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Matthew Stephens

Christopher S Fowler, Barrett A Lee, Stephen A Matthews
Although the trend toward greater ethnoracial diversity in the United States has been documented at a variety of geographic scales, most research tracks diversity one scale at a time. Our study bridges scales, asking how the diversity and segregation patterns of metropolitan areas are influenced by shifts in the racial/ethnic composition of their constituent places. Drawing on 1980-2010 decennial census data, we use a new visual tool to compare the distributions of place diversity for 50 U.S. metro areas over three decades...
October 25, 2016: Demography
Sara Lodi, Shweta Sharma, Jens D Lundgren, Andrew N Phillips, Stephen R Cole, Roger Logan, Brian K Agan, Abdel Babiker, Hartwig Klinker, Haitao Chu, Matthew Law, James D Neaton, Miguel A Hernán
OBJECTIVE: The Strategic Timing of AntiRetroviral Treatment (START) trial found a lower risk of a composite clinical outcome in HIV-positive individuals assigned to immediate initiation of antiretroviral therapy (ART) compared with those assigned to deferred initiation. However, 30% of those assigned to deferred initiation started ART earlier than the protocol specified. To supplement the published intention-to-treat (ITT) effect estimates, here we estimate the per-protocol effect of immediate versus deferred ART initiation in START...
November 13, 2016: AIDS
Wayne B Dyer, Joanne C G Tan, Timothy Day, Lynette Kiers, Matthew C Kiernan, Con Yiannikas, Stephen Reddel, Karl Ng, Phillip Mondy, Peta M Dennington, Melinda M Dean, Halina M Trist, Cristobal Dos Remedios, P Mark Hogarth, Steve Vucic, David O Irving
OBJECTIVE: The objective of the study was to profile leukocyte markers modulated during intravenous immunoglobulin (IVIg) treatment, and to identify markers and immune pathways associated with clinical efficacy of IVIg for chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) with potential for monitoring treatment efficacy. METHODS: Response to IVIg treatment in newly diagnosed IVIg-naïve and established IVIg-experienced patients was assessed by changes in expression of inflammatory leukocyte markers by flow cytometry...
October 2016: Brain and Behavior
Pauline N Serrano, Hongxin Wang, Jason C Crack, Christopher Prior, Matthew I Hutchings, Andrew J Thomson, Saeed Kamali, Yoshitaka Yoda, Jiyong Zhao, Michael Y Hu, Ercan E Alp, Vasily S Oganesyan, Nick E Le Brun, Stephen P Cramer
The reaction of protein-bound iron-sulfur (Fe-S) clusters with nitric oxide (NO) plays key roles in NO-mediated toxicity and signaling. Elucidation of the mechanism of the reaction of NO with DNA regulatory proteins that contain Fe-S clusters has been hampered by a lack of information about the nature of the iron-nitrosyl products formed. Herein, we report nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations that identify NO reaction products in WhiD and NsrR, regulatory proteins that use a [4Fe-4S] cluster to sense NO...
October 25, 2016: Angewandte Chemie
Matthew J Gazzellone, Mehdi Zarrei, Christie L Burton, Susan Walker, Mohammed Uddin, S M Shaheen, Julie Coste, Rageen Rajendram, Reva J Schachter, Marlena Colasanto, Gregory L Hanna, David R Rosenberg, Noam Soreni, Kate D Fitzgerald, Christian R Marshall, Janet A Buchanan, Daniele Merico, Paul D Arnold, Stephen W Scherer
BACKGROUND: Obsessive-compulsive disorder (OCD) is a heterogeneous neuropsychiatric condition, thought to have a significant genetic component. When onset occurs in childhood, affected individuals generally exhibit different characteristics from adult-onset OCD, including higher prevalence in males and increased heritability. Since neuropsychiatric conditions are associated with copy number variations (CNVs), we considered their potential role in the etiology of OCD. METHODS: We genotyped 307 unrelated pediatric probands with idiopathic OCD (including 174 that were part of complete parent-child trios) and compared their genotypes with those of 3861 population controls, to identify rare CNVs (<0...
2016: Journal of Neurodevelopmental Disorders
Jinghui Zhang, Kelly McCastlain, Hiroki Yoshihara, Beisi Xu, Yunchao Chang, Michelle L Churchman, Gang Wu, Yongjin Li, Lei Wei, Ilaria Iacobucci, Yu Liu, Chunxu Qu, Ji Wen, Michael Edmonson, Debbie Payne-Turner, Kerstin B Kaufmann, Shin-Ichiro Takayanagi, Erno Wienholds, Esmé Waanders, Panagiotis Ntziachristos, Sofia Bakogianni, Jingjing Wang, Iannis Aifantis, Kathryn G Roberts, Jing Ma, Guangchun Song, John Easton, Heather L Mulder, Xiang Chen, Scott Newman, Xiaotu Ma, Michael Rusch, Pankaj Gupta, Kristy Boggs, Bhavin Vadodaria, James Dalton, Yanling Liu, Marcus L Valentine, Li Ding, Charles Lu, Robert S Fulton, Lucinda Fulton, Yashodhan Tabib, Kerri Ochoa, Meenakshi Devidas, Deqing Pei, Cheng Cheng, Jun Yang, William E Evans, Mary V Relling, Ching-Hon Pui, Sima Jeha, Richard C Harvey, I-Ming L Chen, Cheryl L Willman, Guido Marcucci, Clara D Bloomfield, Jessica Kohlschmidt, Krzysztof Mrózek, Elisabeth Paietta, Martin S Tallman, Wendy Stock, Matthew C Foster, Janis Racevskis, Jacob M Rowe, Selina Luger, Steven M Kornblau, Sheila A Shurtleff, Susana C Raimondi, Elaine R Mardis, Richard K Wilson, John E Dick, Stephen P Hunger, Mignon L Loh, James R Downing, Charles G Mullighan
Chromosomal rearrangements deregulating hematopoietic transcription factors are common in acute lymphoblastic leukemia (ALL). Here we show that deregulation of the homeobox transcription factor gene DUX4 and the ETS transcription factor gene ERG is a hallmark of a subtype of B-progenitor ALL that comprises up to 7% of B-ALL. DUX4 rearrangement and overexpression was present in all cases and was accompanied by transcriptional deregulation of ERG, expression of a novel ERG isoform, ERGalt, and frequent ERG deletion...
October 24, 2016: Nature Genetics
Diane Lefaudeux, Bertrand De Meulder, Matthew J Loza, Nancy Peffer, Anthony Rowe, Frédéric Baribaud, Aruna T Bansal, Rene Lutter, Ana R Sousa, Julie Corfield, Ioannis Pandis, Per S Bakke, Massimo Caruso, Pascal Chanez, Sven-Erik Dahlén, Louise J Fleming, Stephen J Fowler, Ildiko Horvath, Norbert Krug, Paolo Montuschi, Marek Sanak, Thomas Sandstrom, Dominic E Shaw, Florian Singer, Peter J Sterk, Graham Roberts, Ian M Adcock, Ratko Djukanovic, Charles Auffray, Kian F Chung
BACKGROUND: Asthma is a heterogeneous disease in which there is a differential response to asthma treatments. This heterogeneity needs to be evaluated so that a personalised management approach can be provided. OBJECTIVES: We stratified patients with moderate-to-severe asthma based on clinico-physiological parameters and performed an -omics analysis of sputum. METHODS: Partition-around-medoid clustering was applied to a training set of 266 asthma participants from the European U-BIOPRED adult cohort using 8 pre-specified clinic-physiological variables...
October 20, 2016: Journal of Allergy and Clinical Immunology
Julia I Ellyard, Rebekka Jerjen, Jaime L Martin, Adrian Lee, Matthew A Field, Simon H Jiang, Jean Cappello, Svenja K Naumann, T Daniel Andrews, Hamish S Scott, Marco G Casarotto, Christopher C Goodnow, Jeffrey Chaitow, Virginia Pascual, Paul Hertzog, Stephen I Alexander, Matthew C Cook, Carola G Vinuesa
No abstract text is available yet for this article.
February 2016: Pathology
Stephen Matthew Quinnan
Obtaining optimal results in the treatment of extraarticular distal tibia fractures can be challenging. Plate and screw and intramedullary fixation have proven to be effective treatments, but are associated with significant complication rates when used for open fractures and patient with severe medical comorbidities. External fixation is a third alternative that is less often employed, but provides a very effective means of treatment. Circular external fixation offers great flexibility in obtaining anatomic alignment and stable fixation for even the most challenging distal tibia fractures...
November 2016: Journal of Orthopaedic Trauma
Yanita McLeay, Stephen R Stannard, Toby Mundel, Andrew Foskett, Matthew Barnes
This study was designed to investigate the effects of alcohol consumption on recovery of muscle force when consumed immediately post-exercise in young females. Eight young women completed 300 maximal eccentric actions of the quadriceps femoris muscle on an isokinetic dynamometer on two occasions in a randomized, cross-over design after which an alcoholic beverage (0.88g ethanol/kg body weight) or an iso-caloric placebo was consumed. Maximal isokinetic (concentric and eccentric) torque and isometric tension produced across the knee were measured in both the exercised and control leg pre-damage, 36h-post, and 60h-post damage...
October 21, 2016: International Journal of Sport Nutrition and Exercise Metabolism
Jie Yang, Markus Guehr, Xiaozhe Shen, Renkai Li, Theodore Vecchione, Ryan Coffee, Jeff Corbett, Alan Fry, Nick Hartmann, Carsten Hast, Kareem Hegazy, Keith Jobe, Igor Makasyuk, Joseph Robinson, Matthew S Robinson, Sharon Vetter, Stephen Weathersby, Charles Yoneda, Xijie Wang, Martin Centurion
Observing the motion of the nuclear wave packets during a molecular reaction, in both space and time, is crucial for understanding and controlling the outcome of photoinduced chemical reactions. We have imaged the motion of a vibrational wave packet in isolated iodine molecules using ultrafast electron diffraction with relativistic electrons. The time-varying interatomic distance was measured with a precision 0.07 Å and temporal resolution of 230 fs full width at half maximum. The method is not only sensitive to the position but also the shape of the nuclear wave packet...
October 7, 2016: Physical Review Letters
Nir Hirshoren, Olivia Ruskin, Tsien Fua, Stephen Kleid, Matthew Magarey, Benjamin Dixon
BACKGROUND: Transoral robotic surgery (TORS) is now a well-validated technique for resection of head and neck cancers. Benefits include reduced patient morbidity, swallowing preservation and rationalization of adjuvant therapies. METHODS: This was a single-centre, retrospective review of 35 patients who underwent TORS of oro-, retro- and parapharyngeal tumours between March 2014 and August 2015. Outcome measures included resection margins, swallowing function and impact on post-operative radiotherapy...
October 21, 2016: ANZ Journal of Surgery
Stephen J Hile, Matthew B Feldman, Amanda R Raker, Mary K Irvine
PURPOSE: To collect information that will inform the development of an intervention to support the maintenance of HIV-related health-promoting behaviors. DESIGN: Focused, in-depth individual and group interviews. SETTING: The New York City (NYC) Department of Health and Mental Hygiene (DOHMH) and DOHMH-funded community-based organizations that primarily serve low-income people living with HIV within the five boroughs of NYC. PARTICIPANTS: A total of 42 individuals who had participated in The Positive Life Workshop-an HIV self-management intervention adapted and implemented by the NYC DOHMH...
October 20, 2016: American Journal of Health Promotion: AJHP
Evangelos Vassos, Marta Di Forti, Jonathan Coleman, Conrad Iyegbe, Diana Prata, Jack Euesden, Paul O'Reilly, Charles Curtis, Anna Kolliakou, Hamel Patel, Stephen Newhouse, Matthew Traylor, Olesya Ajnakina, Valeria Mondelli, Tiago Reis Marques, Poonam Gardner-Sood, Katherine J Aitchison, John Powell, Zerrin Atakan, Kathryn E Greenwood, Shubulade Smith, Khalida Ismail, Carmine Pariante, Fiona Gaughran, Paola Dazzan, Hugh S Markus, Anthony S David, Cathryn M Lewis, Robin M Murray, Gerome Breen
BACKGROUND: Polygenic risk scores (PRSs) have successfully summarized genome-wide effects of genetic variants in schizophrenia with significant predictive power. In a clinical sample of first-episode psychosis (FEP) patients, we estimated the ability of PRSs to discriminate case-control status and to predict the development of schizophrenia as opposed to other psychoses. METHODS: The sample (445 case and 265 control subjects) was genotyped on the Illumina HumanCore Exome BeadChip with an additional 828 control subjects of African ancestry genotyped on the Illumina Multi-Ethnic Genotyping Array...
August 6, 2016: Biological Psychiatry
Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B Gerstein, Andrew F Hill, Robert R Kitchen, Jan Lötvall, Tushar Patel, Dena C Procaccini, Peter Quesenberry, Joel Rozowsky, Robert L Raffai, Aleksandra Shypitsyna, Andrew I Su, Clotilde Théry, Kasey Vickers, Marca H M Wauben, Suresh Mathivanan, Aleksandar Milosavljevic, Louise C Laurent
BACKGROUND: To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research. METHODS: By following a consensus-building process, we have worked with several academic societies/consortia, including ERCC, ISEV, and ASEMV, to identify and approve a set of exRNA and extracellular vesicle-related terms and relationships that have been incorporated into GO...
April 12, 2016: Journal of Biomedical Semantics
Denise D Walker, Robert S Stephens, Claire E Blevins, Kelsey E Banes, Lauren Matthews, Roger A Roffman
OBJECTIVE: Brief interventions for adolescent marijuana users offered in schools reach users who would not otherwise present for treatment. The current study builds on previous trials of a school-based, 2-session motivational enhancement therapy (MET) intervention by adding periodic, brief motivational check-ins to reinforce gains and bolster motivation. METHOD: Adolescent participants were randomly assigned to a motivational check-in (MCI; n = 128) or assessment-only check-in (ACI; n = 124) comparison condition...
November 2016: Journal of Consulting and Clinical Psychology
Matthew T Kaufman, Jeffrey S Seely, David Sussillo, Stephen I Ryu, Krishna V Shenoy, Mark M Churchland
Neural activity in monkey motor cortex (M1) and dorsal premotor cortex (PMd) can reflect a chosen movement well before that movement begins. The pattern of neural activity then changes profoundly just before movement onset. We considered the prediction, derived from formal considerations, that the transition from preparation to movement might be accompanied by a large overall change in the neural state that reflects when movement is made rather than which movement is made. Specifically, we examined "components" of the population response: time-varying patterns of activity from which each neuron's response is approximately composed...
July 2016: ENeuro
Xiang Yu, Matthew R Willmann, Stephen J Anderson, Brian D Gregory
RNA turnover is necessary for controlling proper mRNA levels post-transcriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5' end to the 3' end, such as XRN4, or in the opposite direction by the multi-subunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of co-translational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames...
October 7, 2016: Plant Cell
Matthew Stephens
SummaryWe introduce a new Empirical Bayes approach for large-scale hypothesis testing, including estimating false discovery rates (FDRs), and effect sizes. This approach has two key differences from existing approaches to FDR analysis. First, it assumes that the distribution of the actual (unobserved) effects is unimodal, with a mode at 0. This "unimodal assumption" (UA), although natural in many contexts, is not usually incorporated into standard FDR analysis, and we demonstrate how incorporating it brings many benefits...
October 17, 2016: Biostatistics
Ying Ying Leung, Julian Thumboo, Matthew Rouse, Stephen P McKenna
BACKGROUND: To develop Singapore Chinese and English versions of the Psoriatic Arthritis Quality of Life (PsAQoL) scale that were equivalent to and met the same psychometric and acceptability standards as the original UK measure. METHODS: Translation of the original PsAQoL into contextualised English and Chinese versions for use in Singapore was performed by professional and lay translation panels. Ten Chinese speaking and ten English speaking local patients were interviewed to assess face and content validity...
October 18, 2016: BMC Musculoskeletal Disorders
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