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Rna-Seq With Rnase H-Based Ribosomal Rna Depletion Specifically Designed For C. Elegans, Ye Duan, Yongming Sun, Victor R. Ambros 2020 University of Massachusetts Medical School

Rna-Seq With Rnase H-Based Ribosomal Rna Depletion Specifically Designed For C. Elegans, Ye Duan, Yongming Sun, Victor R. Ambros

University of Massachusetts Medical School Faculty Publications

Here we describe a rRNA depletion protocol based on RNase H digestion using antisense oligonucleotides (ASOs) specifically designed for C. elegans cytoplasmic rRNA (Fig. 1A). We suggest that this rRNA depletion protocol is applicable to RNA-seq applications where the yield of mRNA enrichment should be independent of poly(A) status, or any application which benefits from the removal of rRNA sequences, such ribosome profiling, or sequencing of non-coding RNAs other than rRNA.


Timing Of Maximal Weight Reduction Following Bariatric Surgery: A Study In Chinese Patients, Ting Xu, Chen Wang, Hongwei Zhang, Xiaodong Han, Weijie Liu, Junfeng Han, Haoyong Yu, Jin Chen, Pin Zhang, Jianzhong Di 2020 Shanghai Jiao Tong University, China

Timing Of Maximal Weight Reduction Following Bariatric Surgery: A Study In Chinese Patients, Ting Xu, Chen Wang, Hongwei Zhang, Xiaodong Han, Weijie Liu, Junfeng Han, Haoyong Yu, Jin Chen, Pin Zhang, Jianzhong Di

Computer Science Faculty Publications

Introduction: Bariatric surgery is a well-received treatment for obesity with maximal weight loss at 12–36 months postoperatively. We investigated the effect of early bariatric surgery on weight reduction of Chinese patients in accordance with their preoperation characteristics.

Materials and Methods: Altogether, 409 patients with obesity from a prospective cohort in a single bariatric center were enrolled retrospectively and evaluated for up to 4 years. Measurements obtained included surgery type, duration of diabetic condition, besides the usual body mass index data tuple. Weight reduction was expressed as percent total weight loss (%TWL) and percent excess weight loss (%EWL).

Results: RYGB ...


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 2020 University of Kentucky

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 2020 Department of Biochemistry and Biotechnology, The Women University, Multan, Pakistan

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 2020 Rowan University

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 ...


Genomic Survey Of E. Coli From The Bladders Of Women With And Without Lower Urinary Tract Symptoms, Andrea Garretto, Taylor Miller-Ensminger, Adriana Ene, Zubia Merchant, Aashaka Shah, Athina Gerodias, Anthony Biancofiori, Stacey Canchola, Stephanie Canchola, Emanuel Castillo, Tasnim Chowdhury, Nikita Gandhi, Sarah Hamilton, Kyla Hatton, Syed Hyder, Koty Krull, Demetrios Lagios, Thinh Lam, Kennedy Mitchell, Christine Mortensen, Amber Murphy, Joseph Richburg, Meghan Rokas, Suzanne Ryclik, Pauline Sulit, Thomas Szwajnos, Manuel Widuch, Jessica Willis, Mary Woloszyn, Bridget Brassil, Genevieve Johnson, Rita Mormando, Laura Maskeri, Mary Batrich, Nicole Stark, Jason W. Shapiro, Cesar Montelongo Hernandez, Swarnali Banerjee, Alan J. Wolfe, Catherine Putonti 2020 Loyola University Chicago

Genomic Survey Of E. Coli From The Bladders Of Women With And Without Lower Urinary Tract Symptoms, Andrea Garretto, Taylor Miller-Ensminger, Adriana Ene, Zubia Merchant, Aashaka Shah, Athina Gerodias, Anthony Biancofiori, Stacey Canchola, Stephanie Canchola, Emanuel Castillo, Tasnim Chowdhury, Nikita Gandhi, Sarah Hamilton, Kyla Hatton, Syed Hyder, Koty Krull, Demetrios Lagios, Thinh Lam, Kennedy Mitchell, Christine Mortensen, Amber Murphy, Joseph Richburg, Meghan Rokas, Suzanne Ryclik, Pauline Sulit, Thomas Szwajnos, Manuel Widuch, Jessica Willis, Mary Woloszyn, Bridget Brassil, Genevieve Johnson, Rita Mormando, Laura Maskeri, Mary Batrich, Nicole Stark, Jason W. Shapiro, Cesar Montelongo Hernandez, Swarnali Banerjee, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Urinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs are commonly associated with colonization by Escherichia coli, members of this species also have been found within the bladder of individuals with no lower urinary tract symptoms (no LUTS), also known as asymptomatic bacteriuria. Prior studies have found that both uropathogenic E. coli (UPEC) strains and E. coli isolates that are not associated with UTIs encode for virulence factors. Thus, the reason(s) why E. coli sometimes causes UTI-like symptoms remain(s) elusive. In this study, the genomes of 66 E. coli isolates from adult ...


Mechanism Of Translation Inhibition By Type Ii Gnat Toxin Atat2, Stepan V Ovchinnikov, Dmitry Bikmetov, Alexei Livenskyi, Marina Serebryakova, Brendan Wilcox, Kyle Mangano, Dmitrii I Shiriaev, Ilya A Osterman, Petr V Sergiev, Sergei Borukhov, Nora Vazquez-Laslop, Alexander S Mankin, Konstantin Severinov, Svetlana Dubiley 2020 Skolkovo Institute of Science and Technology

Mechanism Of Translation Inhibition By Type Ii Gnat Toxin Atat2, Stepan V Ovchinnikov, Dmitry Bikmetov, Alexei Livenskyi, Marina Serebryakova, Brendan Wilcox, Kyle Mangano, Dmitrii I Shiriaev, Ilya A Osterman, Petr V Sergiev, Sergei Borukhov, Nora Vazquez-Laslop, Alexander S Mankin, Konstantin Severinov, Svetlana Dubiley

School of Osteopathic Medicine Faculty Scholarship

Type II toxin-antitoxins systems are widespread in prokaryotic genomes. Typically, they comprise two proteins, a toxin, and an antitoxin, encoded by adjacent genes and forming a complex in which the enzymatic activity of the toxin is inhibited. Under stress conditions, the antitoxin is degraded liberating the active toxin. Though thousands of various toxin-antitoxins pairs have been predicted bioinformatically, only a handful has been thoroughly characterized. Here, we describe the AtaT2 toxin from a toxin-antitoxin system from Escherichia coli O157:H7. We show that AtaT2 is the first GNAT (Gcn5-related N-acetyltransferase) toxin that specifically targets charged glycyl tRNA. In vivo, the ...


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 2020 Columbia University Medical Center

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 2020 The Graduate Center, City University of New York

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 ...


Mimicking Prophage Induction In The Body: Induction In The Lab With Ph Gradients, Taylor Miller-Ensminger, Andrea Garretto, Nicole Stark, Catherine Putonti 2020 Loyola University Chicago

Mimicking Prophage Induction In The Body: Induction In The Lab With Ph Gradients, Taylor Miller-Ensminger, Andrea Garretto, Nicole Stark, Catherine Putonti

Bioinformatics Faculty Publications

The majority of bacteria within the human body are lysogens, often harboring multiple bacteriophage sequences (prophages) within their genomes. While several different types of environmental stresses can trigger or induce prophages to enter into the lytic cycle, they have yet to be fully explored and understood in the human microbiota. In the laboratory, the most common induction method is the DNA damaging chemical Mitomycin C. Although pH has been listed in the literature as an induction method, it is not widely used. Here, we detail a protocol for prophage induction by culture under different pH conditions. We explored the effects ...


Enrichment Of Ontologies Using Machine Learning And Summarization, Hao Liu 2020 New Jersey Institute of Technology

Enrichment Of Ontologies Using Machine Learning And Summarization, Hao Liu

Dissertations

Biomedical ontologies are structured knowledge systems in biomedicine. They play a major role in enabling precise communications in support of healthcare applications, e.g., Electronic Healthcare Records (EHR) systems. Biomedical ontologies are used in many different contexts to facilitate information and knowledge management. The most widely used clinical ontology is the SNOMED CT. Placing a new concept into its proper position in an ontology is a fundamental task in its lifecycle of curation and enrichment.

A large biomedical ontology, which typically consists of many tens of thousands of concepts and relationships, can be viewed as a complex network with concepts ...


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 2020 University of Connecticut

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 Publications by UMMS Authors

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 [Preprint], Simone Sciabola, Hualin Xi, Dario Cruz, Qing Cao, Christine Lawrence, Tianhong Zhang, Sergio Rotstein, Jason D. Hughes, Daniel R. Caffrey, Robert Stanton 2020 Biogen

Pfred: A Computational Platform For Sirna And Antisense Oligonucleotides Design [Preprint], 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 2020 The University of Western Ontario

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 [Preprint], 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 2020 Paris Sciences et Lettres University

Genome-Wide Mapping Of Human Dna Replication By Optical Replication Mapping Supports A Stochastic Model Of Eukaryotic Replication Timing [Preprint], 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 2020 University of Massachusetts Medical School

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 2020 University of Kentucky

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 ...


Comparative Genomic Study Of Lactobacillus Jensenii And The Newly Defined Lactobacillus Mulieris Species Identifies Species-Specific Functionality, Catherine Putoni, Jason W. Shapiro, Adriana Ene, Oleksandra Tsibere, Alan J. Wolfe 2020 Loyola University Chicago

Comparative Genomic Study Of Lactobacillus Jensenii And The Newly Defined Lactobacillus Mulieris Species Identifies Species-Specific Functionality, Catherine Putoni, Jason W. Shapiro, Adriana Ene, Oleksandra Tsibere, Alan J. Wolfe

Bioinformatics Faculty Publications

Lactobacilli are dominant members of the “healthy” female urogenital microbiota. One of these species, Lactobacillus jensenii, is routinely identified in the urinary microbiota of women both with and without urinary tract symptoms. In March 2020, the new bacterial species Lactobacillus mulieris was introduced, and phylogenetic and average nucleotide identity analysis identified eight L. jensenii strains that should be classified as members of the L. mulieris species. This prompted our phylogenomic study of all publicly available L. jensenii and L. mulieris genome sequences. While there is little variation in the 16S rRNA gene sequences, the core genome shows a clear distinction ...


A Neutrosophic Clinical Decision-Making System For Cardiovascular Diseases Risk Analysis, Florentin Smarandache, Shaista Habib, Wardat-us- Salam, M. Arif Butt, Muhammad Akram 2020 University of New Mexico

A Neutrosophic Clinical Decision-Making System For Cardiovascular Diseases Risk Analysis, Florentin Smarandache, Shaista Habib, Wardat-Us- Salam, M. Arif Butt, Muhammad Akram

Mathematics and Statistics Faculty and Staff Publications

Cardiovascular diseases are the leading cause of death worldwide. Early diagnosis of heart disease can reduce this large number of deaths so that treatment can be carried out. Many decision-making systems have been developed, but they are too complex for medical professionals. To target these objectives, we develop an explainable neutrosophic clinical decision-making system for the timely diagnose of cardiovascular disease risk. We make our system transparent and easy to understand with the help of explainable artificial intelligence techniques so that medical professionals can easily adopt this system. Our system is taking thirtyfive symptoms as input parameters, which are, gender ...


Identification Of Trim24 Domain Essentiality In Primary Trim24coe Carcinosarcoma Cell Lines, Cem Dede 2020 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Identification Of Trim24 Domain Essentiality In Primary Trim24coe Carcinosarcoma Cell Lines, Cem Dede

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Regulation of transcriptional control is a critical feature for organismal development and survival. Because of its effects on chromatin-controlled expression, disruptions of this delicately tuned mechanism are an important factor in development of tumorigenesis. Therefore, there is a growing interest in targeting these control mechanisms for their potential therapeutic values.

Our lab previously discovered the epigenetic regulator function of Tripartite motif protein 24 (TRIM24) through its H3K4me0 and H3K23ac dual histone signature reader function, its negative regulatory effect on the p53 tumor suppressor, in addition to its shown oncogenic driving capacity on immortalized mammary epithelial cells when overexpressed. Although TRIM24 ...


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