Showing papers on "Population published in 2015"

Cancer statistics, 2015.

Abstract: Each year the American Cancer Society estimates the numbers of new cancer cases and deaths that will occur in the United States in the current year and compiles the most recent data on cancer incidence, mortality, and survival. Incidence data were collected by the National Cancer Institute (Surveillance, Epidemiology, and End Results [SEER] Program), the Centers for Disease Control and Prevention (National Program of Cancer Registries), and the North American Association of Central Cancer Registries. Mortality data were collected by the National Center for Health Statistics. A total of 1,658,370 new cancer cases and 589,430 cancer deaths are projected to occur in the United States in 2015. During the most recent 5 years for which there are data (2007-2011), delay-adjusted cancer incidence rates (13 oldest SEER registries) declined by 1.8% per year in men and were stable in women, while cancer death rates nationwide decreased by 1.8% per year in men and by 1.4% per year in women. The overall cancer death rate decreased from 215.1 (per 100,000 population) in 1991 to 168.7 in 2011, a total relative decline of 22%. However, the magnitude of the decline varied by state, and was generally lowest in the South (∼15%) and highest in the Northeast (≥20%). For example, there were declines of 25% to 30% in Maryland, New Jersey, Massachusetts, New York, and Delaware, which collectively averted 29,000 cancer deaths in 2011 as a result of this progress. Further gains can be accelerated by applying existing cancer control knowledge across all segments of the population.

Roary: Rapid large-scale prokaryote pan genome analysis

Abstract: Summary: A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and accessory genes. Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results. Using a single CPU Roary can produce a pan genome consisting of 1000 isolates in 4.5 hours using 13 GB of RAM, with further speedups possible using multiple processors. Availability and implementation: Roary is implemented in Perl and is freely available under an open source GPLv3 license from http://sanger-pathogens.github.io/Roary Contact: ku.ca.regnas@yraor Supplementary information: Supplementary data are available at Bioinformatics online.

Bee declines driven by combined stress from parasites, pesticides, and lack of flowers

Abstract: Bees are subject to numerous pressures in the modern world. The abundance and diversity of flowers has declined, bees are chronically exposed to cocktails of agrochemicals, and they are simultaneously exposed to novel parasites accidentally spread by humans. Climate change is likely to exacerbate these problems in the future. Stressors do not act in isolation; for example pesticide exposure can impair both detoxification mechanisms and immune responses, rendering bees more susceptible to parasites. It seems certain that chronic exposure to multiple, interacting stressors is driving honey bee colony losses and declines of wild pollinators, but such interactions are not addressed by current regulatory procedures and studying these interactions experimentally poses a major challenge. In the meantime, taking steps to reduce stress on bees would seem prudent; incorporating flower-rich habitat into farmland, reducing pesticide use through adopting more sustainable farming methods, and enforcing effective quarantine measures on bee movements are all practical measures that should be adopted. Effective monitoring of wild pollinator populations is urgently needed to inform management strategies into the future.

Current Cigarette Smoking Among Adults - United States, 2016.

Abstract: Tobacco use is the leading cause of preventable disease and death in the United States, resulting in more than 480,000 premature deaths and $289 billion in direct health care expenditures and productivity losses each year. Despite progress over the past several decades, millions of adults still smoke cigarettes, the most commonly used tobacco product in the United States. To assess progress made toward the Healthy People 2020 target of reducing the proportion of U.S. adults who smoke cigarettes to ≤12.0% (objective TU-1.1), CDC used data from the 2013 National Health Interview Survey (NHIS) to provide updated national estimates of cigarette smoking prevalence among adults aged ≥18 years. Additionally, for the first time, estimates of cigarette smoking prevalence were assessed among lesbian, gay, or bisexual persons (LGB) using NHIS data. The proportion of U.S. adults who smoke cigarettes declined from 20.9% in 2005 to 17.8% in 2013, and the proportion of daily smokers declined from 16.9% to 13.7%. Among daily cigarette smokers, the proportion who smoked 20-29 cigarettes per day (CPD) declined from 34.9% to 29.3%, and the proportion who smoked ≥30 CPD declined from 12.7% to 7.1%. However, cigarette smoking remains particularly high among certain groups, including adults who are male, younger, multiracial or American Indian/Alaska Native, have less education, live below the federal poverty level, live in the South or Midwest, have a disability/limitation, or who are LGB. Proven population-based interventions, including tobacco price increases, comprehensive smoke-free policies in worksites and public places, high-impact anti-tobacco mass media campaigns, and easy access to smoking cessation assistance, are critical to reducing cigarette smoking and smoking-related disease and death among U.S. adults, particularly among subpopulations with the greatest burden.

Nivolumab versus chemotherapy in patients with advanced melanoma who progressed after anti-CTLA-4 treatment (CheckMate 037): a randomised, controlled, open-label, phase 3 trial.

Abstract: Summary Background Nivolumab, a fully human IgG4 PD-1 immune checkpoint inhibitor antibody, can result in durable responses in patients with melanoma who have progressed after ipilimumab and BRAF inhibitors. We assessed the efficacy and safety of nivolumab compared with investigator's choice of chemotherapy (ICC) as a second-line or later-line treatment in patients with advanced melanoma. Methods In this randomised, controlled, open-label, phase 3 trial, we recruited patients at 90 sites in 14 countries. Eligible patients were 18 years or older, had unresectable or metastatic melanoma, and progressed after ipilimumab, or ipilimumab and a BRAF inhibitor if they were BRAF V 600 mutation-positive. Participating investigators randomly assigned (with an interactive voice response system) patients 2:1 to receive an intravenous infusion of nivolumab 3 mg/kg every 2 weeks or ICC (dacarbazine 1000 mg/m 2 every 3 weeks or paclitaxel 175 mg/m 2 combined with carboplatin area under the curve 6 every 3 weeks) until progression or unacceptable toxic effects. We stratified randomisation by BRAF mutation status, tumour expression of PD-L1, and previous best overall response to ipilimumab. We used permuted blocks (block size of six) within each stratum. Primary endpoints were the proportion of patients who had an objective response and overall survival. Treatment was given open-label, but those doing tumour assessments were masked to treatment assignment. We assessed objective responses per-protocol after 120 patients had been treated with nivolumab and had a minimum follow-up of 24 weeks, and safety in all patients who had had at least one dose of treatment. The trial is closed and this is the first interim analysis, reporting the objective response primary endpoint. This study is registered with ClinicalTrials.gov, number NCT01721746. Findings Between Dec 21, 2012, and Jan 10, 2014, we screened 631 patients, randomly allocating 272 patients to nivolumab and 133 to ICC. Confirmed objective responses were reported in 38 (31·7%, 95% CI 23·5–40·8) of the first 120 patients in the nivolumab group versus five (10·6%, 3·5–23·1) of 47 patients in the ICC group. Grade 3–4 adverse events related to nivolumab included increased lipase (three [1%] of 268 patients), increased alanine aminotransferase, anaemia, and fatigue (two [1%] each); for ICC, these included neutropenia (14 [14%] of 102), thrombocytopenia (six [6%]), and anaemia (five [5%]). We noted grade 3–4 drug-related serious adverse events in 12 (5%) nivolumab-treated patients and nine (9%) patients in the ICC group. No treatment-related deaths occurred. Interpretation Nivolumab led to a greater proportion of patients achieving an objective response and fewer toxic effects than with alternative available chemotherapy regimens for patients with advanced melanoma that has progressed after ipilimumab or ipilimumab and a BRAF inhibitor. Nivolumab represents a new treatment option with clinically meaningful durable objective responses in a population of high unmet need. Funding Bristol-Myers Squibb.

Annual Research Review: A meta-analysis of the worldwide prevalence of mental disorders in children and adolescents

Abstract: Background The literature on the prevalence of mental disorders affecting children and adolescents has expanded significantly over the last three decades around the world. Despite the field having matured significantly, there has been no meta-analysis to calculate a worldwide-pooled prevalence and to empirically assess the sources of heterogeneity of estimates. Methods We conducted a systematic review of the literature searching in PubMed, PsycINFO, and EMBASE for prevalence studies of mental disorders investigating probabilistic community samples of children and adolescents with standardized assessments methods that derive diagnoses according to the DSM or ICD. Meta-analytical techniques were used to estimate the prevalence rates of any mental disorder and individual diagnostic groups. A meta-regression analysis was performed to estimate the effect of population and sample characteristics, study methods, assessment procedures, and case definition in determining the heterogeneity of estimates. Results We included 41 studies conducted in 27 countries from every world region. The worldwide-pooled prevalence of mental disorders was 13.4% (CI 95% 11.3–15.9). The worldwide prevalence of any anxiety disorder was 6.5% (CI 95% 4.7–9.1), any depressive disorder was 2.6% (CI 95% 1.7–3.9), attention-deficit hyperactivity disorder was 3.4% (CI 95% 2.6–4.5), and any disruptive disorder was 5.7% (CI 95% 4.0–8.1). Significant heterogeneity was detected for all pooled estimates. The multivariate metaregression analyses indicated that sample representativeness, sample frame, and diagnostic interview were significant moderators of prevalence estimates. Estimates did not vary as a function of geographic location of studies and year of data collection. The multivariate model explained 88.89% of prevalence heterogeneity, but residual heterogeneity was still significant. Additional meta-analysis detected significant pooled difference in prevalence rates according to requirement of funcional impairment for the diagnosis of mental disorders. Conclusions Our findings suggest that mental disorders affect a significant number of children and adolescents worldwide. The pooled prevalence estimates and the identification of sources of heterogeneity have important implications to service, training, and research planning around the world.

Burden of Clostridium difficile Infection in the United States

Abstract: Background The magnitude and scope of Clostridium difficile infection in the United States continue to evolve. Methods In 2011, we performed active population- and laboratory-based surveillance across 10 geographic areas in the United States to identify cases of C. difficile infection (stool specimens positive for C. difficile on either toxin or molecular assay in residents ≥1 year of age). Cases were classified as community-associated or health care–associated. In a sample of cases of C. difficile infection, specimens were cultured and isolates underwent molecular typing. We used regression models to calculate estimates of national incidence and total number of infections, first recurrences, and deaths within 30 days after the diagnosis of C. difficile infection. Results A total of 15,461 cases of C. difficile infection were identified in the 10 geographic areas; 65.8% were health care–associated, but only 24.2% had onset during hospitalization. After adjustment for predictors of disease incidence, the estimated number of incident C. difficile infections in the United States was 453,000 (95% confidence interval [CI], 397,100 to 508,500). The incidence was estimated to be higher among females (rate ratio, 1.26; 95% CI, 1.25 to 1.27), whites (rate ratio, 1.72; 95% CI, 1.56 to 2.0), and persons 65 years of age or older (rate ratio, 8.65; 95% CI, 8.16 to 9.31). The estimated number of first recurrences of C. difficile infection was 83,000 (95% CI, 57,000 to 108,900), and the estimated number of deaths was 29,300 (95% CI, 16,500 to 42,100). The North American pulsed-field gel electrophoresis type 1 (NAP1) strain was more prevalent among health care–associated infections than among community-associated infections (30.7% vs. 18.8%, P<0.001) Conclusions C. difficile was responsible for almost half a million infections and was associated with approximately 29,000 deaths in 2011. (Funded by the Centers for Disease Control and Prevention.)

Changes in Burnout and Satisfaction With Work-Life Balance in Physicians and the General US Working Population Between 2011 and 2014

Abstract: Objective To evaluate the prevalence of burnout and satisfaction with work-life balance in physicians and US workers in 2014 relative to 2011. Patients and Methods From August 28, 2014, to October 6, 2014, we surveyed both US physicians and a probability-based sample of the general US population using the methods and measures used in our 2011 study. Burnout was measured using validated metrics, and satisfaction with work-life balance was assessed using standard tools. Results Of the 35,922 physicians who received an invitation to participate, 6880 (19.2%) completed surveys. When assessed using the Maslach Burnout Inventory, 54.4% (n=3680) of the physicians reported at least 1 symptom of burnout in 2014 compared with 45.5% (n=3310) in 2011 ( P P P P Conclusion Burnout and satisfaction with work-life balance in US physicians worsened from 2011 to 2014. More than half of US physicians are now experiencing professional burnout.

Improved Overall Survival in Melanoma with Combined Dabrafenib and Trametinib

Abstract: Background The BRAF inhibitors vemurafenib and dabrafenib have shown efficacy as monotherapies in patients with previously untreated metastatic melanoma with BRAF V600E or V600K mutations. Combining dabrafenib and the MEK inhibitor trametinib, as compared with dabrafenib alone, enhanced antitumor activity in this population of patients. Methods In this open-label, phase 3 trial, we randomly assigned 704 patients with metastatic melanoma with a BRAF V600 mutation to receive either a combination of dabrafenib (150 mg twice daily) and trametinib (2 mg once daily) or vemurafenib (960 mg twice daily) orally as first-line therapy. The primary end point was overall survival. Results At the preplanned interim overall survival analysis, which was performed after 77% of the total number of expected events occurred, the overall survival rate at 12 months was 72% (95% confidence interval [CI], 67 to 77) in the combination-therapy group and 65% (95% CI, 59 to 70) in the vemurafenib group (hazard ratio for death in the combination-therapy group, 0.69; 95% CI, 0.53 to 0.89; P = 0.005). The prespecified interim stopping boundary was crossed, and the study was stopped for efficacy in July 2014. Median progression-free survival was 11.4 months in the combinationtherapy group and 7.3 months in the vemurafenib group (hazard ratio, 0.56; 95% CI, 0.46 to 0.69; P<0.001). The objective response rate was 64% in the combinationtherapy group and 51% in the vemurafenib group (P<0.001). Rates of severe adverse events and study-drug discontinuations were similar in the two groups. Cutaneous squamous-cell carcinoma and keratoacanthoma occurred in 1% of patients in the combination-therapy group and 18% of those in the vemurafenib group. Conclusions Dabrafenib plus trametinib, as compared with vemurafenib monotherapy, significantly improved overall survival in previously untreated patients with metastatic melanoma with BRAF V600E or V600K mutations, without increased overall toxicity. (Funded by GlaxoSmithKline; ClinicalTrials.gov number, NCT01597908.)

Community-acquired pneumonia requiring hospitalization among U.S. adults

Abstract: Background Incidence estimates of hospitalizations for community-acquired pneumonia among children in the United States that are based on prospective data collection are limited. Updated estimates of pneumonia that has been confirmed radiographically and with the use of current laboratory diagnostic tests are needed. Methods We conducted active population-based surveillance for community-acquired pneumonia requiring hospitalization among children younger than 18 years of age in three hospitals in Memphis, Nashville, and Salt Lake City. We excluded children with recent hospitalization or severe immunosuppression. Blood and respiratory specimens were systematically collected for pathogen detection with the use of multiple methods. Chest radiographs were reviewed independently by study radiologists. Results From January 2010 through June 2012, we enrolled 2638 of 3803 eligible children (69%), 2358 of whom (89%) had radiographic evidence of pneumonia. The median age of the children was 2 years (interquartile ...

An integrated map of structural variation in 2,504 human genomes

Abstract: Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

What is the impact of mental health-related stigma on help-seeking? A systematic review of quantitative and qualitative studies.

Abstract: BACKGROUND: Individuals often avoid or delay seeking professional help for mental health problems. Stigma may be a key deterrent to help-seeking but this has not been reviewed systematically. Our systematic review addressed the overarching question: What is the impact of mental health-related stigma on help-seeking for mental health problems? Subquestions were: (a) What is the size and direction of any association between stigma and help-seeking? (b) To what extent is stigma identified as a barrier to help-seeking? (c) What processes underlie the relationship between stigma and help-seeking? (d) Are there population groups for which stigma disproportionately deters help-seeking? METHOD: Five electronic databases were searched from 1980 to 2011 and references of reviews checked. A meta-synthesis of quantitative and qualitative studies, comprising three parallel narrative syntheses and subgroup analyses, was conducted. RESULTS: The review identified 144 studies with 90,189 participants meeting inclusion criteria. The median association between stigma and help-seeking was d = - 0.27, with internalized and treatment stigma being most often associated with reduced help-seeking. Stigma was the fourth highest ranked barrier to help-seeking, with disclosure concerns the most commonly reported stigma barrier. A detailed conceptual model was derived that describes the processes contributing to, and counteracting, the deterrent effect of stigma on help-seeking. Ethnic minorities, youth, men and those in military and health professions were disproportionately deterred by stigma. CONCLUSIONS: Stigma has a small- to moderate-sized negative effect on help-seeking. Review findings can be used to help inform the design of interventions to increase help-seeking.

Mortality in Mental Disorders and Global Disease Burden Implications: A Systematic Review and Meta-analysis

Abstract: Importance Despite the potential importance of understanding excess mortality among people with mental disorders, no comprehensive meta-analyses have been conducted quantifying mortality across mental disorders. Objective To conduct a systematic review and meta-analysis of mortality among people with mental disorders and examine differences in mortality risks by type of death, diagnosis, and study characteristics. Data sources We searched EMBASE, MEDLINE, PsychINFO, and Web of Science from inception through May 7, 2014, including references of eligible articles. Our search strategy included terms for mental disorders (eg, mental disorders, serious mental illness, and severe mental illness), specific diagnoses (eg, schizophrenia, depression, anxiety, and bipolar disorder), and mortality. We also used Google Scholar to identify articles that cited eligible articles. Study selection English-language cohort studies that reported a mortality estimate of mental disorders compared with a general population or controls from the same study setting without mental illness were included. Two reviewers independently reviewed the titles, abstracts, and articles. Of 2481 studies identified, 203 articles met the eligibility criteria and represented 29 countries in 6 continents. Data extraction and synthesis One reviewer conducted a full abstraction of all data, and 2 reviewers verified accuracy. Main outcomes and measures Mortality estimates (eg, standardized mortality ratios, relative risks, hazard ratios, odds ratios, and years of potential life lost) comparing people with mental disorders and the general population or people without mental disorders. We used random-effects meta-analysis models to pool mortality ratios for all, natural, and unnatural causes of death. We also examined years of potential life lost and estimated the population attributable risk of mortality due to mental disorders. Results For all-cause mortality, the pooled relative risk of mortality among those with mental disorders (from 148 studies) was 2.22 (95% CI, 2.12-2.33). Of these, 135 studies revealed that mortality was significantly higher among people with mental disorders than among the comparison population. A total of 67.3% of deaths among people with mental disorders were due to natural causes, 17.5% to unnatural causes, and the remainder to other or unknown causes. The median years of potential life lost was 10 years (n = 24 studies). We estimate that 14.3% of deaths worldwide, or approximately 8 million deaths each year, are attributable to mental disorders. Conclusions and relevance These estimates suggest that mental disorders rank among the most substantial causes of death worldwide. Efforts to quantify and address the global burden of illness need to better consider the role of mental disorders in preventable mortality.

Data Resource Profile: Clinical Practice Research Datalink (CPRD)

Abstract: The Clinical Practice Research Datalink (CPRD) is an ongoing primary care database of anonymised medical records from general practitioners, with coverage of over 11.3 million patients from 674 practices in the UK. With 4.4 million active (alive, currently registered) patients meeting quality criteria, approximately 6.9% of the UK population are included and patients are broadly representative of the UK general population in terms of age, sex and ethnicity. General practitioners are the gatekeepers of primary care and specialist referrals in the UK. The CPRD primary care database is therefore a rich source of health data for research, including data on demographics, symptoms, tests, diagnoses, therapies, health-related behaviours and referrals to secondary care. For over half of patients, linkage with datasets from secondary care, disease-specific cohorts and mortality records enhance the range of data available for research. The CPRD is very widely used internationally for epidemiological research and has been used to produce over 1000 research studies, published in peer-reviewed journals across a broad range of health outcomes. However, researchers must be aware of the complexity of routinely collected electronic health records, including ways to manage variable completeness, misclassification and development of disease definitions for research.

Rising morbidity and mortality in midlife among white non-Hispanic Americans in the 21st century.

Abstract: This paper documents a marked increase in the all-cause mortality of middle-aged white non-Hispanic men and women in the United States between 1999 and 2013. This change reversed decades of progress in mortality and was unique to the United States; no other rich country saw a similar turnaround. The midlife mortality reversal was confined to white non-Hispanics; black non-Hispanics and Hispanics at midlife, and those aged 65 and above in every racial and ethnic group, continued to see mortality rates fall. This increase for whites was largely accounted for by increasing death rates from drug and alcohol poisonings, suicide, and chronic liver diseases and cirrhosis. Although all education groups saw increases in mortality from suicide and poisonings, and an overall increase in external cause mortality, those with less education saw the most marked increases. Rising midlife mortality rates of white non-Hispanics were paralleled by increases in midlife morbidity. Self-reported declines in health, mental health, and ability to conduct activities of daily living, and increases in chronic pain and inability to work, as well as clinically measured deteriorations in liver function, all point to growing distress in this population. We comment on potential economic causes and consequences of this deterioration.

22q11.2 deletion syndrome

Abstract: 22q11.2 deletion syndrome (22q11.2DS) is the most common chromosomal microdeletion disorder, estimated to result mainly from de novo non-homologous meiotic recombination events occurring in approximately 1 in every 1,000 fetuses. The first description in the English language of the constellation of findings now known to be due to this chromosomal difference was made in the 1960s in children with DiGeorge syndrome, who presented with the clinical triad of immunodeficiency, hypoparathyroidism and congenital heart disease. The syndrome is now known to have a heterogeneous presentation that includes multiple additional congenital anomalies and later-onset conditions, such as palatal, gastrointestinal and renal abnormalities, autoimmune disease, variable cognitive delays, behavioural phenotypes and psychiatric illness - all far extending the original description of DiGeorge syndrome. Management requires a multidisciplinary approach involving paediatrics, general medicine, surgery, psychiatry, psychology, interventional therapies (physical, occupational, speech, language and behavioural) and genetic counselling. Although common, lack of recognition of the condition and/or lack of familiarity with genetic testing methods, together with the wide variability of clinical presentation, delays diagnosis. Early diagnosis, preferably prenatally or neonatally, could improve outcomes, thus stressing the importance of universal screening. Equally important, 22q11.2DS has become a model for understanding rare and frequent congenital anomalies, medical conditions, psychiatric and developmental disorders, and may provide a platform to better understand these disorders while affording opportunities for translational strategies across the lifespan for both patients with 22q11.2DS and those with these associated features in the general population.

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes: supplemental material

Abstract: Supplementary Results Refinement for Gene Loss and Duplication Estimates under Opal Stop Codon Recodings Supplementary Methods Identification of Trusted Reference Genomes Refining Marker Sets for Lineage-specific Gene Loss and Duplication Determination of Coding Table Systematic Bias of Completeness and Contamination Estimates Supplemental Figure S1. Distribution of the 104 bacterial and 281 gammaproteobacterial marker genes around the E. coli K12 genome. Supplemental Figure S2. Error in completeness and contamination estimates on simulated genomes with varying levels of completeness and contamination generated under the random contig model. Supplemental Figure S3. Error in completeness and contamination estimates on simulated genomes with varying levels of completeness and contamination generated under the inverse length model. Supplemental Figure S4. Maximum-likelihood genome tree inferred from 5656 reference genomes. Supplemental Figure S5. Error in completeness and contamination estimates on simulated genomes with varying levels of completeness and contamination generated under the random fragment model using a window size of 20 kbp. Supplemental Figure S6. Error in completeness and contamination estimates on simulated genomes with varying levels of completeness and contamination generated under the inverse length model. Supplemental Figure S7. Error in completeness and contamination estimates on simulated genomes from different phyla. Supplemental Figure S8. Bias in completeness and contamination estimates when modelled as a binomial distribution. Supplemental Figure S9. GC-distribution plots of the HMP Capnocytophaga sp. oral taxon 329 genome. Supplemental Figure S10. Phylogenetic placement of the two genomes (Cluster 0 and Cluster 1) identified within the HMP Capnocytophaga sp. oral taxon 329 genome. Supplemental Figure S11. Completeness estimates for 90 putative population genomes recovered from an acetate-amended aquifer. Supplemental Figure S12. Contamination estimates for 90 putative population genomes recovered from an acetate-amended aquifer. Supplemental Figure S13. Identification of the 213 marker genes within the Meyerdierks et al. (2010) ANME-1 genome. Supplemental Figure S14. Refining a marker set for lineage-specific gene loss and duplication. Supplemental Tables Supplemental Table S1. Mean absolute error of completeness (comp.) and contamination (cont.) estimates determined using different universal- and domain-specific marker gene sets. Supplemental Table S2. Number of marker genes and marker sets for taxonomic groups with g 20 reference genomes. Supplemental Table S3. Mean absolute error of completeness (comp.) and contamination (cont.) estimates determined using domain-specific marker genes treated individually (IM) or organized into collocated marker sets (MS). Supplemental Table S4. Mean absolute error and standard deviation of completeness (comp.) and contamination (cont.) estimates determined using domain-specific marker genes treated individually (IM) or organized into collocated marker sets (MS). Supplemental Table S5. Mean absolute error and standard deviation of completeness (comp.) and contamination (cont.) estimates determined using domain-specific marker genes treated individually (IM) or organized into collocated marker sets (MS). Supplemental Table S6. Phylogenetically informative marker genes used to infer the reference genome tree along with matching PhyloSift genes. Supplemental Table S7. Phylogenetically informative genes used in PhyloSift without a matching CheckM gene. Supplemental Table S8. Mean absolute error of completeness (comp.) and contamination (cont.) estimates determined using domain-specific marker sets (dms), the lineage-specific marker set selected by CheckM (sms), and the best performing lineage-specific marker set (bms). Supplemental Table S9. Mean absolute error and standard deviation of completeness (comp.) and contamination (cont.) estimates determined using domain-specific marker sets (dms), the lineage-specific marker set selected by CheckM (sms), and the best performing lineage-specific marker set (bms). Supplemental Table S10. Mean absolute error and standard deviation of completeness (comp.) and contamination (cont.) estimates determined using domain-specific marker sets (dms), the lineage-specific marker set selected by CheckM (sms), and the best performing lineage-specific marker set (bms). Supplemental Table S11. Mean absolute error and standard deviation of completeness (comp.) and contamination (cont.) estimates determined using domain-specific marker sets (dms) and the lineage-specific marker set selected by CheckM (sms). Supplemental Table S12. Mean absolute error and standard deviation of completeness (comp.) and contamination (cont.) estimates determined using domain-specific marker sets (dms) and the lineage-specific marker sets selected by CheckM (sms). Supplemental Table S13. Mean absolute error and standard deviation of completeness (comp.) and contamination (cont.) estimates determined using domain-specific marker sets (dms) and the lineage-specific marker sets selected by CheckM (sms). Supplemental Table S14. Taxonomic rank of the selected lineage-specific marker set used for evaluating the quality of genomes at different degrees of taxonomic novelty. Supplemental Table S15. Mean absolute error and standard deviation of completeness (comp.) and contamination (cont.) estimates for simulated genomes at different degrees of taxonomic novelty. Supplemental Table S16. Lineage-specific completeness and contamination estimates for isolate genomes from large-scale sequencing initiatives. (see Excel file) Supplemental Table S17. Completeness and contamination estimates of the Lactobacillus gasseri MV-22 genome for increasingly basal lineage-specific marker sets. Supplemental Table S18. Bacterial marker genes identified within the HMP Lactobacillus gasseri genomes. Markers missing from a genome or present in multiple copies are highlighted with a grey background. Supplemental Table S19. Lineage-specific completeness and contamination estimates for genomes annotated as finished at IMG, along with predicted translation tables and calculated coding density. (see Excel file) Supplemental Table S20: Lineage-specific completeness and contamination estimates for single-cell genomes from the GEBA-MDM initiative along with traditional assembly statistics. (see Excel file) Supplemental Table S21: Lineage-specific completeness and contamination estimates for population genomes, plasmids, and phage recovered from metagenomic datasets along with traditional assembly statistics. (see Excel file) Supplemental Table S22: Completeness and contamination estimates for population genomes recovered from an acetate-amended aquifer determined using domain-level and lineage-specific marker sets. (see Excel file)

Nonalcoholic Fatty Liver Disease: A Systematic Review

Abstract: Importance Nonalcoholic fatty liver disease and its subtype nonalcoholic steatohepatitis affect approximately 30% and 5%, respectively, of the US population. In patients with nonalcoholic steatohepatitis, half of deaths are due to cardiovascular disease and malignancy, yet awareness of this remains low. Cirrhosis, the third leading cause of death in patients with nonalcoholic fatty liver disease, is predicted to become the most common indication for liver transplantation. Objectives To illustrate how to identify patients with nonalcoholic fatty liver disease at greatest risk of nonalcoholic steatohepatitis and cirrhosis; to discuss the role and limitations of current diagnostics and liver biopsy to diagnose nonalcoholic steatohepatitis; and to provide an outline for the management of patients across the spectrum of nonalcoholic fatty liver disease. Evidence Review PubMed was queried for published articles through February 28, 2015, using the search termsNAFLD and cirrhosis, mortality, biomarkers,andtreatment. A total of 88 references were selected, including 14 randomized clinical trials, 19 cohort or case-control studies, 1 population-based study, 2 practice guidelines, 7 meta-analyses, 43 classified as other, and 2 webpages. Findings Sixty-six percent of patients older than 50 years with diabetes or obesity are thought to have nonalcoholic steatohepatitis with advanced fibrosis. Even though the ability to identify the nonalcoholic steatohepatitis subtype within those with nonalcoholic fatty liver disease still requires liver biopsy, biomarkers to detect advanced fibrosis are increasingly reliable. Lifestyle modification is the foundation of treatment for patients with nonalcoholic steatosis. Available treatments with proven benefit include vitamin E, pioglitazone, and obeticholic acid; however, the effect size is modest ( Conclusions and Relevance Between 75 million and 100 million individuals in the United States are estimated to have nonalcoholic fatty liver disease and its potential morbidity extends beyond the liver. It is important that primary care physicians, endocrinologists, and other specialists be aware of the scope and long-term effects of the disease. Early identification of patients with nonalcoholic steatohepatitis may help improve patient outcomes through treatment intervention, including transplantation for those with decompensated cirrhosis.

Incidence Estimate of Nonmelanoma Skin Cancer (Keratinocyte Carcinomas) in the US Population, 2012

Abstract: Importance Understanding skin cancer incidence is critical for planning prevention and treatment strategies and allocating medical resources. However, owing to lack of national reporting and previously nonspecific diagnosis classification, accurate measurement of the US incidence of nonmelanoma skin cancer (NMSC) has been difficult. Objective To estimate the incidence of NMSC (keratinocyte carcinomas) in the US population in 2012 and the incidence of basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) in the 2012 Medicare fee-for-service population. Design, Setting, and Participants This study analyzes US government administrative data including the Centers for Medicare & Medicaid Services Physicians Claims databases to calculate totals of skin cancer procedures performed for Medicare beneficiaries from 2006 through 2012 and related parameters. The population-based National Ambulatory Medical Care Survey database was used to estimate NMSC-related office visits for 2012. We combined these analyses to estimate totals of new skin cancer diagnoses and affected individuals in the overall US population. Main Outcomes and Measures Incidence of NMSC in the US population in 2012 and BCC and SCC in the 2012 Medicare fee-for-service population. Results The total number of procedures for skin cancer in the Medicare fee-for-service population increased by 13% from 2 048 517 in 2006 to 2 321 058 in 2012. The age-adjusted skin cancer procedure rate per 100 000 beneficiaries increased from 6075 in 2006 to 7320 in 2012. The number of procedures in Medicare beneficiaries specific for NMSC increased by 14% from 1 918 340 in 2006 to 2 191 100 in 2012. The number of persons with at least 1 procedure for NMSC increased by 14% (from 1 177 618 to 1 336 800) from 2006 through 2012. In the 2012 Medicare fee-for-service population, the age-adjusted procedure rate for BCC and SCC were 3280 and 3278 per 100 000 beneficiaries, respectively. The ratio of BCC to SCC treated in Medicare beneficiaries was 1.0. We estimate the total number of NMSCs in the US population in 2012 at 5 434 193 and the total number of persons in the United States treated for NMSC at 3 315 554. Conclusions and Relevance This study is a thorough nationwide estimate of the incidence of NMSC and provides evidence of continued increases in numbers of skin cancer diagnoses and affected patients in the United States. This study also demonstrates equal incidence rates for BCC and SCC in the Medicare population.

Future coastal population growth and exposure to sea-level rise and coastal flooding--a global assessment.

Abstract: Coastal zones are exposed to a range of coastal hazards including sea-level rise with its related effects. At the same time, they are more densely populated than the hinterland and exhibit higher rates of population growth and urbanisation. As this trend is expected to continue into the future, we investigate how coastal populations will be affected by such impacts at global and regional scales by the years 2030 and 2060. Starting from baseline population estimates for the year 2000, we assess future population change in the low-elevation coastal zone and trends in exposure to 100-year coastal floods based on four different sea-level and socio-economic scenarios. Our method accounts for differential growth of coastal areas against the land-locked hinterland and for trends of urbanisation and expansive urban growth, as currently observed, but does not explicitly consider possible displacement or out-migration due to factors such as sea-level rise. We combine spatially explicit estimates of the baseline population with demographic data in order to derive scenario-driven projections of coastal population development. Our scenarios show that the number of people living in the low-elevation coastal zone, as well as the number of people exposed to flooding from 1-in-100 year storm surge events, is highest in Asia. China, India, Bangladesh, Indonesia and Viet Nam are estimated to have the highest total coastal population exposure in the baseline year and this ranking is expected to remain largely unchanged in the future. However, Africa is expected to experience the highest rates of population growth and urbanisation in the coastal zone, particularly in Egypt and sub-Saharan countries in Western and Eastern Africa. The results highlight countries and regions with a high degree of exposure to coastal flooding and help identifying regions where policies and adaptive planning for building resilient coastal communities are not only desirable but essential. Furthermore, we identify needs for further research and scope for improvement in this kind of scenario-based exposure analysis.

Part 8: Post-cardiac arrest care: 2015 American Heart Association guidelines update for cardiopulmonary resuscitation and emergency cardiovascular care

Abstract: The recommendations in this 2015 American Heart Association (AHA) Guidelines Update for Cardiopulmonary Resuscitation and Emergency Cardiovascular Care are based on an extensive evidence review process that was begun by the International Liaison Committee on Resuscitation (ILCOR) after the publication of the 2010 International Consensus on Cardiopulmonary Resuscitation and Emergency Cardiovascular Care Science With Treatment Recommendations 1,2 and was completed in February 2015.3,4 In this in-depth evidence review process, ILCOR examined topics and then generated a prioritized list of questions for systematic review. Questions were first formulated in PICO (population, intervention, comparator, outcome) format,5 and then search strategies and inclusion and exclusion criteria were defined and a search for relevant articles was performed. The evidence was evaluated by the ILCOR task forces by using the standardized methodological approach proposed by the Grading of Recommendations Assessment, Development and Evaluation (GRADE) Working Group.6 The quality of the evidence was categorized based on the study methodologies and the 5 core GRADE domains of risk of bias, inconsistency, indirectness, imprecision, and other considerations (including publication bias). Then, where possible, consensus-based treatment recommendations were created. To create this 2015 Guidelines Update, the AHA formed 15 writing groups, with careful attention to manage conflicts of interest, to assess the ILCOR treatment recommendations and to write AHA treatment recommendations by using the AHA Class of Recommendation (COR) and Level of Evidence (LOE) system. The recommendations made in the Guidelines are informed by the ILCOR recommendations and GRADE classification, in the context of the delivery of medical care in North America. The AHA writing group made new recommendations only on topics specifically reviewed by ILCOR in 2015. This chapter delineates instances where the AHA writing group developed recommendations that are significantly stronger or weaker than the ILCOR statements. In the online …

The cyclin-dependent kinase 4/6 inhibitor palbociclib in combination with letrozole versus letrozole alone as first-line treatment of oestrogen receptor-positive, HER2-negative, advanced breast cancer (PALOMA-1/TRIO-18): a randomised phase 2 study

Abstract: Summary Background Palbociclib (PD-0332991) is an oral, small-molecule inhibitor of cyclin-dependent kinases (CDKs) 4 and 6 with preclinical evidence of growth-inhibitory activity in oestrogen receptor-positive breast cancer cells and synergy with anti-oestrogens. We aimed to assess the safety and efficacy of palbociclib in combination with letrozole as first-line treatment of patients with advanced, oestrogen receptor-positive, HER2-negative breast cancer. Methods In this open-label, randomised phase 2 study, postmenopausal women with advanced oestrogen receptor-positive and HER2-negative breast cancer who had not received any systemic treatment for their advanced disease were eligible to participate. Patients were enrolled in two separate cohorts that accrued sequentially: in cohort 1, patients were enrolled on the basis of their oestrogen receptor-positive and HER2-negative biomarker status alone, whereas in cohort 2 they were also required to have cancers with amplification of cyclin D1 ( CCND1 ), loss of p16 (INK4A or CDKN2A), or both. In both cohorts, patients were randomly assigned 1:1 via an interactive web-based randomisation system, stratified by disease site and disease-free interval, to receive continuous oral letrozole 2·5 mg daily or continuous oral letrozole 2·5 mg daily plus oral palbociclib 125 mg, given once daily for 3 weeks followed by 1 week off over 28-day cycles. The primary endpoint was investigator-assessed progression-free survival in the intention-to-treat population. Accrual to cohort 2 was stopped after an unplanned interim analysis of cohort 1 and the statistical analysis plan for the primary endpoint was amended to a combined analysis of cohorts 1 and 2 (instead of cohort 2 alone). The study is ongoing but closed to accrual; these are the results of the final analysis of progression-free survival. The study is registered with the ClinicalTrials.gov, number NCT00721409. Findings Between Dec 22, 2009, and May 12, 2012, we randomly assigned 165 patients, 84 to palbociclib plus letrozole and 81 to letrozole alone. At the time of the final analysis for progression-free survival (median follow-up 29·6 months [95% CI 27·9–36·0] for the palbociclib plus letrozole group and 27·9 months [25·5–31·1] for the letrozole group), 41 progression-free survival events had occurred in the palbociclib plus letrozole group and 59 in the letrozole group. Median progression-free survival was 10·2 months (95% CI 5·7–12·6) for the letrozole group and 20·2 months (13·8–27·5) for the palbociclib plus letrozole group (HR 0·488, 95% CI 0·319–0·748; one-sided p=0·0004). In cohort 1 (n=66), median progression-free survival was 5·7 months (2·6–10·5) for the letrozole group and 26·1 months (11·2–not estimable) for the palbociclib plus letrozole group (HR 0·299, 0·156–0·572; one-sided p Interpretation The addition of palbociclib to letrozole in this phase 2 study significantly improved progression-free survival in women with advanced oestrogen receptor-positive and HER2-negative breast cancer. A phase 3 trial is currently underway. Funding Pfizer.

Randomized Trial of Peanut Consumption in Infants at Risk for Peanut Allergy

Abstract: Methods We randomly assigned 640 infants with severe eczema, egg allergy, or both to consume or avoid peanuts until 60 months of age. Participants, who were at least 4 months but younger than 11 months of age at randomization, were assigned to separate study cohorts on the basis of preexisting sensitivity to peanut extract, which was determined with the use of a skin-prick test — one consisting of participants with no measurable wheal after testing and the other consisting of those with a wheal measuring 1 to 4 mm in diameter. The primary outcome, which was assessed independently in each cohort, was the proportion of participants with peanut allergy at 60 months of age. Results Among the 530 infants in the intention-to-treat population who initially had negative results on the skin-prick test, the prevalence of peanut allergy at 60 months of age was 13.7% in the avoidance group and 1.9% in the consumption group (P<0.001). Among the 98 participants in the intention-to-treat population who initially had positive test results, the prevalence of peanut allergy was 35.3% in the avoidance group and 10.6% in the consumption group (P = 0.004). There was no significant between-group difference in the incidence of serious adverse events. Increases in levels of peanut-specific IgG4 antibody occurred predominantly in the consumption group; a greater percentage of participants in the avoidance group had elevated titers of peanut-specific IgE antibody. A larger wheal on the skin-prick test and a lower ratio of peanut-specific IgG4:IgE were associated with peanut allergy. Conclusions The early introduction of peanuts significantly decreased the frequency of the development of peanut allergy among children at high risk for this allergy and modulated immune responses to peanuts. (Funded by the National Institute of Allergy and Infectious Diseases and others; ClinicalTrials.gov number, NCT00329784.)

Prevalence of and Trends in Diabetes Among Adults in the United States, 1988-2012

Abstract: Importance Previous studies have shown increasing prevalence of diabetes in the United States. New US data are available to estimate prevalence of and trends in diabetes. Objective To estimate the recent prevalence and update US trends in total diabetes, diagnosed diabetes, and undiagnosed diabetes using National Health and Nutrition Examination Survey (NHANES) data. Design, setting, and participants Cross-sectional surveys conducted between 1988-1994 and 1999-2012 of nationally representative samples of the civilian, noninstitutionalized US population; 2781 adults from 2011-2012 were used to estimate recent prevalence and an additional 23,634 adults from 1988-2010 were used to estimate trends. Main outcomes and measures The prevalence of diabetes was defined using a previous diagnosis of diabetes or, if diabetes was not previously diagnosed, by (1) a hemoglobin A1c level of 6.5% or greater or a fasting plasma glucose (FPG) level of 126 mg/dL or greater (hemoglobin A1c or FPG definition) or (2) additionally including 2-hour plasma glucose (2-hour PG) level of 200 mg/dL or greater (hemoglobin A1c, FPG, or 2-hour PG definition). Prediabetes was defined as a hemoglobin A1c level of 5.7% to 6.4%, an FPG level of 100 mg/dL to 125 mg/dL, or a 2-hour PG level of 140 mg/dL to 199 mg/dL. Results In the overall 2011-2012 population, the unadjusted prevalence (using the hemoglobin A1c, FPG, or 2-hour PG definitions for diabetes and prediabetes) was 14.3% (95% CI, 12.2%-16.8%) for total diabetes, 9.1% (95% CI, 7.8%-10.6%) for diagnosed diabetes, 5.2% (95% CI, 4.0%-6.9%) for undiagnosed diabetes, and 38.0% (95% CI, 34.7%-41.3%) for prediabetes; among those with diabetes, 36.4% (95% CI, 30.5%-42.7%) were undiagnosed. The unadjusted prevalence of total diabetes (using the hemoglobin A1c or FPG definition) was 12.3% (95% CI, 10.8%-14.1%); among those with diabetes, 25.2% (95% CI, 21.1%-29.8%) were undiagnosed. Compared with non-Hispanic white participants (11.3% [95% CI, 9.0%-14.1%]), the age-standardized prevalence of total diabetes (using the hemoglobin A1c, FPG, or 2-hour PG definition) was higher among non-Hispanic black participants (21.8% [95% CI, 17.7%-26.7%]; P Conclusions and relevance In 2011-2012, the estimated prevalence of diabetes was 12% to 14% among US adults, depending on the criteria used, with a higher prevalence among participants who were non-Hispanic black, non-Hispanic Asian, and Hispanic. Between 1988-1994 and 2011-2012, the prevalence of diabetes increased in the overall population and in all subgroups evaluated.