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https://read.qxmd.com/read/30744412/a-high-throughput-protocol-for-isolating-cell-free-circulating-tumor-dna-from-peripheral-blood
#1
Pawan K Pandoh, Richard D Corbett, Helen McDonald, Miguel Alcaide, Heather Kirk, Eva Trinh, Simon Haile, Tina MacLeod, Duane Smailus, Steve Bilobram, Andrew J Mungall, Yussanne Ma, Richard A Moore, Robin Coope, Yongjun Zhao, Steven Jm Jones, Robert A Holt, Aly Karsan, Ryan D Morin, Marco A Marra
The analysis of cell-free circulating tumor DNA (ctDNA) is potentially a less invasive, more dynamic assessment of cancer progression and treatment response than characterizing solid tumor biopsies. Standard isolation methods require separation of plasma by centrifugation, a time-consuming step that complicates automation. To address these limitations, we present an automatable magnetic bead-based ctDNA isolation method that eliminates centrifugation to purify ctDNA directly from peripheral blood (PB). To develop and test our method, ctDNA from cancer patients was purified from PB and plasma...
February 2019: BioTechniques
https://read.qxmd.com/read/30718619/uncovering-regional-variability-in-disturbance-trends-between-parks-and-greater-park-ecosystems-across-canada-1985-2015
#2
Douglas K Bolton, Nicholas C Coops, Txomin Hermosilla, Michael A Wulder, Joanne C White, Colin J Ferster
We assess the protective function of Canada's parks and protected areas (PPAs) by analyzing three decades of stand-replacing disturbance derived from Landsat time series data (1985-2015). Specifically, we compared rates of wildfire and harvest within 1,415 PPAs against rates of disturbance in surrounding greater park ecosystems (GPEs). We found that disturbance rates in GPEs were significantly higher (p < 0.05) than in corresponding PPAs in southern managed forests (six of Canada's 12 forested ecozones)...
February 4, 2019: Scientific Reports
https://read.qxmd.com/read/30691567/imaging-based-3-dimensional-printing-for-improved-maxillofacial-presurgical-planning-a-single-center-case-series
#3
Will Guest, Diana Forbes, Colin Schlosser, Stephen Yip, Robin Coope, Jason Chew
PURPOSE: 3-D printing is an increasingly widespread technology that allows physical models to be constructed based on cross-sectional medical imaging data. We sought to develop a pipeline for production of 3-dimensional (3-D) models for presurgical planning and assess the value of these models for surgeons and patients. METHODS: In this institutional review board-approved, single-center case series, participating surgeons identified cases for 3-D model printing, and after obtaining patient consent, a 3-D model was produced for each of the 7 participating patients based on preoperative cross-sectional imaging...
February 2019: Canadian Association of Radiologists Journal, Journal L'Association Canadienne des Radiologistes
https://read.qxmd.com/read/30684737/the-evaluation-of-tryptase-after-subcutaneous-immunotherapy-associated-systemic-reactions
#4
Sofia Szari, Priscilla H Wong, Howard C Crisp, Edward Champoux, Tonya S Rans, Christopher A Coop
No abstract text is available yet for this article.
January 23, 2019: Annals of Allergy, Asthma & Immunology
https://read.qxmd.com/read/30679259/detecting-adaptive-differentiation-in-structured-populations-with-genomic-data-and-common-gardens
#5
Emily B Josephs, Jeremy J Berg, Jeffrey Ross-Ibarra, Graham Coop
Adaptation in quantitative traits often occurs through subtle shifts in allele frequencies at many loci, a process called polygenic adaptation. While a number of methods have been developed to detect polygenic adaptation in human populations, we lack clear strategies for doing so in many other systems. In particular, there is an opportunity to develop new methods that leverage datasets with genomic data and common garden trait measurements to systematically detect the quantitative traits important for adaptation...
January 24, 2019: Genetics
https://read.qxmd.com/read/30652798/factors-associated-with-the-presence-of-triatomines-in-rural-areas-of-south-argentine-chaco
#6
Liliana Crocco, Julieta Nattero, Ana López, Miriam Cardozo, Carola Soria, Valeria Ortiz, Claudia S Rodriguez
INTRODUCTION: The domestic and peridomestic presence of Triatoma infestans depends on several factors, such as human behavior, vector behavior, ecology, and the environment. METHODS: This work was conducted in 139 domiciliary units, where triatomines were captured and risk factors in domiciles and peridomicilies were recorded. Household dwellers were interviewed to obtain information about practices regarding this disease and entomological indicators were calculated...
January 14, 2019: Revista da Sociedade Brasileira de Medicina Tropical
https://read.qxmd.com/read/30641097/an-evaluation-of-the-electronic-reporting-system-for-the-enhanced-surveillance-of-carbapenemase-producing-gram-negative-bacteria-in-england
#7
Daiga Jermacane, Caroline M Coope, Dean Ironmonger, Paul Cleary, Berit Muller-Pebody, Russell Hope, Susan Hopkins, Richard Puleston, Rachel Freeman, Katie L Hopkins, Alan P Johnson, Neil Woodford, Isabel Oliver
BACKGROUND: An electronic reporting system (ERS) for the enhanced surveillance of carbapenemase-producing Gram-negative bacteria (CPGNB) was launched by Public Health England in May 2015. AIM: This evaluation aimed to assess uptake, timeliness and completeness of data provided and explore potential barriers and facilitators to adopting the system. METHODS: The evaluation comprised a retrospective analysis of surveillance data and semi-structured interviews with ERS users...
January 11, 2019: Journal of Hospital Infection
https://read.qxmd.com/read/30634122/ecoanthromes-of-alberta-an-example-of-disturbance-informed-ecological-regionalization-using-remote-sensing
#8
S P Kearney, N C Coops, G B Stenhouse, T A Nelson
Humans influence ecosystems on magnitudes that often exceed that of natural forces such as climate and geology; however, frameworks rarely include anthropogenic disturbance when delineating unique ecological regions. A critical step toward understanding, managing and monitoring human-altered ecosystems is to incorporate disturbance into ecological regionalizations. Furthermore, quantitative regionalization approaches are desirable to provide cost-effective, repeatable and statistically sound stratification for environmental monitoring...
January 8, 2019: Journal of Environmental Management
https://read.qxmd.com/read/30598449/allele-frequency-dynamics-in-a-pedigreed-natural-population
#9
Nancy Chen, Ivan Juric, Elissa J Cosgrove, Reed Bowman, John W Fitzpatrick, Stephan J Schoech, Andrew G Clark, Graham Coop
A central goal of population genetics is to understand how genetic drift, natural selection, and gene flow shape allele frequencies through time. However, the actual processes underlying these changes-variation in individual survival, reproductive success, and movement-are often difficult to quantify. Fully understanding these processes requires the population pedigree, the set of relationships among all individuals in the population through time. Here, we use extensive pedigree and genomic information from a long-studied natural population of Florida Scrub-Jays ( Aphelocoma coerulescens ) to directly characterize the relative roles of different evolutionary processes in shaping patterns of genetic variation through time...
December 31, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/30562676/addressing-the-nexus-of-risk-biobehavioral-outcomes-from-a-cluster-randomized-trial-of-the-women-s-health-coop-plus-in-pretoria-south-africa
#10
Wendee M Wechsberg, Courtney Peasant Bonner, William A Zule, Charlie van der Horst, Jacqueline Ndirangu, Felicia A Browne, Tracy L Kline, Brittni N Howard, Nathaniel F Rodman
BACKGROUND: HIV prevalence has increased among South African women who use alcohol and other drugs (AOD). However, HIV prevention and treatment efforts have not focused on this population. This study presents the efficacy of the Women's Health CoOp Plus (WHC+) in a cluster-randomized trial to reduce AOD use, gender-based violence, and sexual risk and to increase linkage to HIV care among women who use AODs, compared with HIV counseling and testing alone. METHODS: Black African women (N = 641) were recruited from 14 geographic clusters in Pretoria, South Africa, and underwent either an evidence-based gender-focused HIV prevention intervention that included HIV counseling and testing (WHC+) or HIV counseling and testing alone...
December 3, 2018: Drug and Alcohol Dependence
https://read.qxmd.com/read/30561775/minimal-residual-disease-by-flow-cytometry-and-allelic-specific-oligonucleotide-real-time-quantitative-polymerase-chain-reaction-in-patients-with-myeloma-receiving-lenalidomide-maintenance-a-pooled-analysis
#11
Manuela Gambella, Paola Omedé, Stefano Spada, Vittorio Emanuele Muccio, Milena Gilestro, Elona Saraci, Sara Grammatico, Alessandra Larocca, Concetta Conticello, Annalisa Bernardini, Barbara Gamberi, Rossella Troia, Anna Marina Liberati, Massimo Offidani, Alberto Rocci, Antonio Palumbo, Michele Cavo, Pieter Sonneveld, Mario Boccadoro, Stefania Oliva
BACKGROUND: Minimal residual disease (MRD) is one of the most relevant prognostic factors in patients with multiple myeloma (MM); however, the impact of maintenance therapy on MRD levels remains unclear. Among patients with newly diagnosed MM (NDMM) who received lenalidomide maintenance until they developed disease progression, the role of MRD status as a predictor of progression-free survival (PFS) was evaluated by multiparameter flow cytometry (MFC) and allelic-specific oligonucleotide real-time quantitative polymerase chain reaction (ASO-RQ-PCR) analysis...
December 18, 2018: Cancer
https://read.qxmd.com/read/30557759/mapping-whole-brain-connectivity-changes-the-potential-impact-of-different-surgical-resection-approaches-for-temporal-lobe-epilepsy
#12
Natalie Busby, Ajay D Halai, Geoff J M Parker, David J Coope, Matthew A Lambon Ralph
In neurosurgery there are several situations that require transgression of the temporal cortex. For example, a subset of patients with temporal lobe epilepsy require surgical resection (most typically, en-bloc anterior temporal lobectomy). This procedure is the gold standard to alleviate seizures but is associated with chronic cognitive deficits. In recent years there have been multiple attempts to find the optimum balance between minimising the size of resection in order to preserve cognitive function, while still ensuring seizure freedom...
November 17, 2018: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
https://read.qxmd.com/read/30465861/the-glycerin-associated-pain-gap-study
#13
Christopher A Coop, Karen Barker, Scott Dickson, Troy Baker, Kirk Waibel
No abstract text is available yet for this article.
November 19, 2018: Annals of Allergy, Asthma & Immunology
https://read.qxmd.com/read/30418619/sources-of-erroneous-sequences-and-artifact-chimeric-reads-in-next-generation-sequencing-of-genomic-dna-from-formalin-fixed-paraffin-embedded-samples
#14
Simon Haile, Richard D Corbett, Steve Bilobram, Morgan H Bye, Heather Kirk, Pawan Pandoh, Eva Trinh, Tina MacLeod, Helen McDonald, Miruna Bala, Diane Miller, Karen Novik, Robin J Coope, Richard A Moore, Yongjun Zhao, Andrew J Mungall, Yussanne Ma, Rob A Holt, Steven J Jones, Marco A Marra
Tissues used in pathology laboratories are typically stored in the form of formalin-fixed, paraffin-embedded (FFPE) samples. One important consideration in repurposing FFPE material for next generation sequencing (NGS) analysis is the sequencing artifacts that can arise from the significant damage to nucleic acids due to treatment with formalin, storage at room temperature and extraction. One such class of artifacts consists of chimeric reads that appear to be derived from non-contiguous portions of the genome...
November 12, 2018: Nucleic Acids Research
https://read.qxmd.com/read/30404015/tools-for-rapid-high-resolution-behavioral-phenotyping-of-automatically-isolated-drosophila
#15
W Ryan Williamson, Martin Y Peek, Patrick Breads, Brian Coop, Gwyneth M Card
Sparse manipulation of neuron excitability during free behavior is critical for identifying neural substrates of behavior. Genetic tools for precise neuronal manipulation exist in the fruit fly, Drosophila melanogaster, but behavioral tools are still lacking to identify potentially subtle phenotypes only detectible using high-throughput and high spatiotemporal resolution. We developed three assay components that can be used modularly to study natural and optogenetically induced behaviors. FlyGate automatically releases flies one at a time into an assay...
November 6, 2018: Cell Reports
https://read.qxmd.com/read/30400159/use-of-foaming-disinfectants-and-cleaners-to-reduce-aerobic-bacteria-and-salmonella-on-poultry-transport-coops
#16
Carolee Hinojosa, David Caldwell, James Byrd, Robert Droleskey, Jason Lee, Phil Stayer, Erin Resendiz, Javier Garcia, Stephanie Klein, Denise Caldwell, Megan Pineda, Morgan Farnell
Transport coops are infrequently washed and have been demonstrated to cross-contaminate broiler carcasses. We hypothesized that peracetic acid or a chlorinated cleaner, commonly used within poultry processing plants, can also be used to disinfect transport coops when applied via a compressed air foam system (CAFS). A mixture of fresh layer manure and concentrated Salmonella Typhimurium (ST) was evenly applied to the floors of four pre-cleaned transport coops and allowed to dry for thirty minutes. Treatments consisted of a (1) water rinse only, (2) product application with a water rinse, (3) product application followed by power washing and (4) power washing followed by application of product...
November 2, 2018: Animals: An Open Access Journal From MDPI
https://read.qxmd.com/read/30389971/remotely-sensed-productivity-clusters-capture-global-biodiversity-patterns
#17
Nicholas C Coops, Sean P Kearney, Douglas K Bolton, Volker C Radeloff
Ecological regionalisations delineate areas of similar environmental conditions, ecological processes, and biotic communities, and provide a basis for systematic conservation planning and management. Most regionalisations are made based on subjective criteria, and can not be readily revised, leading to outstanding questions with respect to how to optimally develop and define them. Advances in remote sensing technology, and big data analysis approaches, provide new opportunities for regionalisations, especially in terms of productivity patterns through both photosynthesis and structural surrogates...
November 2, 2018: Scientific Reports
https://read.qxmd.com/read/30389808/reconstructing-the-history-of-polygenic-scores-using-coalescent-trees
#18
Michael D Edge, Graham Coop
Genome-wide association studies (GWAS) have revealed that many traits are highly polygenic, in that their within-population variance is governed in part by small-effect variants at many genetic loci. Standard population-genetic methods for inferring evolutionary history are ill-suited for polygenic traits-when there are many variants of small effect, signatures of natural selection are spread across the genome and subtle at any one locus. In the last several years, several methods have emerged for detecting the action of natural selection on polygenic scores, sums of genotypes weighted by GWAS effect sizes...
November 2, 2018: Genetics
https://read.qxmd.com/read/30388263/inflammation-and-vascular-permeability-correlate-with-growth-in-sporadic-vestibular-schwannoma
#19
Daniel Lewis, Federico Roncaroli, Erjon Agushi, Dominic Mosses, Ricky Williams, Ka-Loh Li, Xiaoping Zhu, Rainer Hinz, Ross Atkinson, Andrea Wadeson, Sharon Hulme, Helen Mayers, Emma Stapleton, Simon K L Lloyd, Simon R Freeman, Scott A Rutherford, Charlotte Hammerbeck-Ward, D Gareth Evans, Omar Pathmanaban, Alan Jackson, Andrew T King, David Coope
Background: Inflammation is hypothesized to be a key event in the growth of sporadic vestibular schwannoma (VS). In this study we sought to investigate the relationship between inflammation and tumor growth in vivo using the PET tracer 11C-(R)-PK11195 and dynamic contrast enhanced (DCE) MRI derived vascular biomarkers. Methods: Nineteen patients with sporadic VS (8 static, 7 growing and 4 shrinking tumors), underwent prospective imaging with dynamic 11C-(R)-PK11195 PET and a comprehensive MR protocol; including high temporal resolution DCE-MRI in fifteen patients...
November 2, 2018: Neuro-oncology
https://read.qxmd.com/read/30311218/an-implementation-study-of-relationship-checkups-as-home-visitations-for-low-income-at-risk-couples
#20
Kristina Coop Gordon, James V Cordova, Patricia N E Roberson, Melanie Miller, Tatiana Gray, Katherine A Lenger, Matt Hawrilenko, Kerri Martin
Couples with the greatest need for relationship health maintenance and intervention are often least able to afford and access it; therefore, accessible, affordable, effective, and brief interventions are needed to improve relationship health for those who need it most. Consequently, this paper examined whether a brief relationship intervention could be effectively implemented with a low-income, underserved population. All enrolled participants (N = 1,312) received the Relationship Checkup, which consists of an assessment and a feedback session delivered in their homes or at a local clinic at their request...
October 11, 2018: Family Process
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