Medicine and Health Sciences Commons^™

Variant-Specific Inflation Factors For Assessing Population Stratification At The Phenotypic Variance Level, Tamar Sofer, Xiuwen Zheng, Cecelia A. Laurie, Stephanie M. Gogarten, Jennifer A. Brody, Matthew P. Conomos, Joshua C. Bis, Timothy A. Thornton, Adam Szpiro, Joanne E. Curran, Michael Mahaney

School of Medicine Publications

In modern Whole Genome Sequencing (WGS) epidemiological studies, participant-level data from multiple studies are often pooled and results are obtained from a single analysis. We consider the impact of differential phenotype variances by study, which we term 'variance stratification'. Unaccounted for, variance stratification can lead to both decreased statistical power, and increased false positives rates, depending on how allele frequencies, sample sizes, and phenotypic variances vary across the studies that are pooled. We develop a procedure to compute variant-specific inflation factors, and show how it can be used for diagnosis of genetic association analyses on pooled individual level data from …

Nanotechnology Synergised Immunoengineering For Cancer, Deepak S. Chauhan, Anupam Dhasmana, Partha Laskar, Rajendra Prasad, Nishant K. Jain, Rohit Srivastava, Meena Jaggi, Subhash C. Chauhan, Murali M. Yallapu

School of Medicine Publications

Novel strategies modulating the immune system yielded enhanced anticancer responses and improved cancer survival. Nevertheless, the success rate of immunotherapy in cancer treatment has been below expectation(s) due to unpredictable efficacy and off-target effects from systemic dosing of immunotherapeutic. As a result, there is an unmet clinical need for improving conventional immunotherapy. Nanotechnology offers several new strategies, multimodality, and multiplex biological targeting advantage to overcome many of these challenges. These efforts enable programming the pharmacodynamics, pharmacokinetics, delivery of immunomodulatory agents/co-delivery of compounds to prime at the tumor sites for improved therapeutic benefits. This review provides an overview of the design …

Knowledge And Anxiety About Covid-19 In The State Of Qatar, And The Middle East And North Africa Region—A Cross Sectional Study, Sathyanarayanan Doraiswamy, Sohaila Cheema, Maisonneuve Patrick, Amit Abraham, Ingmar Weber, Jisun An, Albert B. Lowenfels, Ravinder Mamtani

Research Collection School Of Computing and Information Systems

While the coronavirus disease 2019 (COVID-19) pandemic wreaked havoc across the globe, we have witnessed substantial mis- and disinformation regarding various aspects of the disease. We conducted a cross-sectional study using a self-administered questionnaire for the general public (recruited via social media) and healthcare workers (recruited via email) from the State of Qatar, and the Middle East and North Africa region to understand the knowledge of and anxiety levels around COVID-19 (April–June 2020) during the early stage of the pandemic. The final dataset used for the analysis comprised of 1658 questionnaires (53.0% of 3129 received questionnaires; 1337 [80.6%] from the …

Assessing Real-Time Flow Experience In Human-Computer Interaction: An Electroencephalogram (Eeg) Study, Fiona Fui-Hoon Nah, Tejaswini Yelamanchili, Keng Siau, Langtao Chen

Research Collection School Of Computing and Information Systems

An optimal experience termed flow can be experienced by users who are deeply involved in human-computer interaction (HCI). The electroencephalogram (EEG) provides an innovative way to assess in real-time if users are approaching or experiencing the flow state in various applications of HCI. However, the current literature remains unclear and inconsistent with regard to the relationship between EEG activity and flow experience. The objective of this research is to assess EEG activity corresponding to the state of flow. A laboratory experiment was conducted to collect EEG data of the flow and other states (including baseline) in the context of HCI.

Lipocalin-2 Ameliorates The Signs And Outcomes Of Diabetes Mellitus In An Animal Model, Saeeda Mohammed Al Jaberi

Theses

Lipocalin-2 (LCN2) is a new adipocytokine consisting of 198 amino acids. It is also referred to as neutrophil gelatinase-associated lipocalin, siderocalin, uterocalin, α1-microglobulin related protein, or 24p3. LCN2 belongs to a large group of transport proteins that are capable of carrying small and lipid-soluble molecules in blood circulation. It has two membrane receptors, megalin/glycoprotein GP330, which binds human LCN2 and SLC22A17 or 24p3R, which forms complexes with mouse Lcn2 protein. LCN2 is encoded by a gene located at chromosome locus 9q34.11. LCN2 was initially isolated from neutrophil granules released at the site of infection and inflammation in humans and from …

Lipocalin-2 Ameliorates The Signs And Outcomes Of Diabetes Mellitus In An Animal Model, Saeeda Mohammed Al Jaberi

Theses

Lipocalin-2 (LCN2) is a new adipocytokine consisting of 198 amino acids. It is also referred to as neutrophil gelatinase-associated lipocalin, siderocalin, uterocalin, α1-microglobulin related protein, or 24p3. LCN2 belongs to a large group of transport proteins that are capable of carrying small and lipid soluble molecules in blood circulation. It has two membrane receptors, megalin/glycoprotein GP330, which binds human LCN2 and SLC22A17 or 24p3R, which forms complexes with mouse Lcn2 protein. LCN2 is encoded by a gene located at chromosome locus 9q34.11. LCN2 was initially isolated from neutrophil granules released at site of infection and inflammation in human and from …

Insights Into The Packaging Of Mouse Mammary Tumor Virus (Mmtv) Genomic Rna By Identifying Pr77ᴳᴬᴳ Binding Sites Involved During Its Selective Encapsidation, Akhil Chameettachal

Dissertations

Selective encapsidation and/or packaging of retroviral genomic RNA (gRNA) by Gag during retrovirus assembly is a crucial step for generating infectious virus particles. Despite having been studied extensively, the mechanism by which the retroviral Gag precursor selects and packages the retroviral genome remains largely unclear. Therefore, to understand the molecular mechanism(s) of mouse mammary tumor virus (MMTV) gRNA packaging, as a first step, expression of full-length recombinant Pr77^Gag -His6-tag fusion protein in bacteria was done. The recombinant Gag protein was then purified from the soluble fractions of bacterial cultures using immobilized metal affinity chromatography (IMAC) and size exclusion chromatography …

The Role Of Nutrient Sensitive Protein O-Glcnacylation In Developmental Cortical Neurogenesis, Shama Parween

Dissertations

The nutrient responsive O-GlcNAcylation is a dynamic, posttranslational protein modification present on many nucleocytoplasmic and mitochondrial proteins. Previous research has indicated that hyperglycaemia increases the levels of total O-GlcNAcylation within cells. Transcription factors and histones are among hundreds of proteins that have been reported to be O-GlcNAcylated and have importance in cell fate determination during cell growth, proliferation, and differentiation. However, the role of protein O-GlcNAcylation in epigenome control in response to nutritional perturbations is poorly understood. Hyperglycaemia induced protein O-GlcNAcylation have been linked to several pathologies, including obesity, diabetes, cancer, cardiovascular and neurodegenerative diseases. …

Epigenetic Modifications In Metabolic Syndrome: Identification And Evaluation Of Early Indicators Using A Rodent Model System, Ashok Daniel Pragasam

Dissertations

It is increasingly realized that mechanisms of developmental plasticity rather than pathology independently facilitate the size of developing embryos during early development. Changes in the early developmental environment alter the metabolic traits resulting in diseases, including metabolic syndrome, including type 2 diabetes and obesity in adulthood. Molecular and epidemiological studies have documented an association between Lower Birth Weight (LBW) and increased risk of developing metabolic syndrome. Henceforth, using birth weight as a marker, two groups of normal birth weight range rat pups, Lower Birth Weight (LBW, 5th to 25th percentile) and Average Birth Weight (ABW, 50th to 75th percentile) as …

Construct Validity And Invariance Assessment Of The Social Impacts Of Occupational Heat Stress Scale (Siohss) Among Ghanaian Mining Workers, Victor F. Nunfam, Ebenezer Afrifa-Yamoah, Kwadwo Adusei-Asante, Eddie J. Van Etten, Kwasi Frimpong, Isaac Adjei-Mensah, Jacques Oosthuizen

Research outputs 2014 to 2021

Heat exposure studies over the last decade have shown little attention in assessing and reporting the psychometric properties of the various scales used to measure impacts of occupational heat stress on workers. A descriptive cross-sectional survey including 320 small- and large-scale mining workers was employed to assess the construct validity of the social impacts of occupational heat stress scale (SIOHSS) in the Western Region of Ghana in 2017. A confirmatory factor analysis (CFA) and invariance analysis were carried out using AMOS version 25 and statistical product and service solutions (SPSS) version 26 to examine the model fit and establish consistency …

Air Pollution Exposure And Risk Of Adverse Obstetric And Neonatal Outcomes Among Women With Type 1 Diabetes, Andrew D. Williams, Jenna Kanner, Katherine Grantz, Marion Ouidir, Shanshan Sheehy, Seth Sherman, Candace Robledo, Pauline Mendola

School of Medicine Publications

Aims/Hypothesis:

Women with type 1 diabetes have increased risk for poor obstetric outcomes. Prenatal air pollution exposure is also associated with adverse outcomes for women and infants. We examined whether women with type 1 diabetes are more vulnerable than other women to pollution-associated risks during pregnancy.

Methods:

In singleton deliveries from the Consortium on Safe Labor (2002-2008), obstetric and neonatal outcomes were compared for women with type 1 diabetes (n=507) and women without autoimmune disease (n=204,384). Preconception, trimester, and whole pregnancy average air pollutant exposure (ozone (O3), carbon monoxide (CO), particulate matter >10 microns (PM10), PM >2.5 microns (PM2.5), sulfur …

Effect Of Demographic And Health Dynamics On Cognitive Status In Mexico Between 2001 And 2015: Evidence From The Mexican Health And Aging Study, Silvia Mejia-Arango, Jaqueline Avila, Brian Downer, Marc A. Garcia, Alejandra Michaels-Obregon, Joseph L. Saenz, Rafael Samper-Ternent, Rebeca Wong

School of Medicine Publications

Sources of health disparities such as educational attainment, cardiovascular risk factors, and access to health care affect cognitive impairment among older adults. To examine the extent to which these counteracting changes affect cognitive aging over time among Mexican older adults, we examine how sociodemographic factors, cardiovascular diseases, and their treatment relate to changes in cognitive function of Mexican adults aged 60 and older between 2001 and 2015. Self and proxy respondents were classified as dementia, cognitive impairment no dementia (CIND), and normal cognition. We use logistic regression models to examine the trends in dementia and CIND for men and women …

Genome-Wide Association Study Of More Than 40,000 Bipolar Disorder Cases Provides New Insights Into The Underlying Biology, Niamh Mullins, Andreas J. Forstner, Kevin S. O’Connell, Brandon Coombes, Ney Alliey Rodriguez

School of Medicine Publications

Bipolar disorder is a heritable mental illness with complex etiology. We performed a genome-wide association study of 41,917 bipolar disorder cases and 371,549 controls of European ancestry, which identified 64 associated genomic loci. Bipolar disorder risk alleles were enriched in genes in synaptic signaling pathways and brain-expressed genes, particularly those with high specificity of expression in neurons of the prefrontal cortex and hippocampus. Significant signal enrichment was found in genes encoding targets of antipsychotics, calcium channel blockers, antiepileptics and anesthetics. Integrating expression quantitative trait locus data implicated 15 genes robustly linked to bipolar disorder via gene expression, encoding druggable targets …

Dspace Information Retrieval System: A Study Using Dicom Metadata Standard, Hirak Jyoti Hazarika, Dr. S. Ravikumar, Dr. Akash Handique

Library Philosophy and Practice (e-journal)

The present paper talks about the use of institutional repository software (DSpace) in archiving DICOM images. In the current study, the authors have tried to integrate the DICOM metadata standard with DSpace, which was compatible with DC & OAI PMH. After integrating the DICOM standard with DSpace, and the repository tested with a sample of ten thousand images, the retrieval results using various DICOM tags was very satisfactory. This study paves for the use of OSS in storing and retrieving medical images. Digital Image Communications in Medicine (DICOM) standard has become a centre component for making an application nonpartisan …

The Causes Of Surface Condensation And Mould, And The Responsibility Of Relevant Parties To Alleviate Them, Joseph Little

Reports

All over Ireland large numbers of people live in unsanitary conditions suffering poor indoor air quality, surface condensation and mould. Where the occupants are tenants the cause of the conditions and identification of the parties responsible can cause much stress. Condensation and mould growth on the internal surface of a room are caused by a combination of factors due to specific conditions. In severe cases, one of these factors may lead to surface condensation and/or mould growth, but in general, surface condensation and/or mould growth occurs when two or three of these occur together. Even though multiple causes and shared …

Covid-19 Newsletter (Vol. 74), Center For Disaster Medicine, New York Medical College

COVID-19 Newsletter

No abstract provided.

Week Of June 1, 2021, New York Medical College

InTouch

• NYMC Celebrates 162nd Commencement Virtually
• Golf Tournament and Reception Set for June 28
• Rare Benjamin Rush Textbook Donated to HSL by Peter Bentivegna, M.D. '85
• NYMC Hosts Celebrating Diversity: Then and Now Event
• Twelfth COVID-19 Symposium Set for June 3
• HSL Offers Endnote 20 Training
• SHSP Students Volunteer for COVID-19 Data Collection Project

Social Intervention By The Numbers: Evidence Behind The Specific Public Health Guidelines In The Covid-19 Pandemic., Michael P. Savage, David L. Fischman, Mamas A. Mamas

Department of Medicine Faculty Papers

Coronavirus disease 2019 (COVID-19) has rapidly become a worldwide pandemic ushering in a global health and economic crisis. In the absence of vaccines or definitive drug therapies, current strategies against COVID-19 rely on preventing the transmission of disease through nonpharmaceutical interventions such as social distancing and proper hand hygiene. For practical and perhaps ethical reasons, the clinical efficacy of these public health measures for managing pandemics has not been demonstrated in randomized controlled clinical trials. Accordingly, guideline recommendations for using nonpharmaceutical interventions are based primarily on observational and modeling studies and on expert opinion. A recent position paper from the …

A Case Of Hepatic Cyst-Induced Internal Jugular Venous Thrombosis, Tuyen V Le, Thai Truong, Tam N M Ngo, Quoc Bui, Cassady Palmer, Vien T Truong, Duc H Nguyen

2020-Current year OA Pubs

• Echocardiography can demonstrate hepatic cyst–induced right atrial compression. • Hepatic cyst–induced blood flow stasis can cause internal jugular venous thrombus. • Laparoscopic deroofing of hepatic cysts is a safe and effective treatment.

Report Dose-To-Medium In Clinical Trials Where Available; A Consensus From The Global Harmonisation Group To Maximize Consistency, Stephen F Kry, Jeff Michalski, Et Al.

2020-Current year OA Pubs

PURPOSE: To promote consistency in clinical trials by recommending a uniform framework as it relates to radiation transport and dose calculation in water versus in medium.

METHODS: The Global Quality Assurance of Radiation Therapy Clinical Trials Harmonisation Group (GHG; www.rtqaharmonization.org) compared the differences between dose to water in water (D

RESULTS: No framework was found to be ideal or perfect given the history, complexity, and current status of radiation therapy. Nevertheless, based on the evidence available, the GHG established a recommendation preferring dose to medium in medium (D

CONCLUSIONS: Dose to medium in medium (D

Effects Of Pathogen Reduction Technology And Storage Duration On The Ability Of Cryoprecipitate To Rescue Induced Coagulopathies In Vitro, Kimberly A Thomas, Susan M Shea, Philip C Spinella

2020-Current year OA Pubs

BACKGROUND: Fibrinogen concentrates and cryoprecipitate are currently used for fibrinogen supplementation in bleeding patients with dysfibrinogenemia. Both products provide an abundant source of fibrinogen but take greater than 10 min to prepare for administration. Fibrinogen concentrates lack coagulation factors (i.e., factor VIII [FVIII], factor XIII [FXIII], von Willebrand factor [VWF]) important for robust hemostatic function. Cryoprecipitate products contain these factors but have short shelf lives (<6 h). Pathogen reduction (PR) of cryoprecipitate would provide a shelf-stable immediately available adjunct containing factors important for rescuing hemostatic dysfunction.

STUDY DESIGN AND METHODS: Hemostatic adjunct study products were psoralen-treated PR-cryoprecipitated fibrinogen complex (PR-Cryo FC), cryoprecipitate (Cryo), and fibrinogen concentrates (FibCon). PR-Cryo FC and Cryo were stored for 10 days at 20-24°C. Adjuncts were …

Integration Of Immunotherapy Into Adjuvant Therapy For Resected Non-Small-Cell Lung Cancer: Alchemist Chemo-Io (Accio), Jacob M Sands, Ramaswamy Govindan, Jhanelle Gray, Et Al

2020-Current year OA Pubs

Non-small-cell lung cancer (NSCLC) causes significant mortality each year. After successful resection of disease stage IB (>4 cm) to IIIA (per AJCC 7), adjuvant platinum-based chemotherapy improves median overall survival and is the standard of care, but many patients still experience recurrence of disease. An adjuvant regimen with greater efficacy could substantially improve outcomes. Pembrolizumab, a programmed cell death-1 inhibitor, has become an important option in the treatment of metastatic NSCLC. ALCHEMIST is a clinical trial platform of the National Cancer Institute that includes biomarker analysis for resected NSCLC and supports therapeutic trials including A081801 (ACCIO), a three-arm study …

Dean's Update, June 2021, Jerry Nadler

SOM Dean's Research Newsletter

No abstract provided.

Bolstering Geometric Morphometrics Sample Sizes With Damaged And Pathologic Specimens: Is Near Enough Good Enough?, D. Rex Mitchell, Claire A. Kirchhoff, Siobhán B. Cooke, Claire E. Terhune

Biomedical Sciences Faculty Research and Publications

Obtaining coordinate data for geometric morphometric studies often involves the sampling of dry skeletal specimens from museum collections. But many specimens exhibit damage and/or pathologic conditions. Such specimens can be considered inadequate for the analyses of shape and are excluded from study. However, the influences that damaged specimens may have on the assessment of normal shape variation have only been explored in two-dimensional coordinate data and no studies have addressed the inclusion of pathological specimens to date. We collected three-dimensional coordinate data from the cranium and mandible of 100 crab-eating macaques (Macaca fascicularis). Tests typically employed to analyze shape variation …

Mealtimes In Early Childhood Education Centers During Covid-19: A Mixed-Methods Assessment Of Responsibilities, Interactions, And Best Practices, Joanna Mackie

USF Tampa Graduate Theses and Dissertations

Background: Childhood obesity is a public health problem associated with many co-morbidities. The majority of young children in the United States (U.S.) attend formal early childhood education (ECE) programs, often consuming the majority of daily calories and engaging with teachers during mealtimes. Mealtime best practices support children’s development of healthy eating habits. This dissertation aimed to understand how COVID-19 has influenced mealtimes in ECE centers, including (1) the division of responsibility between adults and children during mealtimes, (2) the child feeding dynamic, and (3) how mealtime best practices have been included during COVID-19.

Methods: This dissertation used a concurrent mixed-methods …

Development Of Stress-Induced Cardiomyopathy After Cytoreductive Surgery And Hyperthermic Intraperitoneal Chemotherapy, Saad Ahmed Naved, Sadiq Shoukat Parpia, Huma Shoukat Ali

Medical College Documents

Pseudomyxoma Peritonei, a massive mucinous peritoneal collection due to a rare epithelial neoplasm, can be effectively treated with Cytoreductive Surgery and Hyperthermic Intraperitoneal Chemotherapy (CRS-HIPEC). A 43-year-old female, previously treated for mucinous ovarian carcinoma with CRS-HIPEC, and total abdominal hysterectomy and bilateral salpingo-oophorectomy, presented with new-onset abdominal distension and early satiety. She was diagnosed with Pseudomyxoma Peritonei. After 48 hours of treatment with CRS-HIPEC, she presented haemodynamically unstable with acute chest pain. Electrocardiogram showed broad complex tachycardia with ST depression in leads V3-6. Severe systolic dysfunction with Ejection Fraction (EF) of 20% along with severe pulmonary hypertension, visualized on Echocardiography. …

Paediatric Pseudo Papillary Pancreatic Tumour: A Case Based Review, Mir Ibrahim Sajid, Ayesha Saleem, Muhammad Arshad

Medical College Documents

Solid pseudopapillary neoplasms are rare and represent approximately 4% of all cystic pancreatic tumours, and predominately affect females. They have an excellent prognosis, however 10-15% of the patients show metastasis at the time of surgery or recurrence of tumour during follow-up after pancreatectomy. Surgical resection is the recommended treatment. We present a rare case of a 15-year-old female, with a pseudopapillary tumour of the pancreas which was diagnosed pre-operatively.

Speckle-Tracking Echocardiography For Detecting Subclinical Left Ventricular Dysfunction In Patients With Familial Hypercholesterolemia, Rongjuan Li, Jinjie Xie, Bo Jiang, Zhonghua Sun, Lvya Wang, Zhaoting Leng, Yueli Wang, Ya Yang

The Texas Heart Institute Journal

Myocardial ischemia and left ventricular dysfunction have been documented in young adults with familial hypercholesterolemia. We investigated whether speckle-tracking echocardiography can be used to detect subclinically impaired global and regional myocardial function in patients with this lipid disorder. This single-center study included 47 patients with familial hypercholesterolemia and 37 healthy control subjects who underwent transthoracic Doppler echocardiography and speckle-tracking echocardiography from January 2003 through December 2016. Conventional echocardiographic and strain parameters in the 2 groups were analyzed and compared. Left ventricular dimensions were significantly larger at end-diastole (P=0.02) and end-systole (P=0.013), left ventricular walls were significantly thicker (P

The Synergy Of Bet Inhibitors With Aurora A Kinase Inhibitors In Mycn-Amplified Neuroblastoma Is Heightened With Functional Tp53, Joanna S Yi, Oscar Sias-Garcia, Nicole Nasholm, Xiaoyu Hu, Amanda Balboni Iniguez, Matthew D Hall, Mindy Davis, Rajarshi Guha, Myrthala Moreno-Smith, Eveline Barbieri, Kevin Duong, Jessica Koach, Jun Qi, James E Bradner, Kimberly Stegmaier, William A Weiss, W Clay Gustafson

Faculty, Staff and Students Publications

Amplification of MYCN is a poor prognostic feature in neuroblastoma (NBL) indicating aggressive disease. We and others have shown BET bromodomain inhibitors (BETi) target MYCN indirectly by downregulating its transcription. Here we sought to identify agents that synergize with BETi and to identify biomarkers of resistance. We previously performed a viability screen of ∼1,900 oncology-focused compounds combined with BET bromodomain inhibitors against MYCN-amplified NBL cell lines. Reanalysis of our screening results prominently identified inhibitors of aurora kinase A (AURKAi) to be highly synergistic with BETi. We confirmed the anti-proliferative effects of several BETi+AURKAi combinations in MYCN-amplified NBL cell lines. Compared …

Two Mechanisms Of Chromosome Fragility At Replication-Termination Sites In Bacteria, Qian Mei, Devon M Fitzgerald, Jingjing Liu, Jun Xia, John P Pribis, Yin Zhai, Ralf B Nehring, Jacob Paiano, Heyuan Li, Andre Nussenzweig, P J Hastings, Susan M Rosenberg

Faculty, Staff and Students Publications

Chromosomal fragile sites are implicated in promoting genome instability, which drives cancers and neurological diseases. Yet, the causes and mechanisms of chromosome fragility remain speculative. Here, we identify three spontaneous fragile sites in the Escherichia coli genome and define their DNA damage and repair intermediates at high resolution. We find that all three sites, all in the region of replication termination, display recurrent four-way DNA or Holliday junctions (HJs) and recurrent DNA breaks. Homology-directed double-strand break repair generates the recurrent HJs at all of these sites; however, distinct mechanisms of DNA breakage are implicated: replication fork collapse at natural replication …