-C phenotypes vary across variants. We aimed to investigate clinical characteristics and outcomes eras.
Importance The COVID-19 pandemic has been associated with an increase in mental health diagnoses among adolescents, though the extent of increase, particularly for severe cases requiring hospitalization, not well characterized. Large-scale federated informatics approaches provide ability to efficiently and securely query care data sets assess monitor hospitalization patterns conditions adolescents. Objective To estimate changes proportion hospitalizations adolescents following onset...
Abstract Background Birth defects are functional and structural abnormalities that impact about 1 in 33 births the United States. They have been attributed to genetic other factors such as drugs, cosmetics, food, environmental pollutants during pregnancy, but for most birth there no known causes. Methods To further characterize associations between small molecule compounds their potential induce specific abnormalities, we gathered knowledge from multiple sources construct a reproductive...
The Homo sapiens Chromosomal Location Ontology (HSCLO) is designed to facilitate the integration of human genomic features into biomedical knowledge graphs from releases GRCh37 and GRCh38 at multiple resolutions. HSCLO comprises two distinct versions, HSCLO37 HSCLO38, each tailored its respective genome release. This ontology supports efficient analysis data across scales ranging entire chromosomes individual base pairs, thereby enhancing retrieval interoperability within large-scale...
A method of designing model‐predictive safety systems that can detect operation hazards proactively is presented. Such a proactive system has two major components: set operability constraints and robust state estimator. The triggers alarm(s) in real time when the process unable to satisfy an constraint over receding time‐horizon into future. In other words, uses model project status generate alarm signals indicating presence present or future hazard. Unlike typical existing systems, it...
HIV-1 Tat protein is released from HIV-1-infected cells and can enter non-permissive including neurons. disrupts neuronal homeostasis may contribute to the neuropathogenesis in people living with HIV (PLWH). The use of cocaine by PLWH exacerbates dysfunction. Here, we examined mechanisms which facilitate alterations homeostatic processes. Bioinformatic interrogation results RNA deep sequencing rat hippocampal neurons exposed alone indicated dysregulation several genes involved lipid...
Over the past decade, there has been substantial growth in both quantity and complexity of available biomedical data. In order to more efficiently harness this extensive data alleviate challenges associated with integration multi-omics data, we developed Petagraph, a knowledge graph that encompasses over 32 million nodes 118 relationships. Petagraph leverages than 180 ontologies standards Unified Biomedical Knowledge Graph (UBKG) embed millions quantitative genomics points. provides cohesive...
Cardiovascular disease remains a leading cause of morbidity and mortality in HIV-positive patients, even those whose viral loads are well controlled with antiretroviral therapy. However, the underlying molecular events responsible for development cardiac setting HIV remain unknown. The HIV-encoded Tat protein plays critical role activation gene expression profoundly impacts homeostasis both HIV-infected cells uninfected that have taken up released via bystander effect. Since cardiomyocyte...
This paper presents a novel efficient method of estimating the joint probability distribution continuous random variables with arbitrary (nonmonotonic or monotonic) relationships. As backbone is set monotonization transformations that "roll out" relationships, named rolling pin method. The allows one to estimate distributions when actual causal structure attributes unknown extremely intricate be determined accurately. Once relationships are monotonized by transformations, an appropriate...
This work addresses the problem of estimating complete probability density functions (PDFs) from historical process data that are incomplete (lack information on rare events), in framework Bayesian networks. In particular, this article presents a method probabilities events for which have no record. The rare‐event prediction becomes more difficult and interesting, when an accurate first‐principles model is not available. To address problem, novel multivariate PDFs proposed. uses maximum...
This paper presents a novel probabilistic modeling and inference method that is computationally more efficient than Bayesian networks (BNs). applicable to systems with continuous variables. It also discrete variables have an adequately high number of states. work, indeed, represents application the rolling pin introduced in our earlier [Mohseni Ahooyi et al., Ind. Eng. Chem. Res, DOI: 10.1021/ie503584q]. Unlike BNs, does not require knowledge causal relationships among variables, because...
HIV‐associated neurocognitive disorders affecting greater than 30% of patients are caused by HIV‐1 infection the CNS, and in part, include neurotoxic effects viral transactivator transcription, Tat protein. In addition to increasing risk for becoming HIV infected, cocaine abuse enhances neuropathogenic impacts HIV‐1. To investigate outcome interference hippocampal neuronal network, cross‐rank‐corrlation was employed develop a systematic framework assess neurons behavior cultured on...
This paper presents a method of estimating discrete multivariate probability distributions from scarce historical data. Of particular interest is the estimation probabilities rare events. The based on maximizing information entropy subject to equality constraints moments estimated distributions. Two criteria are proposed for optimal selections moment functions. models nonlinear and nonmonotonic relations with an level model complexity. Not only does it allow events, but, together Bayesian...
Abstract HIV-1 Tat is known to be released by HIV infected non-neuronal cells in the brain, and after entering neurons, compromises brain homeostasis impairing pro-survival pathways, thus contributing development of HIV-associated CNS disorders commonly observed individuals living with HIV. Here, we demonstrate that synapsins, phosphoproteins are predominantly expressed neuronal play a vital role modulating neurotransmitter release at pre-synaptic terminal, differentiation become targets for...
Abstract HIV-1 Tat is a potent neurotoxic protein that released by infected cells in the brain and perturbs neuronal homeostasis, causing broad range of neurological disorders people living with HIV-1. Furthermore, effects have been addressed numerous studies to investigate molecular events associated survival death. Here, we discovered exposure rat primary neurons resulted up-regulation an uncharacterized long non-coding RNA (lncRNA), LOC102549805 (lncRNA-U1). Our observations showed...
The Homo sapiens Chromosomal Location Ontology for GRCh38 (HSCLO38) represents a knowledge-graph-ready framework connecting genomic features at multiple resolutions. We present the methodology behind development of HSCLO38 and its integration with current standards application in biomedical research. explore performance scalability specific use cases handling large-scale data knowledge graph.
Several factors can contribute to neuroinflammatory disorders, such as cytokine and chemokines that are produced released from peripherally derived immune cells or locally activated microglia perivascular macrophages in the brain. The primary function of these is clear inflammation; however, following inflammation, circulating monocytes recruited central nervous system (CNS). Monocyte-derived CNS play pivotal roles mediating responses. Macrophages heterogeneous both normal pathological...
Abstract The use of biomedical knowledge graphs (BMKG) for representation and data integration has increased drastically in the past several years due to size, diversity, complexity datasets databases. Data extraction from a single dataset or database is usually not particularly challenging. However, if scientific question must rely on integrative analysis across multiple databases datasets, it can often take many hours correctly reproducibly extract integrate towards effective analysis. To...