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A simple objective method for determining a dynamic journal collection

J D Bastille, C J Mankin
1980 Bulletin of the Medical Library Association  
Titles have been ranked by raw use and by density of use with space and cost requirements for each. Data have also been analyzed for five special categories of use.  ...  To account for the effect of the bulk of the journal runs on the number of uses, raw use data have been adjusted using linear shelf space required for each title to produce a factor called density of use  ...  An analysis of the level of activity in changes of rank between the density of use ranking and the raw use ranking was performed.  ... 
pmid:7437589 pmcid:PMC226645 fatcat:yqr7kfx6vfa3xoqdhbxpskqz6i

Comparison of differential accessibility analysis strategies for ATAC-seq data

Paul Gontarz, Shuhua Fu, Xiaoyun Xing, Shaopeng Liu, Benpeng Miao, Viktoriia Bazylianska, Akhil Sharma, Pamela Madden, Kitra Cates, Andrew Yoo, Anna Moszczynska, Ting Wang (+1 others)
2020 Scientific Reports  
We further discussed the statistical and signal density cut-offs in the differential analysis of ATAC-seq by applying them to real data.  ...  Here, we used simulated datasets to systematically measure the sensitivity and specificity of six different methods.  ...  As the recall of true positives 1 CPM and 10 CPM at 20% mean difference and 50% mean difference between higher density and lower density are shown. The ingroup variance was 10%.  ... 
doi:10.1038/s41598-020-66998-4 pmid:32576878 fatcat:rggxubdxsbethnp4iaszourjnq

Tumor necrosis factor receptor family member RANK mediates osteoclast differentiation and activation induced by osteoprotegerin ligand

H. Hsu, D. L. Lacey, C. R. Dunstan, I. Solovyev, A. Colombero, E. Timms, H.-L. Tan, G. Elliott, M. J. Kelley, I. Sarosi, L. Wang, X.-Z. Xia (+9 others)
1999 Proceedings of the National Academy of Sciences of the United States of America  
A receptor that mediates osteoprotegerin ligand (OPGL)-induced osteoclast differentiation and activation has been identified via genomic analysis of a primary osteoclast precursor cell cDNA library and  ...  Furthermore, polyclonal Ab against the RANK extracellular domain promotes osteoclastogenesis in bone marrow cultures suggesting that RANK activation mediates the effects of OPGL on the osteoclast pathway  ...  We thank all members of the Amgen Genome Program for their collective contributions to this work, and to Ms. Judy from Kansas for her pioneering support of OPG clinical studies.  ... 
doi:10.1073/pnas.96.7.3540 pmid:10097072 pmcid:PMC22329 fatcat:2ftjomsgsnhwho7e62cxoltu6a

Creation of RANKL mutants with low affinity for decoy receptor OPG and their potential anti‐fibrosis activity

Yizhou Wang, Timo Michiels, Rita Setroikromo, Ronald van Merkerk, Robbert H. Cool, Wim J. Quax
2019 The FEBS Journal  
The signaling system encompassing Receptor Activator of Nuclear factor NF-κB Ligand (RANKL)/RANK/Osteoprotegerin (OPG) was discovered to play an important role in the regulation of ECM formation and degradation  ...  We show that RANKL_Q236D can activate RAW cells to initiate the process of ECM degradation and is able to escape from the obstruction by exogenous OPG.  ...  YW is a recipient of a scholarship from the Chinese Scholarship Council (CSC). We thank B.N. Melgert and H.  ... 
doi:10.1111/febs.14925 pmid:31081236 pmcid:PMC6852375 fatcat:pde6uxdsxnhjrcsnwrdmjwioja

Guide RNAs with embedded barcodes boost CRISPR-pooled screens

Shiyou Zhu, Zhongzheng Cao, Zhiheng Liu, Yuan He, Yinan Wang, Pengfei Yuan, Wei Li, Feng Tian, Ying Bao, Wensheng Wei
2019 Genome Biology  
This new system is particularly useful when the source of cells is limited or when it is difficult to control viral infection for in vivo screening.  ...  Our iBAR approach outperforms the conventional method by producing screening results with much lower false-positive and false-negative rates especially with a high multiplicity of infection (MOI).  ...  Availability of data and materials The accession number for the raw sequencing data reported in this paper is NCBI Sequence Read Archive (SRA): SRP164294 (PRJNA494953) [35] .  ... 
doi:10.1186/s13059-019-1628-0 fatcat:pcmajwrh25g4tklaaskyf5qcji

Bilateral Image Subtraction and Multivariate Models for the Automated Triaging of Screening Mammograms

José Celaya-Padilla, Antonio Martinez-Torteya, Juan Rodriguez-Rojas, Jorge Galvan-Tejada, Victor Treviño, José Tamez-Peña
2015 BioMed Research International  
In this study, 449 subjects (197 CS, 207 MS, and 45 HS) from a public database were used to train and evaluate the CADx. Percentile-rank (p-rank) andz-normalizations were used.  ...  For thez-normalization, the CS versus HS model achieved an accuracy of 0.825 with an AUC of 0.882 and the MS versus HS model obtained an accuracy of 0.698 and an AUC of 0.807.  ...  Acknowledgments This work was partially supported by the CONACyT Grant SSA/IMSS/ISSSTE 140601 and by Tecnológico de Monterrey Grupo de Investigación y Enfoque Estratégico en Bioinformatica.  ... 
doi:10.1155/2015/231656 pmid:26240818 pmcid:PMC4512565 fatcat:v6zhxdqbgfazre4y52vpjd4r2m

Iterative rank-order normalization of gene expression microarray data

Eric A Welsh, Steven A Eschrich, Anders E Berglund, David A Fenstermacher
2013 BMC Bioinformatics  
A significant strength of this and similar approaches is the use of the entire set of arrays during both normalization and model-based estimation of signal.  ...  However, this leads to differing estimates of expression based on the starting set of arrays, and estimates can change when a single, additional chip is added to the set.  ...  IRON is implemented as part of the libaffy C library and set of tools [17] .  ... 
doi:10.1186/1471-2105-14-153 pmid:23647742 pmcid:PMC3651355 fatcat:gwuoe6n5zzdzhepftchu4uffie

Validation of models for analysis of ranks in horse breeding evaluation

Anne Ricard, Andrés Legarra
2010 Genetics Selection Evolution  
Ranks have been used as phenotypes in the genetic evaluation of horses for a long time through the use of earnings, normal score or raw ranks.  ...  A model, ("underlying model" of an unobservable underlying variable responsible for ranks) exists. Recently, a full Bayesian analysis using this model was developed.  ...  Acknowledgements We gratefully acknowledge the financial support of "Les Haras Nationaux", France.  ... 
doi:10.1186/1297-9686-42-3 pmid:20109204 pmcid:PMC2832620 fatcat:tantkvp4uvalpcjh277swaoiym

Pepitome: Evaluating Improved Spectral Library Search for Identification Complementarity and Quality Assessment

Surendra Dasari, Matthew C. Chambers, Misti A. Martinez, Kristin L. Carpenter, Amy-Joan L. Ham, Lorenzo J. Vega-Montoto, David L. Tabb
2012 Journal of Proteome Research  
Pepitome identifications enabled the automation of quality analysis and quality control (QA/QC) for shotgun proteomics data acquisition pipelines.  ...  Pepitome outperformed the leading library search tool, SpectraST, when analyzing data sets acquired on three different mass spectrometry platforms.  ...  We thank Bing Zhang and Xiaojing Wang from Vanderbilt University for providing access to the RNA-Seq data of the "MMR Cell Lines" sample.  ... 
doi:10.1021/pr200874e pmid:22217208 pmcid:PMC3292681 fatcat:txfa3mz7sbhdbjjlbagoch25vm

Measurements of journal use: an analysis of the correlations between three methods

D D Blecic
1999 Bulletin of the Medical Library Association  
Three key measures are in-house use, circulation, and citation by faculty. This paper examines the correlations between these three measures at an academic health sciences library.  ...  Rapid journal price increases have made essential that libraries have reliable and efficient measures of the importance of individual journals to local clientele.  ...  Library Computer Systems Office for supplying circulation reports, and the Illinois Cooperative Collection Management Program for supplying the ISI citation report.  ... 
pmid:9934525 pmcid:PMC226509 fatcat:gupq222b25gnhif3s4jmdm5fym

YuGene: A simple approach to scale gene expression data derived from different platforms for integrated analyses

Kim-Anh Lê Cao, Florian Rohart, Leo McHugh, Othmar Korn, Christine A. Wells
2014 Genomics  
There are few purpose-built cross-platform normalization strategies, and most of these fit data to an idealised data structure, which in turn may compromise gene expression comparisons between different  ...  Barriers to integrating this data include disparities in data formats and scale, a lack of common identifiers, and the disproportionate contribution of platform to the 'batch effect'.  ...  (a) raw, (b) quantile normalized, (c) YuGene transformation, (d) rank of the data and (e) z-score transformation. The figures are obtained with a kernel density estimation.  ... 
doi:10.1016/j.ygeno.2014.03.001 pmid:24667244 fatcat:dc7w3vut7rckpop62q7rjv6wny

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

Nicolas C Nalpas, Stephen DE Park, David A Magee, Maria Taraktsoglou, John A Browne, Kevin M Conlon, Kévin Rue-Albrecht, Kate E Killick, Karsten Hokamp, Amanda J Lohan, Brendan J Loftus, Eamonn Gormley (+2 others)
2013 BMC Genomics  
Gene ontology analysis of the differentially expressed genes revealed an enrichment of immune, apoptotic and cell signalling genes.  ...  In addition, we compare gene expression profiles generated using RNA-seq with those previously generated by us using the high-density Affymetrix W GeneChip W Bovine Genome Array platform from the same  ...  Paul McGettigan of the UCD Reproductive Biology Research Cluster and the members of the UCD Tuberculosis Diagnostics and Immunology Research Centre.  ... 
doi:10.1186/1471-2164-14-230 pmid:23565803 pmcid:PMC3640917 fatcat:5xmjcfnhkfdhhosowntqepoupm

Minimal genome-wide human CRISPR-Cas9 library

Emanuel Gonçalves, Mark Thomas, Fiona M. Behan, Gabriele Picco, Clare Pacini, Felicity Allen, Alessandro Vinceti, Mamta Sharma, David A. Jackson, Stacey Price, Charlotte M. Beaver, Oliver Dovey (+5 others)
2021 Genome Biology  
MinLibCas9 provides backward compatibility with existing datasets, increases the dynamic range of CRISPR-Cas9 screens and extends their application to complex models and assays.  ...  We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 42% reduction in size compared  ...  Peer review information Yixin Yao and Kevin Pang were the primary editors on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.  ... 
doi:10.1186/s13059-021-02268-4 pmid:33478580 pmcid:PMC7818936 fatcat:xquw27ddhfhn7kc3vbyh76rr6u

Obesity as a driver of international differences in COVID-19 death rates

Julian Gardiner, Jude Oben, Alastair Sutcliffe
2021 Diabetes, obesity and metabolism  
A large proportion of the variation in COVID-19 death rates between countries can be explained by differences in obesity rates, population health, population density, age demographics, the delay in imposing  ...  Some of the unexplained variation is probably attributable to inter-country differences in the definition of COVID-19 deaths and in the completeness of the recording of COVID-19 deaths.  ...  ACKNOWLEDGEMENTS The authors would like to thank the NIHR BRC for supporting the UCL Institute of Child Health.  ... 
doi:10.1111/dom.14357 pmid:33620765 fatcat:afetvgutfneivimckgdhx2kwj4

Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays

Colin S Gillespie, Guiyuan Lei, Richard J Boys, Amanda Greenall, Darren J Wilkinson
2010 BMC Research Notes  
However, proper statistical analysis of time-course data requires the use of more sophisticated tools and complex statistical models.  ...  Findings: Using the open source CRAN and Bioconductor repositories for R, we provide example analysis and protocol which illustrate a variety of methods that can be used to analyse time-course microarray  ...  The authors are affiliated with the Centre for Integrated Systems Biology of Ageing and Nutrition (CISBAN) at Newcastle University, which is supported jointly by the Biotechnology and Biological Sciences  ... 
doi:10.1186/1756-0500-3-81 pmid:20302631 pmcid:PMC2880961 fatcat:tt7p3ykvfng7loqal6egqc4iji
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