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Integrated Multiparametric Radiomics And Informatics System For Characterizing Breast Tumor Characteristics With The Oncotypedx Gene Assay, Michael A. Jacobs, Christopher B. Umbricht, Vishwa S. Parekh, Riham H. El Khouli, Leslie Cope, Katarzyna J. Macura, Susan Harvey, Antonio C. Wolff Sep 2020

Integrated Multiparametric Radiomics And Informatics System For Characterizing Breast Tumor Characteristics With The Oncotypedx Gene Assay, Michael A. Jacobs, Christopher B. Umbricht, Vishwa S. Parekh, Riham H. El Khouli, Leslie Cope, Katarzyna J. Macura, Susan Harvey, Antonio C. Wolff

Radiology Faculty Publications

Optimal use of multiparametric magnetic resonance imaging (mpMRI) can identify key MRI parameters and provide unique tissue signatures defining phenotypes of breast cancer. We have developed and implemented a new machine-learning informatic system, termed Informatics Radiomics Integration System (IRIS) that integrates clinical variables, derived from imaging and electronic medical health records (EHR) with multiparametric radiomics (mpRad) for identifying potential risk of local or systemic recurrence in breast cancer patients. We tested the model in patients (n = 80) who had Estrogen Receptor positive disease and underwent OncotypeDX gene testing, radiomic analysis, and breast mpMRI. The IRIS method was trained using the ...


Atom Identifiers Generated By A Neighborhood-Specific Graph Coloring Method Enable Compound Harmonization Across Metabolic Databases, Huan Jin, Joshua M. Mitchell, Hunter N. B. Moseley Sep 2020

Atom Identifiers Generated By A Neighborhood-Specific Graph Coloring Method Enable Compound Harmonization Across Metabolic Databases, Huan Jin, Joshua M. Mitchell, Hunter N. B. Moseley

Molecular and Cellular Biochemistry Faculty Publications

Metabolic flux analysis requires both a reliable metabolic model and reliable metabolic profiles in characterizing metabolic reprogramming. Advances in analytic methodologies enable production of high-quality metabolomics datasets capturing isotopic flux. However, useful metabolic models can be difficult to derive due to the lack of relatively complete atom-resolved metabolic networks for a variety of organisms, including human. Here, we developed a neighborhood-specific graph coloring method that creates unique identifiers for each atom in a compound facilitating construction of an atom-resolved metabolic network. What is more, this method is guaranteed to generate the same identifier for symmetric atoms, enabling automatic identification of ...


Current Scenario Of Covid-19 With Epidemiological And Phylogenetic Analysis Of Pakistani Coronavirus: A Review, Asma Altaf, Wafa Iqbal, Sidra Younis, Farah Deeba Sep 2020

Current Scenario Of Covid-19 With Epidemiological And Phylogenetic Analysis Of Pakistani Coronavirus: A Review, Asma Altaf, Wafa Iqbal, Sidra Younis, Farah Deeba

Journal of Bioresource Management

A novel corona virus named as 2019 n-CoV was identified to be the actual cause of an outbreak of respiratory illness in Wuhan, China beginning in late December 2019. This respiratory disease was named as COVID-19 by WHO. There are many countries affected by COVID-19 including Pakistan. In this review we have provided a brief introduction of COVID-19 and discussed epidemiological and phylogenetic analysis of Pakistani novel corona virus strain. Our epidemiological analysis of data till 16th May 2020 showed rapidly increasing number of new cases, while at the same time a higher recovery rate than number of deaths ...


Development And Implementation Of A Coarse-Grained Markov State Model, Brian Chen Sep 2020

Development And Implementation Of A Coarse-Grained Markov State Model, Brian Chen

Theses and Dissertations

Markov State Models (MSMs) are constructed from Molecular Dynamics (MD) simulation data, high-resolution spatial and temporal information stored in the form of trajectories, of biological processes, such as ligand-receptor bonding, as a model to understand detailed kinetic information. Traditional MSM implementations involve a clustering step that clusters the MD trajectories into thousands of experimentally unverifiable clusters known as "microstates" before lumping them together into "macrostates". This work details a novel software implementation, using a combination of R, Python, and Tcl, that I have created for the purpose of creating a coarse-grained MSM that directly clusters the MD trajectories into a ...


A Lung Cancer Screening Personalized Decision-Aid Improves Knowledge And Reduces Decisional Conflict Among A Diverse Population Of Smokers At An Urban Academic Medical Center, Madeline Kaufman, Nilan Schnure, Andrea Nicholson, Frank Leone, Carmen Guerra Sep 2020

A Lung Cancer Screening Personalized Decision-Aid Improves Knowledge And Reduces Decisional Conflict Among A Diverse Population Of Smokers At An Urban Academic Medical Center, Madeline Kaufman, Nilan Schnure, Andrea Nicholson, Frank Leone, Carmen Guerra

Journal of Health Disparities Research and Practice

Introduction: Few lung cancer screening decision aids have been tested in diverse populations. The study objective was to determine whether the online decision aid www.shouldiscreen.com impacts knowledge of and decisional conflict around lung cancer screening in a diverse population.

Methods: Eligible patients had significant smoking histories, were at increased risk for lung cancer (ages 45-80, >20 pack-years, smoking within last 15 years) and had no history of prior lung cancer or screening. Data was collected and analyzed in 2017.

Results: 40 patients were enrolled: 80% were female, 62.5% black, 33% white, and 48% had a high school ...


Machine Learning Applications For Drug Repurposing, Hansaim Lim Sep 2020

Machine Learning Applications For Drug Repurposing, Hansaim Lim

Dissertations, Theses, and Capstone Projects

The cost of bringing a drug to market is astounding and the failure rate is intimidating. Drug discovery has been of limited success under the conventional reductionist model of one-drug-one-gene-one-disease paradigm, where a single disease-associated gene is identified and a molecular binder to the specific target is subsequently designed. Under the simplistic paradigm of drug discovery, a drug molecule is assumed to interact only with the intended on-target. However, small molecular drugs often interact with multiple targets, and those off-target interactions are not considered under the conventional paradigm. As a result, drug-induced side effects and adverse reactions are often neglected ...


Machine Learning Model Based On Transthoracic Bioimpedance And Heart Rate Variability For Lung Fluid Accumulation Detection: Prospective Clinical Study, Natasa Reljin, Hugo F. Posada-Quintero, Caitlin Eaton-Robb, Sophia Binici, Emily Ensom, Eric Y. Ding, Anna Hayes, Jarno Riistama, Chad E. Darling, David D. Mcmanus, Ki H. Chon Aug 2020

Machine Learning Model Based On Transthoracic Bioimpedance And Heart Rate Variability For Lung Fluid Accumulation Detection: Prospective Clinical Study, Natasa Reljin, Hugo F. Posada-Quintero, Caitlin Eaton-Robb, Sophia Binici, Emily Ensom, Eric Y. Ding, Anna Hayes, Jarno Riistama, Chad E. Darling, David D. Mcmanus, Ki H. Chon

Open Access Articles

BACKGROUND: Accumulation of excess body fluid and autonomic dysregulation are clinically important characteristics of acute decompensated heart failure. We hypothesized that transthoracic bioimpedance, a noninvasive, simple method for measuring fluid retention in lungs, and heart rate variability, an assessment of autonomic function, can be used for detection of fluid accumulation in patients with acute decompensated heart failure.

OBJECTIVE: We aimed to evaluate the performance of transthoracic bioimpedance and heart rate variability parameters obtained using a fluid accumulation vest with carbon black-polydimethylsiloxane dry electrodes in a prospective clinical study (System for Heart Failure Identification Using an External Lung Fluid Device; SHIELD ...


Pfred: A Computational Platform For Sirna And Antisense Oligonucleotides Design, Simone Sciabola, Hualin Xi, Dario Cruz, Qing Cao, Christine Lawrence, Tianhong Zhang, Sergio Rotstein, Jason D. Hughes, Daniel R. Caffrey, Robert Stanton Aug 2020

Pfred: A Computational Platform For Sirna And Antisense Oligonucleotides Design, Simone Sciabola, Hualin Xi, Dario Cruz, Qing Cao, Christine Lawrence, Tianhong Zhang, Sergio Rotstein, Jason D. Hughes, Daniel R. Caffrey, Robert Stanton

University of Massachusetts Medical School Faculty Publications

PFRED a software application for the design, analysis, and visualization of antisense oligonucleotides and siRNA is described. The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover, the tool facilitates the incorporation of various design criteria that have been shown to be important for stability and potency. PFRED has been made available as an open-source project so the code can be easily modified to address the future needs of the oligonucleotide research community. A compiled version is available for downloading at https://github.com/pfred ...


Computational Methods For Predicting Protein-Protein Interactions And Binding Sites, Yiwei Li Aug 2020

Computational Methods For Predicting Protein-Protein Interactions And Binding Sites, Yiwei Li

Electronic Thesis and Dissertation Repository

Proteins are essential to organisms and participate in virtually every process within cells. Quite often, they keep the cells functioning by interacting with other proteins. This process is called protein-protein interaction (PPI). The bonding amino acid residues during the process of protein-protein interactions are called PPI binding sites. Identifying PPIs and PPI binding sites are fundamental problems in system biology.

Experimental methods for solving these two problems are slow and expensive. Therefore, great efforts are being made towards increasing the performance of computational methods.

We present DELPHI, a deep learning based program for PPI site prediction and SPRINT, an algorithmic ...


Genome-Wide Mapping Of Human Dna Replication By Optical Replication Mapping Supports A Stochastic Model Of Eukaryotic Replication Timing, Weitao Wang, Kyle Klein, Karel Proesmans, Northwestern University, Claire Marchal, Xiaopeng Zhu, Tyler M. Borrman, Alex Hastie, Zhiping Weng, Simon Fraser University, Paris Sciences Et Lettres University, Florida State University, Nicholas R. Rhind Aug 2020

Genome-Wide Mapping Of Human Dna Replication By Optical Replication Mapping Supports A Stochastic Model Of Eukaryotic Replication Timing, Weitao Wang, Kyle Klein, Karel Proesmans, Northwestern University, Claire Marchal, Xiaopeng Zhu, Tyler M. Borrman, Alex Hastie, Zhiping Weng, Simon Fraser University, Paris Sciences Et Lettres University, Florida State University, Nicholas R. Rhind

University of Massachusetts Medical School Faculty Publications

DNA replication is regulated by the location and timing of replication initiation. Therefore, much effort has been invested in identifying and analyzing the sites of human replication initiation. However, the heterogeneous nature of eukaryotic replication kinetics and the low efficiency of individual initiation site utilization in metazoans has made mapping the location and timing of replication initiation in human cells difficult. A potential solution to the problem of human replication mapping is single-molecule analysis. However, current approaches do not provide the throughput required for genome-wide experiments. To address this challenge, we have developed Optical Replication Mapping (ORM), a high-throughput single-molecule ...


An Improved Zebrafish Transcriptome Annotation For Sensitive And Comprehensive Detection Of Cell Type-Specific Genes, Nathan D. Lawson, Rui Li, Masahiro Shin, Ann S. Grosse, Onur Yukselen, Oliver A. Stone, Alper Kucukural, Lihua Julie Zhu Aug 2020

An Improved Zebrafish Transcriptome Annotation For Sensitive And Comprehensive Detection Of Cell Type-Specific Genes, Nathan D. Lawson, Rui Li, Masahiro Shin, Ann S. Grosse, Onur Yukselen, Oliver A. Stone, Alper Kucukural, Lihua Julie Zhu

University of Massachusetts Medical School Faculty Publications

The zebrafish is ideal for studying embryogenesis and is increasingly applied to model human disease. In these contexts, RNA-sequencing (RNA-seq) provides mechanistic insights by identifying transcriptome changes between experimental conditions. Application of RNA-seq relies on accurate transcript annotation for a genome of interest. Here, we find discrepancies in analysis from RNA-seq datasets quantified using Ensembl and RefSeq zebrafish annotations. These issues were due, in part, to variably annotated 3' untranslated regions and thousands of gene models missing from each annotation. Since these discrepancies could compromise downstream analyses and biological reproducibility, we built a more comprehensive zebrafish transcriptome annotation that addresses ...


A Chemical Interpretation Of Protein Electron Density Maps In The Worldwide Protein Data Bank, Sen Yao, Hunter N. B. Moseley Aug 2020

A Chemical Interpretation Of Protein Electron Density Maps In The Worldwide Protein Data Bank, Sen Yao, Hunter N. B. Moseley

Molecular and Cellular Biochemistry Faculty Publications

High-quality three-dimensional structural data is of great value for the functional interpretation of biomacromolecules, especially proteins; however, structural quality varies greatly across the entries in the worldwide Protein Data Bank (wwPDB). Since 2008, the wwPDB has required the inclusion of structure factors with the deposition of x-ray crystallographic structures to support the independent evaluation of structures with respect to the underlying experimental data used to derive those structures. However, interpreting the discrepancies between the structural model and its underlying electron density data is difficult, since derived sigma-scaled electron density maps use arbitrary electron density units which are inconsistent between maps ...


Perspectives On Encode, Encode Project Consortium, Michael P. Snyder, Jill E. Moore, Zhiping Weng Jul 2020

Perspectives On Encode, Encode Project Consortium, Michael P. Snyder, Jill E. Moore, Zhiping Weng

University of Massachusetts Medical School Faculty Publications

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression(1). The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for ...


Expanded Encyclopaedias Of Dna Elements In The Human And Mouse Genomes, Encode Project Consortium, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Xiao-Ou Zhang, Shaimae I. Elhajjajy, Jack Huey, Job Dekker, J. Michael Cherry, Richard M. Myers, Bing Ren, Brenton R. Graveley, Mark B. Gerstein, Len A. Pennacchio, Michael P. Snyder, Bradley E. Bernstein, Barbara Wold, Ross C. Hardison, Thomas R. Gingeras, John A. Stamatoyannopoulos, Zhiping Weng Jul 2020

Expanded Encyclopaedias Of Dna Elements In The Human And Mouse Genomes, Encode Project Consortium, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Xiao-Ou Zhang, Shaimae I. Elhajjajy, Jack Huey, Job Dekker, J. Michael Cherry, Richard M. Myers, Bing Ren, Brenton R. Graveley, Mark B. Gerstein, Len A. Pennacchio, Michael P. Snyder, Bradley E. Bernstein, Barbara Wold, Ross C. Hardison, Thomas R. Gingeras, John A. Stamatoyannopoulos, Zhiping Weng

University of Massachusetts Medical School Faculty Publications

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including ...


Building The Interphase Nucleus: A Study On The Kinetics Of 3d Chromosome Formation, Temporal Relation To Active Transcription, And The Role Of Nuclear Rnas, Kristin N. Abramo Jul 2020

Building The Interphase Nucleus: A Study On The Kinetics Of 3d Chromosome Formation, Temporal Relation To Active Transcription, And The Role Of Nuclear Rnas, Kristin N. Abramo

GSBS Dissertations and Theses

Following the discovery of the one-dimensional sequence of human DNA, much focus has been directed on microscopy and molecular techniques to learn about the spatial organization of chromatin in a 3D cell. The development of these powerful tools has enabled high-resolution, genome-wide analysis of chromosome structure under many different conditions. In this thesis, I focus on how the organization of interphase chromatin is established and maintained following mitosis. Mitotic chromosomes are folded into helical loop arrays creating short and condensed chromosomes, while interphase chromosomes are decondensed and folded into a number of structures at different length scales ranging from loops ...


Identification And Phylogenetic Analysis Of Channa Species From Riverine System Of Pakistan Using Coi Gene As A Dna Barcoding Marker, Muhammad Kamran, Atif Yaqub, Naila Malkani, Khalid Mahmood Anjum, Muhammad Nabeel Awan, Hamed Paknejad Jul 2020

Identification And Phylogenetic Analysis Of Channa Species From Riverine System Of Pakistan Using Coi Gene As A Dna Barcoding Marker, Muhammad Kamran, Atif Yaqub, Naila Malkani, Khalid Mahmood Anjum, Muhammad Nabeel Awan, Hamed Paknejad

Journal of Bioresource Management

Channa are the freshwater and important food fish species in Pakistan belonging to family Channidae. However, identification and phylogenetic analysis based on molecular tools of these species in Pakistan was not well known. Herein, the current investigation was conceptualized, which dealt with mitochondrial DNA sequences from three geographically distinct populations of this species from Pakistan’s water system. DNA from fin tissues was extracted. COI region of mtDNA was amplified using universal primers for fish. PCR products were sequenced. Phylogenetic analysis conducted in the present study, i.e. neighbor-joining (NJ) cladogram, maximum likelihood, K2P genetic divergence and histogram suggests that ...


Β-Amyloid And Tau Drive Early Alzheimer's Disease Decline While Glucose Hypometabolism Drives Late Decline, Tyler C. Hammond, Xin Xing, Chris Wang, David Ma, Kwangsik Nho, Paul K. Crane, Fanny Elahi, David A. Ziegler, Gongbo Liang, Qiang Cheng, Lucille M. Yanckello, Nathan Jacobs, Ai-Ling Lin Jul 2020

Β-Amyloid And Tau Drive Early Alzheimer's Disease Decline While Glucose Hypometabolism Drives Late Decline, Tyler C. Hammond, Xin Xing, Chris Wang, David Ma, Kwangsik Nho, Paul K. Crane, Fanny Elahi, David A. Ziegler, Gongbo Liang, Qiang Cheng, Lucille M. Yanckello, Nathan Jacobs, Ai-Ling Lin

Sanders-Brown Center on Aging Faculty Publications

Clinical trials focusing on therapeutic candidates that modify β-amyloid (Aβ) have repeatedly failed to treat Alzheimer’s disease (AD), suggesting that Aβ may not be the optimal target for treating AD. The evaluation of Aβ, tau, and neurodegenerative (A/T/N) biomarkers has been proposed for classifying AD. However, it remains unclear whether disturbances in each arm of the A/T/N framework contribute equally throughout the progression of AD. Here, using the random forest machine learning method to analyze participants in the Alzheimer’s Disease Neuroimaging Initiative dataset, we show that A/T/N biomarkers show varying importance in ...


Survival-Related Clustering Of Cancer Patients By Integrating Clinical And Biological Datasets, Xinming Wei Jul 2020

Survival-Related Clustering Of Cancer Patients By Integrating Clinical And Biological Datasets, Xinming Wei

Master's Theses (2009 -)

Subtype-based treatments and drug therapies are essential aspects to be considered in cancer patients' clinical trials to provide appropriate personalized therapies. With the advancement of the next-generation sequencing technology, several computational models, integrating genomic and transcriptomic datasets (i.e., multi-omics) in the prediction of subtype-based classification in cancer patients, were emerged. However, integration of the prognostic features from the clinical data, related to survival risks with the multi-omics datasets in the prediction of different subtypes, is limited and an important research area to be explored. In this study, we proposed a data integration pipeline with the prognostic features from the ...


Scalable Learning Of Interpretable Rules For The Dynamic Microbiome Domain, Venkata Suhas Maringanti, Vanni Bucci, Georg K. Gerber Jun 2020

Scalable Learning Of Interpretable Rules For The Dynamic Microbiome Domain, Venkata Suhas Maringanti, Vanni Bucci, Georg K. Gerber

University of Massachusetts Medical School Faculty Publications

The microbiome, which is inherently dynamic, plays essential roles in human physiology and its disruption has been implicated in numerous human diseases. Linking dynamic changes in the microbiome to the status of the human host is an important problem, which is complicated by limitations and complexities of the data. Model interpretability is key in the microbiome field, as practitioners seek to derive testable biological hypotheses from data or develop diagnostic tests that can be understood by clinicians. Interpretable structure must take into account domainspecific information key to biologists and clinicians including evolutionary relationships (phylogeny) and dynamic behavior of the microbiome ...


Introduction To The R-Package: Usdampr, Elliott James Dennis, Bowen Chen Jun 2020

Introduction To The R-Package: Usdampr, Elliott James Dennis, Bowen Chen

Extension Farm and Ranch Management

Why the Need for the Package? In the 1990’s, concern over growing packer concentration and a hog industry market shock resulted in discontent among producers and packers. As a result, the United States Congress passed the Livestock Mandatory Reporting Act of 1999 (1999 Act) [Pub. L. 106-78, Title IX] which is required to be reauthorized every five years. See here for a full history of the Livestock Mandatory Reporting Background.

Market reports were publicly issued in the form of .txt files with varying frequency from April 2000 to April 2020. Current and historical data were also housed in a ...


Translating Clinical And Patient-Reported Data To Tailored Shared Decision Reports With Predictive Analytics For Knee And Hip Arthritis, Patricia D. Franklin, Hua Zheng, Christina Bond, Danielle C. Lavallee Jun 2020

Translating Clinical And Patient-Reported Data To Tailored Shared Decision Reports With Predictive Analytics For Knee And Hip Arthritis, Patricia D. Franklin, Hua Zheng, Christina Bond, Danielle C. Lavallee

University of Massachusetts Medical School Faculty Publications

INTRODUCTION: New informatics tools can transform evidence-based information to individualized predictive reports to serve shared decisions in clinic. We developed a web-based system to collect patient-reported outcomes (PROs) and medical risk factors and to compare responses to national registry data. The system generates predicted outcomes for individual patients and a report for use in clinic to support decisions. We present the report development, presentation, and early experience implementing this PRO-based, shared decision report for knee and hip arthritis patients seeking orthopedic evaluation.

METHODS: Iterative patient and clinician interviews defined report content and visual display. The web-system supports: (a) collection of ...


Maintenance Of Onc Terminology For I2b2 Metadata, James Campbell, Alfred J. Anzalone, Jay Pedersen, James C. Mcclay Jun 2020

Maintenance Of Onc Terminology For I2b2 Metadata, James Campbell, Alfred J. Anzalone, Jay Pedersen, James C. Mcclay

Posters and Presentations: Emergency Medicine

ONC terminologies are constantly adding new content and deactivating existing codes. The University of Nebraska Medical Center (UNMC) deploys three primary code sets that require regular updating to support research: SNOMED CT, RXNORM / NDC, and LOINC. A problem across the i2b2 community is keeping these terminologies up-to-date and loading them into i2b2 for timely analysis of EHR data. We have developed tool kits for rapid deployment of SNOMED CT metadata and will be extending the work to RXNORM/NDC and LOINC.


Contributions Of Gyra And Parc Mutations And Qnrs2 Acquisition To Ciprofloxacin Resistance In Aeromonas Veronii Hm21, Daniel J. Silverstein Jun 2020

Contributions Of Gyra And Parc Mutations And Qnrs2 Acquisition To Ciprofloxacin Resistance In Aeromonas Veronii Hm21, Daniel J. Silverstein

Honors Scholar Theses

In recent years, ciprofloxacin resistant (CpR) Aeromonas veronii and A. hydrophila strains have been isolated from the wounds of patients receiving leech therapy. Genome comparisons of these CpR isolates revealed the presence of chromosomal mutations in gyrA and parC as well as the gain of qnrS2 on either a large, 34 kb, conjugatable, low-copy plasmid, pAv42, or on a small, 6.8 kb, high-copy plasmid, pAh1471. The minimum inhibitory concentration, MIC, for Cp of these clinical isolates ranged from 1 to ≥32 µg/mL and some harbored a qnrS2 containing plasmid. We wanted to assess the contributions of these factors ...


Docking Study Of Selected Citrus Flavonoids Towards Exploring The Potential Anti Estrogen Activity, Indira M., Krupanidhi S, Venkateswarulu T.C., Md. Nazneen Bobby, Keerthi P, Satya Kavya P, Amaze M, Abraham Peele K Jun 2020

Docking Study Of Selected Citrus Flavonoids Towards Exploring The Potential Anti Estrogen Activity, Indira M., Krupanidhi S, Venkateswarulu T.C., Md. Nazneen Bobby, Keerthi P, Satya Kavya P, Amaze M, Abraham Peele K

Karbala International Journal of Modern Science

Breast cancer is one of the serious health issues for the women and it has been characterized with uncontrolled growth of cells in the breast tissue. An elevated level of expression of estrogen promotes survival to breast cancerous cells. The present study is focused on phytochemicals, to screen the inhibition of estrogen receptor activity. The selected phytochemicals’ are citrus flavonoids having anti-cancer, anti-oxidative, anti-proliferative, anti-angiogenic, anti-estrogenic and anti-inflammatory activities. The crystal structure of human estrogen receptor with PDB ID: 2IOG are retrieved from protein data bank (PDB) and citrus flavanoids from Pub Chem database. The drug behavior was studied using ...


Dynamics Of The 4d Genome During In Vivo Lineage Specification And Differentiation, A. Marieke Oudelaar, Daniel Hidalgo, Merav Socolovsky, Douglas R. Higgs, Jim R. Hughes Jun 2020

Dynamics Of The 4d Genome During In Vivo Lineage Specification And Differentiation, A. Marieke Oudelaar, Daniel Hidalgo, Merav Socolovsky, Douglas R. Higgs, Jim R. Hughes

Open Access Articles

Mammalian gene expression patterns are controlled by regulatory elements, which interact within topologically associating domains (TADs). The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. Here, we present Tiled-C, a low-input chromosome conformation capture (3C) technique. We use this approach to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis of chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation. This is followed by structural re-organization within the TAD and formation of ...


A Cas9 With Pam Recognition For Adenine Dinucleotides, Pranam Chatterjee, Jooyoung Lee, Lisa Nip, Sabrina R. T. Koseki, Emma Tysinger, Erik J. Sontheimer, Joseph M. Jacobson, Noah Jakimo May 2020

A Cas9 With Pam Recognition For Adenine Dinucleotides, Pranam Chatterjee, Jooyoung Lee, Lisa Nip, Sabrina R. T. Koseki, Emma Tysinger, Erik J. Sontheimer, Joseph M. Jacobson, Noah Jakimo

Open Access Articles

CRISPR-associated (Cas) DNA-endonucleases are remarkably effective tools for genome engineering, but have limited target ranges due to their protospacer adjacent motif (PAM) requirements. We demonstrate a critical expansion of the targetable sequence space for a type II-A CRISPR-associated enzyme through identification of the natural 5[Formula: see text]-NAAN-3[Formula: see text] PAM preference of Streptococcus macacae Cas9 (SmacCas9). To achieve efficient editing activity, we graft the PAM-interacting domain of SmacCas9 to its well-established ortholog from Streptococcus pyogenes (SpyCas9), and further engineer an increased efficiency variant (iSpyMac) for robust genome editing activity. We establish that our hybrids can target all ...


Lymphatic Filariasis: Host And Parasite Factors And The Pathogenesis Of Systemic Adverse Events Following Treatment, Britt Juul Andersen May 2020

Lymphatic Filariasis: Host And Parasite Factors And The Pathogenesis Of Systemic Adverse Events Following Treatment, Britt Juul Andersen

Arts & Sciences Electronic Theses and Dissertations

Lymphatic filariasis (LF) is a neglected tropical disease caused by the nematode parasites Wuchereria bancrofti, Brugia malayi and B. timori. The primary tool used by the Global Program to Eliminate LF is mass drug administration (MDA), and some 500 million people take the medications each year. Mild to moderate adverse events (AEs) are common after LF treatment, and these pose a major challenge for the LF elimination program. To better understand the pathogenesis of AEs, we studied patients from LF treatment trials in Côte d’Ivoire and Papua New Guinea, where plasma and leucocytes were collected pre and post-treatment and ...


Performance Analysis Of Three Bioinformatic Variant Callers Using A Somatic Reference Standard, Binu Porath, Binu Porath May 2020

Performance Analysis Of Three Bioinformatic Variant Callers Using A Somatic Reference Standard, Binu Porath, Binu Porath

Research Days

No abstract provided.


The Evolving Management Of Aortic Valve Disease: Trends In The Utilization And Cost Of Savr, Tavr, And Medical Therapy, Andrew Goldsweig May 2020

The Evolving Management Of Aortic Valve Disease: Trends In The Utilization And Cost Of Savr, Tavr, And Medical Therapy, Andrew Goldsweig

Theses & Dissertations

Aortic stenosis (AS) and regurgitation (AR) may be treated with surgical aortic valve replacement (SAVR), transcatheter AVR (TAVR), or medical therapy (MT). Data are lacking regarding usage and cost of SAVR, TAVR, and MT for patients hospitalized with aortic valve disease. From the Nationwide Readmissions Database, we determined utilization and cost trends for SAVR, TAVR, and MT in patients with aortic valve disease admitted 2012-2016 for valve replacement, heart failure, unstable angina, non-ST-elevation myocardial infarction, or syncope. From 2012 through 2016, there was a 48.1% increase in the number of patients hospitalized for aortic valve disease annually. Overall, 19 ...


Molecular Characterization Of A Gene Encoding Insulin-Like Peptide 5 (Ilp5) In Drosophila Virilis, Nikolas R. Likourentzos, Jae H. Park May 2020

Molecular Characterization Of A Gene Encoding Insulin-Like Peptide 5 (Ilp5) In Drosophila Virilis, Nikolas R. Likourentzos, Jae H. Park

Pursuit - The Journal of Undergraduate Research at the University of Tennessee

The study of the insulin-like peptides of Drosophila can provide insight of their similarities to mammalian insulin and their potential usage in treating human insulin-related diseases. In this study, we isolated and characterized cDNA encoding insulin-like peptide (ILP) 5 in D. virilis by using RNA purification, reverse transcription, and RACE protocols. Subsequently, various bioinformatic softwares were employed to predict peptide structure. The ILP5 gene (587 base pairs) codes for 121 amino acids that make up prepro-ILP5. After maturation, functional ILP5 is a peptide of two 25 amino acid chains, A- and B-chain, connected by two disulfide bonds. Sequencing genomic DNA ...