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Silent spread of H5N1 in vaccinated poultry

Nicholas J. Savill, Suzanne G. St Rose, Matthew J. Keeling, Mark E. J. Woolhouse
2006 Nature  
doi:10.1038/442757a pmid:16915278 fatcat:loolfmpvgndsdn6uo46a2fnf3y

Distracted Biking

Elizabeth Suzanne Wolfe, Sandra Strack Arabian, Janis L. Breeze, Matthew J. Salzler
2016 Journal of Trauma Nursing  
Cyclists, much like drivers, have always been engaged in multi-tasking activities like using hand-held devices, listening to music, snacking, or reading while bicycling. While distracted drivers endanger themselves and other, distracted bikers, in general present more risk to themselves than to others. Distracted bicycling, however, has not received similar interventions to address safety related issues. This study reviewed the state-of-knowledge on policies, programs, data sources, and
more » ... ources, and identified data collection opportunities and research needs. Literature review conducted in this study revealed only six [6] past studies that investigated the effect of distracted bicycling. The review also found that several agencies/organizations listed the use of portable electronic devices while cycling as unsafe behavior. Some of the agencies/organizations in the United States, Canada, Belgium, Bermuda, Germany, and New Zealand have implemented interventions to curb distracted bicycling such as education, awareness programs, and legislation. The majority of the legislation enacted ban the use of headphones or earphones in or on one or both ears and few ban hand-held phones while cycling. In addition to these, one law common to all U.S. states and District of Columbia restricts cyclists from carrying bundles, articles or objects that prevent them from keeping at least one hand on the handlebars which indirectly addresses distracted bicycling.
doi:10.1097/jtn.0000000000000188 pmid:26953533 pmcid:PMC4785823 fatcat:qglyilc35rgs3ij6jualsozjwi

Quality-of-Life Outcomes After Transcatheter Aortic Valve Replacement in an Unselected Population

Suzanne V. Arnold, John A. Spertus, Sreekanth Vemulapalli, Zhuokai Li, Roland A. Matsouaka, Suzanne J. Baron, Amit N. Vora, Michael J. Mack, Matthew R. Reynolds, John S. Rumsfeld, David J. Cohen
2017 JAMA cardiology  
IMPORTANCE In clinical trials, transcatheter aortic valve replacement (TAVR) has been shown to improve symptoms and quality of life. As this technology moves into general clinical practice, evaluation of the health status outcomes among unselected patients treated with TAVR is of critical importance. OBJECTIVE To examine the short-and long-term health status outcomes of surviving patients after TAVR in the context of an unselected population. DESIGN, SETTING, AND PARTICIPANTS This observational
more » ... This observational cohort study included patients with severe aortic stenosis who underwent TAVR in the Society of Thoracic Surgeons/American College of Cardiology Transcatheter Valve Therapy (TVT) Registry from November 1, 2011, to March 31, 2016, at more than 450 clinical sites. MAIN OUTCOMES AND MEASURES Disease-specific health status was assessed at baseline and at 30 days and 1 year after TAVR using the Kansas City Cardiomyopathy Questionnaire overall summary (KCCQ-OS) score (range, 0-100 points; higher scores indicate less symptom burden and better quality of life). Factors associated with health status at 1 year after TAVR were examined using multivariable linear regression, with adjustment for baseline health status and accounting for clustering of patients within sites. RESULTS The 30-day analytic sample included 31 636 patients, and the 1-year cohort included 7014 surviving patients (3454 women [49.2%] and 3560 men [50.8%]; median [interquartile range] age, 84 [78-88] years). The mean (SD) baseline KCCQ-OS score was 42.3 (23 .7) , indicating substantial health status impairment. Surviving patients had, on average, large improvements in health status at 30 days that persisted to 1 year, with a mean improvement in the KCCQ-OS score of 27.6 (95% CI, 27.3-27.9) points at 30 days and 31.9 (95% CI, 31.3-32.6) points at 1 year. Worse baseline health status, older age, higher ejection fraction, lung disease, home oxygen use, lower mean aortic valve gradients, prior stroke, diabetes, pacemaker use, atrial fibrillation, slow gait speed, and nonfemoral access were significantly associated with worse health status at 1 year. Overall, 62.3% of patients had a favorable outcome at 1 year (alive with reasonable quality of life [KCCQ-OS score, Ն60] and no significant decline [Ն10 points] from baseline), with the lowest rates seen among patients with severe lung disease (51.4%), those undergoing dialysis (47.7%), or those with very poor baseline health status (49.2%). CONCLUSIONS AND RELEVANCE In a national, contemporary clinical practice cohort of unselected patients, improvement in health status after TAVR was similar to that seen in the pivotal clinical trials. Although the health status results were favorable for most patients, approximately 1 in 3 still had a poor outcome 1 year after TAVR. Continued efforts are needed to improve patient selection and procedural/postprocedural care to maximize health status outcomes of this evolving therapy. sis, we added 5-m walk test results to the model to test this association with long-term health status. These results were categorized as at least 0.83 m/s (normal walker; reference group), 0.50 to less than 0.83 m/s (slow walker), and less than 0.50 m/s (slowest walker, including patients unable to walk). walk test data, worse 1-year KCCQ-OS scores were associated with slow gait speed (mean difference, −3.5 points; 95% CI, −5.0 to −2.1 points) and slowest gait speed (mean difference, −5.7 points; 95% CI, −7.6 to −3.7 points).
doi:10.1001/jamacardio.2016.5302 pmid:28146260 pmcid:PMC5408740 fatcat:tja77tej4bahxfw6zxaykj6lgm

Substrate-Specific Gene Expression in Batrachochytrium dendrobatidis, the Chytrid Pathogen of Amphibians

Erica Bree Rosenblum, Thomas J. Poorten, Suzanne Joneson, Matthew Settles, Matthew Charles Fisher
2012 PLoS ONE  
Determining the mechanisms of host-pathogen interaction is critical for understanding and mitigating infectious disease. Mechanisms of fungal pathogenicity are of particular interest given the recent outbreaks of fungal diseases in wildlife populations. Our study focuses on Batrachochytrium dendrobatidis (Bd), the chytrid pathogen responsible for amphibian declines around the world. Previous studies have hypothesized a role for several specific families of secreted proteases as pathogenicity
more » ... as pathogenicity factors in Bd, but the expression of these genes has only been evaluated in laboratory growth conditions. Here we conduct a genome-wide study of Bd gene expression under two different nutrient conditions. We compare Bd gene expression profiles in standard laboratory growth media and in pulverized host tissue (i.e., frog skin). A large proportion of genes in the Bd genome show increased expression when grown in host tissue, indicating the importance of studying pathogens on host substrate. A number of gene classes show particularly high levels of expression in host tissue, including three families of secreted proteases (metallo-, serine-and aspartyl-proteases), adhesion genes, lipase-3 encoding genes, and a group of phylogenetically unusual crinkler-like effectors. We discuss the roles of these different genes as putative pathogenicity factors and discuss what they can teach us about Bd's metabolic targets, host invasion, and pathogenesis. Citation: Rosenblum EB, Poorten TJ, Joneson S, Settles M (2012) Substrate-Specific Gene Expression in Batrachochytrium dendrobatidis, the Chytrid Pathogen of Amphibians. PLoS ONE 7(11): e49924.
doi:10.1371/journal.pone.0049924 pmid:23185485 pmcid:PMC3502224 fatcat:qu2s76gm4jfdxe54di3exe3lkq

Association of Patient-Reported Health Status With Long-Term Mortality After Transcatheter Aortic Valve Replacement

Suzanne V. Arnold, John A. Spertus, Sreekanth Vemulapalli, Dadi Dai, Sean M. O'Brien, Suzanne J. Baron, Ajay J. Kirtane, Michael J. Mack, Philip Green, Matthew R. Reynolds, John S. Rumsfeld, David J. Cohen
2015 Circulation. Cardiovascular Interventions  
doi:10.1161/circinterventions.115.002875 pmid:26643740 pmcid:PMC4673686 fatcat:zf5crhhkaba5tku2j3l65zx57q

Ebola cases and health system demand in Liberia [article]

John M. Drake, RajReni B. Kaul, Laura Alexander, Suzanne M. O'Regan, Andrew M. Kramer, J. Tomlin Pulliam, Matthew J. Ferrari, Andrew W. Park
2014 arXiv   pre-print
In 2014, a major epidemic of human Ebola virus disease emerged in West Africa, where human-to-human transmission has now been been sustained for greater than 10 months. In the summer of 2014, there was great uncertainty about the answers to several key policy questions concerning the path to containment. In recent years, epidemic models have been used to guide public health interventions. But, model-based policy relies on high quality causal understanding of transmission, including the
more » ... luding the availability of appropriate dynamic transmission models and reliable reporting about the sequence of case incidence for model fitting, which were lacking for this epidemic. To investigate the range of potential transmission scenarios, we developed a multi-type branching process model that incorporates key heterogeneities and time-varying parameters to reflect changing human behavior and deliberate interventions. Ensembles of this model were evaluated at a set of parameters that were both epidemiologically plausible and capable of reproducing the observed trajectory. Results suggest that epidemic outcome depends on both hospital capacity and individual behavior. The model predicts that if hospital capacity is not increased soon, then transmission may outpace the rate of isolation and the ability to provide care for the ill, infectious, and dying. Similarly, containment will probably require individuals to adopt behaviors that increase the rates of case identification and isolation and secure burial of the deceased. Given current knowledge, it is uncertain that this epidemic will be contained even with 99% hospitalization rate at the currently projected hospital capacity.
arXiv:1410.8564v1 fatcat:yoehex6rnncnbebumexa23ddsu

An efficient and extensible approach for compressing phylogenetic trees

Suzanne J Matthews, Tiffani L Williams
2011 BMC Bioinformatics  
J. Consider bitstring 000011, which is in row 30 (its h 1 value) in our hash table shown in Figure 3 and has an h 2 value of 42.  ...  (We use characters A through J for compressing our list of tree ids described shortly.) Hence, we encode the bitstring 110000 as K2L4.  ... 
doi:10.1186/1471-2105-12-s10-s16 pmid:22165819 pmcid:PMC3236838 fatcat:jbr42brib5btzhq25obxqromci

Paper Mâché: Creating Dynamic Reproducible Science

Grant R. Brammer, Ralph W. Crosby, Suzanne J. Matthews, Tiffani L. Williams
2011 Procedia Computer Science  
For centuries, the research paper have been the main vehicle for scientific progress. From the paper, readers in the scientific community are expected to extract all the relevant information necessary to reproduce and validate the results presented by the paper's authors. However, the increased use of computer software in science makes reproducing scientific results increasingly difficult. The research paper in its current state is no longer sufficient to fully reproduce, validate, or review a
more » ... idate, or review a paper's experimental results and conclusions. This impedes scientific progress. To remedy these concerns, we introduce Paper Mâché, a new system for creating dynamic, executable research papers. The key novelty of Paper Mâché is its use of virtual machines, which lets readers and reviewers easily view and interact with a paper, and reproduce key experimental results. For authors, the Paper Mâché workbench provides an easy-touse interface to build an executable paper. By transforming the static research paper into a dynamic and interactive entity, Paper Mâché brings the presentation of scientific results into the 21st century. We believe that Paper Mâché will become indispensable to the scientific process, and increase the visibility of key findings among members and non-members of the scientific community.
doi:10.1016/j.procs.2011.04.069 fatcat:xbdtp2gpmfe4hesvibfy36z4fi

A Novel Approach for Compressing Phylogenetic Trees [chapter]

Suzanne J. Matthews, Seung-Jin Sul, Tiffani L. Williams
2010 Lecture Notes in Computer Science  
In The probability of a double collision ( h 1 (B i ) = h 1 (B j ) and h 2 (B i ) = h 2 (B j )) is O( 1 c ), where c can be an arbitrarily large number [1] .  ...  J. Consider bipartition ABCD|EF (bitstring 000011), which is in H [8] in Figure 3 .  ... 
doi:10.1007/978-3-642-13078-6_13 fatcat:htltzu5bazeh5mstitdpdgz3vq

Durability of quality of life benefits of transcatheter aortic valve replacement: Long-term results from the CoreValve US extreme risk trial

Suzanne J. Baron, Suzanne V. Arnold, Matthew R. Reynolds, Kaijun Wang, Michael Deeb, Michael J. Reardon, James Hermiller, Steven J. Yakubov, David H. Adams, Jeffrey J. Popma, David J. Cohen
2017 American Heart Journal  
J. Author manuscript; available in PMC 2018 February 22.  ...  : ratio of the absolute value of change to the standard deviation at baseline Am Heart J. Author manuscript; available in PMC 2018 February 22. .  ... 
doi:10.1016/j.ahj.2017.08.006 pmid:29223434 pmcid:PMC5821894 fatcat:3wuput3kebbo3jjayewkmnnhri

University of Washington School of Medicine

Suzanne M. Allen, Michael J. Ryan, Mark Whipple, Kellie Engle, Lynne Robins, Matthew Cunningham, Marjorie D. Wenrich
2020 Academic Medicine  
doi:10.1097/acm.0000000000003455 pmid:33626763 fatcat:qkxu57yazfgx5lq65xczi736fm

Genome-wide association study of lung lesions and pleurisy in New Zealand lambs1

Kathryn M McRae, Suzanne J Rowe, Hayley J Baird, Matthew J Bixley, Shannon M Clarke
2018 Journal of Animal Science  
Pneumonia is an important issue for sheep production, leading to reduced growth rate and a predisposition to pleurisy. The objective of this study was to identify loci associated with pneumonic lesions and pleurisy in New Zealand progeny test lambs. The lungs from 3,572 progeny-test lambs were scored for presence and severity of pneumonic lesions and pleurisy at slaughter. Animals were genotyped using the Illumina Ovine Infinium HD SNP BeadChip (606,006 markers). The heritability of lung lesion
more » ... lity of lung lesion score and pleurisy were calculated using the genomic relationship matrix, and genome-wide association analyses were conducted using EMMAX and haplotype trend regression. At slaughter, 35% of lambs had pneumonic lesions, with 9% showing lesions on more than half of any individual lobe. The number of lambs recorded as having pleurisy by the processing plants was 9%. Heritability estimates for pneumonic lesions and pleurisy scores adjusted for heteroscedasticity (CPSa and PLEURa) were 0.16 (± 0.03) and 0.05 (± 0.02), respectively. Five single-nucleotide polymorphisms (SNPs) were significantly associated with pneumonic lesions at the genome-wide level, and additional 37 SNPs were suggestively significant. Four SNPs were significantly associated with pleurisy, with an additional 11 SNPs reaching the suggestive level of significance. There were no regions that overlapped between the 2 traits. Multiple SNPs were in regions that contained genes involved in either the DNA damage response or the innate immune response, including several that had previously been reported to have associations with respiratory disease. Both EMMAX and HTR analyses of pleurisy data showed a significant peak on chromosome 2, located downstream from the transcription factor SP3. SP3 activates or suppresses the expression of numerous genes, including several genes with known functions in the immune system. This study identified several SNPs associated with genes involved in both the innate immune response and the response to DNA damage that are associated with pneumonic lesions and pleurisy in lambs at slaughter. Additionally, the identification in sheep of several SNPs within genes that have previously been associated with the respiratory system in cattle, pigs, rats, and mice indicates that there may be common pathways that underlie the response to invasion by respiratory pathogens in multiple species.
doi:10.1093/jas/sky323 pmid:30099550 fatcat:zn2gla5fpjdyhkh624wu523n3y

COVID-19

J. Matthew Lacy, Erin G. Brooks, Joshua Akers, Danielle Armstrong, Lauren Decker, Adam Gonzalez, William Humphrey, Romana Mayer, Matthew Miller, Catherine Perez, Jose Antonio Ruiz Arango, Lakshmanan Sathyavagiswaran (+2 others)
2020 American Journal of Forensic Medicine and Pathology  
J Clin Pathol. 2020 Mar 20. pii: jclinpath-2020-206522. doi: 10.1136/jclinpath-2020-206522. [Epub ahead of print] 20. World Health Organization (WHO).  ...  J Clin Pathol. 2004;57(3):260-265. Available at: http://www.centerforhealthsecurity.org/resources/COVID-19/Serologybased-tests-for-COVID-19.html#sec5.  ... 
doi:10.1097/paf.0000000000000567 fatcat:x7ovwixhwfgprekepm2ztqynuy

MrsRF: an efficient MapReduce algorithm for analyzing large collections of evolutionary trees

Suzanne J Matthews, Tiffani L Williams
2010 BMC Bioinformatics  
Acknowledgements We would like to thank Matthew Gitzendanner, Paul Lewis, and David Soltis for providing us with the Bayesian tree collections used in this paper.  ...  The RF distance between trees T i and T j is: RF T T T i T j T j T i i j ( , ) . = − + − B B B B 2 In this paper, we develop a multi-core algorithm to compute the t × t RF matrix for a collection of t  ...  Each increment to entry (i, j) in the similarity matrix represents that the pair of trees T i and T j share a bipartition.  ... 
doi:10.1186/1471-2105-11-s1-s15 pmid:20122186 pmcid:PMC3009486 fatcat:azp2oflnezdljldlvjf7473hqe

Multisource Feedback in Evaluating the Performance of Doctors

Christine Wright, Suzanne H. Richards, Jacqueline J. Hill, Martin J. Roberts, Geoff R. Norman, Michael Greco, Matthew R.S. Taylor, John L. Campbell
2012 Academic Medicine  
doi:10.1097/acm.0b013e3182724cc0 pmid:23095930 fatcat:blsmtaz435fqhl3knxxfultfje
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