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TransCell:In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning

Genomics, Proteomics & Bioinformatics 2024年第2期22卷 157-170页

作者： Shan-Ju Yeh Shreya Paithankar Ruoqiao Chen Jing Xing Mengying Sun Ke Liu Jiayu Zhou Bin Chen Department of Pediatrics and Human Development Michigan State UniversityGrand RapidsMI 49503USA Department of Pharmacology and Toxicology Michigan State UniversityGrand RapidsMI 49503USA Department of Computer Science and Engineering Michigan State UniversityEast LansingMI 48824USA

Gene expression profiling of new or modified cell lines becomes routine today;however,obtaining comprehensive molecular characterization and cellular responses for a variety of cell lines,including those derived from underrepresented groups,is not trivial when resources are *** gene expression to predict other measurements has been actively explored;however,systematic investigation of its predictive power in various measurements has not been well ***,we evaluated commonly used machine learning methods and presented TransCell,a two-step deep transfer learning framework that utilized the knowledge derived from pan-cancer tumor samples to predict molecular features and *** these models,TransCell had the best performance in predicting metabolite,gene effect score(or genetic dependency),and drug sensitivity,and had comparable performance in predicting mutation,copy number variation,and protein ***,TransCell improved the performance by over 50%in drug sensitivity prediction and achieved a correlation of 0.7 in gene effect score ***,predicted drug sensitivities revealed potential repurposing candidates for new 100 pediatric cancer cell lines,and predicted gene effect scores reflected BRAF resistance in melanoma cell ***,we investigated the predictive power of gene expression in six molecular measurement types and developed a web portal(http://***/transcell/)that enables the prediction of 352,000 genomic and cellular response features solely from gene expression profiles.

关键词： Genomics Transcriptomics Cancer dependency Drug repurposing Transfer learning

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Using molecular dynamics simulations to show differences of movement over time in the CCR5 variants of genetically edited children

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BIOS 2023年第2期94卷 49-56页

作者： Caitlin Turner Sara Cline Jeremy Prokop Biology Department Athens State University Athens AL 35611 Department of Pediatrics and Human Development Michigan State University Grand Rapids MI 49503

In 2018 He Jiankui presented a study where he claimed he successfully used CRISPR to genetically modify a set of twins, intending to provide them with resistance against HIV. Dr. He modified CCR5, C-C chemokine receptor type 5, in two patients which have been given the names “Lulu” and “Nana”. It has not been clinically confirmed that the variants introduced provide a protective effect. Because of the barriers to collecting human clinical data, here we use homology modeling to predict the effects of these proteins. Molecular dynamics simulations are used to compare these new variants to known variants using 3D protein models produced from predicted translations. This allows us to follow and compare the individual amino acid movement of the variants within a simulated aqueous environment over time. The simulations of the novel variants in twins Lulu and Nana showed differences in the amino acid residue movement of the protein over a 20-nanosecond interval when compared with known variants. This allows us to determine the stability of the protein by following the way the amino acids within the protein move in the simulated aqueous environment. Stability and amino acid movement affects the regulation and expression of the protein and can be altered when specific amino acids are targeted. The differences in the model simulations presented here suggest potential changes in functionality or stability.

关键词： Cas9 cross-correlation matrices human genome editing Δ32

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Building the COVID-19 Portal By Integrating Literature, Clinical Trials, and Knowledge Graphs 21

Building the COVID-19 Portal By Integrating Literature, Clin...

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Proceedings of the 2021 ACM/IEEE Joint Conference on Digital Libraries

作者： Aoshen Wan Yan Zhan Sanjana Tripathi Jiarong Yang Mona Sachdev Shreya Paithankar Joel Duerksen Bin Chen Ying Ding School of Information University of Texas at Austin Austin TX Department of Pediatrics and Human Development Michigan State University Grand Rapids MI Data2Discovery Greater Orlando Florida Department of Pediatrics and Human Development Michigan State University Grand Rapids Michigan School of Information University of Texas at Austin Austin Texas

ISBN: (纸本)9781665417709

The outbreak of COVID-19 has a severe impact on our families, communities, and businesses. Researchers, practitioners, and administrators need a tool to help them digest this enormous amount of knowledge to address various scientific questions related to COVID-19. With CORD-19 dataset, this paper showcases the COVID-19 portal to portray the research profiles of scientists, bio entities (e.g., gene, drug, disease), and institutions based on the integration of CORD-19 research literature, COVID-19 related clinical trials, PubMed knowledge graph, and the drug discovery knowledge graph. This portal provides the following profiles related to COVID-19: 1) the profile of a research scientist with his/her COVID-19 related publications and clinical trials with tweets amount; 2) the profile of a bio entity which could be a gene, a drug, or a disease with articles and clinical trials; and 3) the profile of an institution with papers authored by researchers from this institution.

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Maternal perspectives on COVID-19 kindergarten learning impacts: a qualitative study of families with low income

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Discover Education 2025年第1期4卷 1-16页

作者： Turnbull, Khara L. P. Jaworski, Brianna Cubides Mateus, Deiby Mayaris Coolman, Frances L. LoCasale-Crouch, Jennifer Moon, Rachel Y. Hauck, Fern R. Kellams, Ann Colson, Eve R. School of Education and Human Development Center for Advanced Study of Teaching and Learning University of Virginia PO Box 800784 Charlottesville 22908 VA United States Department of Pediatrics University of Virginia School of Medicine Charlottesville Charlottesville VA United States Department of Family Medicine University of Virginia School of Medicine Charlottesville VA United States Department of Pediatrics WashU Medicine St. Louis MO United States Present Affiliation College of Education University of South Florida Tampa FL United States Present Affiliation School of Education Virginia Commonwealth University Richmond VA United States

In this paper, we aim to understand maternal perspectives on: (1) COVID-19 pandemic learning impacts for kindergartners from low-income households;and (2) Factors that mitigated or exacerbated impacts on learning. We conducted a qualitative study with 22 mothers of low-income households in the United States who had kindergarten-age children. Through in-depth, semi-structured interviews, mothers reflected on their experiences during the 2020–21 school year. We used an iterative approach for developing and revising codes and themes emerging from the transcribed interview data until we reached thematic saturation. Many mothers noted negative learning impacts, but some noted positive impacts that they attributed to active parental engagement in their child’s learning. Mothers described several family-level and school-level supports and barriers to their child’s learning. Fewer mothers described supports and barriers pertaining to their social circle or their larger community. The most commonly reported supports included: economic and social supports that allowed the time and financial means to engage actively in their child’s learning, mental health supports to strengthen family functioning, and regular, timely, and open home-school communication. © The Author(s) 2025.

关键词： COVID-19 pandemic Home learning environment Kindergarten Parents' experiences Qualitative

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Childhood acute myeloid leukemia with 5q deletion and HNRNPH1-MLLT10 fusion: the first case report (vol 6 pg 3162. 2022)

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BLOOD ADVANCES 2022年第24期6卷 6209-6209页

作者： Kudo, K. Kubota, Y. Toki, T. Department of Pediatrics Hirosaki University Graduate School of Medicine Hirosaki Japan Department of Pediatrics Hirosaki University Graduate School of Medicine Hirosaki Japan Department of Pediatrics Graduate School of Medicine The University of Tokyo Bunkyo City Tokyo Japan Department of Pediatrics Graduate School of Medicine The University of Tokyo Bunkyo City Tokyo Japan Department of Pediatrics Yokohama City University Graduate School of Medicine Yokohama Japan National Center for Child Health and Development Children's Cancer Center Tokyo Japan Department of Human Health Sciences Graduate School of Medicine Kyoto University Kyoto Japan Department of Pathology and Tumor Biology Graduate School of Medicine Kyoto University Kyoto Japan Institute for the Advanced Study of Human Biology (WPI ASHBi) Kyoto University Kyoto Japan Center for Hematology and Regenerative Medicine Karolinska Institute Stockholm Sweden Department of Pediatrics Graduate School of Medicine Kyoto University Kyoto Japan Department of Pediatrics Hirosaki University Graduate School of Medicine 5 Zaifucho Hirosaki Aomori Japan

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Exploring the increased prevalence of autism in the fee-for-service Medicare population with open data, 2007 to 2018

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Disability and Health Journal 2025年第3期18卷 101776页

作者： Yoo, Ethan M. The Boggs Center on Disability and Human Development Department of Pediatrics Rutgers Robert Wood Johnson Medical School 335 George Street Suite 3500 New Brunswick 08901 NJ United States

Background: The Autism and developmental Disabilities Monitoring (ADDM) Network continues to report increases in the percentage of U.S. children identified with autism spectrum disorder (ASD). Few studies, however, have examined prevalence among U.S. adults. Objective: To use open data on ASD prevalence among fee-for-service Medicare beneficiaries, considering trends in the context of sociodemographic factors and dual enrollment in Medicaid. Methods: Administrative prevalence estimates from the Centers for Medicare and Medicaid Services (CMS) were used to explore changes in ASD prevalence among fee-for-service Medicare beneficiaries. These rates were compared with corresponding childhood prevalence estimates from the ADDM Network. Results: In 2018, there were 87,108 fee-for-service Medicare beneficiaries with autism diagnoses, representing a 236.1% increase from 2008. For 8-year-old children in the ADDM Network, the 2008–2018 change was 32.41%. National ASD prevalence increased in the fee-for-service Medicare population every year from 2007 through 2018, most substantially for beneficiaries under the age of 65. While only 10 states had a prevalence at or above 1 in 1000 beneficiaries in 2007, 48 states and the District of Columbia had a prevalence above that value in 2018. Prevalence in the Medicare population also increased from 2016 to 2018, a period in which program enrollment declined. Conclusions: Even more so than among children, autism prevalence increased in the fee-for-service Medicare population from 2007 through 2018. While geographic and sociodemographic differences in ASD identification existed, prevalence grew across states and most subgroups. Further research is needed to address questions involving the identification and support of autistic adults. © 2025 The Author

关键词： Adults Autism spectrum disorder (ASD) Medicare Open data Prevalence

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Increasing Access and Reach: Implementing School-Based CBT for Anxiety in Students with ASD or Suspected ASD

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Evidence-Based Practice in Child and Adolescent Mental Health 2022年第1期7卷 56-75页

作者： Reaven, Judy Meyer, Allison T. Pickard, Katherine Boles, Richard E. Hayutin, Lisa Middleton, Caitlin Reyes, Nuri M. Hepburn, Susan L. Tanda, Tanea Stahmer, Aubyn Blakeley-Smith, Audrey JFK Partners Department of Psychiatry and Pediatrics University of Colorado Anschutz Medical Campus Aurora CO United States Department of Pediatrics University of Colorado Anschutz Medical Campus Aurora CO United States Department of Human Development and Family Studies Colorado State University Fort Collins CO United States Department of Psychiatry and Behavioral Sciences MIND Institute University of California Davis Sacramento California United States

Youth with Autism Spectrum Disorder (ASD) are at high risk for experiencing clinical anxiety, interfering with friendships, family functioning, and school performance. Many children with ASD and anxiety have difficulty accessing appropriate mental health care and schools are often the ideal location to receive services. The implementation of evidence-based practices to manage anxiety in students with ASD in schools is just beginning. The primary purpose of the current study was to train interdisciplinary school providers to effectively deliver a 13 session evidence-based, group cognitive behavioral therapy (CBT) program adapted for schools [Facing Your Fears–School-Based program (FYF-SB)], to students with anxiety and ASD, or suspected ASD, using a quasi-experimental design. Provider CBT knowledge, feasibility, and effectiveness of FYF-SB were examined. Twenty-five interdisciplinary school providers, from nine elementary/middle urban public schools were trained to deliver FYF-SB. Twenty-nine students (aged 8–14), with clinically significant anxietyASD, or ASD characteristics, participated. Provider CBT knowledge significantly improved following FYF-SB training. Six of 9 school teams exceeded the minimum standard for acceptable treatment adherence (80%) and 8 of the 9 participating teams delivered adequate intervention dosage for student sessions, although parent attendance was more variable. School providers indicated that FYF-SB was feasible, acceptable, and appropriate for participating students. Parents and students reported significant reductions in student anxiety following program participation. Implementation and treatment outcomes are encouraging and suggest that traditionally underserved students with ASD or ASD characteristics may be able to access much needed mental health interventions in their own communities. © 2021 Society of Clinical Child & Adolescent Psychology.

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ACMG practice resource: Genetic evaluation of short stature (vol 11, pg 465, 2009)

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GENETICS IN MEDICINE 2021年第5期23卷 813-815页

作者： Mintz, Cassie S. Seaver, Laurie H. Irons, Mira Grimberg, Adda Lozano, Reymundo Departments of Genetics and Genomic Sciences and Pediatrics Icahn School of Medicine at Mount Sinai Hospital New York NY USA Spectrum Health Medical Genetics and Genomics/Helen Devos Children’s Hospital and Department of Pediatrics and Human Development Michigan State University College of Human Medicine Grand Rapids MI USA American Medical Association Chicago IL USA Department of Pediatrics Perelman School of Medicine University of Pennsylvania and Division of Endocrinology and Diabetes Children’s Hospital of Philadelphia Philadelphia PA USA Departments of Genetics and Genomic Sciences Pediatrics and Psychiatry Icahn School of Medicine at Mount Sinai Hospital New York NY USA

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White Matter Tract Properties and Mathematics Skills: A Longitudinal Study of Children Born Preterm and Full-term 43

White Matter Tract Properties and Mathematics Skills: A Long...

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43rd Annual Meeting of the Cognitive Science Society: Comparative Cognition: Animal Minds, CogSci 2021

作者： Adrian, Julia Anna Sawyer, Carolyn Akshoomoff, Natacha Center for Human Development Department of Cognitive Science Department of Pediatrics Department of Psychiatry University of California 9500 Gilman Drive La Jolla San DiegoCA92093 United States

Children born preterm are at increased risk for white matter injury, impaired cognitive development and lower academic achievement. Here, we examined the association between fractional anisotropy and volume of select white matter tracts at age 5 with mathematics skills at age 7 in children born preterm ( © Cognitive Science Society: Comparative Cognition: Animal Minds, CogSci *** rights reserved.

关键词： Magnetic resonance imaging

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Frequency of Thrombotic Events in Hospitalized Patients with Sickle Cell Disease

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BLOOD 2020年 136卷 13-13页

作者： Inoue, Susumu Anagonye, Christina Department of Pediatrics Hurley Medical Center Flint MI Department of Pediatrics/Human Development Michigan State University College of Human Medicine Flint MI MSU Flint Area Medical Education Michigan State University College of Human Medicine Flint MI

Background Thrombosis is one of the most common complications described in patients with sickle cell disease. However, little is known about the prevalence, variety and severity of thrombus particularly in sickle cell patients hospitalized with vaso-occlusive crisis. Methods We made a retrospective chart review of patients (age 21 years or older) admitted with sickle cell disease at Hurley Medical Center (Flint, Michigan) and was diagnosed with a thrombotic event between April 2012 and April 2020. To obtain a logistic model, we identified all patients with the the final discharge diagnosis of thrombosis (ICD-9 or ICD-10 code indicating any thrombosis, such as DVT, arterial thrombosis, catheter-related thrombus, pulmonary embolism, and stroke), combined with the diagnosis of sickle cell disease. Findings 37/137 (27%) sickle cell patients were found to have had at least one thrombotic event during their hospitalization. As predicted, patients with sickle cell disease appeared to have very high frequency of thrombotic complications, though we lack a control group to compare with. Genotypes of sickle cell disease was also measured in this study. Patients with the Hb-SS disease had a much higher rate of this complication(25/68=37%) compared with those with Hb SC disease patients (12/49=24%). There were no thrombotic events reported in patients with Hb S/beta thalassemia+, or 0 patients or in patients with Hb SS with HPFH. Interpretation The risk of a thromboembolic event in patients with SCD is high, Sickle cell anemia is a procoagulant condition, which is a risk factor for thrombosis. More research is required to determine if preventive modalities could reduce thrombotic risk. Disclosures No relevant conflicts of interest to declare.

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