Other Medical Specialties Commons^™

Isomirmap-Fast, Deterministic, And Exhaustive Mining Of Isomirs From Short Rna-Seq Datasets., Phillipe Loher, Nestoras Karathanasis, Eric R Londin, Paul Bray, Venetia Pliatsika, Aristeidis G. Telonis, Isidore Rigoutsos

Computational Medicine Center Faculty Papers

MOTIVATION: MicroRNA (miRNA) precursor arms give rise to multiple isoforms simultaneously called "isomiRs." IsomiRs from the same arm typically differ by a few nucleotides at either their 5´ or 3´ termini, or both. In humans, the identities and abundances of isomiRs depend on a person's sex, population of origin, race/ethnicity, and on tissue type, tissue state, and disease type/subtype. Moreover, nearly half of the time the most abundant isomiR differs from the miRNA sequence found in public databases. Accurate mining of isomiRs from deep sequencing data is thus important.

RESULTS: We developed isoMiRmap, a fast, standalone, user-friendly mining tool that …

Sepsis In Two Hospitals In Rwanda: A Retrospective Cohort Study Of Presentation, Management, Outcomes, And Predictors Of Mortality., Dennis A Hopkinson, Jean Paul Mvukiyehe, Sudha P Jayaraman, Aamer A Syed, Myles Dworkin, Willy Mucyo, Thierry Cyuzuzo, Anne Tuyizere, Christian Mukwesi, Gaston Nyirigira, Paulin R Banguti, Elisabeth D Riviello

Student Papers, Posters & Projects

PURPOSE: Few studies have assessed the presentation, management, and outcomes of sepsis in low-income countries (LICs). We sought to characterize these aspects of sepsis and to assess mortality predictors in sepsis in two referral hospitals in Rwanda.

MATERIALS AND METHODS: This was a retrospective cohort study in two public academic referral hospitals in Rwanda. Data was abstracted from paper medical records of adult patients who met our criteria for sepsis.

RESULTS: Of the 181 subjects who met eligibility criteria, 111 (61.3%) met our criteria for sepsis without shock and 70 (38.7%) met our criteria for septic shock. Thirty-five subjects (19.3%) …

Effects Of Combining Meditation Techniques On Short-Term Memory, Attention, And Affect In Healthy College Students., Samani Unnata Pragya, Neelam D Mehta, Bassam Abomoelak, Parvin Uddin, Pushya Veeramachaneni, Naina Mehta, Stephanie Moore, Melissa Jean-Francois, Stephanie Garcia, Samani Chaitanya Pragya, Devendra I Mehta

Department of Medicine Faculty Papers

Meditation refers to a family of self-regulation practices that focuses on training attention and awareness to foster psycho-emotional well-being and to develop specific capacities such as calmness, clarity, and concentration. We report a prospective convenience-controlled study in which we analyzed the effect of two components of Preksha Dhyāna – buzzing bee sound meditation (Mahapran dhvani) and color meditation (leśyā dhyāna) on healthy college students. Mahapran and leśya dhyāna are two Preksha Dhyāna practices that are based on sound and green color, respectively. The study population represents a suitable target as college students experience different stress factors during the school year. …

Biomolecules As Model Indicators Of In Vitro And In Vivo Cold Plasma Safety, Caitlin Heslin, Daniela Boehm, Julianne Megaw, Brendan F. Gilmore, Theresa A. Freeman, Noreen J. Hickok, P. J. Cullen, Paula Bourke

Department of Medicine Faculty Papers

No abstract provided.

Evaluating The Relationship Between Participation In Student-Run Free Clinics And Changes In Empathy In Medical Students., Anita Modi, Michele Fascelli, Zachary Daitch, Mohammadreza Hojat Professor

Department of Medicine Faculty Papers

PURPOSE: We explored differences in changes in medical student empathy in the third year of medical school between volunteers at JeffHOPE, a multisite medical student-run free clinic of Sidney Kimmel Medical College (SKMC), and nonvolunteers.

METHOD: Volunteerism and leadership experience at JeffHOPE were documented for medical students in the Class of 2015 (n = 272) across their medical educations. Students completed the Jefferson Scale of Empathy at the beginning of medical school and at the end of the third year. Students who reported participation in other Jefferson-affiliated clinics (n = 44) were excluded from this study. Complete data were available …

Consequential Considerations When Mapping Trna Fragments., Aristeidis G Telonis, Phillipe Loher, Yohei Kirino, Phd, Isidore Rigoutsos

Computational Medicine Center Faculty Papers

We examine several of the choices that went into the design of tDRmapper, a recently reported tool for identifying transfer RNA (tRNA) fragments in deep sequencing data, evaluate them in the context of currently available knowledge, and discuss their potential impact on the output that the tool generates.

Cannibalism, Kuru, And Mad Cows: Prion Disease As A "Choose-Your-Own-Experiment" Case Study To Simulate Scientific Inquiry In Large Lectures., Antonio Serrano, Jeffrey Liebner, Justin K Hines

Department of Medicine Faculty Papers

Despite significant efforts to reform undergraduate science education, students often perform worse on assessments of perceptions of science after introductory courses, demonstrating a need for new educational interventions to reverse this trend. To address this need, we created An Inexplicable Disease, an engaging, active-learning case study that is unusual because it aims to simulate scientific inquiry by allowing students to iteratively investigate the Kuru epidemic of 1957 in a choose-your-own-experiment format in large lectures. The case emphasizes the importance of specialization and communication in science and is broadly applicable to courses of any size and sub-discipline of the life sciences.

Targeting The Mrna-Binding Protein Hur Impairs Malignant Characteristics Of Pancreatic Ductal Adenocarcinoma Cells., Masaya Jimbo, Fernando F Blanco, Yu-Hung Huang, Aristeidis G Telonis, Brad A Screnci, Gabriela L Cosma, Vitali Alexeev, Gregory E Gonye, Charles Yeo, Janet A Sawicki, Jordan M Winter, Jonathan Brody, Md

Computational Medicine Center Faculty Papers

Post-transcriptional regulation is a powerful mediator of gene expression, and can rapidly alter the expression of numerous transcripts involved in tumorigenesis. We have previously shown that the mRNA-binding protein HuR (ELAVL1) is elevated in human pancreatic ductal adenocarcinoma (PDA) specimens compared to normal pancreatic tissues, and its cytoplasmic localization is associated with increased tumor stage. To gain a better insight into HuR's role in PDA biology and to assess it as a candidate therapeutic target, we altered HuR expression in PDA cell lines and characterized the resulting phenotype in preclinical models. HuR silencing by short hairpin and small interfering RNAs …

Trna-Derived Short Non-Coding Rna As Interacting Partners Of Argonaute Proteins., Megumi Shigematsu, Yohei Kirino, Phd

Computational Medicine Center Faculty Papers

The advent of next-generation sequencing technologies has not only accelerated findings on various novel non-coding RNA (ncRNA) species but also led to the revision of the biological significance and versatility of fundamental RNA species with canonical function, such as transfer RNAs (tRNAs). Although tRNAs are best known as adapter components of translational machinery, recent studies suggest that tRNAs are not always end products but can further serve as a source for short ncRNAs. In many organisms, various tRNA-derived ncRNA species are produced from mature tRNAs or their precursor transcripts as functional molecules involved in various biological processes beyond translation. In …

Isomir Expression Profiles In Human Lymphoblastoid Cell Lines Exhibit Population And Gender Dependencies., Phillipe Loher, Eric R Londin, Isidore Rigoutsos

Computational Medicine Center Faculty Papers

For many years it was believed that each mature microRNA (miRNA) existed as a single entity with fixed endpoints and a 'static' and unchangeable primary sequence. However, recent evidence suggests that mature miRNAs are more 'dynamic' and that each miRNA precursor arm gives rise to multiple isoforms, the isomiRs. Here we report on our identification of numerous and abundant isomiRs in the lymphoblastoid cell lines (LCLs) of 452 men and women from five different population groups. Unexpectedly, we find that these isomiRs exhibit an expression profile that is population-dependent and gender-dependent. This is important as it indicates that the LCLs …

Nuclear And Mitochondrial Trna-Lookalikes In The Human Genome., Aristeidis G Telonis, Phillipe Loher, Yohei Kirino, Isidore Rigoutsos

Computational Medicine Center Faculty Papers

We are interested in identifying and characterizing loci of the human genome that harbor sequences resembling known mitochondrial and nuclear tRNAs. To this end, we used the known nuclear and mitochondrial tRNA genes (the "tRNA-Reference" set) to search for "tRNA-lookalikes" and found many such loci at different levels of sequence conservation. We find that the large majority of these tRNA-lookalikes resemble mitochondrial tRNAs and exhibit a skewed over-representation in favor of some mitochondrial anticodons. Our analysis shows that the tRNA-lookalikes have infiltrated specific chromosomes and are preferentially located in close proximity to known nuclear tRNAs (z-score ≤ -2.54, P-value ≤ …