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https://www.readbyqxmd.com/read/28538734/zika-virus-evolution-and-spread-in-the-americas
#1
Hayden C Metsky, Christian B Matranga, Shirlee Wohl, Stephen F Schaffner, Catherine A Freije, Sarah M Winnicki, Kendra West, James Qu, Mary Lynn Baniecki, Adrianne Gladden-Young, Aaron E Lin, Christopher H Tomkins-Tinch, Simon H Ye, Daniel J Park, Cynthia Y Luo, Kayla G Barnes, Rickey R Shah, Bridget Chak, Giselle Barbosa-Lima, Edson Delatorre, Yasmine R Vieira, Lauren M Paul, Amanda L Tan, Carolyn M Barcellona, Mario C Porcelli, Chalmers Vasquez, Andrew C Cannons, Marshall R Cone, Kelly N Hogan, Edgar W Kopp, Joshua J Anzinger, Kimberly F Garcia, Leda A Parham, Rosa M Gélvez Ramírez, Maria C Miranda Montoya, Diana P Rojas, Catherine M Brown, Scott Hennigan, Brandon Sabina, Sarah Scotland, Karthik Gangavarapu, Nathan D Grubaugh, Glenn Oliveira, Refugio Robles-Sikisaka, Andrew Rambaut, Lee Gehrke, Sandra Smole, M Elizabeth Halloran, Luis Villar, Salim Mattar, Ivette Lorenzana, Jose Cerbino-Neto, Clarissa Valim, Wim Degrave, Patricia T Bozza, Andreas Gnirke, Kristian G Andersen, Sharon Isern, Scott F Michael, Fernando A Bozza, Thiago M L Souza, Irene Bosch, Nathan L Yozwiak, Bronwyn L MacInnis, Pardis C Sabeti
Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analysed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental United States...
May 24, 2017: Nature
https://www.readbyqxmd.com/read/28538723/genomic-epidemiology-reveals-multiple-introductions-of-zika-virus-into-the-united-states
#2
Nathan D Grubaugh, Jason T Ladner, Moritz U G Kraemer, Gytis Dudas, Amanda L Tan, Karthik Gangavarapu, Michael R Wiley, Stephen White, Julien Thézé, Diogo M Magnani, Karla Prieto, Daniel Reyes, Andrea M Bingham, Lauren M Paul, Refugio Robles-Sikisaka, Glenn Oliveira, Darryl Pronty, Carolyn M Barcellona, Hayden C Metsky, Mary Lynn Baniecki, Kayla G Barnes, Bridget Chak, Catherine A Freije, Adrianne Gladden-Young, Andreas Gnirke, Cynthia Luo, Bronwyn MacInnis, Christian B Matranga, Daniel J Park, James Qu, Stephen F Schaffner, Christopher Tomkins-Tinch, Kendra L West, Sarah M Winnicki, Shirlee Wohl, Nathan L Yozwiak, Joshua Quick, Joseph R Fauver, Kamran Khan, Shannon E Brent, Robert C Reiner, Paola N Lichtenberger, Michael J Ricciardi, Varian K Bailey, David I Watkins, Marshall R Cone, Edgar W Kopp, Kelly N Hogan, Andrew C Cannons, Reynald Jean, Andrew J Monaghan, Robert F Garry, Nicholas J Loman, Nuno R Faria, Mario C Porcelli, Chalmers Vasquez, Elyse R Nagle, Derek A T Cummings, Danielle Stanek, Andrew Rambaut, Mariano Sanchez-Lockhart, Pardis C Sabeti, Leah D Gillis, Scott F Michael, Trevor Bedford, Oliver G Pybus, Sharon Isern, Gustavo Palacios, Kristian G Andersen
Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016-several months before its initial detection...
May 24, 2017: Nature
https://www.readbyqxmd.com/read/28526802/macrolide-resistance-in-pseudomonas-aeruginosa-implications-for-practice
#3
EDITORIAL
James D Chalmers
No abstract text is available yet for this article.
May 2017: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/28506850/neutrophil-extracellular-traps-are-associated-with-disease-severity-and-microbiota-diversity-in-chronic-obstructive-pulmonary-disease
#4
Alison J Dicker, Megan L Crichton, Eleanor G Pumphrey, Andrew J Cassidy, Guillermo Suarez-Cuartin, Oriol Sibila, Elizabeth Furrie, Christopher J Fong, Wasyla Ibrahim, Gill Brady, Gisli G Einarsson, J Stuart Elborn, Stuart Schembri, Sara E Marshall, Colin Na Palmer, James D Chalmers
BACKGROUND: Neutrophil extracellular traps (NETs) have been observed in the airway in COPD, but their clinical and pathophysiological implications have not been defined. OBJECTIVE: To determine if NETs are associated with disease severity in COPD, and how they are associated with microbiota composition and airway neutrophil function. METHODS: NET protein complexes (DNA-Elastase and Histone-Elastase complexes), cell free DNA and neutrophil biomarkers were quantified in soluble sputum and serum from COPD patients during periods of disease stability and during exacerbations, and compared to clinical measures of disease severity and sputum microbiome...
May 12, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28502416/the-heterogeneity-of-systemic-inflammation-in-bronchiectasis
#5
Aarash D Saleh, James D Chalmers, Anthony De Soyza, Thomas C Fardon, Spiro O Koustas, Jonathan Scott, A John Simpson, Jeremy S Brown, John R Hurst
BACKGROUND: Systemic inflammation in bronchiectasis is poorly studied in relation to aetiology and severity. We hypothesized that molecular patterns of inflammation may define particular aetiology and severity groups in bronchiectasis. METHOD: We assayed blood concentrations of 31 proteins from 90 bronchiectasis patients (derivation cohort) and conducted PCA to examine relationships between these markers, disease aetiology and severity. Key results were validated in two separate cohorts of 97 and 79 patients from other centres...
June 2017: Respiratory Medicine
https://www.readbyqxmd.com/read/28481709/reply-to-a-chalmers-et-al
#6
William J Magnuson, Nataniel H Lester-Coll, James B Yu, Veronica L Chiang
No abstract text is available yet for this article.
May 8, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28420421/analysis-of-100-000-human-cancer-genomes-reveals-the-landscape-of-tumor-mutational-burden
#7
Zachary R Chalmers, Caitlin F Connelly, David Fabrizio, Laurie Gay, Siraj M Ali, Riley Ennis, Alexa Schrock, Brittany Campbell, Adam Shlien, Juliann Chmielecki, Franklin Huang, Yuting He, James Sun, Uri Tabori, Mark Kennedy, Daniel S Lieber, Steven Roels, Jared White, Geoffrey A Otto, Jeffrey S Ross, Levi Garraway, Vincent A Miller, Phillip J Stephens, Garrett M Frampton
BACKGROUND: High tumor mutational burden (TMB) is an emerging biomarker of sensitivity to immune checkpoint inhibitors and has been shown to be more significantly associated with response to PD-1 and PD-L1 blockade immunotherapy than PD-1 or PD-L1 expression, as measured by immunohistochemistry (IHC). The distribution of TMB and the subset of patients with high TMB has not been well characterized in the majority of cancer types. METHODS: In this study, we compare TMB measured by a targeted comprehensive genomic profiling (CGP) assay to TMB measured by exome sequencing and simulate the expected variance in TMB when sequencing less than the whole exome...
April 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28406394/a-randomised-controlled-trial-to-compare-the-safety-effectiveness-and-cost-effectiveness-of-doxycycline-200%C3%A2-mg-day-with-that-of-oral-prednisolone-0-5%C3%A2-mg-kg-day-for-initial-treatment-of-bullous-pemphigoid-the-bullous-pemphigoid-steroids-and-tetracyclines-blister
#8
Joanne R Chalmers, Fenella Wojnarowska, Gudula Kirtschig, James Mason, Margaret Childs, Diane Whitham, Karen Harman, Anna Chapman, Shernaz Walton, Enno Schmidt, Thomas R Godec, Andrew J Nunn, Hywel C Williams
BACKGROUND: Bullous pemphigoid (BP) is an autoimmune blistering skin disorder with increased morbidity and mortality in the elderly. OBJECTIVES: To evaluate the effectiveness, safety and cost-effectiveness of a strategy of initiating BP treatment with oral doxycycline or oral prednisolone. We hypothesised that starting treatment with doxycycline gives acceptable short-term blister control while conferring long-term safety advantages over starting treatment with oral prednisolone...
March 2017: Health Technology Assessment: HTA
https://www.readbyqxmd.com/read/28404649/the-microbiome-in-respiratory-medicine-current-challenges-and-future-perspectives
#9
REVIEW
Rosa Faner, Oriol Sibila, Alvar Agustí, Eric Bernasconi, James D Chalmers, Gary B Huffnagle, Chaysavanh Manichanh, Philip L Molyneaux, Roger Paredes, Vicente Pérez Brocal, Julia Ponomarenko, Sanjay Sethi, Jordi Dorca, Eduard Monsó
The healthy lung has previously been considered to be a sterile organ because standard microbiological culture techniques consistently yield negative results. However, culture-independent techniques report that large numbers of microorganisms coexist in the lung. There are many unknown aspects in the field, but available reports show that the lower respiratory tract microbiota: 1) is similar in healthy subjects to the oropharyngeal microbiota and dominated by members of the Firmicutes, Bacteroidetes and Proteobacteria phyla; 2) shows changes in smokers and well-defined differences in chronic respiratory diseases, although the temporal and spatial kinetics of these changes are only partially known; and 3) shows relatively abundant non-cultivable bacteria in chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, cystic fibrosis and bronchiectasis, with specific patterns for each disease...
April 2017: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/28393141/using-cluster-analysis-of-cytokines-to-identify-patterns-of-inflammation-in-hospitalized-patients-with-community-acquired-pneumonia-a-pilot-study
#10
Timothy L Wiemken, Robert R Kelley, Rafael Fernandez-Botran, William A Mattingly, Forest W Arnold, Stephen P Furmanek, Marcos I Restrepo, James D Chalmers, Paula Peyrani, Rodrigo Cavallazzi, Jose Bordon, Stefano Aliberti, Julio A Ramirez
INTRODUCTION: Patients with severe community-acquired pneumonia (CAP) are believed to have an exaggerated inflammatory response to bacterial infection. Therapies aiming to modulate the inflammatory response have been largely unsuccessful, perhaps reflecting that CAP is a heterogeneous disorder that cannot be modulated by a single anti-inflammatory approach. We hypothesize that the host inflammatory response to pneumonia may be characterized by distinct cytokine patterns, which can be harnessed for personalized therapies...
2017: Univ Louisville J Respir Infect
https://www.readbyqxmd.com/read/28338705/cohort-profile-scottish-diabetes-research-network-type-1-bioresource-study-sdrnt1bio
#11
Tahira Akbar, Stuart McGurnaghan, Colin N A Palmer, Shona J Livingstone, John Petrie, John Chalmers, Robert S Lindsay, John A McKnight, Donald W M Pearson, Alan W Patrick, James Walker, Helen C Looker, Helen M Colhoun
No abstract text is available yet for this article.
September 26, 2016: International Journal of Epidemiology
https://www.readbyqxmd.com/read/28306354/bronchiectasis-phenotyping-a-complex-disease
#12
James D Chalmers
Bronchiectasis is a long-neglected disease currently experiencing a surge in interest. It is a highly complex condition with numerous aetiologies, co-morbidities and a heterogeneous disease presentation and clinical course. The past few years have seen major advances in our understanding of the disease, primarily through large real-life cohort studies. The main outcomes of interest in bronchiectasis are symptoms, exacerbations, treatment response, disease progression and death. We are now more able to identify clearly the radiological, clinical, microbiological and inflammatory contributors to these outcomes...
March 15, 2017: COPD
https://www.readbyqxmd.com/read/28306353/management-of-chronic-airway-diseases-what-can-we-learn-from-real-life-data
#13
James D Chalmers
No abstract text is available yet for this article.
March 15, 2017: COPD
https://www.readbyqxmd.com/read/28289927/nmr-assignments-of-sparsely-labeled-proteins-using-a-genetic-algorithm
#14
Qi Gao, Gordon R Chalmers, Kelley W Moremen, James H Prestegard
Sparse isotopic labeling of proteins for NMR studies using single types of amino acid ((15)N or (13)C enriched) has several advantages. Resolution is enhanced by reducing numbers of resonances for large proteins, and isotopic labeling becomes economically feasible for glycoproteins that must be expressed in mammalian cells. However, without access to the traditional triple resonance strategies that require uniform isotopic labeling, NMR assignment of crosspeaks in heteronuclear single quantum coherence (HSQC) spectra is challenging...
April 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28279484/doxycycline-versus-prednisolone-as-an-initial-treatment-strategy-for-bullous-pemphigoid-a-pragmatic-non-inferiority-randomised-controlled-trial
#15
Hywel C Williams, Fenella Wojnarowska, Gudula Kirtschig, James Mason, Thomas R Godec, Enno Schmidt, Joanne R Chalmers, Margaret Childs, Shernaz Walton, Karen Harman, Anna Chapman, Diane Whitham, Andrew J Nunn
BACKGROUND: Bullous pemphigoid is a blistering skin disorder with increased mortality. We tested whether a strategy of starting treatment with doxycycline gives acceptable short-term blister control while conferring long-term safety advantages over starting treatment with oral corticosteroids. METHODS: We did a pragmatic, multicentre, parallel-group randomised controlled trial of adults with bullous pemphigoid (three or more blisters at two or more sites and linear basement membrane IgG or C3)...
April 22, 2017: Lancet
https://www.readbyqxmd.com/read/28270656/raising-awareness-of-bronchiectasis-in-primary-care-overview-of-diagnosis-and-management-strategies-in-adults
#16
James D Chalmers, Sanjay Sethi
Bronchiectasis is a chronic lung disease characterised by recurrent infection, inflammation, persistent cough and sputum production. The disease is increasing in prevalence, requiring a greater awareness of the disease across primary and secondary care. Mild and moderate cases of bronchiectasis in adults can often be managed by primary care clinicians. Initial assessments and long-term treatment plans that include both pharmacological and non-pharmacological treatments, however, should be undertaken in collaboration with a secondary care team that includes physiotherapists and specialists in respiratory medicine...
December 2017: NPJ Primary Care Respiratory Medicine
https://www.readbyqxmd.com/read/28244617/year-in-review-2016-respiratory-infections-acute-respiratory-distress-syndrome-pleural-diseases-lung-cancer-and-interventional-pulmonology
#17
REVIEW
Marcos I Restrepo, James D Chalmers, Yuanlin Song, Christopher Mallow, Justin Hewlett, Fabien Maldonado, Lonny Yarmus
No abstract text is available yet for this article.
April 2017: Respirology: Official Journal of the Asian Pacific Society of Respirology
https://www.readbyqxmd.com/read/28212153/new-therapies-for-the-prevention-and-treatment-of-exacerbations-of-bronchiectasis
#18
Hani Abo-Leyah, James D Chalmers
PURPOSE OF REVIEW: Exacerbations of bronchiectasis have a major impact on quality of life, healthcare costs, and long-term risk of complications. Preventing exacerbations is one of the major goals of treatment. Bronchiectasis is increasingly recognized and the impact of bronchiectasis exacerbations on daily clinical practice is also increasing. RECENT FINDINGS: Preventing bronchiectasis exacerbations are dependent on appropriate risk assessment, identifying the patients at highest risk to rationally target preventive therapies...
May 2017: Current Opinion in Pulmonary Medicine
https://www.readbyqxmd.com/read/28210295/global-impact-of-bronchiectasis-and-cystic-fibrosis
#19
REVIEW
Margarida Redondo, Holly Keyt, Raja Dhar, James D Chalmers
EDUCATIONAL AIMS: To recognise the clinical and radiological presentation of the spectrum of diseases associated with bronchiectasis.To understand variation in the aetiology, microbiology and burden of bronchiectasis and cystic fibrosis across different global healthcare systems. Bronchiectasis is the term used to refer to dilatation of the bronchi that is usually permanent and is associated with a clinical syndrome of cough, sputum production and recurrent respiratory infections. It can be caused by a range of inherited and acquired disorders, or may be idiopathic in nature...
September 2016: Breathe
https://www.readbyqxmd.com/read/28110337/investigating-the-etiology-of-bronchiectasis-you-do-not-find-what-you-do-not-look-for
#20
Francesco Amati, Elisa Franceschi, Andrea Gramegna, James D Chalmers, Stefano Aliberti
No abstract text is available yet for this article.
2017: Respiration; International Review of Thoracic Diseases
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