Survey design and analysis procedures: a comprehensive review of good practice

This paper provides a major review of acoustic survey and-data analysis procedures, it has been prepared as a result of discussions in the FAST working group of ICES. A review of published literature is combined with an assessment of methodology. A consideration of information available a priori and its impact on the choice of survey area and survey design is presented. The subject of predetermined survey tracks using both systematic and random strategies is addressed, indicating the assumptions implied by these choices. Adaptive strategies that might be required for mobile or less predictable spatia1 distributions are discussed along with the advantages and the costs of an adaptive approach. The methods of determining of stock species composition are examined. The methods for assessing the degree of homogeneity species size and proportion are presented. The important choice of averaging method i.e. how the samples provide information on the true density within an area is examined. Sources of error within the estimate are discussed. Firstly, methods for computing the spatial sampling error are examined, and secondly, a summary of other sources of error is presented. A appraisal of these errors is presented and provides an intrinsic error analysis. Finally a brief comparison of the results of acoustic surveys with the results of other techniques is presented. Throughout the paper the assumptions implicit in each choice are discussed, and appropriate selections of survey design and analysis methods are presented in tabular form. The paper concludes with a summary of recommended procedures

ICES coordinated acoustic survey of ICES divisions IIIa, IVa, IVb AND Via (North) 2002 Results and long term trends

Six surveys were carried out during late June and July covering most of the continental shelf north of 54oN in the North Sea and to the west of Scotland to a northern limit of 62oN. The eastern edge of the survey area was bounded by the Norwegian and Danish, Swedish and German coasts, and to the west by the shelf edge between 200 and 400 m depth. The surveys are reported individually in the report of the planning group for herring surveys, and a combined report has been prepared from the data from all surveys. The combined survey results provide spatial distributions of herring abundance by number and biomass at age by statistical rectangle; and distributions of mean weight and fraction mature at age. The estimates of North Sea autumn spawning herring are consistent with previous years at 2.9 million tonnes and 17,200 million herring. The survey also shows two exceptional year classes of herring (the 1998 and 2000 year classes) in the North Sea, which is consistent with the observation of exceptionally large year classes observed in the MIK and IBTS surveys. The estimates of Western Baltic spring spawning herring SSB are 255,000 tonnes and 2.9 millions (Table 2) and show a large increase compared with the previous year. The Western Baltic survey produces a rather noisy signal but the indications are of a stock that is higher now than between 1996 to 2000. The West of Scotland survey estimates of 548,000 tonnes and 2,900 million and shows the high 1995 year class again this year. The 1998 year class now (3 ring) is also a large one. Total adult mortality shows much lower mortality than last year (0.1 compared to 0.5 ) but the mean mortality over the last 4 years has been 0.3: this is consistent with the 2002 assessment that the stock is lightly exploited. The overall time series of abundance by age from 1989 to 2002 are summarised by simple models describing the spatial distribution over time. The changes over time with latitude, longitude and area occupied are compared with changes in abundance

ICES coordinated acoustic survey of ICES divisions IIIa, IVa, IVb AND Via (North) 2002 Results and long term trends

Six surveys were carried out during late June and July covering most of the continental shelf north of 54oN in the North Sea and to the west of Scotland to a northern limit of 62oN. The eastern edge of the survey area was bounded by the Norwegian and Danish, Swedish and German coasts, and to the west by the shelf edge between 200 and 400 m depth. The surveys are reported individually in the report of the planning group for herring surveys, and a combined report has been prepared from the data from all surveys. The combined survey results provide spatial distributions of herring abundance by number and biomass at age by statistical rectangle; and distributions of mean weight and fraction mature at age. The estimates of North Sea autumn spawning herring are consistent with previous years at 2.9 million tonnes and 17,200 million herring. The survey also shows two exceptional year classes of herring (the 1998 and 2000 year classes) in the North Sea, which is consistent with the observation of exceptionally large year classes observed in the MIK and IBTS surveys. The estimates of Western Baltic spring spawning herring SSB are 255,000 tonnes and 2.9 millions (Table 2) and show a large increase compared with the previous year. The Western Baltic survey produces a rather noisy signal but the indications are of a stock that is higher now than between 1996 to 2000. The West of Scotland survey estimates of 548,000 tonnes and 2,900 million and shows the high 1995 year class again this year. The 1998 year class now (3 ring) is also a large one. Total adult mortality shows much lower mortality than last year (0.1 compared to 0.5 ) but the mean mortality over the last 4 years has been 0.3: this is consistent with the 2002 assessment that the stock is lightly exploited. The overall time series of abundance by age from 1989 to 2002 are summarised by simple models describing the spatial distribution over time. The changes over time with latitude, longitude and area occupied are compared with changes in abundance

Genetics, recombination and clinical features of human rhinovirus species C (HRV-C) infections; interactions of HRV-C with other respiratory viruses

To estimate the frequency, molecular epidemiological and clinical associations of infection with the newly described species C variants of human rhinoviruses (HRV), 3243 diagnostic respiratory samples referred for diagnostic testing in Edinburgh were screened using a VP4-encoding region-based selective polymerase chain reaction (PCR) for HRV-C along with parallel PCR testing for 13 other respiratory viruses. HRV-C was the third most frequently detected behind respiratory syncytial virus (RSV) and adenovirus, with 141 infection episodes detected among 1885 subjects over 13 months (7.5%). Infections predominantly targeted the very young (median age 6–12 months; 80% of infections in those <2 years), occurred throughout the year but with peak incidence in early winter months. HRV-C was detected significantly more frequently among subjects with lower (LRT) and upper respiratory tract (URT) disease than controls without respiratory symptoms; HRV-C mono-infections were the second most frequently detected virus (behind RSV) in both disease presentations (6.9% and 7.8% of all cases respectively). HRV variants were classified by VP4/VP2 sequencing into 39 genotypically defined types, increasing the current total worldwide to 60. Through sequence comparisons of the 5′untranslated region (5′UTR), the majority grouped with species A (n = 96; 68%, described as HRV-Ca), the remainder forming a phylogenetically distinct 5′UTR group (HRV-Cc). Multiple and bidirectional recombination events between HRV-Ca and HRV-Cc variants and with HRV species A represents the most parsimonious explanation for their interspersed phylogeny relationships in the VP4/VP2-encoding region. No difference in age distribution, seasonality or disease associations was identified between HRV-Ca and HRV-Cc variants. HRV-C-infected subjects showed markedly reduced detection frequencies of RSV and other respiratory viruses, providing evidence for a major interfering effect of HRV-C on susceptibility to other respiratory virus infections. HRV-C's disease associations, its prevalence and evidence for interfering effects on other respiratory viruses mandates incorporation of rhinoviruses into future diagnostic virology screening

An international/multicentre report on patients with cystic fibrosis (CF) over the age of 40 years

AbstractBackgroundThe lifespan of patients with cystic fibrosis (CF) is increasing significantly. The objective of this international pilot study was to study the characteristics of these long-term survivors.MethodsFour centres with large CF clinics from London (UK), Minneapolis (USA), Toronto (Canada) and Verona (Italy) identified 366 patients who had survived 40years and longer.ResultsAt all centres males survived longer than females. There were more pancreatic sufficient patients in Verona (60%) and Toronto (40%) than in London (16%) and Minneapolis (21%). The percentage of ΔF508 homozygous patients varied between 47% in London and 45% in Minneapolis to only 26% in Toronto and 9% in Verona.Average FEV1 and BMI values of the surviving population appeared to stabilise after 40years of age. FEV1 was on average 12% higher in patients who were pancreatic sufficient (p > 0.0001). There was no difference in survival between the centres. The overall median survival after the age of 40 was 13years. The estimated annual death rate was approximately 3.4% from the age of 40–60years.ConclusionsSignificant numbers of patients are now surviving to 40years or more, and it is hoped that an in-depth study of these patients may identify the factors contributing to longer survival

Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi

<p>Abstract</p> <p>Background</p> <p>Of the > 2000 serovars of <it>Salmonella enterica </it>subspecies I, most cause self-limiting gastrointestinal disease in a wide range of mammalian hosts. However, <it>S. enterica </it>serovars Typhi and Paratyphi A are restricted to the human host and cause the similar systemic diseases typhoid and paratyphoid fever. Genome sequence similarity between Paratyphi A and Typhi has been attributed to convergent evolution via relatively recent recombination of a quarter of their genomes. The accumulation of pseudogenes is a key feature of these and other host-adapted pathogens, and overlapping pseudogene complements are evident in Paratyphi A and Typhi.</p> <p>Results</p> <p>We report the 4.5 Mbp genome of a clinical isolate of Paratyphi A, strain AKU_12601, completely sequenced using capillary techniques and subsequently checked using Illumina/Solexa resequencing. Comparison with the published genome of Paratyphi A ATCC9150 revealed the two are collinear and highly similar, with 188 single nucleotide polymorphisms and 39 insertions/deletions. A comparative analysis of pseudogene complements of these and two finished Typhi genomes (CT18, Ty2) identified several pseudogenes that had been overlooked in prior genome annotations of one or both serovars, and identified 66 pseudogenes shared between serovars. By determining whether each shared and serovar-specific pseudogene had been recombined between Paratyphi A and Typhi, we found evidence that most pseudogenes have accumulated after the recombination between serovars. We also divided pseudogenes into relative-time groups: ancestral pseudogenes inherited from a common ancestor, pseudogenes recombined between serovars which likely arose between initial divergence and later recombination, serovar-specific pseudogenes arising after recombination but prior to the last evolutionary bottlenecks in each population, and more recent strain-specific pseudogenes.</p> <p>Conclusion</p> <p>Recombination and pseudogene-formation have been important mechanisms of genetic convergence between Paratyphi A and Typhi, with most pseudogenes arising independently after extensive recombination between the serovars. The recombination events, along with divergence of and within each serovar, provide a relative time scale for pseudogene-forming mutations, affording rare insights into the progression of functional gene loss associated with host adaptation in <it>Salmonella</it>.</p

Early and nonreversible decrease of CD161++ /MAIT cells in HIV infection

HIV infection is associated with immune dysfunction, perturbation of immune-cell subsets and opportunistic infections. CD161++ CD8+ T cells are a tissue-infiltrating population that produce IL17A, IL22, IFN, and TNFα, cytokines important in mucosal immunity. In adults they dominantly express the semi-invariant TCR Vα7.2, the canonical feature of mucosal associated invariant T (MAIT) cells and have been recently implicated in host defense against pathogens. We analyzed the frequency and function of CD161++ /MAIT cells in peripheral blood and tissue from patients with early stage or chronic-stage HIV infection. We show that the CD161++ /MAIT cell population is significantly decreased in early HIV infection and fails to recover despite otherwise successful treatment. We provide evidence that CD161++ /MAIT cells are not preferentially infected but may be depleted through diverse mechanisms including accumulation in tissues and activation-induced cell death. This loss may impact mucosal defense and could be important in susceptibility to specific opportunistic infections in HIV

In vivo imaging reveals increased eosinophil uptake in the lungs of obese asthmatic patients.

To The Editor: Eosinophils play an important pathogenic role in pulmonary and systemic conditions including eosinophilic asthma and eosinophilic granulomatosis with polyangiitis.1,2 While progress has been made in understanding the mechanisms responsible for the activation of these cells, existing biomarkers of eosinophilic inflammation are indirect and/or invasive and do not always correlate with tissue eosinophilia. Hence, there is a need to develop non-invasive biomarkers of tissue eosinophilia. We have previously demonstrated the capacity of SPECT (single photon emission computed tomography) to quantify neutrophil uptake into the lungs of COPD patients.3 We sought to determine whether this methodology could be used to quantify eosinophil kinetics and pulmonary uptake, which may differ amongst diseases characterized by eosinophilic inflammation. In particular, the role of the eosinophil in asthma with obesity, a distinct asthma endotype associated with increased severity,4 is controversial. We hypothesized that injection of radiolabeled eosinophils, coupled with SPECT/CT, would reveal changes in eosinophil kinetics in patients compared to healthy volunteers.This work was supported by Asthma UK [08/11], the Medical Research Council [grant number MR/J00345X/1], the Wellcome Trust [grant number 098351/Z/12/Z], Cambridge NIHR Biomedical Research Centre, Wellcome Trust Senior Fellowship (to CEB) [grant number WT082265], AirPROM 7th EU Framework grant and Leicester NIHR Biomedical Research Centre

Phylodynamics of Hepatitis C Virus Subtype 2c in the Province of Córdoba, Argentina

The Hepatitis C Virus Genotype 2 subtype 2c (HCV-2c) is detected as a low prevalence subtype in many countries, except in Southern Europe and Western Africa. The current epidemiology of HCV in Argentina, a low-prevalence country, shows the expected low prevalence for this subtype. However, this subtype is the most prevalent in the central province of Córdoba. Cruz del Eje (CdE), a small rural city of this province, shows a prevalence for HCV infections of 5%, being 90% of the samples classified as HCV-2c. In other locations of Córdoba Province (OLC) with lower prevalence for HCV, HCV-2c was recorded in about 50% of the samples. The phylogenetic analysis of samples from Córdoba Province consistently conformed a monophyletic group with HCV-2c sequences from all the countries where HCV-2c has been sequenced. The phylogeographic analysis showed an overall association between geographical traits and phylogeny, being these associations significant (α = 0.05) for Italy, France, Argentina (places other than Córdoba), Martinique, CdE and OLC. The coalescence analysis for samples from CdE, OLC and France yielded a Time for the Most Common Recent Ancestor of about 140 years, whereas its demographic reconstruction showed a “lag” phase in the viral population until 1880 and then an exponential growth until 1940. These results were also obtained when each geographical area was analyzed separately, suggesting that HCV-2c came into Córdoba province during the migration process, mainly from Europe, which is compatible with the history of Argentina of the early 20th century. This also suggests that the spread of HCV-2c occurred in Europe and South America almost simultaneously, possibly as a result of the advances in medicine technology of the first half of the 20th century