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The impact of Docker containers on the performance of genomic pipelines

Paolo Di Tommaso, Emilio Palumbo, Maria Chatzou, Pablo Prieto, Michael L. Heuer, Cedric Notredame
2015 PeerJ  
. • Emilio Palumbo, Maria Chatzou and Michael L.  ...  Heuer contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper. • Pablo Prieto analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared  ... 
doi:10.7717/peerj.1273 pmid:26421241 pmcid:PMC4586803 fatcat:4qxyd3khznhplnuq4liu5f6f3q

BOSC 2019, the 20th annual Bioinformatics Open Source Conference

Nomi L. Harris, Peter J.A. Cock, Christopher J. Fields, Bastian Greshake Tzovaras, Michael Heuer, Karsten Hokamp, Monica Munoz-Torres, Alexander Peltzer, Bastian Rieck, Heather Wiencko, Yo Yehudi
2019 F1000Research  
Source Conference (BOSC) Nomi L.  ...  From left to right: Peter Cock, Karsten Hokamp, Yo Yehudi, Nomi Harris, Monica Munoz-Torres, Heather Wiencko, Michael Heuer, Bastian Greshake Tzovaras; not shown: Chris Fields.  ... 
doi:10.12688/f1000research.21568.1 pmid:32025286 pmcid:PMC6971845 fatcat:5yy5psbptrbc5m6424wcyigav4

Provider perceptions of limited health literacy in community health centers

Jennifer A. Schlichting, Michael T. Quinn, Loretta J. Heuer, Cynthia T. Schaefer, Melinda L. Drum, Marshall H. Chin
2007 Patient Education and Counseling  
Objective-To examine techniques used by community health center (HC) providers to care for patients with limited health literacy (LHL). Methods-Survey mailed to 803 HC providers in 10 Midwestern states. Response rate was 47.5%. Associations between variables were examined using generalized estimating equations (GEE) models to account for clustering of respondents within health centers. Results-The average provider estimates of LHL prevalence among English-speaking and Spanishspeaking patients
more » ... re 41% ±24% (mean ± SD) and 48% ±30%, respectively. Those with training in health literacy were more likely to have patients repeat instructions back to check understanding (OR=2.05, p=0.04) and were more likely to give out health education materials designed for patients with LHL (OR=2.80, p=0.0002). Providers differed by type in encouraging patients to bring friends or family members to appointments (p=0.02). Conclusions-Providers estimate LHL to be highly prevalent in their HCs, and use various techniques to assist patients. Practice Implications-Training in health literacy is associated with increased usage of evidencebased techniques to assist patients with LHL. Providers at all levels would likely benefit from LHL training. Most providers believe providing health education materials designed specifically for patients with LHL would be very helpful.
doi:10.1016/j.pec.2007.08.003 pmid:17889494 pmcid:PMC2246059 fatcat:hypyt23lvrfmjimetpbfphe7nu

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

Peter J. A. Cock, Christopher J. Fields, Naohisa Goto, Michael L. Heuer, Peter M. Rice
2009 Nucleic Acids Research  
FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger standard, the Solexa/ Illumina variants and conversion between them, based on publicly available information such as the MAQ documentation and conventions recently agreed by the Open
more » ... informatics Foundation projects Biopython, BioPerl, BioRuby, BioJava and EMBOSS. Being an open access publication, it is hoped that this description, with the example files provided as Supplementary Data, will serve in future as a reference for this important file format.
doi:10.1093/nar/gkp1137 pmid:20015970 pmcid:PMC2847217 fatcat:hh5eesuklnbkxmiarcsk63gfhq

Predicting Changes in Staff Morale and Burnout at Community Health Centers Participating in the Health Disparities Collaboratives

Jessica E. Graber, Elbert S. Huang, Melinda L. Drum, Marshall H. Chin, Amy E. Walters, Loretta Heuer, Hui Tang, Cynthia T. Schaefer, Michael T. Quinn
2008 Health Services Research  
Heuer was a Robert Wood Johnson Executive Nurse Fellow. Disclosures: There are no financial or other conflicts to report. Disclaimers: There are no disclaimers to report.  ... 
doi:10.1111/j.1475-6773.2007.00828.x pmid:18248402 pmcid:PMC2517268 fatcat:diwhi34eyneb5deqpra3bxlfgu

Combating Obesity at Community Health Centers (COACH): A Quality Improvement Collaborative for Weight Management Programs

Abigail E. Wilkes, Priya M. John, Anusha M. Vable, Amanda Campbell, Loretta Heuer, Cynthia Schaefer, Lisa Vinci, Melinda L. Drum, Marshall H. Chin, Michael T. Quinn, Deborah L. Burnet
2013 Journal of health care for the poor and underserved  
Community health centers (CHCs) seek effective strategies to address obesity. MidWest Clinicians' Network partnered with [an academic medical center] to test feasibility of a weight management quality improvement (QI) collaborative. MidWest Clinicians' Network members expressed interest in an obesity QI program. This pilot study aimed to determine whether the QI model can be feasibly implemented with limited resources at CHCs to improve weight management programs. Five health centers with
more » ... management programs enrolled with CHC staff as primary study participants; this study did not attempt to measure patient outcomes. Participants attended learning sessions and monthly conference calls to build QI skills and share
doi:10.1353/hpu.2013.0101 pmid:23727964 pmcid:PMC3750964 fatcat:onea2ersfjc7fldmsyyptaepo4

The Perceived Financial Impact of Quality Improvement Efforts in Community Health Centers

Karen Cheung, Adil Moiduddin, Marshall H. Chin, Melinda L. Drum, Sydney E. S. Brown, Jessica E. Graber, Loretta Heuer, Michael T. Quinn, Cynthia T. Schaefer, Amy E. Schlotthauer, Elbert S. Huang
2008 The journal of ambulatory care management  
We administered surveys to 100 chief executive officers (CEOs) of community health centers to determine their perceptions of the financial impact of the Health Disparities Collaboratives, a national quality improvement initiative. One third of the CEOs believed that the HDC had a negative financial impact on their health center, and this perception was significantly correlated with centers having a higher proportion of uninsured patients. Performance-based payment incentives may improve care
more » ... may also add new financial burdens to facilities that treat the uninsured population. As such, a provider's payer mix may need to be considered in the design of QI programs if they are to be sustainable.
doi:10.1097/01.jac.0000314701.50042.0b pmid:18360172 pmcid:PMC2291345 fatcat:ydluwea3ofbufinpsbq2qpiwwa

Peripheral Innate Immune Activation Correlates With Disease Severity in GRN Haploinsufficiency

Peter A. Ljubenkov, Zachary Miller, Paige Mumford, Jane Zhang, Isabel Elaine Allen, Laura Mitic, Adam Staffaroni, Hilary Heuer, Julio C. Rojas, Yann Cobigo, Anna Karydas, Rodney Pearlman (+5 others)
2019 Frontiers in Neurology  
Objective: To investigate associations between peripheral innate immune activation and frontotemporal lobar degeneration (FTLD) in progranulin gene (GRN) haploinsufficiency. Methods: In this cross-sectional study, ELISA was used to measure six markers of innate immunity (sCD163, CCL18, LBP, sCD14, IL-18, and CRP) in plasma from 30 GRN mutation carriers (17 asymptomatic, 13 symptomatic) and 29 controls. Voxel based morphometry was used to model associations between marker levels and brain
more » ... in mutation carriers relative to controls. Linear regression was used to model relationships between plasma marker levels with mean frontal white matter integrity [fractional anisotropy (FA)] and the FTLD modified Clinical Dementia Rating Scale sum of boxes score (FTLD-CDR SB). Results: Plasma sCD163 was higher in symptomatic GRN carriers [mean 321 ng/ml (SD 125)] compared to controls [mean 248 ng/ml (SD 58); p < 0.05]. Plasma CCL18 was higher in symptomatic GRN carriers [mean 56.9 pg/ml (SD 19)] compared to controls [mean 40.5 pg/ml (SD 14); p < 0.05]. Elevation of plasma LBP was associated with white matter atrophy in the right frontal pole and left inferior frontal gyrus (p FWE corrected <0.05) in all mutation carriers relative to controls. Plasma LBP levels inversely correlated with bilateral frontal white matter FA (R2 = 0.59, p = 0.009) in mutation carriers. Elevation in plasma was positively correlated with CDR-FTLD SB (b = 2.27 CDR units/μg LBP/ml plasma, R2 = 0.76, p = 0.003) in symptomatic carriers. Conclusion: FTLD-GRN is associated with elevations in peripheral biomarkers of macrophage-mediated innate immunity, including sCD163 and CCL18. Clinical disease severity and white matter integrity are correlated with blood LBP, suggesting a role for peripheral immune activation in FTLD-GRN.
doi:10.3389/fneur.2019.01004 pmid:31620075 pmcid:PMC6759464 fatcat:joh6zrgepjaxfndjqsbeohfjh4

Community Health Center Provider and Staff's Spanish Language Ability and Cultural Awareness

Arshiya A. Baig, Amanda Benitez, Cara A. Locklin, Amanda Campbell, Cynthia T. Schaefer, Loretta J. Heuer, Sang Mee Lee, Marla C. Solomon, Michael T. Quinn, Deborah L. Burnet, Marshall H. Chin
2014 Journal of health care for the poor and underserved  
Many community health center providers and staff care for Latinos with diabetes, but their Spanish language ability and awareness of Latino culture are unknown. We surveyed 512 Midwestern health center providers and staff who managed Latino patients with diabetes. Few respondents had high Spanish language (13%) or cultural awareness scores (22%). Of respondents who self-reported 76-100% of their patients were Latino, 48% had moderate/low Spanish language and 49% had moderate/low cultural
more » ... ncy scores. Among these respondents, 3% lacked access to interpreters and 27% had neither received cultural competency training nor had access to training. Among all respondents, Spanish skills and Latino cultural awareness were low. Respondents who saw a significant number of Latinos had good access to interpretation services but not cultural competency training. Improved Spanish-language skills and increased access to cultural competency training and Latino cultural knowledge are needed to provide linguistically and culturally tailored care to Latino patients. The Latino population is the largest and fastest growing ethnic minority in the United States. 1 By 2050, Latinos are predicted to be one-third of the U.S. population. 2 The health care system must be prepared to care for this population and its disproportionate burden of diabetes. 3 Latinos are almost twice as likely to have a diagnosis of diabetes, have higher rates of complications, and have a 65% higher diabetes-related mortality rate than non-Hispanic Whites. 4, 5 Cultural awareness score High Moderate or low High Moderate or low n % n % p-value n % n % p-value All Respondents
doi:10.1353/hpu.2014.0086 pmid:24858866 pmcid:PMC4128238 fatcat:rvyuoi25grg5beq4xltbbqkwpu

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1

Ethan Cerami, Jianjiong Gao, Ugur Dogrusoz, Benjamin E. Gross, Selcuk Onur Sumer, Bülent Arman Aksoy, Anders Jacobsen, Caitlin J. Byrne, Michael L. Heuer, Erik Larsson, Yevgeniy Antipin, Boris Reva (+3 others)
2012 Cancer Discovery  
The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 5,000 tumor samples from 20 cancer studies. The cBio Cancer Genomics Portal significantly lowers the barriers between complex genomic data and cancer researchers who want rapid, intuitive, and high-quality access to molecular profiles and clinical attributes from large-scale cancer genomics
more » ... projects and empowers researchers to translate these rich data sets into biologic insights and clinical applications. Cancer Discov; 2(5);
doi:10.1158/2159-8290.cd-12-0095 pmid:22588877 pmcid:PMC3956037 fatcat:jblbbzlvavbspno7io3bhkrbyu

Sleeping BeautyInsertional Mutagenesis in Mice Identifies Drivers of Steatosis-Associated Hepatic Tumors

Barbara R. Tschida, Nuri A. Temiz, Timothy P. Kuka, Lindsey A. Lee, Jesse D. Riordan, Carlos A. Tierrablanca, Robert Hullsiek, Sandra Wagner, Wendy A. Hudson, Michael A. Linden, Khalid Amin, Pauline J. Beckmann (+8 others)
2017 Cancer Research  
E, NAT10 immunohistochemical stain intensity of nontumor liver tissue (L) or liver tumors (T) from Nat10/shp53 (n ¼ 11 L; n ¼ 17 T) or GFP/shp53-injected mice (n ¼ 6 L) from both diets combined.  ...  E, p-PKA immunohistochemistry stain intensity of nontumor liver tissue (L) or liver tumors (T) from PKA/shp53 (n ¼ 17 each) or GFP/shp53-injected mice (n ¼ 13) from both diets combined.  ... 
doi:10.1158/0008-5472.can-17-2281 pmid:28993411 fatcat:2zt4p2cukngrjay5gn7tpua5l4

Minimum Information for Reporting Next Generation Sequence Genotyping (MIRING): Guidelines for Reporting HLA and KIR Genotyping via Next Generation Sequencing [article]

Steven J. Mack, Robert P Milius, Benjamin D Gifford, Jürgen Sauter, Jan Hofmann, Kazutoyo Osoegawa, James Robinson, Mathjis Groeneweg, Gregory S Turenchalk, Alex Adai, Cherie Holcomb, Erik H Rozemuller (+13 others)
2015 bioRxiv   pre-print
y p o l y m o r p h i c h u m a n l e u c o c y t e a n t i g e n ( H L A ) a n d k i l l e r -c e l l i m m u n o g l o b u l i n -l  ...  I n o r d e r t o e v a l I ) f o r t h e G L S t r i n g s h o u l d b e i n c l u d e d a s w e l l .  ... 
doi:10.1101/015230 fatcat:t36xnsrzd5flzpyiv6ek4upyte

Minimum information for reporting next generation sequence genotyping (MIRING): Guidelines for reporting HLA and KIR genotyping via next generation sequencing

Steven J. Mack, Robert P. Milius, Benjamin D. Gifford, Jürgen Sauter, Jan Hofmann, Kazutoyo Osoegawa, James Robinson, Mathijs Groeneweg, Gregory S. Turenchalk, Alex Adai, Cherie Holcomb, Erik H. Rozemuller (+13 others)
2015 Human Immunology  
The development of next-generation sequencing (NGS) technologies for HLA and KIR genotyping is rapidly advancing knowledge of genetic variation of these highly polymorphic loci. NGS genotyping is poised to replace older methods for clinical use, but standard methods for reporting and exchanging these new, high quality genotype data are needed. The Immunogenomic NGS Consortium, a broad collaboration of histocompatibility and immunogenetics clinicians, researchers, instrument manufacturers and
more » ... tware developers, has developed the Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines. MIRING is a checklist that specifies the content of NGS genotyping results as well as a set of messaging guidelines for reporting the results. A MIRING message includes five categories of structured information -message annotation, reference context, full genotype, http://dx.
doi:10.1016/j.humimm.2015.09.011 pmid:26407912 pmcid:PMC4674382 fatcat:bscs4sxibvckdi2kh2toyoj7vy

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

Gustavo Glusman, Peter W. Rose, Andreas Prlić, Jennifer Dougherty, José M. Duarte, Andrew S. Hoffman, Geoffrey J. Barton, Emøke Bendixen, Timothy Bergquist, Christian Bock, Elizabeth Brunk, Marija Buljan (+25 others)
2017 Genome Medicine  
The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic
more » ... databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods.
doi:10.1186/s13073-017-0509-y pmid:29254494 pmcid:PMC5735928 fatcat:zb2s4ibp4bhyhgmfhwbp5xdv34

Davunetide in patients with progressive supranuclear palsy: a randomised, double-blind, placebo-controlled phase 2/3 trial

Adam L Boxer, Anthony E Lang, Murray Grossman, David S Knopman, Bruce L Miller, Lon S Schneider, Rachelle S Doody, Andrew Lees, Lawrence I Golbe, David R Williams, Jean-Cristophe Corvol, Albert Ludolph (+18 others)
2014 Lancet Neurology  
In preclinical studies, davunetide promoted microtubule stability and reduced tau phosphorylation. Because progressive supranuclear palsy (PSP) is linked to tau pathology, davunetide could be a treatment for PSP. We assessed the safety and effi cacy of davunetide in patients with PSP. Methods In a double-blind, parallel group, phase 2/3 trial, participants were randomly assigned with permuted blocks in a 1:1 ratio to davunetide (30 mg twice daily, intranasally) or placebo for 52 weeks at 48
more » ... res in Australia, Canada, France, Germany, the UK, and the USA. Participants met the modifi ed Neuroprotection and Natural History in Parkinson Plus Syndrome study criteria for PSP. Primary endpoints were the change from baseline in PSP Rating Scale (PSPRS) and Schwab and England Activities of Daily Living (SEADL) scale at up to 52 weeks. All participants and study personnel were masked to treatment assignment. Analysis was by intention to treat. The trial is registered with Clinicaltrials.gov, number NCT01110720. Findings 313 participants were randomly assigned to davunetide (n=157) or to placebo (n=156), and 241 (77%) completed the study (118 and 156 in the davunetide and placebo groups, respectively). There were no diff erences in the davunetide and placebo groups in the baseline PSPRS and SEADL. The davunetide and placebo groups did not diff er in the change from baseline in PSPRS (median 11·8 [95% CI 10·5 to 13·0] vs 11·8 [10·5 to 13·0], respectively, p=0·41) or SEADL (-0·20 [-0·20 to -0·17] vs -0·20 [-0·22 to -0·17], respectively, p=0·92). 54 serious adverse events were reported in each of the treatment groups, including 11 deaths in the davunetide group and ten in the placebo group. The frequency of nasal adverse events was greater in the davunetide group than in the placebo group ( epistaxis 18 [12%] of 156 vs 13 [8%] of 156, rhinorrhoea 15 [10%] vs eight [5%], and nasal discomfort 15 [10%] vs one [<1%]). Interpretation Davunetide is not an eff ective treatment for PSP. Clinical trials of disease-modifying treatment are feasible in patients with PSP and should be pursued with other promising tau-directed treatments. Funding Allon Therapeutics.
doi:10.1016/s1474-4422(14)70088-2 pmid:24873720 pmcid:PMC4129545 fatcat:sjebyvk2fzahdjqdqv52x6ivua
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