Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors

Background: One of the most provocative recent observations in cancer epigenetics is the discovery of large hypomethylated blocks, including single copy genes, in colorectal cancer, that correspond in location to heterochromatic LOCKs (large organized chromatin lysine-modifications) and LADs (lamin-associated domains). Methods: Here we performed a comprehensive genome-scale analysis of 10 breast, 28 colon, nine lung, 38 thyroid, 18 pancreas cancers, and five pancreas neuroendocrine tumors as well as matched normal tissue from most of these cases, as well as 51 premalignant lesions. We used a new statistical approach that allows the identification of large hypomethylated blocks on the Illumina HumanMethylation450 BeadChip platform. Results: We find that hypomethylated blocks are a universal feature of common solid human cancer, and that they occur at the earliest stage of premalignant tumors and progress through clinical stages of thyroid and colon cancer development. We also find that the disrupted CpG islands widely reported previously, including hypermethylated island bodies and hypomethylated shores, are enriched in hypomethylated blocks, with flattening of the methylation signal within and flanking the islands. Finally, we found that genes showing higher between individual gene expression variability are enriched within these hypomethylated blocks. Conclusion: Thus hypomethylated blocks appear to be a universal defining epigenetic alteration in human cancer, at least for common solid tumors. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0061-y) contains supplementary material, which is available to authorized users

M/L, H-alpha Rotation Curves, and HI Measurements for 329 Nearby Cluster and Field Spirals: II. Evidence for Galaxy Infall

We have conducted a study of optical and HI properties of spiral galaxies (size, luminosity, H-alpha flux distribution, circular velocity, HI gas mass) to explore the role of gas stripping as a driver of morphological evolution in clusters. We find a strong correlation between the spiral and S0 fractions within clusters, and the spiral fraction scales tightly with cluster X-ray gas luminosity. We explore young star formation and identify spirals that are (1) asymmetric, with truncated H-alpha emission and HI gas reservoirs on the leading edge of the disk, on a first pass through the dense intracluster medium in the cores of rich clusters; (2) strongly HI deficient and stripped, with star formation confined to the inner 5 kpc/h and 3 disk scale lengths; (3) reddened, extremely HI deficient and quenched, where star formation has been halted across the entire disk. We propose that these spirals are in successive stages of morphological transformation, between infalling field spirals and cluster S0s, and that the process which acts to remove the HI gas reservoir suppresses new star formation on a similarly fast timescale. These data suggest that gas stripping plays a significant role in morphological transformation and rapid truncation of star formation across the disk.Comment: 24 pages, 12 figures; accepted for publication in AJ; higher-resolution figures available at http://astronomy.nmsu.edu/nicol

Arterial line pressure control enhanced extracorporeal blood flow prescription in hemodialysis patients

<p>Abstract</p> <p>Background</p> <p>In hemodialysis, extracorporeal blood flow (Qb) recommendation is 300–500 mL/min. To achieve the best Qb, we based our prescription on dynamic arterial line pressure (DALP).</p> <p>Methods</p> <p>This prospective study included 72 patients with catheter Group 1 (G1), 1877 treatments and 35 arterio-venous (AV) fistulae Group 2 (G2), 1868 treatments. The dialysis staff was trained to prescribe Qb sufficient to obtain DALP between -200 to -250 mmHg. We measured ionic clearance (IK: mL/min), access recirculation, DALP (mmHg) and Qb (mL/min). Six prescription zones were identified: from an optimal A zone (Qb > 400, DALP -200 to -250) to zones with lower Qb E (Qb < 300, DALP -200 to -250) and F (Qb < 300, DALP > -199).</p> <p>Results</p> <p>Treatments distribution in A was 695 (37%) in G1 vs. 704 (37.7%) in G2 (<it>P </it>= 0.7). In B 150 (8%) in G1 vs. 458 (24.5%) in G2 (<it>P </it>< 0.0001). Recirculation in A was 10.0% (Inter quartile rank, IQR 6.5, 14.2) in G1 vs. 9.8% (IQR 7.5, 14.1) in G2 (<it>P </it>= 0.62). IK in A was 214 ± 34 (G1) vs. 213 ± 35 (G2) (<it>P </it>= 0.65). IK Anova between G2 zones was: A vs. C and D (<it>P </it>< 0.000001). Staff prescription adherence was 81.3% (G1) vs. 84.1% (G2) (<it>P </it>= 0.02).</p> <p>Conclusion</p> <p>In conclusion, an optimal Qb can de prescribed with DALP of -200 mmHg. Staff adherence to DLAP treatment prescription could be reached up to 81.3% in catheters and 84.1% in AV fistulae.</p

Comparison of Current-Use Pesticide and Other Toxicant Urinary Metabolite Levels among Pregnant Women in the CHAMACOS Cohort and NHANES

BackgroundWe measured 34 metabolites of current-use pesticides and other precursor compounds in urine samples collected twice during pregnancy from 538 women living in the Salinas Valley of California, a highly agricultural area (1999-2001). Precursors of these metabolites included fungicides, carbamate, organochlorine, organophosphorus (OP), and pyrethroid insecticides, and triazine and chloroacetanilide herbicides. We also measured ethylenethiourea, a metabolite of the ethylene-bisdithiocarbamate fungicides. Repeat measurements of the compounds presented here have not been reported in pregnant women previously. To understand the impact of the women's regional environment on these findings, we compared metabolite concentrations from the CHAMACOS (Center for the Health Assessment of Mothers and Children of Salinas) cohort with U.S. national reference data for 342 pregnant women sampled by the National Health and Nutrition Examination Survey (1999-2002).ResultsThe eight metabolites detected in &gt; 50% of samples [2,4-dichlorophenol (2,4-DCP); 2,5-dichlorophenol (2,5-DCP); 1- and 2-naphthol; ortho-phenylphenol (ORTH); para-nitrophenol (PNP); 2,4,6-trichlorophenol (2,4,6-TCP); and 3,4,6-trichloro-2-pyridinol (TCPy)] may be related to home or agricultural pesticide use in the Salinas Valley, household products, and other sources of chlorinated phenols. More than 78% of women in this study had detectable levels of at least one of the OP pesticide-specific metabolites that we measured, and &gt; 30% had two or more. The 95th percentile values of six of the most commonly detected (&gt; 50%) compounds were significantly higher among the CHAMACOS women after controlling for age, race, socioeconomic status, and smoking [(2,4-DCP; 2,5-DCP; ORTH; PNP; 2,4,6-TCP; and TCPy); quantile regression p &lt; 0.05].ConclusionsFindings suggest that the CHAMACOS cohort has an additional burden of precursor pesticide exposure compared with the national sample, possibly from living and/or working in an agricultural area

Determinants of Organophosphorus Pesticide Urinary Metabolite Levels in Young Children Living in an Agricultural Community

Organophosphorus (OP) pesticides are used in agriculture and several are registered for home use. As young children age they may experience different pesticide exposures due to varying diet, behavior, and other factors. We measured six OP dialkylphosphate (DAP) metabolites (three dimethyl alkylphosphates (DMAP) and three diethyl alkylphosphates (DEAP)) in urine samples collected from ∼400 children living in an agricultural community when they were 6, 12, and 24 months old. We examined bivariate associations between DAP metabolite levels and determinants such as age, diet, season, and parent occupation. To evaluate independent impacts, we then used generalized linear mixed multivariable models including interaction terms with age. The final models indicated that DMAP metabolite levels increased with age. DMAP levels were also positively associated with daily servings of produce at 6- and 24-months. Among the 6-month olds, DMAP metabolite levels were higher when samples were collected during the summer/spring versus the winter/fall months. Among the 12-month olds, DMAP and DEAP metabolites were higher when children lived ≤60 meters from an agricultural field. Among the 24-month-olds, DEAP metabolite levels were higher during the summer/spring months. Our findings suggest that there are multiple determinants of OP pesticide exposures, notably dietary intake and temporal and spatial proximity to agricultural use. The impact of these determinants varied by age and class of DAP metabolite

Evaluation of the Impact of Genetically Modified Cotton After 20 Years of Cultivation in Mexico

For more than 20 years cotton has been the most widely sown genetically modified (GM) crop in Mexico. Its cultivation has fulfilled all requirements and has gone through the different regulatory stages. During the last 20 years, both research-institutions and biotech-companies have generated scientific and technical information regarding GM cotton cultivation in Mexico. In this work, we collected data in order to analyze the environmental and agronomic effects of the use of GM cotton in Mexico. In 1996, the introduction of Bt cotton made it possible to reactivate this crop, which in previous years was greatly reduced due to pest problems, production costs and environmental concerns. Bt cotton is a widely accepted tool for cotton producers and has proven to be efficient for the control of lepidopteran pests. The economic benefits of its use are variable, and depend on factors such as the international cotton-prices and other costs associated with its inputs. So far, the management strategies used to prevent development of insect resistance to GM cotton has been successful, and there are no reports of insect resistance development to Bt cotton in Mexico. In addition, no effects have been observed on non-target organisms. For herbicide tolerant cotton, the prevention of herbicide resistance has also been successful since unlike other countries, the onset of resistance weeds is still slow, apparently due to cultural practices and rotation of different herbicides. Environmental benefits have been achieved with a reduction in chemical insecticide applications and the subsequent decrease in primary pest populations, so that the inclusion of other technologies—e.g., use of non-Bt cotton- can be explored. Nevertheless, control measures need to be implemented during transport of the bolls and fiber to prevent dispersal of volunteer plants and subsequent gene flow to wild relatives distributed outside the GM cotton growing areas. It is still necessary to implement national research programs, so that biotechnology and plant breeding advances can be used in the development of cotton varieties adapted to the Mexican particular environmental conditions and to control insect pests of regional importance

Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation

Open access to sequence data is a cornerstone of biology and biodiversity research, but has created tension under the United Nations Convention on Biological Diversity (CBD). Policy decisions could compromise research and development, unless a practical multilateral solution is implemented.This workwas funded by the German Federal Ministry of Education and Research (BMBF) WiLDSI 031B0862 (A.H.S., J.O., and J.F.) and Horizon Europe EVA-GLOBAL 871029 (A.H.S.). I.K.M. was supported by the National Center for Biotechnology Information of the National Library of Medicine, National Institutes of Health

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Clinical practice guideline for surgical antimicrobial prophylaxis

La infección del sitio quirúrgico (ISQ) es una de las principales causas de infecciones asociadas a la atención en salud (IAAS), con un impacto significativo en la mortalidad y morbilidad del paciente quirúrgico, así como en los costos asociados a la atención en salud. El adecuado uso de la profilaxis quirúrgica antimicrobiana es un aspecto fundamental en la reducción del riesgo de ISQ, dado que su utilización inapropiada o indiscriminada puede representar un riesgo para los pacientes y contribuir al desarrollo de resistencia a los antimicrobianos, por lo que resulta de importancia generar directrices que permitan orientar el uso adecuado de antimicrobianos en la profilaxis del paciente quirúrgico, con el objetivo de obtener mejores desenlaces clínicos y propender por un uso racional de antibióticos. La presente guía contiene recomendaciones para profilaxis antibiótica de pacientes sometidos a procedimiento quirúrgico, basadas en la evidencia, realizadas mediante el proceso de adaptación de guías de práctica clínica para el contexto colombiano.Q4Pacientes sometidos a Profilaxis quirúrgica antimicrobianaSurgical site infection (SSI) is one of the main causes of healthcare associated infections (HAI), with a significant impact on the mortality and morbidity of the surgi-cal patient, as well as on the costs associated with health care. The adequate use of surgical antimicrobial prophylaxis being a fundamental aspect in reducing the risk of SSI, taking into account that the inappropriate or indiscriminate use of antibiotics in surgical prophylaxis may represent a risk for patients and contribute to the development of antimicrobial resistance, so it is important to generate guidelines that guide the appropriate antimicrobial prophylaxis in the surgical patient, with the aim of obtaining better clinical outcomes and promoting a rational use of antibiotics. This guide contains recommendations for antibiotic prophylaxis in patients undergoing a surgical procedure, based on evidence, carried out through the process of adapting clinical practice guidelines for the Colombian context.https://orcid.org/0000-0002-5392-7083https://orcid.org/0000-0003-2568-4667Revista Nacional - IndexadaCN