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https://www.readbyqxmd.com/read/28345046/canopy-near-infrared-reflectance-and-terrestrial-photosynthesis
#1
Grayson Badgley, Christopher B Field, Joseph A Berry
Global estimates of terrestrial gross primary production (GPP) remain highly uncertain, despite decades of satellite measurements and intensive in situ monitoring. We report a new approach for quantifying the near-infrared reflectance of terrestrial vegetation (NIRV). NIRV provides a foundation for a new approach to estimate GPP that consistently untangles the confounding effects of background brightness, leaf area, and the distribution of photosynthetic capacity with depth in canopies using existing moderate spatial and spectral resolution satellite sensors...
March 2017: Science Advances
https://www.readbyqxmd.com/read/28344990/inspiired-a-pipeline-for-quantitative-analysis-of-sites-of-new-dna-integration-in-cellular-genomes
#2
Eric Sherman, Christopher Nobles, Charles C Berry, Emmanuelle Six, Yinghua Wu, Anatoly Dryga, Nirav Malani, Frances Male, Shantan Reddy, Aubrey Bailey, Kyle Bittinger, John K Everett, Laure Caccavelli, Mary J Drake, Paul Bates, Salima Hacein-Bey-Abina, Marina Cavazzana, Frederic D Bushman
Integration of new DNA into cellular genomes mediates replication of retroviruses and transposons; integration reactions have also been adapted for use in human gene therapy. Tracking the distributions of integration sites is important to characterize populations of transduced cells and to monitor potential outgrow of pathogenic cell clones. Here, we describe a pipeline for quantitative analysis of integration site distributions named INSPIIRED (integration site pipeline for paired-end reads). We describe optimized biochemical steps for site isolation using Illumina paired-end sequencing, including new technology for suppressing recovery of unwanted contaminants, then software for alignment, quality control, and management of integration site sequences...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28344988/inspiired-quantification-and-visualization-tools-for-analyzing-integration-site-distributions
#3
Charles C Berry, Christopher Nobles, Emmanuelle Six, Yinghua Wu, Nirav Malani, Eric Sherman, Anatoly Dryga, John K Everett, Frances Male, Aubrey Bailey, Kyle Bittinger, Mary J Drake, Laure Caccavelli, Paul Bates, Salima Hacein-Bey-Abina, Marina Cavazzana, Frederic D Bushman
Analysis of sites of newly integrated DNA in cellular genomes is important to several fields, but methods for analyzing and visualizing these datasets are still under development. Here, we describe tools for data analysis and visualization that take as input integration site data from our INSPIIRED pipeline. Paired-end sequencing allows inference of the numbers of transduced cells as well as the distributions of integration sites in target genomes. We present interactive heatmaps that allow comparison of distributions of integration sites to genomic features and that support numerous user-defined statistical tests...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28344030/antibacterial-activity-of-medicinal-plants-from-the-physicians-of-myddvai-a-13-th-century-welsh-medical-manuscript
#4
Charles Wagner, Jillian De Gezelle, Maureen Robertson, Keith Robertson, Mickey Wilson, Slavko Komarnytsky
ETHNOPHARMACOLOGICAL RELEVANCE: Antimicrobial drug resistance is a growing threat to global public health. Historical records and herbal texts relating to traditional Celtic medicine indicate an extensive pharmacopeia of plants for treating infections likely caused by microbes. However, a major barrier for successful integration of these remedies into mainstream practice is the current lack of accurate interpretation and scientific validation. MATERIALS AND METHODS: We applied Mobile Discovery approach to the Isle of Arran, Scotland, for in situ targeted screening of 83 out of 138 plants identified in Meddygion Myddvai (a 13(th) century Welsh manuscript) to treat conditions related to microbial infections, and an additional 18 plants from modern ethnobotanical knowledge on the island...
March 24, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28344021/pharmaceutical-cocrystals-salts-and-multicomponent-systems-intermolecular-interactions-and-property-based-design
#5
REVIEW
David J Berry, Jonathan W Steed
As small molecule drugs become harder to develop and less cost effective for patient use, efficient strategies for their property improvement become increasingly important to global health initiatives. Improvements in the physical properties of Active Pharmaceutical Ingredients (APIs), without changes in the covalent chemistry, have long been possible through the application of binary component solids. This was first achieved through the use of pharmaceutical salts, within the last 10-15years with cocrystals and more recently coamorphous systems have also been consciously applied to this problem...
March 23, 2017: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/28342717/slow-chromatin-dynamics-allow-polycomb-target-genes-to-filter-fluctuations-in-transcription-factor-activity
#6
Scott Berry, Caroline Dean, Martin Howard
Genes targeted by Polycomb repressive complex 2 (PRC2) are regulated in cis by chromatin modifications and also in trans by diffusible regulators such as transcription factors. Here, we introduce a mathematical model in which transcription directly antagonizes Polycomb silencing, thereby linking these cis- and trans-regulatory inputs to gene expression. The model is parameterized by recent experimental data showing that PRC2-mediated repressive chromatin modifications accumulate extremely slowly. The model generates self-perpetuating, bistable active and repressed chromatin states that persist through DNA replication, thereby ensuring high-fidelity transmission of the current chromatin state...
March 21, 2017: Cell Systems
https://www.readbyqxmd.com/read/28342694/nursing-led-home-visits-post-hospitalization-for-children-with-medical-complexity
#7
Sarah Wells, Margaret O'Neill, Jayne Rogers, Kevin Blaine, Amy Hoffman, Sarah McBride, Meghan M Tschudy, Igor Shumskiy, Sangeeta Mauskar, Jay G Berry
PURPOSE: Hospital discharge for children with medical complexity (CMC) can be challenging for families. Home visits could potentially benefit CMC and their families after leaving the hospital. We assessed the utility of post-discharge home visits to identify and address health problems for recently hospitalized CMC. DESIGN AND METHODS: A prospective study of 36 CMC admitted to a children's hospital from 4/15/2015 to 4/14/2016 identified with a possible high risk of hospital readmission and offered a post-discharge home visit within 72h of discharge...
March 23, 2017: Journal of Pediatric Nursing
https://www.readbyqxmd.com/read/28341910/effectiveness-and-cost-benefit-evaluation-of-a-comprehensive-workers-health-surveillance-program-for-sustainable-employability-of-meat-processing-workers
#8
Berry J van Holland, Michiel F Reneman, Remko Soer, Sandra Brouwer, Michiel R de Boer
Objective To evaluate the effectiveness of a comprehensive workers' health surveillance (WHS) program on aspects of sustainable employability and cost-benefit. Methods A cluster randomized stepped wedge trial was performed in a Dutch meat processing company from february 2012 until march 2015. In total 305 workers participated in the trial. Outcomes were retrieved during a WHS program, by multiple questionnaires, and from company registries. Primary outcomes were sickness absence, work ability, and productivity...
March 24, 2017: Journal of Occupational Rehabilitation
https://www.readbyqxmd.com/read/28341805/correction-the-high-polyphenol-content-of-grapevine-cultivar-tannat-berries-is-conferred-primarily-by-genes-that-are-not-shared-with-the-reference-genome
#9
https://www.readbyqxmd.com/read/28341277/seasonality-of-periprosthetic-femur-fractures-in-12-700-primary-and-revision-total-hip-arthroplasties
#10
William H Trousdale, Matthew P Abdel, Anthony Viste, Robert T Trousdale, John J Callaghan, Daniel J Berry
BACKGROUND: Periprosthetic femur fractures after primary and revision total hip arthroplasty (THA) are one of the most common long-term reasons for reoperation after THA. Previous investigations have analyzed the incidence and risk factors of these fractures. No previous study, however, has analyzed a variation in periprosthetic femur fractures between meteorologic seasons. The aim of this study was to compare the incidence of periprosthetic femur fractures after primary and revision THAs depending on the meteorologic season...
February 28, 2017: Journal of Arthroplasty
https://www.readbyqxmd.com/read/28341127/effects-of-coal-contamination-on-early-life-history-processes-of-a-reef-building-coral-acropora-tenuis
#11
Kathryn L E Berry, Mia O Hoogenboom, Diane L Brinkman, Kathryn A Burns, Andrew P Negri
Successful reproduction and larval dispersal are important for the persistence of marine invertebrate populations, and these early life history processes can be sensitive to marine pollution. Coal is emerging as a contaminant of interest due to the proximity of ports and shipping lanes to coral reefs. To assess the potential hazard of this contaminant, gametes, newly developed embryos, larvae and juveniles of the coral Acropora tenuis were exposed to a range of coal leachate, suspended coal, and coal smothering treatments...
January 15, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28340790/on-line-in-syringe-sugaring-out-liquid-liquid-extraction-coupled-with-hplc-ms-ms-for-the-determination-of-pesticides-in-fruit-and-berry-juices
#12
Irina Timofeeva, Andrey Shishov, Daria Kanashina, Daria Dzema, Andrey Bulatov
A fully automated method for the determination of pesticides (malathion, diazinon, imidacloprid and triadimefon) in fruit and berry juices has been developed. In the current study, the on-line in-syringe sugaring-out liquid-liquid extraction was successfully combined with a HPLC-MS/MS system for the first time. The procedure assumes the liquid-liquid extraction of analytes in water-miscible organic solvent acetonitrile followed by phase separation using glucose as sugaring-out reagent. After the phase separation in a syringe of a flow system, the extract containing pesticides was injected into the HPLC-MS/MS system...
May 15, 2017: Talanta
https://www.readbyqxmd.com/read/28340350/a-viral-immunoevasin-controls-innate-immunity-by-targeting-the-prototypical-natural-killer-cell-receptor-family
#13
Oscar A Aguilar, Richard Berry, Mir Munir A Rahim, Johanna J Reichel, Branka Popović, Miho Tanaka, Zhihui Fu, Gautham R Balaji, Timothy N H Lau, Megan M Tu, Christina L Kirkham, Ahmad Bakur Mahmoud, Aruz Mesci, Astrid Krmpotić, David S J Allan, Andrew P Makrigiannis, Stipan Jonjić, Jamie Rossjohn, James R Carlyle
Natural killer (NK) cells play a key role in innate immunity by detecting alterations in self and non-self ligands via paired NK cell receptors (NKRs). Despite identification of numerous NKR-ligand interactions, physiological ligands for the prototypical NK1.1 orphan receptor remain elusive. Here, we identify a viral ligand for the inhibitory and activating NKR-P1 (NK1.1) receptors. This murine cytomegalovirus (MCMV)-encoded protein, m12, restrains NK cell effector function by directly engaging the inhibitory NKR-P1B receptor...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28339623/the-molecular-and-clinical-epidemiology-of-extended-spectrum-cephalosporin-and-carbapenem-resistant-enterobacteriaceae-at-4-us-pediatric-hospitals
#14
Danielle M Zerr, Scott J Weissman, Chuan Zhou, Matthew P Kronman, Amanda L Adler, Jessica E Berry, Jaipreet Rayar, Jeff Myers, Wren L Haaland, Carey-Ann D Burnham, Alexis Elward, Jason Newland, Rangaraj Selvarangan, Kaede V Sullivan, Theoklis Zaoutis, Xuan Qin
Objective.: In this report, we aim to describe the epidemiology of extended-spectrum cephalosporin-resistant (ESC-R) and carbapenem-resistant (CR) Enterobacteriaceae infections in children. Methods.: ESC-R and CR Enterobacteriaceae isolates from normally sterile sites of patients aged <22 years from 4 freestanding pediatric medical centers were collected along with the associated clinical data. Results.: The overall frequencies of ESC-R and CR isolates according to hospital over the 4-year study period ranged from 0...
January 19, 2017: Journal of the Pediatric Infectious Diseases Society
https://www.readbyqxmd.com/read/28338755/red-blotch-disease-alters-grape-berry-development-and-metabolism-by-interfering-with-the-transcriptional-and-hormonal-regulation-of-ripening
#15
Barbara Blanco-Ulate, Helene Hopfer, Rosa Figueroa-Balderas, Zirou Ye, Rosa M Rivero, Alfonso Albacete, Francisco Pérez-Alfocea, Renata Koyama, Michael M Anderson, Rhonda J Smith, Susan E Ebeler, Dario Cantu
Grapevine red blotch-associated virus (GRBaV) is a major threat to the wine industry in the USA. GRBaV infections (aka red blotch disease) compromise crop yield and berry chemical composition, affecting the flavor and aroma properties of must and wine. In this study, we combined genome-wide transcriptional profiling with targeted metabolite analyses and biochemical assays to characterize the impact of the disease on red-skinned berry ripening and metabolism. Using naturally infected berries collected from two vineyards, we were able to identify consistent berry responses to GRBaV across different environmental and cultural conditions...
January 27, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338417/a-3d-tissue-printing-approach-for-validation-of-diffusion-tensor-imaging-in-skeletal-muscle
#16
David B Berry, Shangting You, John Warner, Lawrence R Frank, Shaochen Chen, Samuel R Ward
The ability to noninvasively assess skeletal muscle microstructure, which predicts function and disease, would be of significant clinical value. One method that holds this promise is diffusion tensor magnetic resonance imaging (DT-MRI), which is sensitive to the microscopic diffusion of water within tissues and has become ubiquitous in neuroimaging as a way of assessing neuronal structure and damage. However, its application to the assessment of changes in muscle microstructure associated with injury, pathology, or age remains poorly defined, because it is difficult to precisely control muscle microstructural features in vivo...
March 24, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28338229/response-to-endurance-exercise-training-in-older-adults-with-heart-failure-with-preserved-or-reduced-ejection-fraction
#17
Ambarish Pandey, Dalane W Kitzman, Peter Brubaker, Mark J Haykowsky, Timothy Morgan, J Thomas Becton, Jarett D Berry
OBJECTIVES: To systematically examine the relative magnitude and predictors of responses to exercise training in older adult with heart failure (HF) with reduced ejection fraction (HFrEF), and preserved EF (HFpEF). DESIGN: Secondary analysis of a randomized controlled trial. SETTING: Outpatient cardiac rehabilitation program. PARTICIPANTS: Individuals with HF (24 HFrEF, 24 HFpEF) who underwent supervised exercise training...
March 24, 2017: Journal of the American Geriatrics Society
https://www.readbyqxmd.com/read/28337994/the-new-phases-due-to-symmetry-protected-piecewise-berry-phases-enhanced-pumping-and-non-reciprocity-in-trimer-lattices
#18
Xuele Liu, G S Agarwal
Finding new phase of matter is a fundamental task in physics. Generally, various phases or states of matter (for instance solid/liquid/gas phases) have different symmetries, the phase transitions among them can be explained by Landau's symmetry breaking theory. The topological phases discovered in recent years show that different phases may have the same symmetry. The different topological phases are characterized by different integer values of the Berry phases. By studying one dimensional (1D) trimer lattices we report new phases beyond topological phases...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337390/an-rbcl-reference-library-to-aid-in-the-identification-of-plant-species-mixtures-by-dna-metabarcoding
#19
Karen L Bell, Virginia M Loeffler, Berry J Brosi
PREMISE OF THE STUDY: DNA metabarcoding has broad-ranging applications in ecology, aerobiology, biosecurity, and forensics. A bioinformatics pipeline has recently been published for identification using a comprehensive database of ITS2, one of the common plant DNA barcoding markers. There is, however, no corresponding database for rbcL, the other primary marker used in plants. METHODS: Using publicly available data, we compiled a reference library of rbcL sequences and trained databases for use with UTAX and RDP classifier algorithms...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337183/are-oligotypes-meaningful-ecological-and-phylogenetic-units-a-case-study-of-microcystis-in-freshwater-lakes
#20
Michelle A Berry, Jeffrey D White, Timothy W Davis, Sunit Jain, Thomas H Johengen, Gregory J Dick, Orlando Sarnelle, Vincent J Denef
Oligotyping is a computational method used to increase the resolution of marker gene microbiome studies. Although oligotyping can distinguish highly similar sequence variants, the resulting units are not necessarily phylogenetically and ecologically informative due to limitations of the selected marker gene. In this perspective, we examine how oligotyping data is interpreted in recent literature, and we illustrate some of the method's constraints with a case study of the harmful bloom-forming cyanobacterium Microcystis...
2017: Frontiers in Microbiology
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