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https://www.readbyqxmd.com/read/28545117/on-tests-of-treatment-covariate-interactions-an-illustration-of-appropriate-power-and-sample-size-calculations
#1
Gwowen Shieh
The appraisals of treatment-covariate interaction have theoretical and substantial implications in all scientific fields. Methodologically, the detection of interaction between categorical treatment levels and continuous covariate variables is analogous to the homogeneity of regression slopes test in the context of ANCOVA. A fundamental assumption of ANCOVA is that the regression slopes associating the response variable with the covariate variable are presumed constant across treatment groups. The validity of homogeneous regression slopes accordingly is the most essential concern in traditional ANCOVA and inevitably determines the practical usefulness of research findings...
2017: PloS One
https://www.readbyqxmd.com/read/28544613/qtl-and-systems-genetics-analysis-of-mouse-grooming-and-behavioral-responses-to-novelty-in-an-open-field
#2
Anna Delprato, Marie-Paule Algéo, Brice Bonheur, Jason A Bubier, Lu Lu, Robert W Williams, Elissa J Chesler, Wim E Crusio
The open field is a classic test used to assess exploratory behavior, anxiety, and locomotor activity in rodents. Here we mapped quantitative trait loci (QTLs) underlying behaviors displayed in an open field, using a panel of 53 BXD recombinant inbred mouse strains with deep replication (10 per strain and sex). The use of these strains permits the integration and comparison of data obtained in different laboratories, and also offers the possibility to study trait covariance by exploiting powerful bioinformatics tools and resources...
May 24, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28544284/the-national-healthcare-system-claims-databases-in-france-sniiram-and-egb-powerful-tools-for-pharmacoepidemiology
#3
Julien Bezin, Mai Duong, Régis Lassalle, Cécile Droz, Antoine Pariente, Patrick Blin, Nicholas Moore
The French health care system is based on universal coverage by one of several health care insurance plans. The SNIIRAM database merges anonymous information of reimbursed claims from all these plans, linked to the national hospital-discharge summaries database system (PMSI) and the national death registry. It now covers 98.8% of the French population, over 66 million persons, from birth (or immigration) to death (or emigration), making it possibly the world's largest continuous homogeneous claims database...
May 24, 2017: Pharmacoepidemiology and Drug Safety
https://www.readbyqxmd.com/read/28544058/beyond-differences-in-means-robust-graphical-methods-to-compare-two-groups-in-neuroscience
#4
Guillaume A Rousselet, Cyril R Pernet, Rand R Wilcox
If many changes are necessary to improve the quality of neuroscience research, one relatively simple step could have great pay-offs: to promote the adoption of detailed graphical methods, combined with robust inferential statistics. Here we illustrate how such methods can lead to a much more detailed understanding of group differences than bar graphs and t-tests on means. To complement the neuroscientist's toolbox, we present two powerful tools that can help us understand how groups of observations differ: the shift function and the difference asymmetry function...
May 24, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/28544016/recent-advances-of-crispr-cas9-genome-editing-technologies-for-biological-and-biomedical-investigations
#5
Vijai Singh, Nisarg Gohil, Robert Ramírez García, Darren Braddick, Christian Kuete Fofié
The Type II CRISPR-Cas9 system is a simple, efficient, and versatile tool for targeted genome editing in a wide range of organisms and cell types. It continues to gain more scientific interest and has established itself as an extremely powerful technology within our synthetic biology toolkit. It works upon a targeted site and generates a double strand breaks that become repaired by either the NHEJ or HDR pathway, modifying or permanently replacing the genomic target sequences of interest. These can include viral targets, single-mutation genetic diseases, and multiple-site corrections for wide scale disease states, offering the potential to manage and cure some of mankind's most persistent biomedical menaces...
May 24, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28543827/estimations-of-linkage-disequilibrium-effective-population-size-and-roh-based-inbreeding-coefficients-in-spanish-churra-sheep-using-imputed-high-density-snp-genotypes
#6
P K Chitneedi, J J Arranz, A Suarez-Vega, E García-Gámez, B Gutiérrez-Gil
In this study, the availability of the Ovine HD SNP BeadChip (HD-chip) and the development of an imputation strategy provided an opportunity to further investigate the extent of linkage disequilibrium (LD) at short distances in the genome of the Spanish Churra dairy sheep breed. A population of 1686 animals, including 16 rams and their half-sib daughters, previously genotyped for the 50K-chip, was imputed to the HD-chip density based on a reference population of 335 individuals. After assessing the imputation accuracy for beagle v4...
May 22, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28543811/the-structural-flexibility-of-the-human-copper-chaperone-atox1-insights-from-combined-pulsed-epr-studies-and-computations
#7
Ariel R Levy, Meital Turgeman, Lada Gevorkyan-Aiapetov, Sharon Ruthstein
Metallochaperones are responsible for shuttling metal ions to target proteins. Thus, a metallochaperone's structure must be sufficiently flexible both to hold onto its ion while traversing the cytoplasm and to transfer the ion to or from a partner protein. Here, we sought to shed light on the structure of Atox1, a metallochaperone involved in the human copper regulation system. Atox1 shuttles copper ions from the main copper transporter, Ctr1, to the ATP7b transporter in the Golgi apparatus. Conventional biophysical tools such as X-ray or NMR cannot always target the various conformational states of metallochaperones, owing to a requirement for crystallography or low sensitivity and resolution...
May 20, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28543787/accurate-determination-of-brain-metabolite-concentrations-using-eretic-as-external-reference
#8
Niklaus Zoelch, Andreas Hock, Susanne Heinzer-Schweizer, Nikolai Avdievitch, Anke Henning
Magnetic Resonance Spectroscopy (MRS) can provide in vivo metabolite concentrations in standard concentration units if a reliable reference signal is available. For (1) H MRS in the human brain, typically the signal from the tissue water is used as the (internal) reference signal. However, a concentration determination based on the tissue water signal most often requires a reliable estimate of the water concentration present in the investigated tissue. Especially in clinically interesting cases, this estimation might be difficult...
May 25, 2017: NMR in Biomedicine
https://www.readbyqxmd.com/read/28543738/crispr-editing-in-biological-and-biomedical-investigation
#9
Xing-Da Ju, Jing Xu, Zhong Sheng Sun
The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR--associated protein) system, a prokaryotic RNA-based adaptive immune system against viral infection, is emerging as a powerful genome editing tool in broad research areas. To further improve and expand its functionality, various CRISPR delivery strategies have been tested and optimized, and key CRISPR system components such as Cas protein have been engineered with different purposes. Benefiting from more in-depth understanding and further development of CRISPR, versatile CRISPR-based platforms for genome editing have been rapidly developed to advance investigations in biology and biomedicine...
May 20, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28543694/genetically-engineered-mouse-models-of-melanoma
#10
REVIEW
Eva Pérez-Guijarro, Chi-Ping Day, Glenn Merlino, M Raza Zaidi
Melanoma is a complex disease that exhibits highly heterogeneous etiological, histopathological, and genetic features, as well as therapeutic responses. Genetically engineered mouse (GEM) models provide powerful tools to unravel the molecular mechanisms critical for melanoma development and drug resistance. Here, we expound briefly the basis of the mouse modeling design, the available technology for genetic engineering, and the aspects influencing the use of GEMs to model melanoma. Furthermore, we describe in detail the currently available GEM models of melanoma...
June 1, 2017: Cancer
https://www.readbyqxmd.com/read/28543544/the-prognostic-utility-of-the-tumor-burden-score-based-on-preoperative-radiographic-features-of-colorectal-liver-metastases
#11
Kazunari Sasaki, Georgios A Margonis, Nikolaos Andreatos, Xu-Feng Zhang, Stefan Buettner, Jaeyun Wang, Amar Deshwar, Jin He, Christopher L Wolfgang, Matthew Weiss, Timothy M Pawlik
BACKGROUND: Recently, a tumor-burden "metro ticket" score (TBS) based on final pathology was proposed to predict outcome following resection of colorectal liver metastasis (CRLM). We sought to validate the TBS prognostic tool using preoperative radiologic cross-sectional imaging. METHODS: Imaging TBS was defined on a Cartesian plane that incorporated both maximum tumor size (x-axis) and lesion number (y-axis) assessed by pre-operative imaging. The discriminatory power (area under the curve [AUC]) and goodness-of-fit (Harrel's C statistic and Somer's D statistics) of the imaging TBS model was assessed...
May 25, 2017: Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28543099/evidence-of-altered-mitochondrial-protein-expression-after-chronic-ethanol-consumption-in-the-aged-estrogen-deficient-female-rat-heart
#12
Alexandra M Garvin, J L Miller-Lee, D R Sharda, G M Kanski, J C Hunter, Donna H Korzick
BACKGROUND: Estrogen loss has been implicated to increase the risk of alcoholic cardiomyopathy in post-menopausal women. The purpose of this study was to identify novel mitochondrial protein targets for the treatment of alcoholic cardiomyopathy in aged women using a state-of-the-art proteomics approach. We hypothesized that chronic ethanol (EtOH) ingestion exacerbates maladaptive mitochondrial protein expression in the aged female heart METHODS: Adult (3 mo) and aged (18 mo) F344 ovary-intact or ovariectomized (OVX) rats were randomly assigned an EtOH or control Lieber-DeCarli 'all liquid' diet for 20 wks...
May 19, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28542547/determination-of-diagnostic-standards-on-saturated-soil-extracts-for-cut-roses-grown-in-greenhouses
#13
John Jairo Franco-Hermida, María Fernanda Quintero, Raúl Iskander Cabrera, José Miguel Guzman
This work comprises the theoretical determination and validation of diagnostic standards for the analysis of saturated soil extracts for cut rose flower crops (Rosa spp.) growing in the Bogota Plateau, Colombia. The data included 684 plant tissue analyses and 684 corresponding analyses of saturated soil extracts, all collected between January 2009 and June 2013. The tissue and soil samples were selected from 13 rose farms, and from cultivars grafted on the 'Natal Briar' rootstock. These concurrent samples of soil and plant tissues represented 251 production units (locations) of approximately 10,000 m2 distributed across the study area...
2017: PloS One
https://www.readbyqxmd.com/read/28542495/dna-barcoding-and-lc-ms-metabolite-profiling-of-the-lichen-forming-genus-melanelia-specimen-identification-and-discrimination-focusing-on-icelandic-taxa
#14
Maonian Xu, Starri Heidmarsson, Margret Thorsteinsdottir, Finnur F Eiriksson, Sesselja Omarsdottir, Elin S Olafsdottir
Taxa in the genus Melanelia (Parmeliaceae, Ascomycota) belong to a group of saxicolous lichens with brown to black foliose thalli, which have recently undergone extensive changes in circumscription. Taxa belonging to Parmeliaceae are prolific producers of bioactive compounds, which have also been traditionally used for chemotaxonomic purposes. However, the chemical diversity of the genus Melanelia and the use of chemical data for species discrimination in this genus are largely unexplored. In addition, identification based on morphological characters is challenging due to few taxonomically informative characters...
2017: PloS One
https://www.readbyqxmd.com/read/28542466/toner-a-tool-for-identifying-nucleotide-enrichment-signals-in-feature-enriched-rna-seq-data
#15
Yuttachon Promworn, Pavita Kaewprommal, Philip J Shaw, Apichart Intarapanich, Sissades Tongsima, Jittima Piriyapongsa
BACKGROUND: Biochemical methods are available for enriching 5' ends of RNAs in prokaryotes, which are employed in the differential RNA-seq (dRNA-seq) and the more recent Cappable-seq protocols. Computational methods are needed to locate RNA 5' ends from these data by statistical analysis of the enrichment. Although statistical-based analysis methods have been developed for dRNA-seq, they may not be suitable for Cappable-seq data. The more efficient enrichment method employed in Cappable-seq compared with dRNA-seq could affect data distribution and thus algorithm performance...
2017: PloS One
https://www.readbyqxmd.com/read/28542329/novel-agoshrna-molecules-for-silencing-of-the-ccr5-co-receptor-for-hiv-1-infection
#16
Elena Herrera-Carrillo, Ben Berkhout
Allogeneic transplantation of blood stem cells from a CCR5-Δ32 homozygous donor to an HIV-infected individual, the "Berlin patient", led to a cure. Since then there has been a search for approaches that mimic this intervention in a gene therapy setting. RNA interference (RNAi) has evolved as a powerful tool to regulate gene expression in a sequence-specific manner and can be used to inactivate the CCR5 mRNA. Short hairpin RNA (shRNA) molecules can impair CCR5 expression, but these molecules may cause unintended side effects and they will not be processed in cells that lack Dicer, such as monocytes...
2017: PloS One
https://www.readbyqxmd.com/read/28542057/knowing-your-community-community-health-assessment-as-a-powerful-tool
#17
Kaye Bender
No abstract text is available yet for this article.
July 2017: Journal of Public Health Management and Practice: JPHMP
https://www.readbyqxmd.com/read/28541721/a-joint-bayesian-model-for-integrating-microarray-and-rna-sequencing-transcriptomic-data
#18
Tianzhou Ma, Faming Liang, Steffi Oesterreich, George C Tseng
As the sequencing cost continued to drop in the past decade, RNA sequencing (RNA-seq) has replaced microarray to become the standard high-throughput experimental tool to analyze transcriptomic profile. As more and more datasets are generated and accumulated in the public domain, meta-analysis to combine multiple transcriptomic studies to increase statistical power has received increasing popularity. In this article, we propose a Bayesian hierarchical model to jointly integrate microarray and RNA-seq studies...
May 25, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28541490/glanet-genomic-loci-annotation-and-enrichment-tool
#19
Burçak Otlu, Can Firtina, Sündüz Keles, Oznur Tastan
Motivation: Genomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations. Results: We present GLANET as a comprehensive annotation and enrichment analysis tool which implements a sampling-based enrichment test that accounts for GC content and/or mappability biases, jointly or separately...
May 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28541284/a-scalable-double-barcode-sequencing-platform-for-characterization-of-dynamic-protein-protein-interactions
#20
Ulrich Schlecht, Zhimin Liu, Jamie R Blundell, Robert P St Onge, Sasha F Levy
Several large-scale efforts have systematically catalogued protein-protein interactions (PPIs) of a cell in a single environment. However, little is known about how the protein interactome changes across environmental perturbations. Current technologies, which assay one PPI at a time, are too low throughput to make it practical to study protein interactome dynamics. Here, we develop a highly parallel protein-protein interaction sequencing (PPiSeq) platform that uses a novel double barcoding system in conjunction with the dihydrofolate reductase protein-fragment complementation assay in Saccharomyces cerevisiae...
May 25, 2017: Nature Communications
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