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Andy Clark

Joshua K Sabari, Michael Offin, Dennis Stephens, Andy Ni, Adrian Lee, Nick Pavlakis, Stephen Clarke, Connie I Diakos, Sutirtha Datta, Nidhi Tandon, Andres Martinez, Mackenzie L Myers, Alex Makhnin, Ysleni Leger, Helena A Yu, Paul K Paik, Jamie E Chaft, Mark G Kris, Jeong O Jeon, Laetitia A Borsu, Marc Ladanyi, Maria E Arcila, Jennifer Hernandez, Samantha Henderson, Tristan Shaffer, Kavita Garg, Dan DiPasquo, Christopher K Raymond, Lee P Lim, Mark Li, Matthew D Hellmann, Alexander Drilon, Gregory J Riely, Valerie W Rusch, David R Jones, Andreas Rimner, Charles M Rudin, James M Isbell, Bob T Li
Background: Liquid biopsy for plasma circulating tumor DNA (ctDNA) next-generation sequencing (NGS) is commercially available and increasingly adopted in clinical practice despite a paucity of prospective data to support its use. Methods: Patients with advanced lung cancers who had no known oncogenic driver or developed resistance to current targeted therapy (n = 210) underwent plasma NGS, targeting 21 genes. A subset of patients had concurrent tissue NGS testing using a 468-gene panel (n = 106)...
November 28, 2018: Journal of the National Cancer Institute
Jeffry G Weers, Yoen-Ju Son, Mark Glusker, Alfred Haynes, Daniel Huang, Nani Kadrichu, John Le, Xue Li, Richard Malcolmson, Danforth P Miller, Thomas E Tarara, Keith Ung, Andy Clark
This review discusses how advances in formulation and device design can be utilized to dramatically improve lung targeting and dose consistency relative to current marketed dry powder inhalers (DPIs). Central to the review is the development of engineered particles that effectively bypass deposition in the upper respiratory tract (URT). This not only reduces the potential for off-target effects but it also reduces variability in dose delivery to the lungs resulting from anatomical differences in the soft tissue in the mouth and throat...
November 27, 2018: Journal of Aerosol Medicine and Pulmonary Drug Delivery
Charlotte K Brierley, Francesca M Jones, Katharine Hanlon, Andy J Peniket, Chris Hatton, Graham P Collins, Anna Schuh, Patrick Medd, Andrew Clark, Janice Ward, Sridar Chaganti, Ram Malladi, Anne Parker, Charles Craddock, Robert Danby, Vanderson Rocha
Allogeneic haematopoietic stem cell transplant (allo-HSCT) offers potentially curative therapy for patients with relapsed/refractory lymphoid malignancies. Reduced-intensity conditioning (RIC) with Alemtuzumab reduces transplant-related mortality and graft-versus-host disease (GvHD), but may be associated with increased risk of relapse. With the aim of studying the effect of GVHD and donor lymphocyte infusions (DLI) on relapse, we performed a retrospective study of 288 patients (57% non-Hodgkin lymphoma, 24% Hodgkin lymphoma and 19% chronic lymphocytic leukaemia; 58% were relapsed/refractory) who underwent RIC-Alemtuzumab-HSCT between 2000 and 2012...
November 22, 2018: British Journal of Haematology
Andy Madrid, Kirk J Hogan, Ligia A Papale, Lindsay R Clark, Sanjay Asthana, Sterling C Johnson, Reid S Alisch
Differentially methylated positions (DMPs) between persons with and without late-onset Alzheimer's disease (LOAD) were observed at 477 of 769,190 loci in a plurality of genes. Of these, 17 were shared with DMPs identified using clinical LOAD markers analyzed independently as continuous variables comprising Rey Auditory Verbal Learning Test scores, cerebrospinal fluid total tau (t-tau) and phosphorylated tau 181 (p-tau181) levels, and t-tau/Aβ1-42 (Aβ42), p-tau181/Aβ42, and Aβ42/Aβ1-40 (Aβ40) ratios. In patients with LOAD, 12 of the shared 17 DMPs were hypomethylated in B3GALT4 (Beta-1,3-galatcosyltransferase 4) (EC 2...
2018: Journal of Alzheimer's Disease: JAD
Benjamin A Chalmers, Hui Xing, Sevan Houston, Charlotte Clark, Sussan Ghassabian, Andy Kuo, Benjamin Cao, Andrea Reitsma, Cody-Ellen P Murray, Jeanette E Stok, Glen M Boyle, Carly J Pierce, Stuart W Littler, David A Winkler, Paul V Bernhardt, Cielo Pasay, James J De Voss, James McCarthy, Peter G Parsons, Gimme H Walter, Maree T Smith, Helen M Cooper, Susan K Nilsson, John Tsanaktsidis, G Paul Savage, Craig M Williams
No abstract text is available yet for this article.
July 9, 2018: Angewandte Chemie
Philippe Jousset, Thomas Reinsch, Trond Ryberg, Hanna Blanck, Andy Clarke, Rufat Aghayev, Gylfi P Hersir, Jan Henninges, Michael Weber, Charlotte M Krawczyk
Natural hazard prediction and efficient crust exploration require dense seismic observations both in time and space. Seismological techniques provide ground-motion data, whose accuracy depends on sensor characteristics and spatial distribution. Here we demonstrate that dynamic strain determination is possible with conventional fibre-optic cables deployed for telecommunication. Extending recently distributed acoustic sensing (DAS) studies, we present high resolution spatially un-aliased broadband strain data...
July 3, 2018: Nature Communications
John A Ford, Andy Jones, Geoff Wong, Allan Clark, Tom Porter, Nick Steel
BACKGROUND: Realist approaches seek to answer questions such as 'how?', 'why?', 'for whom?', 'in what circumstances?' and 'to what extent?' interventions 'work' using context-mechanism-outcome (CMO) configurations. Quantitative methods are not well-established in realist approaches, but structural equation modelling (SEM) may be useful to explore CMO configurations. Our aim was to assess the feasibility and appropriateness of SEM to explore CMO configurations and, if appropriate, make recommendations based on our access to primary care research...
June 19, 2018: BMC Medical Research Methodology
Zev N Kronenberg, Ian T Fiddes, David Gordon, Shwetha Murali, Stuart Cantsilieris, Olivia S Meyerson, Jason G Underwood, Bradley J Nelson, Mark J P Chaisson, Max L Dougherty, Katherine M Munson, Alex R Hastie, Mark Diekhans, Fereydoun Hormozdiari, Nicola Lorusso, Kendra Hoekzema, Ruolan Qiu, Karen Clark, Archana Raja, AnneMarie E Welch, Melanie Sorensen, Carl Baker, Robert S Fulton, Joel Armstrong, Tina A Graves-Lindsay, Ahmet M Denli, Emma R Hoppe, PingHsun Hsieh, Christopher M Hill, Andy Wing Chun Pang, Joyce Lee, Ernest T Lam, Susan K Dutcher, Fred H Gage, Wesley C Warren, Jay Shendure, David Haussler, Valerie A Schneider, Han Cao, Mario Ventura, Richard K Wilson, Benedict Paten, Alex Pollen, Evan E Eichler
Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants...
June 8, 2018: Science
Kylie S Foo, Miia L Lehtinen, Chuen Yan Leung, Xiaojun Lian, Jiejia Xu, Wendy Keung, Lin Geng, Terje R S Kolstad, Sebastian Thams, Andy On-Tik Wong, Nicodemus Wong, Kristine Bylund, Chikai Zhou, Xiaobing He, Shao-Bo Jin, Jonathan Clarke, Urban Lendahl, Ronald A Li, William E Louch, Kenneth R Chien
The generation of human pluripotent stem cell (hPSC)-derived ventricular progenitors and their assembly into a 3-dimensional in vivo functional ventricular heart patch has remained an elusive goal. Herein, we report the generation of an enriched pool of hPSC-derived ventricular progenitors (HVPs), which can expand, differentiate, self-assemble, and mature into a functional ventricular patch in vivo without the aid of any gel or matrix. We documented a specific temporal window, in which the HVPs will engraft in vivo...
July 5, 2018: Molecular Therapy: the Journal of the American Society of Gene Therapy
Ryan J Longman, Thomas W Giambelluca, Michael A Nullet, Abby G Frazier, Kevin Kodama, Shelley D Crausbay, Paul D Krushelnycky, Susan Cordell, Martyn P Clark, Andy J Newman, Jeffrey R Arnold
Long-term, accurate observations of atmospheric phenomena are essential for a myriad of applications, including historic and future climate assessments, resource management, and infrastructure planning. In Hawai'i, climate data are available from individual researchers, local, State, and Federal agencies, and from large electronic repositories such as the National Centers for Environmental Information (NCEI). Researchers attempting to make use of available data are faced with a series of challenges that include: (1) identifying potential data sources; (2) acquiring data; (3) establishing data quality assurance and quality control (QA/QC) protocols; and (4) implementing robust gap filling techniques...
February 13, 2018: Scientific Data
Andy Reisinger, Harry Clark
Agriculture directly contributes about 10%-12% of current global anthropogenic greenhouse gas emissions, mostly from livestock. However, such percentage estimates are based on global warming potentials (GWPs), which do not measure the actual warming caused by emissions and ignore the fact that methane does not accumulate in the atmosphere in the same way as CO2 . Here, we employ a simple carbon cycle-climate model, historical estimates and future projections of livestock emissions to infer the fraction of actual warming that is attributable to direct livestock non-CO2 emissions now and in future, and to CO2 from pasture conversions, without relying on GWPs...
April 2018: Global Change Biology
Ronan MacLoughlin, Colin Telfer, Andy Clark, James Fink
BACKGROUND: Local delivery of drugs to the lungs of newborn infant represents an unmet need as no drugs have been approved. Potential benefits could be large. Development of aerosol for delivery of drugs to infants and newborn offers huge potential for better therapy. Newborn infants present unique challenges with regard to aerosol therapy. Efficient deposition of aerosolized medications on the neonate airway surface is hampered by anatomical features such as small airway geometries and physiological features such as exquisitely small tidal volumes, rapid breathing and unfavorable inhalation:exhalation ratios...
2017: Current Pharmaceutical Design
Jon Wilson, Tim Clarke, Rebecca Lower, Uju Ugochukwu, Sarah Maxwell, Jo Hodgekins, Karen Wheeler, Andy Goff, Robert Mack, Rebecca Horne, David Fowler
Young people attempting to access mental health services in the United Kingdom often find traditional models of care outdated, rigid, inaccessible and unappealing. Policy recommendations, research and service user opinion suggest that reform is needed to reflect the changing needs of young people. There is significant motivation in the United Kingdom to transform mental health services for young people, and this paper aims to describe the rationale, development and implementation of a novel youth mental health service in the United Kingdom, the Norfolk Youth Service...
August 2018: Early Intervention in Psychiatry
Christopher T Sempos, Joseph M Betz, Johanna E Camara, Graham D Carter, Etienne Cavalier, Michael W Clarke, Kirsten G Dowling, Ramon A Durazo-Arvizu, Andrew N Hoofnagle, Andy Liu, Karen W Phinney, Kurtis Sarafin, Stephen A Wise, Paul M Coates
The Vitamin D Standardization Program (VDSP) has collaborated with numerous groups and agencies to assemble a set of tools, i.e., a reference measurement system, that can be used to establish the traceability of 25-hydroxyvitamin D [25(OH)D] assays to relevant reference measurement procedures and reference materials. This is done with the goal of verifying end-user laboratory performance using precise statistical criteria to determine whether a specific assay is standardized. The purpose of this paper was to outline a set of steps that routine clinical and research laboratories can use to standardize their 25(OH)D assays using these tools...
September 1, 2017: Journal of AOAC International
Bogdan-Alexandru Luca, Daniel S Brewer, Dylan R Edwards, Sandra Edwards, Hayley C Whitaker, Sue Merson, Nening Dennis, Rosalin A Cooper, Steven Hazell, Anne Y Warren, Rosalind Eeles, Andy G Lynch, Helen Ross-Adams, Alastair D Lamb, David E Neal, Krishna Sethia, Robert D Mills, Richard Y Ball, Helen Curley, Jeremy Clark, Vincent Moulton, Colin S Cooper
BACKGROUND: A critical problem in the clinical management of prostate cancer is that it is highly heterogeneous. Accurate prediction of individual cancer behaviour is therefore not achievable at the time of diagnosis leading to substantial overtreatment. It remains an enigma that, in contrast to breast cancer, unsupervised analyses of global expression profiles have not currently defined robust categories of prostate cancer with distinct clinical outcomes. OBJECTIVE: To devise a novel classification framework for human prostate cancer based on unsupervised mathematical approaches...
March 6, 2017: European Urology Focus
Andy Clark
Ransom, Fazelpour, and Mole (this journal - 2017) raise an important puzzle for the 'prediction error minimization' account of cognitive processing. That account depicts all cognitive processing as fundamentally in the business of minimizing prediction errors concerning the evolving flow of sensory information. One of the cornerstones of these highly ambitious, would-be unifying accounts is their depiction of attention as nothing other than the process of optimizing the precision (inverse variance) of critical prediction error signals...
November 2017: Consciousness and Cognition
James M Brown, Ewan Ross, Guillaume Desanti, Atif Saghir, Andy Clark, Chris Buckley, Andrew Filer, Amy Naylor, Ela Claridge
Rheumatoid arthritis (RA) is an autoimmune disease in which chronic inflammation of the synovial joints can lead to destruction of cartilage and bone. Pre-clinical studies attempt to uncover the underlying causes by emulating the disease in genetically different mouse strains and characterising the nature and severity of bone shape changes as indicators of pathology. This paper presents a fully automated method for obtaining quantitative measurements of bone destruction from volumetric micro-CT images of a mouse hind paw...
August 2017: Medical Image Analysis
Rebecca A Slattery, Andy VanLoocke, Carl J Bernacchi, Xin-Guang Zhu, Donald R Ort
Reducing chlorophyll (chl) content may improve the conversion efficiency of absorbed photosynthetically active radiation into biomass and therefore yield in dense monoculture crops by improving light penetration and distribution within the canopy. The effects of reduced chl on leaf and canopy photosynthesis and photosynthetic efficiency were studied in two reportedly robust reduced-chl soybean mutants, Y11y11 and y9y9, in comparison to the wild-type (WT) "Clark" cultivar. Both mutants were characterized during the 2012 growing season whereas only the Y11y11 mutant was characterized during the 2013 growing season...
2017: Frontiers in Plant Science
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