Regular breakfast consumption and type 2 diabetes risk markers in 9- to 10-year-old children in the child heart and health study in England (CHASE): a cross-sectional analysis.

BACKGROUND: Regular breakfast consumption may protect against type 2 diabetes risk in adults but little is known about its influence on type 2 diabetes risk markers in children. We investigated the associations between breakfast consumption (frequency and content) and risk markers for type 2 diabetes (particularly insulin resistance and glycaemia) and cardiovascular disease in children. METHODS AND FINDINGS: We conducted a cross-sectional study of 4,116 UK primary school children aged 9-10 years. Participants provided information on breakfast frequency, had measurements of body composition, and gave fasting blood samples for measurements of blood lipids, insulin, glucose, and glycated haemoglobin (HbA1c). A subgroup of 2,004 children also completed a 24-hour dietary recall. Among 4,116 children studied, 3,056 (74%) ate breakfast daily, 450 (11%) most days, 372 (9%) some days, and 238 (6%) not usually. Graded associations between breakfast frequency and risk markers were observed; children who reported not usually having breakfast had higher fasting insulin (percent difference 26.4%, 95% CI 16.6%-37.0%), insulin resistance (percent difference 26.7%, 95% CI 17.0%-37.2%), HbA1c (percent difference 1.2%, 95% CI 0.4%-2.0%), glucose (percent difference 1.0%, 95% CI 0.0%-2.0%), and urate (percent difference 6%, 95% CI 3%-10%) than those who reported having breakfast daily; these differences were little affected by adjustment for adiposity, socioeconomic status, and physical activity levels. When the higher levels of triglyceride, systolic blood pressure, and C-reactive protein for those who usually did not eat breakfast relative to those who ate breakfast daily were adjusted for adiposity, the differences were no longer significant. Children eating a high fibre cereal breakfast had lower insulin resistance than those eating other breakfast types (p for heterogeneity <0.01). Differences in nutrient intakes between breakfast frequency groups did not account for the differences in type 2 diabetes markers. CONCLUSIONS: Children who ate breakfast daily, particularly a high fibre cereal breakfast, had a more favourable type 2 diabetes risk profile. Trials are needed to quantify the protective effect of breakfast on emerging type 2 diabetes risk. Please see later in the article for the Editors' Summary

Evaluation and application of microsatellite and major histocompatability complex variation for stock identification of coho salmon

Abstract.-Variation at eight microsatellite loci and two linked exons of a major histocompatibility complex (MHC) locus was surveyed in approximately 21,000 coho salmon Oncorhynchus kisutch sampled from 138 localities ranging from southeast Alaska to the Columbia River, the majority of the sites being in British Columbia. The observed regional population structure enabled evaluation of the utility of using microsatellite and MHC variation for estimating the stock composition of coho salmon in mixed-stock fisheries. Both MHC exons were more effective for stock identification than any of the eight microsatellite loci examined. The two MHC exons combined were nearly as effective, on average, as the eight microsatellite loci combined. Some loci were particularly effective at discriminating stocks from specific regions. Mixed-stock analysis provided accurate estimates of contributions from the threatened Thompson River and upper Skeena River stocks, even when they composed less than 5% of the sampled fish. From about 17,000 coho salmon sampled from mixed-stock fisheries in British Columbia and Washington during 1997-1999, we found that the highest estimated proportions of coho salmon originating in southeast Alaska were in Canadian fishing areas adjacent to the international border in northern British Columbia; the highest proportions of Washington-origin coho salmon were observed closest to the international border in southern British Columbia. Within major river drainages, MHC variation within appropriately sampled fisheries can be used to determine the timing of spawning returns of specific stocks and the relative or absolute stock escapements. The application of molecular genetic markers to stock structure analysis and mixed-stock analysis of anadromous salmonids has been extensive because of the economic importance of these fish and the relative ease of sampling temporally or spatially segregated spawning aggregations In 1995, we began to develop a comprehensive genetic database for coho salmon in British Columbia that would assist in identifying and selecting conservation and management units of British Columbia coho salmon. We believed the database would also provide sufficiently accurate and precise estimates of stock composition in mixed-stock samples and thereby enhance conservation-based fisheries management. We chose to survey variation at eight microsatellite loci and 1117 STOCK IDENTIFICATION OF COHO SALMON two exons (coding portion of a gene) of a major histocompatibilty complex (MHC) locus. We used a PCR-based (polymerase chain reaction) approach to ensure cost effectiveness and speed in establishing the database and to enable nonlethal sampling for mixed-stock analysis. Microsatellite loci are abundant, highly polymorphic, and noncoding (considered selectively neutral), and provide genetic information on nonselective forces, including mutation and drift. As such, they can be used to generate estimates of gene flow, effective population size, and phylogenetic relationships. Vertebrate MHC genes encode cell-surface glycoproteins that are functional in the adaptive immune system. They evolve rapidly, are highly polymorphic, and because they encode adaptive variation, are subject to natural selection. The adaptive nature of MHC genes compromises use of MHC allele frequencies to estimate parameters for which an assumption of selective neutrality is required. However, MHC allele frequencies have the potential to enhance stock specificity and thus their utility in mixed-stock analyses. Moreover, variation in MHC allele and genotype frequencies attributable to selective forces provides quantitative information on the adaptive variation among salmonid stocks that conservation efforts are directed at preserving (Miller et al. in press). The two linked class-I MHC exons surveyed in this study exhibit high levels of polymorphism, heterozygosity, and temporally stable differentiation among coho salmon populations After having received scientific advice in 1998 that the abundance of Thompson River and upper Skeena River coho salmon was at critically low levels (Stocker and Peacock 1998), the Minister of the Department of Fisheries and Oceans directed that the management of Canadian fisheries in 1998 was to be conducted with the objective of achieving a zero mortality of those salmon. Fisheries were curtailed in areas where Thompson River and upper Skeena River coho salmon were believed to be prevalent. Salmon fisheries in other areas could proceed if they were unlikely to intercept significant numbers of coho salmon, and generally, all coho salmon caught in any British Columbia fishery were to be released. Coded wire tag (CWT) analysis depends upon recovery of CWTs from dead fish, so under the 1998 management objectives, the traditional stock identification information from CWTs would not be available. However, by 1998, extensive surveys of microsatellite and MHC variation had been conducted, the general units of population structure of coho salmon had been defined, and the feasibility of DNA-based MSA had been assessed In this study, we evaluate the utility of using microsatellite and MHC data for coho salmon stock identification through simulation analyses, apply the technologies to estimate stock composition of known-origin samples of coded-wiretagged coho salmon, and outline the applications to estimating stock composition for coho salmon fisheries sampled in British Columbia and Washington during 1997-1999. Methods Collection of DNA samples and laboratory analysis.-Genomic DNA was extracted from either liver, scales, operculum punches, or fin clips from coho salmon sampled between 1987 and 1999 using the phenol-chloroform protocol of class-I MHC exons was surveyed by denaturing gradient gel electrophoresis (DGGE) Collection of the CWT sample.-In 1997, coho salmon could still be landed and retained in British Columbia fisheries. The program to recover codedwire-tagged fish was in operation, and we were able to obtain operculum punches from coho salmon that had previously been marked with CWTs and for which the CWT had been recovered and decoded for marking location (source population). We subsequently used this sample of 264 fish to evaluate the accuracy of estimated stock compositions using a sample of known origin. Collection of fishery samples.-In 1997, samples were collected from the recreational fishery off southwestern Vancouver Island and in test fisheries in the lower Fraser River in southern British Columbia. In 1998, when coho salmon were not to be retained in most fisheries in the province, sampling coho salmon from the fisheries was challenging. Sampling effort was expanded considerably; observers aboard troll, purse seine, and gillnet vessels sampled the bycatch of coho salmon before their release. Obtaining samples from the recreational fishery was difficult; there were no landings to sample, and it was not practical to place observers aboard individual vessels. Samples from these fisheries were generally obtained either from individual guides or charter boat operators, or from members of the British Columbia Wildlife Federation. The DNA samples from the 1998 and 1999 fisheries were obtained from either operculum punches or fin clips preserved in 70% ethanol. To facilitate rapid analysis of fishery samples, we generally screened them for variability at both MHC exons and at four microsatellite loci. The microsatellite loci screened for the 1997-1998 samples were Ots2, Ots3, Ots101, and Ots103, whereas the loci screened for the 1999 samples were Oki1, Oki10, Oki100, Oki101. Baseline populations.-Applying DNA variation to estimates of stock composition in mixedstock fisheries requires surveying variation in contributing populations at a sufficient number of genetic markers to provide reliable determination of population structure and, thus, estimates of stock composition. The baseline survey consisted of analysis of approximately 21,000 coho salmon in 138 populations from geographic areas where coho salmon are likely to occur in British Columbia fisheries. These populations included 1 from Oregon, 17 from Washington, 111 from British Columbia, and 9 from southeast Alaska ( Conversion of allele sizes between manual and automated sizing systems.-The ABI 377 automated sequencer was obtained in our laboratory during the 1998 fishery to shorten the processing time for the approximately 9,000 samples collected from fisheries throughout British Columbia. At that time the baseline microsatellite data consisted of manual gel data for only four (Ots2, Ots3, Ots101, and Ots103) of the eight microsatellite loci used in this analysis. For the 1998 fishery samples, we surveyed variation at Ots3, Ots101, and Ots103 on the automated sequencer and retained Ots2 on manual gels. Given the wide distribution of allele sizes of Ots101 and Ots103 and the limitation of three fluorescent dyes for microsatellites on the sequencer, we were not able at that time to analyze Ots2 on the sequencer. Estimated allele sizes at Ots3, Ots101, and Ots103 differed between the manual nondenaturing gels stained with ethidium bromide and the automated sequencer denaturing gels with fluorescently labeled alleles. To convert allele sizes between the two systems, we analyzed approximately 600 fish on both systems and determined the distributions of allele frequencies. By inspection of the allele frequencies, we were able to match specific allele sizes obtained from the sequencer to specific allele sizes from the manual gels and then convert the sizing in the automated sequencer data set to match that obtained from the manual gels. Estimated allele sizes from both systems were very highly correlated (r 2 ϭ 0.987 for Ots3, 0.998 for Ots101, and 0.999 for Ots103). In general, sizes for the same allele from the sequencer were larger than those estimated from manual gels, and the differential increased directly with allele size. Estimating stock composition.-Genotypic frequencies were determined at each locus in each population. The statistical package for the analysis of mixtures software program (SPAM; Reported stock compositions for the CWT and actual fishery samples are the point estimates of each mixture analyzed; variance estimates were derived from 100 bootstrap simulations. Each baseline population and fishery sample was sampled with replacement in order to simulate random variation involved in the collection of the baseline and fishery samples. Reported stock composition for simulated mixtures was the bootstrap mean and standard deviation. Coastal British Columbia is divided into statistical areas for salmon catch reporting and management ( Results Population Structure If a regional genetic structure among populations contributing to a fishery exists, then it is unnecessary to survey all individual populations that contribute to the fishery. The portion of the mixed-stock sample derived from unsampled populations is allocated to sampled populations from the same region, reducing the cost and complexity of establishing a baseline sufficient for mixture analysis. The sampled populations constitute the baseline used to estimate stock compositions in mixed-fishery samples. Regional structure was observed in the baseline populations, the Thompson River populations being the most distinct of 15 geographically based groups or stocks (Table 2; Comparison of Individual Loci Determining the relative power of individual loci for regional discrimination is of prime importance for practical stock identification applications. Of the 10 markers surveyed in our study, the MHC exons were individually more effective for stock identification than any of the eight microsatellite loci Coho salmon from some regions were more easily differentiated than those from other regions. The distinctive Thompson River coho were clearly well differentiated from coho salmon in other regions, regardless of the loci examined. When all 10 loci surveyed were used, coho salmon from the west coast of Vancouver Island (WCVI) were the most difficult to discriminate when mixed with populations from other regions, whereas those from the east coast of Vancouver Island (ECVI) populations were accurately discriminated Some loci were particularly effective at discriminating populations from specific regions. For example, the two MHC exons were more powerful for identifying coastal Washington and Columbia River populations than were microsatellite loci. However, the combined microsatellite loci were more effective at identifying Vancouver Island coho salmon than were the MHC exons. Although the overall discriminatory ability of Ots101 was only moderate, it was particularly effective for discriminating Thompson River coho salmon (e.g., the average estimated composition of pure samples of Thompson River coho salmon was 98% using only this single locus in the 138-population baseline; Thompson and Upper Skeena River Identifications Since 1998, Canadian salmon fisheries have been conducted to minimize mortality of Thompson River and upper Skeena River coho salmon. Accurate estimates of these two stock components in mixed-fishery samples were thus essential for proper management. We were also interested in separating Thompson River from upper Fraser River populations, a stock of uncertain status that has genetic characteristics most similar to Thompson River populations Estimates of Regional Stock Composition We evaluated whether the genetic differentiation observed among the 138 coho salmon populations included in the baseline was sufficient for mixedstock analysis aimed at estimating regional contributions to fishery samples. Three fishery-mixture samples were simulated, and stock compositions were estimated for 16 regions. For stock contributions ranging from 0% to 20% of the mixture, the estimated bootstrap mean of a region was usually within 0.0-1.5% of the actual composition in the mixture For eight regional groups of coho salmon we evaluated the accuracy of estimated stock compositions in simulated mixtures, based on compositions of the target region ranging from 0-100% and only 6 of the 10 loci surveyed being used. Very little bias was observed when the region composed less than 40% of the mixture ( Identification of Specific Populations Accurate differentiation of mixture samples to specific populations was generally not possible because not all populations contributing to a fishery sample were included in the baseline. However, situations could occur in which all populations contributing to a fishery sample could be sampled. Such a case arose for the proposed &apos;&apos;mark-only&apos;&apos; fishery for coho salmon in southern British Columbia and Washington State in which hatchery fish, marked by a clipped adipose fin, may be retained but naturally spawned fish, identified by the presence of an adipose fin, must be released. We evaluated the accuracy of the estimated stock composition for each Canadian population by simulating mixtures for six southern British Columbia hatcheries for which population-specific estimates of stock composition are required. The baseline was substantially reduced to include only the six Canadian populations, but all populations from Washington were retained. Analysis of three simulated mixtures indicated that accurate hatcheryspecific estimates of stock composition could be obtained if applied to samples from mark-only fisheries Analysis of a Sample of Known Origin The superiority of using expected over observed genotypic frequencies for baseline samples was confirmed for the mixture sample containing fish identified by their CWTs. The sum of errors in estimated stock composition was always less when expected genotypic frequencies for all loci were used than when observed genotypic frequencies for some loci were used Analysis of Fishery Samples: Southern Baseline The estimated proportion of Thompson River coho salmon in mixed-stock samples was of key importance to Canadian fishery managers in 1998 and 1999. In 1998, we were unable to distinguish reliably between Thompson River and upper Fraser River using the loci surveyed in the mixedstock sample. Indeed, it was only after the introduction of DNA analysis to the mixed-stock samples that separation of the two closely related stock groups was considered of management importance. Therefore, upper Fraser and Thompson stock estimates were combined in the 1998 mixedfishery samples, but reported separately for the 1999 samples because of the change in the loci surveyed. Estimated stock compositions of Thompson River coho salmon were never above 2% in the Pacific Salmon Commission (PSC) seine test fishery conducted from late July to late August in Area 20 (Strait of Juan de Fuca) and rarely above 2% for the PSC gill-net test fishery conducted from early July through mid-August in a similar area Recreational fishery sampling in the Strait of Georgia (Areas 14-19) indicated that coho from Vancouver Island, the lower British Columbia mainland, the lower Fraser River, and Puget Sound predominated the catch in the summer, but October samples in Area 14 indicated that ECVI stock was predominant, composing 85% of the sample (Appendix 1). By October, coho salmon from other areas have probably moved from the Strait of Georgia and closer to their respective spawning grounds. The major contributor to fisheries in Canada&apos;s Area 20 in the Strait of Juan de Fuca was the Puget Sound stock, composing nearly 40% of the coho sampled in the seine and gill-net test fisheries (Appendix 1). However, the relative proportion of the Puget Sound stock in Canadian recreational fish-1130 BEACHAM ET AL. TABLE 7.-Percentage composition (SD) of a sample of coded-wire-tagged coho salmon obtained from fisheries in British Columbia in 1997 and estimated with three sets of loci for three groups of baseline populations. Because all fish in the sample were marked with coded wire tags, the actual composition of the sample is known. Set-1 loci include ␣1, ␣2, Ots2, Ots3, Ots101, and Ots103; set-2 loci include ␣1, ␣2, Oki1, Oki10, Oki100, and Oki101; set-3 loci include ␣1, ␣2, and all eight microsatellite loci. In state 1, the expected Hardy-Weinberg genotypic frequencies were used for all loci for the appropriate baseline populations. In state 2, observed genotypic frequencies for Oki100 and Ots103 were used. Analysis of Fishery Samples: Central Baseline A major interception fishery occurs in the Queen Charlotte Strait and Johnstone Strait (Areas 11-13; The troll fishery is the predominant fishery occurring off the west coast of Vancouver Island (Areas 124-127). The area and time of highest Thompson River proportion in the fishery samples was the first two weeks in August in the northern (Area 125-127) troll fishery, the Thompson stock estimated at 3% in the samples. Generally, the upper Skeena stock was estimated at negligible levels in the samples. Most of the fish sampled originated from Vancouver Island, the southern mainland, the lower Fraser River, and Puget Sound. Higher proportions of Canadian-origin coho salmon were sampled in this fishery compared with the more southerly fishery in the Strait of Juan de Fuca (Area 20) (Appendix 2). Off the west coast of Vancouver Island, about 70-80% of the sample was estimated to be of Canadian origin, compared with about 40-50% for samples from the Strait of Juan de Fuca. Analysis of Fishery Samples: Northern Baseline In northern fisheries, the upper Skeena stock was of greatest management concern. For fisheries adjacent to the Queen Charlotte Islands (Areas 1, 2W, and 2E), this stock was only detected in a late July troll fishery on the west coast of the Queen Charlottes (2W), and then was estimated to have composed 3% of the 99-fish sample (Appendix 3). However, in Area 3, this stock composed 15% of a 153-fish sample from a seine fishery in the last half of July 1998 and 8-25% of much smaller samples from gill-net fisheries in Areas 3 and 4 taken at the same time. The Thompson River stock was estimated to have contributed only negligible amounts to these fishery samples. There were clear differences in stock composition between fisheries on the east coast and west coast of the Queen Charlotte Islands. On the east coast (2E), samples from both the seine and gillnet fisheries from mid-September to mid-October 1998 indicated that coho salmon from the Queen Charlotte Islands predominated the fishery, composing about 70% of the samples from both fisheries (Appendix 3). However, on the west coast (2W), the Queen Charlotte Islands stock composed less than 20% of the fishery samples from late July and August 1998. The estimated contributions of Alaskan-origin coho salmon were highest in Canadian fishing areas closest to the northern border. Alaskan-origin coho salmon composed up to 20% of the sample from Area 3, and although only 21 fish were sampled in Area 1, nearly 20% of that sample was estimated to have been derived from Alaskan populations. In northern British Columbia, the northcentral coast stock was the predominant contributor to fisheries; coho salmon from Alaska, the lower Skeena River, WCVI, and NVI composed, at times, significant proportions of samples. Central coast fishery samples (Areas 6 and 7) were predominated by the northcentral coast stock, with Vancouver Island and southern mainland populations at times making significant contributions (Appendix 3). Analysis within Major Watersheds: Fraser River Baseline The key question in sampling fisheries within the Fraser River drainage related to the relative abundance of Thompson River coho salmon, particularly the migration timing of the stock through the lower Fraser River. Three years of sampling by a test fishery in the lower

Incidence of anogenital warts in Germany: a population-based cohort study

<p>Abstract</p> <p>Background</p> <p>Human papilloma virus (HPV) types 6 and 11 account for 90 percent of anogenital warts (AGW). Assessment of a potential reduction of the incidence of AGW following introduction of HPV vaccines requires population-based incidence rates. The aim of this study was to estimate incidence rates of AGW in Germany, stratified by age, sex, and region. Additionally, the medical practitioner (gynaecologist, dermatologist, urologist etc.) who made the initial diagnosis of AGW was assessed.</p> <p>Methods</p> <p>Retrospective cohort study in a population aged 10 to 79 years in a population-based healthcare insurance database. The database included more than 14 million insurance members from all over Germany during the years 2004-2006. A case of AGW was considered incident if a disease-free period of twelve months preceded the diagnosis. To assess regional variation, analyses were performed by federal state.</p> <p>Results</p> <p>The estimated incidence rate was 169.5/100,000 person-years for the German population aged 10 to 79 years. Most cases occurred in the 15 to 40 years age group. The incidence rate was higher and showed a peak at younger ages in females than in males. The highest incidence rates for both sexes were observed in the city-states Berlin, Hamburg and Bremen. In females, initial diagnosis of AGW was most frequently made by a gynaecologist (71.7%), whereas in males, AGW were most frequently diagnosed by a dermatologist (44.8%) or urologist (25.1%).</p> <p>Conclusions</p> <p>Incidence of AGW in Germany is comparable with findings for other countries. As expected, most cases occurred in the younger age groups. The frequency of diagnoses of AGW differs between sexes and women and men receive treatment by doctors of different specialties.</p

Patient Age, Sex, and Inflammatory Bowel Disease Phenotype Associate With Course of Primary Sclerosing Cholangitis

BACKGROUND & AIMS: Primary sclerosing cholangitis (PSC) is an orphan hepatobiliary disorder associated with inflammatory bowel disease (IBD). We aimed to estimate the risk of disease progression based on distinct clinical phenotypes in a large international cohort of patients with PSC. METHODS: We performed a retrospective outcome analysis of patients diagnosed with PSC from 1980 through 2010 at 37 centers in Europe, North America, and Australia. For each patient, we collected data on sex, clinician-reported age at and date of PSC and IBD diagnoses, phenotypes of IBD and PSC, and date and indication of IBD-related surgeries. The primary and secondary endpoints were liver transplantation or death (LTD) and hepatopancreatobiliary malignancy, respectively. Cox proportional hazards models were applied to determine the effects of individual covariates on rates of clinical events, with time-to-event analysis ascertained through Kaplan-Meier estimates. RESULTS: Of the 7121 patients in the cohort, 2616 met the primary endpoint (median time to event of 14.5 years) and 721 developed hepatopancreatobiliary malignancy. The most common malignancy was cholangiocarcinoma (n = 594); patients of advanced age at diagnosis had an increased incidence compared with younger patients (incidence rate: 1.2 per 100 patient-years for patients younger than 20 years old, 6.0 per 100 patient-years for patients 21-30 years old, 9.0 per 100 patient-years for patients 31-40 years old, 14.0 per 100 patient-years for patients 4150 years old, 15.2 per 100 patient-years for patients 51-60 years old, and 21.0 per 100 patient-years for patients older than 60 years). Of all patients with PSC studied, 65.5% were men, 89.8% had classical or large-duct disease, and 70.0% developed IBD at some point. Assessing the development of IBD as a time-dependent covariate, Crohn's disease and no IBD (both vs ulcerative colitis) were associated with a lower risk of LTD (unadjusted hazard ratio [HR], 0.62; PPeer reviewe

Supplement: "Localization and broadband follow-up of the gravitational-wave transient GW150914" (2016, ApJL, 826, L13)

This Supplement provides supporting material for Abbott et al. (2016a). We briefly summarize past electromagnetic (EM) follow-up efforts as well as the organization and policy of the current EM follow-up program. We compare the four probability sky maps produced for the gravitational-wave transient GW150914, and provide additional details of the EM follow-up observations that were performed in the different bands

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.

Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Archives of Virology (2021) 166:3567–3579. https://doi.org/10.1007/s00705-021-05266-wIn March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.This work was supported in part through Laulima Government Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. This work was also supported in part with federal funds from the National Cancer Institute (NCI), National Institutes of Health (NIH), under Contract No. 75N91019D00024, Task Order No. 75N91019F00130 to I.C., who was supported by the Clinical Monitoring Research Program Directorate, Frederick National Lab for Cancer Research. This work was also funded in part by Contract No. HSHQDC-15-C-00064 awarded by DHS S&T for the management and operation of The National Biodefense Analysis and Countermeasures Center, a federally funded research and development center operated by the Battelle National Biodefense Institute (V.W.); and NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (N.V., R.B.T.). S.S. acknowledges partial support from the Special Research Initiative of Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University, and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. Part of this work was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001030), the UK Medical Research Council (FC001030), and the Wellcome Trust (FC001030).S

Rare and low-frequency coding variants alter human adult height

Height is a highly heritable, classic polygenic trait with ~700 common associated variants identified so far through genome - wide association studies . Here , we report 83 height - associated coding variants with lower minor allele frequenc ies ( range of 0.1 - 4.8% ) and effects of up to 2 16 cm /allele ( e.g. in IHH , STC2 , AR and CRISPLD2 ) , >10 times the average effect of common variants . In functional follow - up studies, rare height - increasing alleles of STC2 (+1 - 2 cm/allele) compromise d proteolytic inhibition of PAPP - A and increased cleavage of IGFBP - 4 in vitro , resulting in higher bioavailability of insulin - like growth factors . The se 83 height - associated variants overlap genes mutated in monogenic growth disorders and highlight new biological candidates ( e.g. ADAMTS3, IL11RA, NOX4 ) and pathways ( e.g . proteoglycan/ glycosaminoglycan synthesis ) involved in growth . Our results demonstrate that sufficiently large sample sizes can uncover rare and low - frequency variants of moderate to large effect associated with polygenic human phenotypes , and that these variants implicate relevant genes and pathways

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes