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An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions

Nicola Senior, Kalesh Sasidharan, Richard Saint, Andrew Scott, Mitali Sarkar-Tyson, Philip Ireland, Helen Bullifent, Z. Rong Yang, Karen Moore, Petra Oyston, Timothy Atkins, Helen Atkins, Orkun Soyer & Richard Titball
Abstract Background The World Health Organization has categorized plague as a re-emerging disease and the potential for Yersinia pestis to also be used as a bioweapon makes the identification of new drug targets against this pathogen a priority. Environmental temperature is a key signal which regulates virulence of the bacterium. The bacterium normally grows outside the human host at 28 °C. Therefore, understanding the mechanisms that the bacterium used to adapt to a mammalian host at...

Additional file 2: of Epidemiology of taeniosis/cysticercosis in Europe, a systematic review: Western Europe

Minerva Laranjo-González, Brecht Devleesschauwer, Chiara Trevisan, Alberto Allepuz, Smaragda Sotiraki, Annette Abraham, Mariana Afonso, Joachim Blocher, Luís Cardoso, José Correia Da Costa, Pierre Dorny, Sarah Gabriël, Jacinto Gomes, María Gómez-Morales, Pikka Jokelainen, Miriam Kaminski, Brane Krt, Pascal Magnussen, Lucy Robertson, Veronika Schmidt, Erich Schmutzhard, G. Smit, Barbara Šoba, Christen Stensvold, Jože Starič … & Veronique Dermauw
Country sheets template. (DOCX 47 kb)

Staphylococcus aureus Prostatic abscess: a clinical case report and a review of the literature

David Carroll, Ian Marr, G Khai Lin Huang, Deborah Holt, Steven Tong & Craig Boutlis
Abstract Background Prostatic abscess is a rare complication of acute bacterial prostatitis and is most commonly caused by Enterobacteriaceae. We report on a case of prostatic abscess caused by Staphylococcus aureus and conduct a review of the literature. Case presentation We present a case of S. aureus prostatic abscess that was successfully treated with a combination of antibiotic and surgical therapy. The isolate was nonâ multidrug-resistant, methicillin-resistant Staphylococcus aureus and was genotyped as clonal complex...

Additional file 2: Figure S2. of Staphylococcus aureus Prostatic abscess: a clinical case report and a review of the literature

David Carroll, Ian Marr, G Khai Lin Huang, Deborah Holt, Steven Tong & Craig Boutlis
CT of pelvis showing persistence of prostatic abscess in the left lobe of the prostate. (PNG 447 kb)

Additional file 5: Figure S2. of An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions

Nicola Senior, Kalesh Sasidharan, Richard Saint, Andrew Scott, Mitali Sarkar-Tyson, Philip Ireland, Helen Bullifent, Z. Rong Yang, Karen Moore, Petra Oyston, Timothy Atkins, Helen Atkins, Orkun Soyer & Richard Titball
Analysis of gene essentiality using the genome-scale model and 2 million randomly generated media (using available exchange reactions in the model). The x-axis list the number of genes identified as essential in a set of media (y-axis). (TIFF 95 kb)

MOESM1 of Estimating the cost-effectiveness of daclatasvir + sofosbuvir versus sofosbuvir + ribavirin for patients with genotype 3 hepatitis C virus

Phil McEwan, Samantha Webster, Thomas Ward, Michael Brenner, Anupama Kalsekar & Yong Yuan
Additional file 1: Figure S1. Schematic of the cohort-based Markov simulation model.

Estimating the cost-effectiveness of daclatasvir + sofosbuvir versus sofosbuvir + ribavirin for patients with genotype 3 hepatitis C virus

Phil McEwan, Samantha Webster, Thomas Ward, Michael Brenner, Anupama Kalsekar & Yong Yuan
Abstract Background As treatments for chronic hepatitis C are moving away from interferon-containing regimens, the most appropriate allocation of resources to higher cost, interferon-free, direct-acting antiviral (DAA) regimens needs to be assessed. Hepatitis C virus (HCV) genotype 3 is associated with faster disease progression and has fewer treatment options, historically, than other HCV genotypes. This analysis aims to estimate the comparative cost-effectiveness of two recently licenced interferon-free regimens for the treatment of HCV genotype 3....

Additional file 1: Figure S1. of Staphylococcus aureus Prostatic abscess: a clinical case report and a review of the literature

David Carroll, Ian Marr, G Khai Lin Huang, Deborah Holt, Steven Tong & Craig Boutlis
CT of pelvis showing prostatic abscess in the left lobe of the prostate. (PNG 477 kb)

Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Hideaki Abe, Daiki Aoya, Hiro-Aki Takeuchi & Miho Inoue-Murayama
Abstract Background Neuregulin 3 (NRG3) plays a key role in central nervous system development and is a strong candidate for human mental disorders. Thus, genetic variation in NRG3 may have some impact on a variety of phenotypes in non-mammalian vertebrates. Recently, genome-wide screening for short insertions and deletions in chicken (Gallus gallus) genomes has provided useful information about structural variation in functionally important genes. NRG3 is one such gene that has a putative frameshift deletion...

Additional file 5 of Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Hideaki Abe, Daiki Aoya, Hiro-Aki Takeuchi & Miho Inoue-Murayama
: Figure S3. Example electrophoresis gel after qPCR using dup_Int2F and dup_Int2R. (PDF 382 kb)

Additional file 4: Figure S1. of An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions

Nicola Senior, Kalesh Sasidharan, Richard Saint, Andrew Scott, Mitali Sarkar-Tyson, Philip Ireland, Helen Bullifent, Z. Rong Yang, Karen Moore, Petra Oyston, Timothy Atkins, Helen Atkins, Orkun Soyer & Richard Titball
Analysis of gene essentiality using the genome-scale model and 2 million randomly generated media. A. Number of essential genes (blue bars; y-axis) predicted by the model using a specific random media composition derived from the available exchange reactions in the model (x-axis). The overlap with experimentally identified genes in BAB broth media is shown as well (red bars). B. Number of essential genes (y-axis) predicted by the model using a specific media composition that is...

Additional file 4 of Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Hideaki Abe, Daiki Aoya, Hiro-Aki Takeuchi & Miho Inoue-Murayama
: Table S2. List of the oligonucleotide primers used in this study. (PDF 45 kb)

Effectiveness and cost-effectiveness of daily all-over-body application of emollient during the first year of life for preventing atopic eczema in high-risk children (The BEEP trial): protocol for a randomised controlled trial

Joanne Chalmers, Rachel Haines, Eleanor Mitchell, Kim Thomas, Sara Brown, Matthew Ridd, Sandra Lawton, Eric Simpson, Michael Cork, Tracey Sach, Lucy Bradshaw, Alan Montgomery, Robert Boyle & Hywel Williams
Abstract Background Atopic eczema (AE) is a common skin problem that impairs quality of life and is associated with the development of other atopic diseases including asthma, food allergy and allergic rhinitis. AE treatment is a significant cost burden for health care providers. The purpose of the trial is to investigate whether daily application of emollients for the first year of life can prevent AE developing in high-risk infants (first-degree relative with asthma, AE or...

Additional file 1: Table S1. of Epidemiology of taeniosis/cysticercosis in Europe, a systematic review: Western Europe

Minerva Laranjo-González, Brecht Devleesschauwer, Chiara Trevisan, Alberto Allepuz, Smaragda Sotiraki, Annette Abraham, Mariana Afonso, Joachim Blocher, Luís Cardoso, José Correia Da Costa, Pierre Dorny, Sarah Gabriël, Jacinto Gomes, María Gómez-Morales, Pikka Jokelainen, Miriam Kaminski, Brane Krt, Pascal Magnussen, Lucy Robertson, Veronika Schmidt, Erich Schmutzhard, G. Smit, Barbara Šoba, Christen Stensvold, Jože Starič … & Veronique Dermauw
PRISMA 2009 Checklist. (DOC 64 kb)

Additional file 3 of Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Hideaki Abe, Daiki Aoya, Hiro-Aki Takeuchi & Miho Inoue-Murayama
: Table S1. Estimated number of del alleles in each individual of the chicken breeds. (PDF 46 kb)

Additional file 3: Table S3. of An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions

Nicola Senior, Kalesh Sasidharan, Richard Saint, Andrew Scott, Mitali Sarkar-Tyson, Philip Ireland, Helen Bullifent, Z. Rong Yang, Karen Moore, Petra Oyston, Timothy Atkins, Helen Atkins, Orkun Soyer & Richard Titball
Essential genes identified in different strains of Y. pestis by different methods. Genes in KIM10 identified in in vitro expansion of a himar1-derived transposon library grown on TB agar containing 2.5 mM CaCl2 and 25 μg/ml zeocin at 37 °C, then analysed using the Hidden Markov model (50). Genes in CO92 identified after in vitro growth in BAB broth at both 28 °C and 37 °C, then analysed using the DEM algorithm (14) (DOCX 48 kb)

Additional file 2: Table S2. of An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions

Nicola Senior, Kalesh Sasidharan, Richard Saint, Andrew Scott, Mitali Sarkar-Tyson, Philip Ireland, Helen Bullifent, Z. Rong Yang, Karen Moore, Petra Oyston, Timothy Atkins, Helen Atkins, Orkun Soyer & Richard Titball
Primer sequences used during preparation of libraries for sequencing (DOCX 12 kb)

Additional file 2 of Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Hideaki Abe, Daiki Aoya, Hiro-Aki Takeuchi & Miho Inoue-Murayama
: Figure S2. Distribution of transcription factor binding sites in intron 1 of chicken NRG3. (PDF 568 kb)

Additional file 4: of Effectiveness and cost-effectiveness of daily all-over-body application of emollient during the first year of life for preventing atopic eczema in high-risk children (The BEEP trial): protocol for a randomised controlled trial

Joanne Chalmers, Rachel Haines, Eleanor Mitchell, Kim Thomas, Sara Brown, Matthew Ridd, Sandra Lawton, Eric Simpson, Michael Cork, Tracey Sach, Lucy Bradshaw, Alan Montgomery, Robert Boyle & Hywel Williams
The Patient Oriented Eczema Measure (POEM); patient-reported symptoms severity scale. (DOCX 1521 kb)

Additional file 1: of Impact of the change of copay policy in Medicare Part D on zoster vaccine uptake among Medicare beneficiaries in a managed care organization

Rulin Hechter, Lei Qian, Songkai Yan, Yi Luo, Girishanthy Krishnarajah & Hung-Fu Tseng
Focus on the Patient. Patient-focused highlights providing the context, the outcomes and the impact of the study in the plainest language possible. (DOCX 13 kb)

Additional file 1 of Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Hideaki Abe, Daiki Aoya, Hiro-Aki Takeuchi & Miho Inoue-Murayama
: Figure S1. Alignments of duplicated exons 1 and 2 found in the upstream region of chicken NRG3 and ΨNRG3. (PDF 400 kb)

Additional file 1: Table S1. of An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions

Nicola Senior, Kalesh Sasidharan, Richard Saint, Andrew Scott, Mitali Sarkar-Tyson, Philip Ireland, Helen Bullifent, Z. Rong Yang, Karen Moore, Petra Oyston, Timothy Atkins, Helen Atkins, Orkun Soyer & Richard Titball
Sequences of adapters used during library preparation in this study. (DOCX 11 kb)

Impact of the change of copay policy in Medicare Part D on zoster vaccine uptake among Medicare beneficiaries in a managed care organization

Rulin Hechter, Lei Qian, Songkai Yan, Yi Luo, Girishanthy Krishnarajah & Hung-Fu Tseng
Abstract Background Kaiser Permanente Southern California (KPSC) adopted the Medicare Part D Tier-6 with zero patient copay for zoster vaccination in 2012. We assessed the impact of the implementation on zoster vaccination rate (GSK study identifier: HO-13-14,182). Methods Zoster vaccination rate was examined among an open cohort of ≥65-year-old Medicare Part D beneficiaries during 01/01/2008–06/30/2014, compared to ≥65-year-old commercial health plan members and 60–64-year-old members. The demographics, vaccination records, and insurance and benefit type were...

Additional file 3: Figure S3. of Evaluation of left atrial volume and function using single-beat real-time three-dimensional echocardiography in atrial fibrillation patients

Qian Zhang, Ju-Fang Wang, Qing-Qing Dong, Qing Yan, Xiang-Hong Luo, Xue-Ying Wu, Jian Liu & Ya-Ping Sun
Manual tracking of the left atrial endocardium from healthy controls (A) and patient cases (B). (ZIP 1184 kb)

Evaluation of left atrial volume and function using single-beat real-time three-dimensional echocardiography in atrial fibrillation patients

Qian Zhang, Ju-Fang Wang, Qing-Qing Dong, Qing Yan, Xiang-Hong Luo, Xue-Ying Wu, Jian Liu & Ya-Ping Sun
Abstract Background This study was aimed to evaluate the feasibility and accuracy of real-time three-dimensional echocardiography (RT-3DE) measurement of left atrial (LA) volume and function in comparison with two-dimensional echocardiography (2DE) measurements in atrial fibrillation (AF) patients. Methods A total of 50 pairs of AF patients and healthy controls were enrolled in this study. Indexed LA end-diastole volume (ILAEDV) and indexed LA end-systolic volume (ILAESV), as well as LA function indices such as segmental LA...

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