Matching LOFAR sources across radio bands

Aims. With the recent preliminary release of the LOFAR LBA Sky Survey (LoLSS), the first wide-area, ultra-low frequency observations from LOFAR were published. Our aim is to combine this data set with other surveys at higher frequencies to study the spectral properties of a large sample of radio sources. Methods. We present a new cross-matching algorithm taking into account the sizes of the radio sources and apply it to the LoLSS-PR, LoTSS-DR1, LoTSS-DR2 (all LOFAR), TGSS-ADR1 (GMRT), WENSS (WSRT) and NVSS (VLA) catalogues. We then study the number of matched counterparts for LoLSS radio sources and their spectral properties. Results. We find counterparts for 22 607 (89.5%) LoLSS sources. The remaining 2 640 sources (10.5%) are identified either as an artefact in the LoLSS survey (3.6%) or flagged due to their closeness to bright sources (6.9%). We find an average spectral index of $\alpha = -0.77 \pm 0.18$ between LoLSS and NVSS. Between LoLSS and LoTSS-DR2 we find $\alpha = -0.71 \pm 0.31$. The average spectral index is flux density independent above $S_{54} = 181$ mJy. Comparison of the spectral slopes from LoLSS--LoTSS-DR2 with LoTSS-DR2--NVSS indicates that the probed population of radio sources exhibits evidence for a negative spectral curvature.Comment: 13 pages, 22 figures and 2 tables. Accepted for publication in A&

Prevalence and clinical features of patients with concurrent HBsAg and anti‐HBs: Evaluation of the hepatitis B research network cohort

The prevalence of concurrent HBsAg and anti‐HBs in plasma of persons with chronic hepatitis B virus (HBV) infection is variable and its clinical significance enigmatic. We examined the prevalence and clinical and virological features of concurrent HBsAg and anti‐HBs in children and adults with chronic HBV infection living in North America. A total of 1462 HBsAg positive participants in the Hepatitis B Research Network paediatric and adult cohorts were included (median age 41 (range 4‐80) years, 48% female, 11% white, 13% black, 73% Asians). Only 18 (1.2%) were found to be anti‐HBs positive (≥10 mIU/mL) at initial study evaluation. Distributions of sex, race, HBV genotype and ALT were similar between participants with and without concurrent anti‐HBs. Those who were anti‐HBs positive appeared to be older (median age 50 vs 41 years, P = .06), have lower platelet counts (median 197 vs 222 × 103/mm3, P = .07) and have higher prevalence of HBeAg (44% vs 26%, P = .10). They also had lower HBsAg levels (median 2.0 vs 3.5 log10 IU/mL, P = .02). Testing of follow‐up samples after a median of 4 years (range 1‐6) in 12 of the 18 participants with initial concurrent anti‐HBs showed anti‐HBs became undetectable in 6, decreased to <10 mIU/mL in 1 and remained positive in 5 participants. Two patients lost HBsAg during follow‐up. In conclusion, prevalence of concurrent HBsAg and anti‐HBs was low at 1.2%, with anti‐HBs disappearing in some during follow‐up, in this large cohort of racially diverse children and adults with chronic HBV infection living in North America. Presence of concurrent HBsAg and anti‐HBs did not identify a specific phenotype of chronic hepatitis B, nor did it appear to affect clinical outcomes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156489/3/jvh13312.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156489/2/jvh13312-sup-0001-FigS1-S3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156489/1/jvh13312_am.pd

Systematic review of reviews of intervention components associated with increased effectiveness in dietary and physical activity interventions.

BACKGROUND: To develop more efficient programmes for promoting dietary and/or physical activity change (in order to prevent type 2 diabetes) it is critical to ensure that the intervention components and characteristics most strongly associated with effectiveness are included. The aim of this systematic review of reviews was to identify intervention components that are associated with increased change in diet and/or physical activity in individuals at risk of type 2 diabetes. METHODS: MEDLINE, EMBASE, CINAHL, PsycInfo, and the Cochrane Library were searched for systematic reviews of interventions targeting diet and/or physical activity in adults at risk of developing type 2 diabetes from 1998 to 2008. Two reviewers independently selected reviews and rated methodological quality. Individual analyses from reviews relating effectiveness to intervention components were extracted, graded for evidence quality and summarised. RESULTS: Of 3856 identified articles, 30 met the inclusion criteria and 129 analyses related intervention components to effectiveness. These included causal analyses (based on randomisation of participants to different intervention conditions) and associative analyses (e.g. meta-regression). Overall, interventions produced clinically meaningful weight loss (3-5 kg at 12 months; 2-3 kg at 36 months) and increased physical activity (30-60 mins/week of moderate activity at 12-18 months). Based on causal analyses, intervention effectiveness was increased by engaging social support, targeting both diet and physical activity, and using well-defined/established behaviour change techniques. Increased effectiveness was also associated with increased contact frequency and using a specific cluster of "self-regulatory" behaviour change techniques (e.g. goal-setting, self-monitoring). No clear relationships were found between effectiveness and intervention setting, delivery mode, study population or delivery provider. Evidence on long-term effectiveness suggested the need for greater consideration of behaviour maintenance strategies. CONCLUSIONS: This comprehensive review of reviews identifies specific components which are associated with increased effectiveness in interventions to promote change in diet and/or physical activity. To maximise the efficiency of programmes for diabetes prevention, practitioners and commissioning organisations should consider including these components.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Targeted next generation sequencing as a tool for precision medicine

Background: Targeted next-generation sequencing (NGS) enables rapid identification of common and rare genetic variation. The detection of variants contributing to therapeutic drug response or adverse effects is essential for implementation of individualized pharmacotherapy. Successful application of short-read based NGS to pharmacogenes with high sequence homology, nearby pseudogenes and complex structure has been previously shown despite anticipated technical challenges. However, little is known regarding the utility of such panels to detect copy number variation (CNV) in the highly polymorphic cytochrome P450 (CYP) 2D6 gene, or to identify the promoter (TA)7 TAA repeat polymorphism UDP glucuronosyltransferase (UGT) 1A1∗28. Here we developed and validated PGxSeq, a targeted exome panel for pharmacogenes pertinent to drug disposition and/or response. Methods: A panel of capture probes was generated to assess 422 kb of total coding region in 100 pharmacogenes. NGS was carried out in 235 subjects, and sequencing performance and accuracy of variant discovery validated in clinically relevant pharmacogenes. CYP2D6 CNV was determined using the bioinformatics tool CNV caller (VarSeq). Identified SNVs were assessed in terms of population allele frequency and predicted functional effects through in silico algorithms. Results: Adequate performance of the PGxSeq panel was demonstrated with a depth-of-coverage (DOC) ≥ 20× for at least 94% of the target sequence. We showed accurate detection of 39 clinically relevant gene variants compared to standard genotyping techniques (99.9% concordance), including CYP2D6 CNV and UGT1A1∗28. Allele frequency of rare or novel variants and predicted function in 235 subjects mirrored findings from large genomic datasets. A large proportion of patients (78%, 183 out of 235) were identified as homozygous carriers of at least one variant necessitating altered pharmacotherapy. Conclusions: PGxSeq can serve as a comprehensive, rapid, and reliable approach for the detection of common and novel SNVs in pharmacogenes benefiting the emerging field of precision medicine

Guidelines for Physical Activity During Pregnancy: Comparisons From Around the World

Introduction. Women attain numerous benefits from physical activity during pregnancy. However, because of physical changes that occur during pregnancy, special precautions are also needed. This review summarizes current guidelines for physical activity among pregnant women worldwide. Methods. We searched PubMed (MedLINE) for country-specific governmental and clinical guidelines on physical activity during pregnancy through the year 2012. We cross-referenced with articles referring to guidelines, with only the most recent included. An abstraction form was used to extract key details and summarize. Results. In total, 11 guidelines were identified from 9 countries (Australia, Canada, Denmark, France, Japan, Norway, Spain, United Kingdom, United States). Most guidelines supported moderate-intensity physical activity during pregnancy (10/11) and indicated specific frequency (9/11) and duration/time (9/11) recommendations. Most guidelines provided advice on initiating an exercise program during pregnancy (10/11). Six guidelines included absolute and relative contraindications to exercise. All guidelines generally ruled-out sports with risks of falls, trauma, or collisions. Six guidelines included indications for stopping exercise during pregnancy. Conclusion. This review contrasted pregnancy-related physical activity guidelines from around the world, and can help inform new guidelines as they are created or updated and facilitate the development of a worldwide guideline. © 2013 The Author(s)

Multilevel latent class casemix modelling: a novel approach to accommodate patient casemix

<p>Abstract</p> <p>Background</p> <p>Using routinely collected patient data we explore the utility of multilevel latent class (MLLC) models to adjust for patient casemix and rank Trust performance. We contrast this with ranks derived from Trust standardised mortality ratios (SMRs).</p> <p>Methods</p> <p>Patients with colorectal cancer diagnosed between 1998 and 2004 and resident in Northern and Yorkshire regions were identified from the cancer registry database (n = 24,640). Patient age, sex, stage-at-diagnosis (Dukes), and Trust of diagnosis/treatment were extracted. Socioeconomic background was derived using the Townsend Index. Outcome was survival at 3 years after diagnosis. MLLC-modelled and SMR-generated Trust ranks were compared.</p> <p>Results</p> <p>Patients were assigned to two classes of similar size: one with reasonable prognosis (63.0% died within 3 years), and one with better prognosis (39.3% died within 3 years). In patient class one, all patients diagnosed at stage B or C died within 3 years; in patient class two, all patients diagnosed at stage A, B or C survived. Trusts were assigned two classes with 51.3% and 53.2% of patients respectively dying within 3 years. Differences in the ranked Trust performance between the MLLC model and SMRs were all within estimated 95% CIs.</p> <p>Conclusions</p> <p>A novel approach to casemix adjustment is illustrated, ranking Trust performance whilst facilitating the evaluation of factors associated with the patient journey (e.g. treatments) and factors associated with the processes of healthcare delivery (e.g. delays). Further research can demonstrate the value of modelling patient pathways and evaluating healthcare processes across provider institutions.</p

Cephalopod genomics: a plan of strategies and organization

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, "Paths to Cephalopod Genomics-Strategies, Choices, Organization," held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described in this white paper

Cephalopod genomics : a plan of strategies and organization

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 7 (2012): 175-188, doi:10.4056/sigs.3136559.The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod molluscs. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described in this White Paper.The Catalysis Group Meeting was supported by the National Science Foundation through the National Evolutionary Synthesis Center (NESCent) under grant number NSF #EF-0905606

Macrophage Activation and Differentiation Signals Regulate Schlafen-4 Gene Expression: Evidence for Schlafen-4 as a Modulator of Myelopoiesis

Background: The ten mouse and six human members of the Schlafen (Slfn) gene family all contain an AAA domain. Little is known of their function, but previous studies suggest roles in immune cell development. In this report, we assessed Slfn regulation and function in macrophages, which are key cellular regulators of innate immunity

A Deficiency of Ceramide Biosynthesis Causes Cerebellar Purkinje Cell Neurodegeneration and Lipofuscin Accumulation

Sphingolipids, lipids with a common sphingoid base (also termed long chain base) backbone, play essential cellular structural and signaling functions. Alterations of sphingolipid levels have been implicated in many diseases, including neurodegenerative disorders. However, it remains largely unclear whether sphingolipid changes in these diseases are pathological events or homeostatic responses. Furthermore, how changes in sphingolipid homeostasis shape the progression of aging and neurodegeneration remains to be clarified. We identified two mouse strains, flincher (fln) and toppler (to), with spontaneous recessive mutations that cause cerebellar ataxia and Purkinje cell degeneration. Positional cloning demonstrated that these mutations reside in the Lass1 gene. Lass1 encodes (dihydro)ceramide synthase 1 (CerS1), which is highly expressed in neurons. Both fln and to mutations caused complete loss of CerS1 catalytic activity, which resulted in a reduction in sphingolipid biosynthesis in the brain and dramatic changes in steady-state levels of sphingolipids and sphingoid bases. In addition to Purkinje cell death, deficiency of CerS1 function also induced accumulation of lipofuscin with ubiquitylated proteins in many brain regions. Our results demonstrate clearly that ceramide biosynthesis deficiency can cause neurodegeneration and suggest a novel mechanism of lipofuscin formation, a common phenomenon that occurs during normal aging and in some neurodegenerative diseases