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Matthew Stephens

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https://www.readbyqxmd.com/read/28333934/visualizing-the-structure-of-rna-seq-expression-data-using-grade-of-membership-models
#1
Kushal K Dey, Chiaowen Joyce Hsiao, Matthew Stephens
Grade of membership models, also known as "admixture models", "topic models" or "Latent Dirichlet Allocation", are a generalization of cluster models that allow each sample to have membership in multiple clusters. These models are widely used in population genetics to model admixed individuals who have ancestry from multiple "populations", and in natural language processing to model documents having words from multiple "topics". Here we illustrate the potential for these models to cluster samples of RNA-seq gene expression data, measured on either bulk samples or single cells...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28333548/utility-of-pet-ct-after-cryoablation-for-early-identification-of-local-tumor-progression-in-osseous-metastatic-disease
#2
Ann T Packard, Stephen M Broski, Matthew R Callstrom, Thomas D Atwell, Grant D Schmit, John J Schmitz, Jonathan M Morris, Christopher H Hunt, A Nicholas Kurup
OBJECTIVE: The purpose of this study is to evaluate the utility of combined PET/CT for the detection of early local tumor progression after cryoablation of bone metastases. MATERIALS AND METHODS: A retrospective single-institution review revealed 61 consecutive patients with 80 separate bone metastases treated with cryoablation who were evaluated with a preablation PET/CT and at least two postablation PET/CT examinations between September 2007 and July 2015. Patients were excluded if they had local therapy or pathologic fracture after ablation...
March 23, 2017: AJR. American Journal of Roentgenology
https://www.readbyqxmd.com/read/28325313/a-structural-basis-for-the-amphiphilic-character-of-alginates-implications-for-membrane-fouling
#3
Matthew B Stewart, Darli T Myat, Michael Kuiper, Richard J Manning, Stephen R Gray, John D Orbell
Ostensibly hydrophilic alginates are known to foul hydrophobic membranes, under various conditions. Here, controlled experiments have been conducted at high and low pH on the fouling of a polypropylene membrane by alginate and the results suggest that the observed fouling is due to an intrinsic property of the alginate. Thus quantum chemical calculations on the M and G monomers of alginate reveal that M adopts an equilibrium geometry that is hydrophilic on one face and hydrophobic on the other, i.e. is potentially amphiphilic...
May 15, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28325276/limiting-thymic-precursor-supply-increases-the-risk-of-lymphoid-malignancy-in-murine-x-linked-severe-combined-immunodeficiency
#4
Samantha L Ginn, Claus V Hallwirth, Sophia H Y Liao, Erdahl T Teber, Jonathan W Arthur, Jianmin Wu, Hong Ching Lee, Szun S Tay, Min Hu, Roger R Reddel, Matthew P McCormack, Adrian J Thrasher, Marina Cavazzana, Stephen I Alexander, Ian E Alexander
In early gene therapy trials for SCID-X1, using γ-retroviral vectors, T cell leukemias developed in a subset of patients secondary to insertional proto-oncogene activation. In contrast, we have reported development of T cell leukemias in SCID-X1 mice following lentivirus-mediated gene therapy independent of insertional mutagenesis. A distinguishing feature in our study was that only a proportion of transplanted γc-deficient progenitors were transduced and therefore competent for reconstitution. We hypothesized that reconstitution of SCID-X1 mice with limiting numbers of hematopoietic progenitors might be a risk factor for lymphoid malignancy...
March 17, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28323699/use-of-nanocrystalline-hydroxyapatite-with-autologous-bma-and-local-bone-in-the-lumbar-spine-a-retrospective-ct-analysis-of-posterolateral-fusion-results
#5
Stephen Robbins, Carl Lauryssen, Matthew N Songer
STUDY DESIGN: A retrospective, multicenter, medical record review and independent analysis of computed tomographic scans was performed in 46 patients to determine radiographic arthrodesis rates after 1-segment, 2-segment, or 3-segment instrumented posterolateral fusions (PLF) using autograft, bone marrow aspirate (BMA), and a nanocrystalline hydroxyapatite bone void filler (nHA). OBJECTIVE: To determine the radiographic arthrodesis rates after instrumented lumbar PLF using local autograft, BMA, and nHA...
April 2017: Clinical Spine Surgery
https://www.readbyqxmd.com/read/28322596/motor-imagery-during-action-observation-increases-eccentric-hamstring-force-an-acute-non-physical-intervention
#6
Matthew Scott, Stephen Taylor, Paul Chesterton, Stefan Vogt, Daniel Lloyd Eaves
PURPOSE: Rehabilitation professionals typically use motor imagery (MI) or action observation (AO) to increase physical strength for injury prevention and recovery. Here we compared hamstring force gains for MI during AO (AO + MI) against two pure MI training groups. MATERIALS AND METHODS: Over a 3-week intervention physically fit adults imagined Nordic hamstring exercises in both legs and synchronized this with a demonstration of the same action (AO + MI), or they purely imagined this action (pure MI), or imagined upper-limb actions (pure MI-control)...
March 21, 2017: Disability and Rehabilitation
https://www.readbyqxmd.com/read/28314478/osteoinductive-effects-of-glyceollins-on-adult-mesenchymal-stromal-stem-cells-from-adipose-tissue-and-bone-marrow
#7
Marjorie E Bateman, Amy L Strong, Ryan S Hunter, Melyssa R Bratton, Rajesh Komati, Jayalakshmi Sridhar, Kevin E Riley, Guangdi Wang, Daniel J Hayes, Stephen M Boue, Matthew E Burow, Bruce A Bunnell
BACKGROUND: While current therapies for osteoporosis focus on reducing bone resorption, the development of therapies to regenerate bone may also be beneficial. Promising anabolic therapy candidates include phytoestrogens, such as daidzein, which effectively induce osteogenesis of adipose-derived stromal cells (ASCs) and bone marrow stromal cells (BMSCs). PURPOSE: To investigate the effects of glyceollins, structural derivatives of daidzein, on osteogenesis of ASCs and BMSCs...
April 15, 2017: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
https://www.readbyqxmd.com/read/28302712/improved-survival-after-acute-graft-vs-host-disease-diagnosis-in-the-modern-era
#8
Hanna J Khoury, Tao Wang, Michael T Hemmer, Daniel Couriel, Amin Alousi, Corey Cutler, Mahmoud Aljurf, Joseph H Antin, Mouhab Ayas, Minoo Battiwalla, Jean-Yves Cahn, Mitchell Cairo, Yi-Bin Chen, Robert Peter Gale, Shahrukh Hashmi, Robert J Hayashi, Madan Jagasia, Mark Juckett, Rammurti T Kamble, Mohamed Kharfan-Dabaja, Mark Litzow, Navneet Majhail, Alan Miller, Taiga Nishihori, Muna Qayed, Helene Schoemans, Harry C Schouten, Gérard Socié, Jan Storek, Leo Verdonck, Ravi Vij, William A Wood, Lolie Yu, Rodrigo Martino, Matthew Carabasi, Christopher Dandoy, Usama Gergis, Peiman Hematti, Melham Solh, Kareem Jamani, Leslie Lehmann, Bipin Savani, Kirk R Schultz, Baldeep M Wirk, Stephen Spellman, Mukta Arora, Joseph Pidala
Acute graft vs. host disease remains a major threat to successful outcome after allogeneic hematopoietic cell transplantation. While improvements in treatment and supportive care have occurred, it is unknown whether these advances have resulted in improved outcome specifically among those diagnosed with acute graft vs. host disease. We examined outcome following diagnosis of grade II-IV acute graft vs. host disease according to time period, and examine effects according to original graft vs. host disease prophylaxis regimen and maximum overall grade of acute GVHD...
March 16, 2017: Haematologica
https://www.readbyqxmd.com/read/28297711/bumblebee-family-lineage-survival-is-enhanced-in-high-quality-landscapes
#9
Claire Carvell, Andrew F G Bourke, Stephanie Dreier, Stephen N Freeman, Sarah Hulmes, William C Jordan, John W Redhead, Seirian Sumner, Jinliang Wang, Matthew S Heard
Insect pollinators such as bumblebees (Bombus spp.) are in global decline. A major cause of this decline is habitat loss due to agricultural intensification. A range of global and national initiatives aimed at restoring pollinator habitats and populations have been developed. However, the success of these initiatives depends critically upon understanding how landscape change affects key population-level parameters, such as survival between lifecycle stages, in target species. This knowledge is lacking for bumblebees, because of the difficulty of systematically finding and monitoring colonies in the wild...
March 15, 2017: Nature
https://www.readbyqxmd.com/read/28295614/body-mass-index-and-rural-status-on-self-reported-health-in-older-adults-2004-2013-medicare-expenditure-panel-survey
#10
John A Batsis, Karen L Whiteman, Matthew C Lohman, Emily A Scherer, Stephen J Bartels
PURPOSE: To ascertain whether rural status impacts self-reported health and whether the effect of rural status on self-reported health differs by obesity status. METHODS: We identified 22,307 subjects aged ≥60 from the Medical Expenditure Panel Survey 2004-2013. Body mass index (BMI) was categorized as underweight, normal, overweight, or obese. Physical and mental component scores of the Short Form-12 assessed self-reported health status. Rural/urban status was defined using metropolitan statistical area...
March 15, 2017: Journal of Rural Health
https://www.readbyqxmd.com/read/28291233/lysogeny-in-nature-mechanisms-impact-and-ecology-of-temperate-phages
#11
Cristina Howard-Varona, Katherine R Hargreaves, Stephen T Abedon, Matthew B Sullivan
Viruses that infect bacteria (phages) can influence bacterial community dynamics, bacterial genome evolution and ecosystem biogeochemistry. These influences differ depending on whether phages establish lytic, chronic or lysogenic infections. Although the first two produce virion progeny, with lytic infections resulting in cell destruction, phages undergoing lysogenic infections replicate with cells without producing virions. The impacts of lysogeny are numerous and well-studied at the cellular level, but ecosystem-level consequences remain underexplored compared to those of lytic infections...
March 14, 2017: ISME Journal
https://www.readbyqxmd.com/read/28291052/first-line-antiretroviral-treatment-outcomes-and-durability-in-hiv-infectedchildren-treatedthrough-theuniversal-coverage-health-program-in-thailand
#12
Sirinya Teeraananchai, Torsak Bunupuradah, Thanyawee Puthanakit, Stephen J Kerr, Kiat Ruxrungtham, Suchada Chaivooth, Sorakij Bhakeecheep, Matthew G Law, Kulkanya Chokephaibulkit
BACKGROUND: We assessed the treatment outcomes on first-line antiretroviral therapy (ART), and factors associated with switching regimen in HIV-infected children treated through the universal coverage health program (UC) in Thailand. METHODS: Children aged <15 years at ART initiation who had been receiving ART for at least 6 months between 2008 and 2014 through UC were included in the analysis. The Kaplan-Meier method was used to estimate immunological recovery (IMR), immunologic failure (IMF) and virologic failure (VF)...
March 10, 2017: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/28290723/accuracy-of-18-f-fdg-pet-ct-to-detect-bone-marrow-clearance-in-patients-with-peripheral-t-cell-lymphoma-tissue-remains-the-issue
#13
Anthony Q Pham, Stephen M Broski, Thomas M Habermann, Dragan Jevremovic, Gregory A Wiseman, Andrew L Feldman, Matthew J Maurer, Kay M Ristow, Thomas E Witzig
Staging of peripheral T-cell non-Hodgkin lymphoma (PTCL) is determined by 18-F FDG PET scan and bone marrow biopsy. This study addressed the accuracy of PET at detecting bone marrow (BM) involvement at restaging in patients with known involvement pretreatment. We identified patients with biopsy proven BM PTCL at diagnosis and concomitant BM and PET at the end of therapy. Pre-treatment PET demonstrated 50% (8/16) had a false-negative PET scan of the BM. After induction, repeat biopsy revealed 62.5% (10/16) with BM involvement...
March 14, 2017: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/28287405/t-cells-control-the-generation-of-nanomolar-affinity-anti-glycan-antibodies
#14
Zinaida Polonskaya, Shenglou Deng, Anita Sarkar, Lisa Kain, Marta Comellas-Aragones, Craig S McKay, Katarzyna Kaczanowska, Marie Holt, Ryan McBride, Valle Palomo, Kevin M Self, Seth Taylor, Adriana Irimia, Sanjay R Mehta, Jennifer M Dan, Matthew Brigger, Shane Crotty, Stephen P Schoenberger, James C Paulson, Ian A Wilson, Paul B Savage, M G Finn, Luc Teyton
Vaccines targeting glycan structures at the surface of pathogenic microbes must overcome the inherent T cell-independent nature of immune responses against glycans. Carbohydrate conjugate vaccines achieve this by coupling bacterial polysaccharides to a carrier protein that recruits heterologous CD4 T cells to help B cell maturation. Yet they most often produce low- to medium-affinity immune responses of limited duration in immunologically fit individuals and disappointing results in the elderly and immunocompromised patients...
March 13, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28284533/sublingual-immunotherapy-a-focused-allergen-immunotherapy-practice-parameter-update
#15
Matthew Greenhawt, John Oppenheimer, Michael Nelson, Hal Nelson, Richard Lockey, Phil Lieberman, Anna Nowak-Wegrzyn, Anju Peters, Charlotte Collins, David I Bernstein, Joann Blessing-Moore, David Khan, David Lang, Richard A Nicklas, Jay M Portnoy, Christopher R Randolph, Diane E Schuller, Sheldon L Spector, Stephen A Tilles, Dana Wallace
No abstract text is available yet for this article.
March 2017: Annals of Allergy, Asthma & Immunology
https://www.readbyqxmd.com/read/28283060/decoupling-the-functional-pleiotropy-of-stem-cell-factor-by-tuning-c-kit-signaling
#16
Chia Chi M Ho, Akanksha Chhabra, Philipp Starkl, Peter-John Schnorr, Stephan Wilmes, Ignacio Moraga, Hye-Sook Kwon, Nicolas Gaudenzio, Riccardo Sibilano, Tom S Wehrman, Milica Gakovic, Jonathan T Sockolosky, Matthew R Tiffany, Aaron M Ring, Jacob Piehler, Irving L Weissman, Stephen J Galli, Judith A Shizuru, K Christopher Garcia
Most secreted growth factors and cytokines are functionally pleiotropic because their receptors are expressed on diverse cell types. While important for normal mammalian physiology, pleiotropy limits the efficacy of cytokines and growth factors as therapeutics. Stem cell factor (SCF) is a growth factor that acts through the c-Kit receptor tyrosine kinase to elicit hematopoietic progenitor expansion but can be toxic when administered in vivo because it concurrently activates mast cells. We engineered a mechanism-based SCF partial agonist that impaired c-Kit dimerization, truncating downstream signaling amplitude...
March 9, 2017: Cell
https://www.readbyqxmd.com/read/28278486/differences-between-gait-on-stairs-and-flat-surfaces-in-relation-to-fall-risk-and-future-falls
#17
Kejia Wang, Kim Delbaere, Matthew Brodie, Nigel Lovell, Lauren Kark, Stephen Lord, Stephen Redmond
We used body-worn inertial sensors to quantify differences in semi-free-living gait between stairs and on normal flat ground in older adults, and investigated the utility of assessing gait on these terrains for predicting the occurrence of multiple falls. 82 community-dwelling older adults wore two inertial sensors, on the lower back and the right ankle, during several bouts of walking on flat surfaces and up and down stairs, in between rests and activities of daily living. Derived from the vertical acceleration at the lower back, step rate was calculated from the signal's fundamental frequency...
March 3, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28277954/physiological-responses-to-fasting-and-estivation-for-the-three-toed-amphiuma-amphiuma-tridactylum
#18
Matthew E Smith, Stephen M Secor
Species of Amphiuma enter a state of subterranean estivation with the drying of their aquatic habitat. Characteristic of amphibian fasting and estivation is an initial depression of metabolism and tissue mass and function with fasting, followed by a more pronounced adaptive decrease in metabolism and tissue function with estivation. We hypothesized that Amphiuma likewise experiences a two-stage set of responses to estivation. Therefore, we examined the physiological responses of the three-toed amphiuma (Amphiuma tridactylum) to fasting and estivation treatments...
March 2017: Physiological and Biochemical Zoology: PBZ
https://www.readbyqxmd.com/read/28273481/matching-dietary-amino-acid-balance-to-the-in-silico-translated-exome-optimizes-growth-and-reproduction-without-cost-to-lifespan
#19
Matthew D W Piper, George A Soultoukis, Eric Blanc, Andrea Mesaros, Samantha L Herbert, Paula Juricic, Xiaoli He, Ilian Atanassov, Hanna Salmonowicz, Mingyao Yang, Stephen J Simpson, Carlos Ribeiro, Linda Partridge
Balancing the quantity and quality of dietary protein relative to other nutrients is a key determinant of evolutionary fitness. A theoretical framework for defining a balanced diet would both reduce the enormous workload to optimize diets empirically and represent a breakthrough toward tailoring diets to the needs of consumers. Here, we report a simple and powerful in silico technique that uses the genome information of an organism to define its dietary amino acid requirements. We show for the fruit fly Drosophila melanogaster that such "exome-matched" diets are more satiating, enhance growth, and increase reproduction relative to non-matched diets...
March 7, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28273385/effect-of-aerosolized-antipseudomonals-on-pseudomonas-positivity-and-bronchiolitis-obliterans-syndrome-after-lung-transplantation
#20
Cody A Moore, Joseph M Pilewski, Raman Venkataraman, Keven M Robinson, Matthew R Morrell, Stephen R Wisniewski, Adriana Zeevi, John F McDyer, Christopher R Ensor
PURPOSE: To describe the effects of aerosolized antipseudomonals (AAP) on Pseudomonas (PS) culture positivity, bronchiolitis obliterans syndrome (BOS), and acute cellular rejection (ACR) in lung transplant recipients (LTRs). METHODS: Single-center, retrospective cohort study of adult LTRs treated with either AAP for ≥28 days vs no AAP therapy or AAP therapy <28 days, indexed to a matched median date post lung transplantation (LT). Primary outcome was freedom from PS positivity by positive bronchoalveolar lavage (BAL) or bronchial wash at 1 year...
March 8, 2017: Transplant Infectious Disease: An Official Journal of the Transplantation Society
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