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David A Rubin

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https://www.readbyqxmd.com/read/28628098/short-chain-alkanes-fuel-mussel-and-sponge-cycloclasticus-symbionts-from-deep-sea-gas-and-oil-seeps
#1
Maxim Rubin-Blum, Chakkiath Paul Antony, Christian Borowski, Lizbeth Sayavedra, Thomas Pape, Heiko Sahling, Gerhard Bohrmann, Manuel Kleiner, Molly C Redmond, David L Valentine, Nicole Dubilier
Cycloclasticus bacteria are ubiquitous in oil-rich regions of the ocean and are known for their ability to degrade polycyclic aromatic hydrocarbons (PAHs). In this study, we describe Cycloclasticus that have established a symbiosis with Bathymodiolus heckerae mussels and poecilosclerid sponges from asphalt-rich, deep-sea oil seeps at Campeche Knolls in the southern Gulf of Mexico. Genomic and transcriptomic analyses revealed that, in contrast to all previously known Cycloclasticus, the symbiotic Cycloclasticus appears to lack the genes needed for PAH degradation...
June 19, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28618253/hypoxia-inducible-factor-1%C3%AE-signaling-promotes-repair-of-the-alveolar-epithelium-after-acute-lung-injury
#2
Jazalle McClendon, Nicole L Jansing, Elizabeth F Redente, Aneta Gandjeva, Yoko Ito, Sean P Colgan, Aftab Ahmad, David W H Riches, Harold A Chapman, Robert J Mason, Rubin M Tuder, Rachel L Zemans
During acute respiratory distress syndrome, epithelial cells, primarily alveolar type (AT) I cells, die and slough off the basement membrane, resulting in enhanced permeability. ATII cells proliferate and spread onto the denuded basement membrane to reseal the barrier. Repair of the alveolar epithelium is critical for clinical recovery; however, the mechanisms underlying ATII cell proliferation and spreading are not well understood. We hypothesized that hypoxia-inducible factor (HIF)1α promotes proliferation and spreading of ATII cells during repair after lung injury...
June 12, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28609654/intertumoral-heterogeneity-within-medulloblastoma-subgroups
#3
Florence M G Cavalli, Marc Remke, Ladislav Rampasek, John Peacock, David J H Shih, Betty Luu, Livia Garzia, Jonathon Torchia, Carolina Nor, A Sorana Morrissy, Sameer Agnihotri, Yuan Yao Thompson, Claudia M Kuzan-Fischer, Hamza Farooq, Keren Isaev, Craig Daniels, Byung-Kyu Cho, Seung-Ki Kim, Kyu-Chang Wang, Ji Yeoun Lee, Wieslawa A Grajkowska, Marta Perek-Polnik, Alexandre Vasiljevic, Cecile Faure-Conter, Anne Jouvet, Caterina Giannini, Amulya A Nageswara Rao, Kay Ka Wai Li, Ho-Keung Ng, Charles G Eberhart, Ian F Pollack, Ronald L Hamilton, G Yancey Gillespie, James M Olson, Sarah Leary, William A Weiss, Boleslaw Lach, Lola B Chambless, Reid C Thompson, Michael K Cooper, Rajeev Vibhakar, Peter Hauser, Marie-Lise C van Veelen, Johan M Kros, Pim J French, Young Shin Ra, Toshihiro Kumabe, Enrique López-Aguilar, Karel Zitterbart, Jaroslav Sterba, Gaetano Finocchiaro, Maura Massimino, Erwin G Van Meir, Satoru Osuka, Tomoko Shofuda, Almos Klekner, Massimo Zollo, Jeffrey R Leonard, Joshua B Rubin, Nada Jabado, Steffen Albrecht, Jaume Mora, Timothy E Van Meter, Shin Jung, Andrew S Moore, Andrew R Hallahan, Jennifer A Chan, Daniela P C Tirapelli, Carlos G Carlotti, Maryam Fouladi, José Pimentel, Claudia C Faria, Ali G Saad, Luca Massimi, Linda M Liau, Helen Wheeler, Hideo Nakamura, Samer K Elbabaa, Mario Perezpeña-Diazconti, Fernando Chico Ponce de León, Shenandoah Robinson, Michal Zapotocky, Alvaro Lassaletta, Annie Huang, Cynthia E Hawkins, Uri Tabori, Eric Bouffet, Ute Bartels, Peter B Dirks, James T Rutka, Gary D Bader, Jüri Reimand, Anna Goldenberg, Vijay Ramaswamy, Michael D Taylor
While molecular subgrouping has revolutionized medulloblastoma classification, the extent of heterogeneity within subgroups is unknown. Similarity network fusion (SNF) applied to genome-wide DNA methylation and gene expression data across 763 primary samples identifies very homogeneous clusters of patients, supporting the presence of medulloblastoma subtypes. After integration of somatic copy-number alterations, and clinical features specific to each cluster, we identify 12 different subtypes of medulloblastoma...
June 12, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28600480/mir-193a-3p-is-a-key-tumor-suppressor-in-ulcerative-colitis-associated-colon-cancer-and-promotes-carcinogenesis-through-up-regulation-of-il17rd
#4
Joel Pekow, Katherine Meckel, Urszula Dougherty, Yong Huang, Xindi Chen, Anas Almoghrabi, Reba Mustafi, Fatma Ayaloglu-Butun, Zifeng Deng, Haider I Haider, John Hart, David T Rubin, John H Kwon, Marc Bissonnette
Purpose: Patients with ulcerative colitis (UC) are at increased risk for colorectal cancer, although mechanisms underlying neoplastic transformation are poorly understood. We sought to evaluate the role of microRNAs in neoplasia development in this high-risk population.   <p>Experimental Design: Tissue from 12 controls, 9 UC patients without neoplasia, and 11 UC patients with neoplasia was analyzed. miRNA array analysis was performed and select miRNAs assayed by real-time PCR on the discovery cohort and a validation cohort...
June 9, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28594651/mir-4728-3p-functions-as-a-tumor-suppressor-in-ulcerative-colitis-associated-colorectal-neoplasia-through-regulation-of-focal-adhesion-signaling
#5
Joel Pekow, Alan L Hutchison, Katherine Meckel, Kymberly Harrington, Zifeng Deng, Nitya Talasila, David T Rubin, Stephen B Hanauer, Roger Hurst, Konstantin Umanskiy, Alessandro Fichera, John Hart, Aaron R Dinner, Marc Bissonnette
BACKGROUND: As mechanisms of neoplasia in patients with ulcerative colitis (UC) remain poorly understood, we sought to identify pathways of carcinogenesis in this high-risk population. METHODS: MicroRNA (miRNA) and mRNA expression was examined in nondysplastic rectosigmoid mucosa from UC patients with (n = 19) or without remote colon neoplasia (n = 23). We developed a method to identify miRNA-regulated pathways based on differentially expressed miRNAs and their putative mRNAs targets in the same samples...
June 9, 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28586335/biology-and-evolution-of-poorly-differentiated-neuroendocrine-tumors
#6
David S Rickman, Himisha Beltran, Francesca Demichelis, Mark A Rubin
Neuroendocrine (NE) cancers are a diverse group of neoplasms typically diagnosed and treated on the basis of their site of origin. This Perspective focuses on advances in our understanding of the tumorigenesis and treatment of poorly differentiated neuroendocrine tumors. Recent evidence from sequencing indicates that, although neuroendocrine tumors can arise de novo, they can also develop as a result of lineage plasticity in response to pressure from targeted therapies. We discuss the shared genomic alterations of these tumors independently of their site of origin, and we explore potential therapeutic strategies on the basis of recent biological findings...
June 6, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28569525/web-based-alcohol-intervention-for-veterans-ptsd-combat-exposure-and-alcohol-outcomes
#7
Deborah J Brief, Marika Solhan, Denis Rybin, Justin L Enggasser, Amy Rubin, Monica Roy, Eric Helmuth, Amy Schreiner, Meagan Heilman, Lisa Vittorio, David Rosenbloom, Terence M Keane
OBJECTIVE: The purpose of the current study was to evaluate the relationship between baseline levels of posttraumatic stress disorder (PTSD), combat exposure, and alcohol outcomes in a sample of Operation Enduring Freedom (OEF) and Operation Iraqi Freedom (OIF) veterans using a web-based self-management intervention (VetChange) for problem drinking. METHOD: The current study focuses on 523 veterans who participated in a larger randomized clinical trial. Analyses in the current study include (a) multivariable linear regression models to assess the relationship between PTSD, combat exposure, and alcohol variables at baseline, and (b) general linear models accounting for correlated data within subjects to analyze change over time for alcohol outcomes as a function of baseline PTSD symptoms, combat exposure, and covariates...
June 1, 2017: Psychological Trauma: Theory, Research, Practice and Policy
https://www.readbyqxmd.com/read/28555642/tgf-%C3%AE-activation-by-bone-marrow-derived-thrombospondin-1-causes-schistosoma-and-hypoxia-induced-pulmonary-hypertension
#8
Rahul Kumar, Claudia Mickael, Biruk Kassa, Liya Gebreab, Jeffrey C Robinson, Daniel E Koyanagi, Linda Sanders, Lea Barthel, Christina Meadows, Daniel Fox, David Irwin, Min Li, B Alexandre McKeon, Suzette Riddle, R Dale Brown, Leslie E Morgan, Christopher M Evans, Daniel Hernandez-Saavedra, Angela Bandeira, James P Maloney, Todd M Bull, William J Janssen, Kurt R Stenmark, Rubin M Tuder, Brian B Graham
Pulmonary arterial hypertension (PAH) is an obstructive disease of the precapillary pulmonary arteries. Schistosomiasis-associated PAH shares altered vascular TGF-β signalling with idiopathic, heritable and autoimmune-associated etiologies; moreover, TGF-β blockade can prevent experimental pulmonary hypertension (PH) in pre-clinical models. TGF-β is regulated at the level of activation, but how TGF-β is activated in this disease is unknown. Here we show TGF-β activation by thrombospondin-1 (TSP-1) is both required and sufficient for the development of PH in Schistosoma-exposed mice...
May 30, 2017: Nature Communications
https://www.readbyqxmd.com/read/28554877/comparison-of-ecological-momentary-assessment-versus-direct-measurement-of-e-cigarette-use-with-a-bluetooth-enabled-e-cigarette-a-pilot-study
#9
Jennifer L Pearson, Hoda Elmasry, Babita Das, Sabrina L Smiley, Leslie F Rubin, Teresa DeAtley, Emily Harvey, Yitong Zhou, Raymond Niaura, David B Abrams
BACKGROUND: Assessing the frequency and intensity of e-cigarette use presents special challenges beyond those posed by cigarette use. Accurate measurement of e-cigarette consumption, puff duration, and the stability of these measures over time will be informative for estimating the behavioral and health effects of e-cigarette use. OBJECTIVE: The purpose of this pilot study was to compare the accuracy of self-reported e-cigarette puff counts collected via ecological momentary assessment (EMA) to objective puff count data collected by a Bluetooth-enabled e-cigarette device and to examine the feasibility and acceptability of using a second-generation e-cigarette among adult smokers...
May 29, 2017: JMIR Research Protocols
https://www.readbyqxmd.com/read/28549156/early-subjective-sensory-experiences-with-cigalike-e-cigarettes-among-african-american-menthol-smokers-a-qualitative-study
#10
Sabrina L Smiley, Teresa DeAtley, Leslie F Rubin, Emily Harvey, Elexis C Kierstead, Monica Webb Hooper, Raymond S Niaura, David B Abrams, Jennifer L Pearson
Introduction: Despite smoker interest in e-cigarettes as a harm reduction or cessation aid, many smokers prematurely discontinue vaping after trying a product. This study explored the role of early subjective sensory experience in vaping persistence and desistence. Methods: African American menthol cigarette smokers aged ≥18 years (n=15; M=54.1 years; SD=8.2), motivated to quit smoking, and interested in trying e-cigarettes were recruited in Washington, D.C. Participants were followed for three weeks and provided menthol cigalike e-cigarettes after week one...
May 26, 2017: Nicotine & Tobacco Research: Official Journal of the Society for Research on Nicotine and Tobacco
https://www.readbyqxmd.com/read/28545492/non-participants-in-policy-efforts-to-promote-evidence-based-practices-in-a-large-behavioral-health-system
#11
Rebecca E Stewart, Danielle R Adams, David S Mandell, Gayatri Nangia, Lauren Shaffer, Arthur C Evans, Ronnie Rubin, Shawna Weaver, Trevor R Hadley, Rinad S Beidas
BACKGROUND: System-wide training initiatives to support and implement evidence-based practices (EBPs) in behavioral health systems have become increasingly widespread. Understanding more about organizations who do not participate in EBP training initiatives is a critical piece of the dissemination and implementation puzzle if we endeavor to increase access in community settings. METHODS: We conducted 30 1-h semi-structured interviews with leaders in non-participating agencies who did not formally participate in system-wide training initiatives to implement EBPs in the City of Philadelphia, with the goal to understand why they did not participate...
May 25, 2017: Implementation Science: IS
https://www.readbyqxmd.com/read/28530494/review-anal-intraepithelial-neoplasia-in-hiv-infected-men-who-have-sex-with-men-is-screening-and-treatment-justified
#12
Peter Wasserman, David S Rubin, Glenn Turett
Anal squamous cell carcinoma (SCC) is the fourth most prevalent cancer in human immunodeficiency virus (HIV)-infected men who have sex with men (MSM). Human papillomavirus (HPV) has been detected in over 90% of anal carcinoma biopsy specimens from MSM, and is considered a necessary, but alone, insufficient factor for carcinogenesis. Anal intraepithelial neoplasia (AIN) may be precursive for SCC, and screening cytology with referral of persons with abnormality for high-resolution anoscopy-guided biopsy, and AIN treatment, has been recommended for prevention...
June 2017: AIDS Patient Care and STDs
https://www.readbyqxmd.com/read/28522728/draft-genome-sequence-of-mycobacterium-abscessus-bamboo
#13
Michelle Yee, David Klinzing, Jun-Rong Wei, Martin Gengenbacher, Eric J Rubin, Thomas Dick
Mycobacterium abscessus, an intrinsically multidrug-resistant pathogen, causes chronic incurable lung disease. New drugs for this emerging pathogen represent an urgent unmet medical need. Here, we report a draft genome sequence of M. abscessus Bamboo, a clinical isolate used as a screening strain for drug discovery.
May 18, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28520829/association-between-combined-tmprss2-erg-and-pca3-rna-urinary-testing-and-detection-of-aggressive-prostate-cancer
#14
Martin G Sanda, Ziding Feng, David H Howard, Scott A Tomlins, Lori J Sokoll, Daniel W Chan, Meredith M Regan, Jack Groskopf, Jonathan Chipman, Dattatraya H Patil, Simpa S Salami, Douglas S Scherr, Jacob Kagan, Sudhir Srivastava, Ian M Thompson, Javed Siddiqui, Jing Fan, Aron Y Joon, Leonidas E Bantis, Mark A Rubin, Arul M Chinnayian, John T Wei, Mohamed Bidair, Adam Kibel, Daniel W Lin, Yair Lotan, Alan Partin, Samir Taneja
Importance: Potential survival benefits from treating aggressive (Gleason score, ≥7) early-stage prostate cancer are undermined by harms from unnecessary prostate biopsy and overdiagnosis of indolent disease. Objective: To evaluate the a priori primary hypothesis that combined measurement of PCA3 and TMPRSS2:ERG (T2:ERG) RNA in the urine after digital rectal examination would improve specificity over measurement of prostate-specific antigen alone for detecting cancer with Gleason score of 7 or higher...
May 18, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28499401/are-general-and-strategic-measures-of-organizational-context-and-leadership-associated-with-knowledge-and-attitudes-toward-evidence-based-practices-in-public-behavioral-health-settings-a-cross-sectional-observational-study
#15
Byron J Powell, David S Mandell, Trevor R Hadley, Ronnie M Rubin, Arthur C Evans, Matthew O Hurford, Rinad S Beidas
BACKGROUND: Examining the role of modifiable barriers and facilitators is a necessary step toward developing effective implementation strategies. This study examines whether both general (organizational culture, organizational climate, and transformational leadership) and strategic (implementation climate and implementation leadership) organizational-level factors predict therapist-level determinants of implementation (knowledge of and attitudes toward evidence-based practices). METHODS: Within the context of a system-wide effort to increase the use of evidence-based practices (EBPs) and recovery-oriented care, we conducted an observational, cross-sectional study of 19 child-serving agencies in the City of Philadelphia, including 23 sites, 130 therapists, 36 supervisors, and 22 executive administrators...
May 12, 2017: Implementation Science: IS
https://www.readbyqxmd.com/read/28486648/faecal-microbiota-transplantation-for-inflammatory-bowel-disease-a-systematic-review-and-meta-analysis
#16
Sudarshan Paramsothy, Ramesh Paramsothy, David T Rubin, Michael A Kamm, Nadeem O Kaakoush, Hazel M Mitchell, Natalia Castaño-Rodríguez
BACKGROUND: Faecal microbiota transplantation (FMT) has been investigated as a potential treatment for inflammatory bowel disease (IBD). We thus performed a systematic review and meta-analysis assessing the effectiveness and safety of FMT in IBD. METHODS: A systematic review was conducted until Jan 2017. Studies were excluded if patients had co-infection or data was pooled across disease subtypes (ulcerative colitis (UC), Crohn's disease (CD), pouchitis). Clinical remission was established as the primary outcome...
May 9, 2017: Journal of Crohn's & Colitis
https://www.readbyqxmd.com/read/28473000/tracking-microbial-colonization-in-fecal-microbiota-transplantation-experiments-via-genome-resolved-metagenomics
#17
Sonny T M Lee, Stacy A Kahn, Tom O Delmont, Alon Shaiber, Özcan C Esen, Nathaniel A Hubert, Hilary G Morrison, Dionysios A Antonopoulos, David T Rubin, A Murat Eren
BACKGROUND: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits...
May 4, 2017: Microbiome
https://www.readbyqxmd.com/read/28464947/erratum-to-unraveling-the-clonal-hierarchy-of-somatic-genomic-aberrations
#18
Davide Prandi, Sylvan C Baca, Alessandro Romanel, Christopher E Barbieri, Juan-Miguel Mosquera, Jacqueline Fontugne, Himisha Beltran, Andrea Sboner, Levi A Garraway, Mark A Rubin, Francesca Demichelis
No abstract text is available yet for this article.
May 2, 2017: Genome Biology
https://www.readbyqxmd.com/read/28445381/regulatory-advocacy-update-american-society-of-plastic-surgeons-comments-in-response-to-the-u-s-food-and-drug-administration-draft-guidance-documents-on-human-cell-and-tissue-products
#19
J Peter Rubin, Richard A D'Amico, Ricardo Rodriguez, Sydney R Coleman, Paul Cederna, Scot Glasberg, Michael Neumeister, David H Song, Charles Butler, Keith M Hume
The U.S. Food and Drug Administration released draft guidance documents on human cells, tissues, and cellular and tissue-based products regulations. These proposed guidance documents can impact the practice of plastic surgery in the area of tissue grafting procedures. This article describes the relevant issues in these draft guidance documents, and presents the comments provided to the U.S. Food and Drug Administration by the American Society of Plastic Surgeons.
May 2017: Plastic and Reconstructive Surgery
https://www.readbyqxmd.com/read/28441679/the-drivers-of-discretionary-utilization-clinical-history-versus-physician-supply
#20
Gregory W Ruhnke, Willard G Manning, David T Rubin, David O Meltzer
PURPOSE: Because the effect of physician supply on utilization remains controversial, literature based on non-Medicare populations is sparse, and a physician supply expansion is under way, the potential for physician-induced demand across diverse populations is important to understand. A substantial proportion of gastrointestinal endoscopies may be inappropriate. The authors analyzed the impact of physician supply, practice patterns, and clinical history on esophagogastroduodenoscopy (EGD, defined as discretionary) among patients hospitalized with lower gastrointestinal bleeding (LGIB)...
May 2017: Academic Medicine: Journal of the Association of American Medical Colleges
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