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Gene expression microarrays and the integration of biological knowledge

Michiel O Noordewier, Patrick V Warren
<span title="">2001</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/va62z7g5ofgoday6mzmc4uzqgm" style="color: black;">Trends in Biotechnology</a> </i> &nbsp;
Noordewier and Patrick V. Warren Review criteria, including sequence, MeSH headings, keywords and content.  ...  TRENDS in Biotechnology Cell lines A C D H B E F G + + + + ----Compounds U ----+ + -+ V + + ---+ --W -----+ + -X --+ + -+ --Y -+ + + + -+ Fig. 3 . 3 Microarrays of cDNAs  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0167-7799(01)01735-8">doi:10.1016/s0167-7799(01)01735-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11587767">pmid:11587767</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6lro76xkszbudhxhq77kweai7a">fatcat:6lro76xkszbudhxhq77kweai7a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060909055053/http://genomics10.bu.edu/mschaff/microarraypapers/Microarray%20General/Noordewier_TIB-Arrays_Review.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/37/03/3703cd8772e1f4e05e437c22f111859ae130757c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0167-7799(01)01735-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Evolution of Two-Component Signal Transduction

Kristin K. Koretke, Andrei N. Lupas, Patrick V. Warren, Martin Rosenberg, James R. Brown
<span title="2000-12-01">2000</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4bimmtjdczetrfmnc3ijbmwpoy" style="color: black;">Molecular biology and evolution</a> </i> &nbsp;
Two-component signal transduction (TCST) systems are the principal means for coordinating responses to environmental changes in bacteria as well as some plants, fungi, protozoa, and archaea. These systems typically consist of a receptor histidine kinase, which reacts to an extracellular signal by phosphorylating a cytoplasmic response regulator, causing a change in cellular behavior. Although several model systems, including sporulation and chemotaxis, have been extensively studied, the
more &raquo; ... nary relationships between specific TCST systems are not well understood, and the ancestry of the signal transduction components is unclear. Phylogenetic trees of TCST components from 14 complete and 6 partial genomes, containing 183 histidine kinases and 220 response regulators, were constructed using distance methods. The trees showed extensive congruence in the positions of 11 recognizable phylogenetic clusters. Eukaryotic sequences were found almost exclusively in one cluster, which also showed the greatest extent of domain variability in its component proteins, and archaeal sequences mainly formed speciesspecific clusters. Three clusters in different parts of the kinase tree contained proteins with serine-phosphorylating activity. All kinases were found to be monophyletic with respect to other members of their superfamily, such as type II topoisomerases and Hsp90. Structural analysis further revealed significant similarity to the ATP-binding domain of eukaryotic protein kinases. TCST systems are of bacterial origin and radiated into archaea and eukaryotes by lateral gene transfer. Their components show extensive coevolution, suggesting that recombination has not been a major factor in their differentiation. Although histidine kinase activity is prevalent, serine kinases have evolved multiple times independently within this family, accompanied by a loss of the cognate response regulator(s). The structural and functional similarity between TCST kinases and eukaryotic protein kinases raises the possibility of a distant evolutionary relationship.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/oxfordjournals.molbev.a026297">doi:10.1093/oxfordjournals.molbev.a026297</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11110912">pmid:11110912</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/24lcp3jz5rhv7lgklpi5sioz3y">fatcat:24lcp3jz5rhv7lgklpi5sioz3y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100216062748/http://mbe.oxfordjournals.org:80/cgi/reprint/17/12/1956.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a9/f6/a9f647904e5f695f4087b1a544372358c3611e4d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/oxfordjournals.molbev.a026297"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Conserved syntenic clusters of protein coding genes are missing in birds

Peter V Lovell, Morgan Wirthlin, Larry Wilhelm, Patrick Minx, Nathan H Lazar, Lucia Carbone, Wesley C Warren, Claudio V Mello
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bzsiicmhvczjnsm7jbog7ysaa" style="color: black;">Genome Biology</a> </i> &nbsp;
We note that we used the most recent version of the chicken genome (gal-Gal4), and an improved version of the zebra finch genome (Mello and Warren, unpublished data) in which additional Illumina sequence  ...  the best-covered avian genome, we also conducted mega-BLAST searches of the individual genome sequencing reads for chicken and zebra finch [51] , and an Illumina SOAP de novo chicken genome assembly (Warren  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13059-014-0565-1">doi:10.1186/s13059-014-0565-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25518852">pmid:25518852</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4290089/">pmcid:PMC4290089</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oyz6xst7kvhnnbx25kkwmkutyi">fatcat:oyz6xst7kvhnnbx25kkwmkutyi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171017101456/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/aa7/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvczEzMDU5LTAxNC0wNTY1LTEucGRm.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cf/b2/cfb20d6cf686713231525d3f010b0256da428ef9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13059-014-0565-1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290089" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Women with high exercise tolerance and the role of myocardial perfusion imaging

Sofia N. Chatziioannou, Warren H. Moore, Ramesh D. Dhekne, Patrick V. Ford
<span title="">2001</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fsrkshzmvbcynhtiupsyvtdedu" style="color: black;">Clinical Cardiology</a> </i> &nbsp;
Myocardial perfusion imaging (MPI) provides incremental diagnostic and prognostic information, even in patients with high exercise tolerance. Hypothesis: Myocardial perfusion imaging provides significant diagnostic value, specifically in women with high exercise tolerance. Methods: Our study population consisted of all women who underwent exercise MPI in our Department from January 1992 to June 1996 and reached at least Stage IV in the Bruce protocol. Patients were divided into those with known
more &raquo; ... and those with possible coronary artery disease (CAD). All patients were followed for 3 years from the performance of h4PI. Results: Of 4,803 women who underwent myocardial perfusion imaging, 3, I83 had exercise stressing, and of those, 3 1 1 reached at least Stage IV in the Bruce protocol. Of these 3 1 1 MPI scans, only 23 (7.4%) were abnormal (reversible, fixed, or mixed) and the remaining 288 (92.6%) were normal. Of the 82 patients with known CAD, 13 (15.8%) had an abnormal MPI, while only 10 (4.4%) of the 229 patients with possible CAD. No myocardial infarction or cardiac death occurred within 3 years; one patient with normal MPI needed revascularization. Conclusion: In women with high exercise tolerance, especially in those without already known CAD, the yield of MPI is very low. Women with high exercise tolerance have an excellent prognosis.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/clc.4960240611">doi:10.1002/clc.4960240611</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11403510">pmid:11403510</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u7laozu6gjdhhmswjcblab3wia">fatcat:u7laozu6gjdhhmswjcblab3wia</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191024012747/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6655181&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0e/17/0e17b5411392882942c3fc657b87de12ff8836a6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/clc.4960240611"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a>

ApoE genotype-specific inhibition of apoptosis

Robert M. DeKroon, Mirta Mihovilovic, Zoe V. Goodger, Jennifer B. Robinette, Patrick M. Sullivan, Ann M. Saunders, Warren J. Strittmatter
<span title="2003-05-16">2003</span> <i title="American Society for Biochemistry &amp; Molecular Biology (ASBMB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dhy2q44wbjhqnktingq26ppurq" style="color: black;">Journal of Lipid Research</a> </i> &nbsp;
Endothelial cell apoptosis can be initiated by withdrawing growth factors or serum, and is inhibited by HDL. Our results show that the total lipoprotein population from apolipoprotein E 4/4 (APOE4/4) sera is less anti-apoptotic than total lipoproteins from other APOE genotypes, as measured by caspase 3/7 activity. Moreover, APOE4/4 VLDL antagonizes the antiapoptotic activity of HDL by a mechanism requiring binding of apoE4 on VLDL particles to an LDL family receptor. This ability of APOE4/4
more &raquo; ... to inhibit the antiapoptotic effects of HDL presents a potential mechanism by which the expression of several diseases, including atherosclerosis, is enhanced by the APOE4 genotype.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1194/jlr.m300097-jlr200">doi:10.1194/jlr.m300097-jlr200</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12754278">pmid:12754278</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ro7kmymgdvel5dfsx44s3l74h4">fatcat:ro7kmymgdvel5dfsx44s3l74h4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720090128/http://www.jlr.org/content/44/8/1566.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/06/a8/06a8d67c7e797499db68a62d258503e62dc5e5c1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1194/jlr.m300097-jlr200"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

The complete genome of the hyperthermophilic bacterium Aquifex aeolicus

Gerard Deckert, Patrick V. Warren, Terry Gaasterland, William G. Young, Anna L. Lenox, David E. Graham, Ross Overbeek, Marjory A. Snead, Martin Keller, Monette Aujay, Robert Huber, Robert A. Feldman (+3 others)
<span title="">1998</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/drfdii35rzaibj3aml5uhvr5xm" style="color: black;">Nature</a> </i> &nbsp;
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/32831">doi:10.1038/32831</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9537320">pmid:9537320</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4kmtuov5zvbctjhw7kwndwz4nm">fatcat:4kmtuov5zvbctjhw7kwndwz4nm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200316020332/https://www.nature.com/articles/32831.pdf?error=cookies_not_supported&amp;code=037c7ba7-a28f-44d1-9f7b-76786360fed9" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ef/c8/efc847f4e15990b9eacc85f60364eb39fe42a46f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/32831"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a>

Reconstitution of electron transport in photosystem I with PsaC and PsaD proteins expressed inEscherichia coli

Jindong Zhao, Patrick V. Warren, Ning Li, Donald A. Bryant, John H. Golbeck
<span title="1990-12-10">1990</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kn6dhptylrb77b5atyiom5ysjm" style="color: black;">FEBS Letters</a> </i> &nbsp;
concentration of 0.01%; (iii) the PsaCl apoprotein was added at an 80-fold molar excess (relative to P700); (iv) after 10 min an aliquot of 30 mM FeCls was slowly added to a final concentration of 0.15 mM; (v)  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/0014-5793(90)80536-r">doi:10.1016/0014-5793(90)80536-r</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/2125006">pmid:2125006</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e3ngl7qxdvetvgmpacgwyz7h5y">fatcat:e3ngl7qxdvetvgmpacgwyz7h5y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190216193257/https://core.ac.uk/download/pdf/82426346.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/01/ac/01ac868b0a89959995b33307ea0dd891124b35a2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/0014-5793(90)80536-r"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Experience and Compliance With Scanning Vaccines' Two-Dimensional Barcodes to Record Data

Heather V. Evanson, Loren Rodgers, Jenica Reed, Ashley Daily, Kenneth Gerlach, Michael Greene, Patrick Koeppl, Regina Cox, Warren Williams
<span title="">2017</span> <i title="Ovid Technologies (Wolters Kluwer Health)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gii7dlrmufbqhinvkvwqb4rhgu" style="color: black;">Computers, Informatics, Nursing</a> </i> &nbsp;
Automated population of data into health information system fields offers the potential to increase efficiencies and save time. Increasingly, as 2D barcoded vaccine products and barcode scanning technology become more widely available, manual recording of vaccine data can be reduced. This evaluation explores how often 2D barcodes on vaccine vials and syringes were scanned and the perceived benefits and challenges reported by vaccine providers. Eighty-two facilities that administer vaccines
more &raquo; ... eted the evaluation. Twenty-seven of those facilities provided records from vaccines administered between July 2014 and January 2015. Among the 63,179 2D barcoded vaccine administrations recorded, 12,408 (19%) were scanned. We received 116 user surveys from 63 facilities; using content analysis we identified perceived benefits of scanning, workflow challenges, scanning challenges, and other challenges. The findings of this evaluation can guide health information system developers, vaccine manufacturers, and vaccine providers on how to remove potential barriers to using 2D barcode scanning.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1097/cin.0000000000000395">doi:10.1097/cin.0000000000000395</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29049085">pmid:29049085</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5896297/">pmcid:PMC5896297</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/n46xzhiajjdc7evtuxzna52x6a">fatcat:n46xzhiajjdc7evtuxzna52x6a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208070306/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5896297&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c1/ed/c1ed7575a372bfde8b6b61374a3b3d0c73fe7395.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1097/cin.0000000000000395"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5896297" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Prognostic Value of Myocardial Perfusion Imaging in Patients With High Exercise Tolerance

Sofia N. Chatziioannou, Warren H. Moore, Patrick V. Ford, Ronald E. Fisher, Vei-Vei Lee, Carina Alfaro-Franco, Ramesh D. Dhekne
<span title="1999-02-23">1999</span> <i title="Ovid Technologies (Wolters Kluwer Health)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yp7myvwge5ef7jsub32vmdbdhy" style="color: black;">Circulation</a> </i> &nbsp;
Background-Although high exercise tolerance is associated with an excellent prognosis, the significance of abnormal myocardial perfusion imaging (MPI) in patients with high exercise tolerance has not been established. This study retrospectively compares the utility of MPI and exercise ECG (EECG) in these patients. Methods and Results-Of 388 consecutive patients who underwent exercise MPI and reached at least Bruce stage IV, 157 (40.5%) had abnormal results and 231 (59.5%) had normal results.
more &raquo; ... low-up was performed at 18Ϯ2.7 months. Adverse events, including revascularization, myocardial infarction, and cardiac death, occurred in 40 patients. Nineteen patients had revascularization related to the MPI results or the patient's condition at the time of MPI and were not included in further analysis. Seventeen patients (12.2%) with abnormal MPI and 4 (1.7%) with normal MPI had adverse cardiac events (PϽ0.001). Cox proportional-hazards regression analysis showed that MPI was an excellent predictor of cardiac events (global 2 ϭ13.2; PϽ0.001; relative riskϭ8; 95% CIϭ3 to 23) but EECG had no predictive power (global 2 ϭ0.05; Pϭ0.8; relative riskϭ1; 95% CIϭ0.4 to 3.0). The addition of Duke's treadmill score risk categories did not improve the predictive power of EECG (global 2 ϭ0.17). The predictive power of the combination of EECG (including Duke score categories) and MPI was no better than that of MPI alone (global 2 ϭ13.5). Conclusions-Unlike EECG, MPI is an excellent prognostic indicator for adverse cardiac events in patients with known or suspected CAD and high exercise tolerance. (Circulation. 1999;99:867-872.)
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1161/01.cir.99.7.867">doi:10.1161/01.cir.99.7.867</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10027807">pmid:10027807</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kwxoe3a5gzgexasi2sahxnllry">fatcat:kwxoe3a5gzgexasi2sahxnllry</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724032044/http://circ.ahajournals.org/content/circulationaha/99/7/867.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9c/99/9c991da4628edc34f1e20efad991e2c693b5addd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1161/01.cir.99.7.867"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Efficient digest of high-throughput sequencing data in a reproducible report

Zhe Zhang, Jeremy Leipzig, Ariella Sasson, Angela M Yu, Juan C Perin, Hongbo M Xie, Mahdi Sarmady, Patrick V Warren, Peter S White
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
High-throughput sequencing (HTS) technologies are spearheading the accelerated development of biomedical research. Processing and summarizing the large amount of data generated by HTS presents a nontrivial challenge to bioinformatics. A commonly adopted standard is to store sequencing reads aligned to a reference genome in SAM (Sequence Alignment/Map) or BAM (Binary Alignment/Map) files. Quality control of SAM/BAM files is a critical checkpoint before downstream analysis. The goal of the
more &raquo; ... project is to facilitate and standardize this process. Results: We developed bamchop, a robust program to efficiently summarize key statistical metrics of HTS data stored in BAM files, and to visually present the results in a formatted report. The report documents information about various aspects of HTS data, such as sequencing quality, mapping to a reference genome, sequencing coverage, and base frequency. Bamchop uses the R language and Bioconductor packages to calculate statistical matrices and the Sweave utility and associated LaTeX markup for documentation. Bamchop's efficiency and robustness were tested on BAM files generated by local sequencing facilities and the 1000 Genomes Project. Source code, instruction and example reports of bamchop are freely available from https://github.com/CBMi-BiG/ bamchop. Conclusions: Bamchop enables biomedical researchers to quickly and rigorously evaluate HTS data by providing a convenient synopsis and user-friendly reports.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s11-s3">doi:10.1186/1471-2105-14-s11-s3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24564231">pmid:24564231</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3846741/">pmcid:PMC3846741</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/glvvga2zxjeotkdd4mvso26yde">fatcat:glvvga2zxjeotkdd4mvso26yde</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3846741/PMC3846741-1471-2105-14-S11-S3.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b0/5b/b05b5493fb31d125124f85dfc6f3c53aa73d54db.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s11-s3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3846741" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Evaluation of scanning 2D barcoded vaccines to improve data accuracy of vaccines administered

Ashley Daily, Erin D. Kennedy, Leslie A. Fierro, Jenica Huddleston Reed, Michael Greene, Warren W. Williams, Heather V. Evanson, Regina Cox, Patrick Koeppl, Ken Gerlach
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wqdavxmwkrh4ndbs3jgtlylvmq" style="color: black;">Vaccine</a> </i> &nbsp;
and Objective-Accurately recording vaccine lot number, expiration date, and product identifiers, in patient records is an important step in improving supply chain management and patient safety in the event of a recall. These data are being encoded on two-dimensional (2D) barcodes on most vaccine vials and syringes. Using electronic vaccine administration records, we evaluated the accuracy of lot number and expiration date entered using 2D barcode scanning compared to traditional manual or
more &raquo; ... own list entry methods. Methods-We analyzed 128,573 electronic records of vaccines administered at 32 facilities. We compared the accuracy of records entered using 2D barcode scanning with those entered using traditional methods using chi-square tests and multilevel logistic regression. Results-When 2D barcodes were scanned, lot number data accuracy was 1.8 percentage points higher (94.3% to 96.1%, P < .001) and expiration date data accuracy was 11 percentage points higher (84.8% to 95.8%, P < .001) compared with traditional methods. In multivariate analysis, lot number was more likely to be accurate (aOR = 1.75; 99% CI, 1.57-1.96) as was expiration date (aOR = 2.39; 99% CI, 2.12-2.68). When controlling for scanning and other factors, manufacturer,
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.vaccine.2016.09.052">doi:10.1016/j.vaccine.2016.09.052</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27742219">pmid:27742219</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5297213/">pmcid:PMC5297213</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fifbhlfd5nfixbjli3km3y4hjm">fatcat:fifbhlfd5nfixbjli3km3y4hjm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208052252/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5297213&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/51/b5/51b58faa694704f6914fd611fe8bf2cf220d1e11.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.vaccine.2016.09.052"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5297213" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The pānānā or 'sighting wall' at Hanamauloa, Kahikinui, Maui: archaeological investigation of a possible navigational monument

Patrick V. Kirch, Clive Ruggles, Warren D. Sharp
<span title="">2013</span> <i title="The Polynesian Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4nrb7ddyu5h7rdbej6etvp4hqq" style="color: black;">The Journal of the Polynesian Society</a> </i> &nbsp;
The Pänänä or 'Sighting Wall' at Hanamauloa Patrick V.Kirch, Clive Ruggles and Warren D. Sharp  ...  In addition, we are joined by geochronologist Warren Sharp, who has assisted us in dating branch coral associated with the site, giving a possible age of construction or use of the pänänä.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.15286/jps.122.1.45-68">doi:10.15286/jps.122.1.45-68</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/borkspi3njcqrcigr2qfwrzxle">fatcat:borkspi3njcqrcigr2qfwrzxle</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429024435/http://thepolynesiansociety.org/jps/index.php/JPS/article/download/50/50" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/87/01/8701084d472d5441f64f9938b24ff9eb9d8ffa7f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.15286/jps.122.1.45-68"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Harmonization of cortical thickness measurements across scanners and sites [article]

Jean-Philippe Fortin, Nicholas Cullen, Yvette I. Sheline, Warren D. Taylor, Irem Aselcioglu, Phil Adams, Crystal Cooper, Mauricio Fava, Patrick J. McGrath, Melvin McInnis, Ramin V. Parsey, Mary L. Phillips (+3 others)
<span title="2017-06-10">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
ij β v + Z T ij θ v + ijv (2) where α v is the average cortical thickness for the reference site for feature v, where θ v is the k × 1 vector of the coefficients associated with Z for feature v and where  ...  Using the previous notation, the model can be written as y ijv = α v + X T ij β v + Z T ij θ v + δ iv ijv , (3) where α v is the average cortical thickness for the reference site for feature v, where θ  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/148502">doi:10.1101/148502</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2s6ynnpgezcd3ax2owiv76bk6e">fatcat:2s6ynnpgezcd3ax2owiv76bk6e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501220521/https://www.biorxiv.org/content/biorxiv/early/2017/06/10/148502.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/148502"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Domain Architecture and Biochemical Characterization of Vertebrate Mcm10

Patrick D. Robertson, Eric M. Warren, Haijiang Zhang, David B. Friedman, Jeffrey W. Lary, James L. Cole, Antonin V. Tutter, Johannes C. Walter, Ellen Fanning, Brandt F. Eichman
<span title="2007-12-06">2007</span> <i title="American Society for Biochemistry &amp; Molecular Biology (ASBMB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mryncoafc5cxdicldzfm4vlsze" style="color: black;">Journal of Biological Chemistry</a> </i> &nbsp;
Proteases were inactivated by adding 10 l of SDS-PAGE sample buffer (63 mM Tris-HCl, pH 6.8, 700 mM ␤-mercaptoethanol, 2% w/v SDS, 0.03% w/v bromphenol blue, and 10% glycerol) and heating for 5 min at  ...  Reactions were concentrated in 0.1% trifluoroacetic acid, mixed with 3 l of saturated sinapinic acid in 60:40 (v/v) acetonitrile:1% trifluoroacetic acid/distilled H 2 O, and 1 l was deposited onto a gold  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/jbc.m706267200">doi:10.1074/jbc.m706267200</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18065420">pmid:18065420</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2753450/">pmcid:PMC2753450</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p5jf4a5jwzgw7b7cq5kherzkrq">fatcat:p5jf4a5jwzgw7b7cq5kherzkrq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724232155/http://www.jbc.org/content/283/6/3338.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f0/78/f078d3ab9e6e96a71cc252598c3fcb2088e28e71.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/jbc.m706267200"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753450" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Statistical Design Features of the Healthy Communities Study

Warren J. Strauss, Christopher J. Sroka, Edward A. Frongillo, S. Sonia Arteaga, Catherine M. Loria, Eric S. Leifer, Colin O. Wu, Heather Patrick, Howard A. Fishbein, Lisa V. John
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3udjmbs5yjcnjgfox7chccjfqy" style="color: black;">American Journal of Preventive Medicine</a> </i> &nbsp;
The Healthy Communities Study is designed to assess relationships between characteristics of community programs and policies targeting childhood obesity and children's BMI, diet, and physical activity. The study involved a complex data collection protocol implemented over a 2-year period (2013-2015) across a diverse sample of 130 communities, defined as public high school catchment areas. The protocol involved baseline assessment within each community that included in-person or telephone
more &raquo; ... ews regarding community programs and policies and in-home collection of BMI, nutritional, and physical activity outcomes from a sample of up to 81 children enrolled in kindergarten through eighth grade in public schools. The protocol also involved medical record reviews to establish a longitudinal trajectory of BMI for an estimated 70% of participating children. Staged sampling was used to collect less detailed measures of physical activity and nutrition across the entire sample of children, with a subset assessed using more costly, burdensome, and detailed measures. Data from the Healthy Community Study will be analyzed using both crosssectional and longitudinal models that account for the complex design and correct for measurement error and bias using a likelihood-based Markov-chain Monte Carlo methodology. This methods paper provides insights into the complex design features of the Healthy Communities Study and may serve as an example for future large-scale studies that assess the relationship between community-based programs and policies and health outcomes of community residents. (Am J Prev Med 2015;49(4):624-630) &
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.amepre.2015.06.021">doi:10.1016/j.amepre.2015.06.021</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26384932">pmid:26384932</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4575768/">pmcid:PMC4575768</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y5l3b2debvd23csbo76lhzwi3m">fatcat:y5l3b2debvd23csbo76lhzwi3m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170927120657/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/525/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDc0OTM3OTcxNTAwMzMxMQ%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/50/e7/50e71039342d88261e5508af7823d0aab076358e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.amepre.2015.06.021"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4575768" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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