Estimation of the specificity of an antibody ELISA for paratuberculosis generated from a sector of the UK cattle population using results from a paratuberculosis control programme

In the United Kingdom (UK) a voluntary programme to control paratuberculosis in cattle based on herd management and serological screening has been operating since 1998. The programme assigns a risk level to each participating herd according to the within herd seroprevalence and the confirmation of the presence of infection with Mycobacterium avium subspecies paratuberculosis (MAP) by faecal culture or polymerase chain reaction (PCR). From the outset a general concern over the specificity of the paratuberculosis antibody enzyme-linked immunosorbent assay (ELISA) resulted in the use of a faecal screen for the causal organism to negate or confirm infection in individual seropositive animals. Progress in improving the diagnostic tests has been gradual throughout the life of the programme and the under-pinning approach to using tests to determine the risk of paratuberculosis for a herd required to be re-examined. This study used a large data set of more than 143,000 test results over five years from the lowest paratuberculosis risk level category of herds to estimate the specificity of a commercially available paratuberculosis antibody ELISA for cattle. In each year of the study the estimated specificity reached or exceeded 0.998. We also examined the apparent impact that annual or more frequent application of the single intradermal comparative cervical tuberculin (SICCT) test for tuberculosis (TB), using purified protein derivatives of Mycobacterium bovis and Mycobacterium avium subspecies avium, had on specificity of the antibody ELISA for paratuberculosis. We found a statistically significant difference in three of the five years with herds that were officially tuberculosis free and not subject to frequent SICCT testing. This difference was small and considered to be of little practical importance for the paratuberculosis assurance programme. We concluded that, in the UK the mandatory TB surveillance programme of cattle herds is not a limiting factor in the use of serological testing to support herd-level assurance schemes for paratuberculosis. Furthermore, in paratuberculosis, where shedding of MAP is intermittent and the sensitivity of the commercially available PCR tests for detection MAP is highly variable, faecal screening of seropositive animals is an unreliable method for negating infection in seropositive cattle

Development and initial validation of the bronchiectasis exacerbation and symptom tool (BEST)

BACKGROUND: Recurrent bronchiectasis exacerbations are related to deterioration of lung function, progression of the disease, impairment of quality of life, and to an increased mortality. Improved detection of exacerbations has been accomplished in chronic obstructive pulmonary disease through the use of patient completed diaries. These tools may enhance exacerbation reporting and identification. The aim of this study was to develop a novel symptom diary for bronchiectasis symptom burden and detection of exacerbations, named the BEST diary. METHODS: Prospective observational study of patients with bronchiectasis conducted at Ninewells Hospital, Dundee. We included patients with confirmed bronchiectasis by computed tomography, who were symptomatic and had at least 1 documented exacerbation of bronchiectasis in the previous 12\u2009months to participate. Symptoms were recorded daily in a diary incorporating cough, sputum volume, sputum colour, dyspnoea, fatigue and systemic disturbance scored from 0 to 26. RESULTS: Twenty-one patients were included in the study. We identified 29 reported (treated exacerbations) and 23 unreported (untreated) exacerbations over 6-month follow-up. The BEST diary score showed a good correlation with the established and validated questionnaires and measures of health status (COPD Assessment Test, r =\u20090.61, p =\u20090.0037, Leicester Cough Questionnaire, r =\u2009-\u20090.52,p =\u20090.0015, St Georges Respiratory Questionnaire, r =\u20090.61,p <\u20090.0001 and 6\u2009min walk test, r =\u2009-\u20090.46,p =\u20090.037). The mean BEST score at baseline was 7.1 points (SD 2.2). The peak symptom score during exacerbation was a mean of 16.4 (3.1), and the change from baseline to exacerbation was a mean of 9.1 points (SD 2.5). Mean duration of exacerbations based on time for a return to baseline symptoms was 15.3\u2009days (SD 5.7). A minimum clinically important difference of 4 points is proposed. CONCLUSIONS: The BEST symptom diary has shown concurrent validity with current health questionnaires and is responsive at onset and recovery from exacerbation. The BEST diary may be useful to detect and characterise exacerbations in bronchiectasis clinical trials

Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees

BACKGROUND: Class III Homeodomain Leucine Zipper (HD-Zip III) proteins have been implicated in the regulation of cambium identity, as well as primary and secondary vascular differentiation and patterning in herbaceous plants. They have been proposed to regulate wood formation but relatively little evidence is available to validate such a role. We characterised and compared HD-Zip III gene family in an angiosperm tree, Populus spp. (poplar), and the gymnosperm Picea glauca (white spruce), representing two highly evolutionarily divergent groups. RESULTS: Full-length cDNA sequences were isolated from poplar and white spruce. Phylogenetic reconstruction indicated that some of the gymnosperm sequences were derived from lineages that diverged earlier than angiosperm sequences, and seem to have been lost in angiosperm lineages. Transcript accumulation profiles were assessed by RT-qPCR on tissue panels from both species and in poplar trees in response to an inhibitor of polar auxin transport. The overall transcript profiles HD-Zip III complexes in white spruce and poplar exhibited substantial differences, reflecting their evolutionary history. Furthermore, two poplar sequences homologous to HD-Zip III genes involved in xylem development in Arabidopsis and Zinnia were over-expressed in poplar plants. PtaHB1 over-expression produced noticeable effects on petiole and primary shoot fibre development, suggesting that PtaHB1 is involved in primary xylem development. We also obtained evidence indicating that expression of PtaHB1 affected the transcriptome by altering the accumulation of 48 distinct transcripts, many of which are predicted to be involved in growth and cell wall synthesis. Most of them were down-regulated, as was the case for several of the poplar HD-Zip III sequences. No visible physiological effect of over-expression was observed on PtaHB7 transgenic trees, suggesting that PtaHB1 and PtaHB7 likely have distinct roles in tree development, which is in agreement with the functions that have been assigned to close homologs in herbaceous plants. CONCLUSIONS: This study provides an overview of HD-zip III genes related to woody plant development and identifies sequences putatively involved in secondary vascular growth in angiosperms and in gymnosperms. These gene sequences are candidate regulators of wood formation and could be a source of molecular markers for tree breeding related to wood properties

Twisted Yangians for symmetric pairs of types B, C, D

We study a class of quantized enveloping algebras, called twisted Yangians, associated with the symmetric pairs of types B, C, D in Cartan's classification. These algebras can be regarded as coideal subalgebras of the extended Yangian for orthogonal or symplectic Lie algebras. They can also be presented as quotients of a reflection algebra by additional symmetry relations. We prove an analogue of the Poincare-Birkoff-Witt Theorem, determine their centres and study also extended reflection algebras

Integrability of Green-Schwarz Sigma Models with Boundaries

We construct integrability preserving boundary conditions for Green-Schwarz sigma-models on semi-symmetric spaces. The boundary conditions are expressed as gluing conditions of the flat-connection, using an involutive metric preserving automorphism. We show that the boundary conditions preserve half of the space-time supersymmetry and an infinite set of conserved charges. We find integrable D-brane configurations for AdS_5 x S^5 and AdS_4 x CP^3 backgrounds.Comment: 24 pages. v2 references added. v3 typos fixed, sec. 3 improved, references added, published versio

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

Human rhinovirus infection in young African children with acute wheezing

<p>Abstract</p> <p>Background</p> <p>Infections caused by human rhinoviruses (HRVs) are important triggers of wheezing in young children. Wheezy illness has increasingly been recognised as an important cause of morbidity in African children, but there is little information on the contribution of HRV to this. The aim of this study was to determine the role of HRV as a cause of acute wheezing in South African children.</p> <p>Methods</p> <p>Two hundred and twenty children presenting consecutively at a tertiary children's hospital with a wheezing illness from May 2004 to November 2005 were prospectively enrolled. A nasal swab was taken and reverse transcription PCR used to screen the samples for HRV. The presence of human metapneumovirus, human bocavirus and human coronavirus-NL63 was assessed in all samples using PCR-based assays. A general shell vial culture using a pool of monoclonal antibodies was used to detect other common respiratory viruses on 26% of samples. Phylogenetic analysis to determine circulating HRV species was performed on a portion of HRV-positive samples. Categorical characteristics were analysed using Fisher's Exact test.</p> <p>Results</p> <p>HRV was detected in 128 (58.2%) of children, most (72%) of whom were under 2 years of age. Presenting symptoms between the HRV-positive and negative groups were similar. Most illness was managed with ambulatory therapy, but 45 (35%) were hospitalized for treatment and 3 (2%) were admitted to intensive care. There were no in-hospital deaths. All 3 species of HRV were detected with HRV-C being the most common (52%) followed by HRV-A (37%) and HRV-B (11%). Infection with other respiratory viruses occurred in 20/128 (16%) of HRV-positive children and in 26/92 (28%) of HRV-negative samples.</p> <p>Conclusion</p> <p>HRV may be the commonest viral infection in young South African children with acute wheezing. Infection is associated with mild or moderate clinical disease.</p

A global compilation of diatom silica oxygen isotope records from lake sediment - trends and implications for climate reconstruction

\ua9 Copyright: Oxygen isotopes in biogenic silica (δ18OBSi) from lake sediments allow for quantitative reconstruction of past hydroclimate and proxy-model comparison in terrestrial environments. The signals of individual records have been attributed to different factors, such as air temperature (Tair), atmospheric circulation patterns, hydrological changes, and lake evaporation. While every lake has its own local set of drivers of δ18O variability, here we explore the extent to which regional or even global signals emerge from a series of paleoenvironmental records. This study provides a comprehensive compilation and combined statistical evaluation of the existing lake sediment δ18OBSi records, largely missing in other summary publications (i.e. PAGES network). For this purpose, we have identified and compiled 71 down-core records published to date and complemented these datasets with additional lake basin parameters (e.g. lake water residence time and catchment size) to best characterize the signal properties. Records feature widely different temporal coverage and resolution, ranging from decadal-scale records covering the past 150 years to records with multi-millennial-scale resolution spanning glacial-interglacial cycles. The best coverage in number of records (NCombining double low line37) and data points (NCombining double low line2112) is available for Northern Hemispheric (NH) extratropical regions throughout the Holocene (roughly corresponding to Marine Isotope Stage 1; MIS 1). To address the different variabilities and temporal offsets, records were brought to a common temporal resolution by binning and subsequently filtered for hydrologically open lakes with lake water residence times &lt;100 years. For mid- to high-latitude (&gt;45\ub0N) lakes, we find common δ18OBSi patterns among the lake records during both the Holocene and Common Era (CE). These include maxima and minima corresponding to known climate episodes, such as the Holocene Thermal Maximum (HTM), Neoglacial Cooling, Medieval Climate Anomaly (MCA) and the Little Ice Age (LIA). These patterns are in line with long-term air temperature changes supported by previously published climate reconstructions from other archives, as well as Holocene summer insolation changes. In conclusion, oxygen isotope records from NH extratropical lake sediments feature a common climate signal at centennial (for CE) and millennial (for Holocene) timescales despite stemming from different lakes in different geographic locations and hence constitute a valuable proxy for past climate reconstructions

The expression of mismatched repair genes and their correlation with clinicopathological parameters and response to neo-adjuvant chemotherapy in breast cancer

BACKGROUND: The DNA mismatch repair (MMR) pathway is an important post-replicative repair process. It is involved in the maintenance of genomic stability and MMR genes have therefore been named the proofreaders of replicating DNA. These genes repair the replicative errors of DNA and are thus imperative for genomic stability. The MMR genes have been found to be involved in promoting cytotoxicity, apoptosis, p53 phosphorylation and cell cycle arrest following exposure to exogenous DNA damaging agents. Loss of MMR function prevents the correction of replicative errors leading to instability of the genome, and can be detected by polymorphisms in micro satellites (1–6 nucleotide repeat sequences scattered in whole of the genome). This phenomenon, known as micro satellite instability (MSI), is a hallmark of MMR dysfunction and can be used as a marker of MMR dysfunction in colorectal and other malignancies. An alternative method for detection of MMR dysfunction is to test the expression of protein products of the MMR genes by immunohistochemistry (IHC), as mutations in these genes lead to reduced or absent expression of their gene products. Correlation between loss of MMR function and clinical, histopathological, behavioral parameters of the tumor and its response to chemotherapy in breast cancers may be of value in predicting tumor behavior and response to neoadjuvant chemotherapy (NACT). Neoadjuvant chemotherapy is an integral part of multimodal therapy for locally advanced breast cancer and predicting response may help in tailoring regimens in patients for optimum response. MATERIALS: After approval by the IRB(Institutional Review Board) and ethical committee of the hospital, 31 cases of locally advanced breast carcinoma (LABC) were studied to assess the correlation between MMR dysfunction, clinicopathological parameters and objective clinical response to neoadjuvant chemotherapy using immunohistochemistry. The immunohistochemical analysis for four MMR protein products -MLH1, MSH2, MSH6 and PMS2 was done in the pre NACT trucut biopsy specimen and after three cycles of NACT with C AF (cyclophosphamide, adriamycin, 5-fluorouracil) regimen, in the modified radical mastectomy specimen. RESULTS AND CONCLUSION: There was no significant correlation observed between expression of MMR proteins and age, family history, tumor size or histological type. However there was a statistically significant negative correlation between MLH1, MSH2 expression and histological grade. There was also a negative correlation observed between PMS2 expression after neo-adjuvant chemotherapy and clinical response. Cases with high post NACT expression of PMS2 were poor responders to chemotherapy. MSH6 was the most frequently altered MMR gene, with a negativity rate of 48% and the patients with high expression responded poorly to NACT. The study highlights the possible role of MMR expression in predicting aggressive tumor behavior (histological grade) and response to neoadjuvant chemotherapy in patients with LABC

Human Rhinovirus Infections in Rural Thailand: Epidemiological Evidence for Rhinovirus as Both Pathogen and Bystander

BACKGROUND: We describe human rhinovirus (HRV) detections in SaKaeo province, Thailand. METHODS: From September 1, 2003-August 31, 2005, we tested hospitalized patients with acute lower respiratory illness and outpatient controls without fever or respiratory symptoms for HRVs with polymerase chain reaction and molecularly-typed select HRVs. We compared HRV detection among hospitalized patients and controls and estimated enrollment adjusted incidence. RESULTS: HRVs were detected in 315 (16%) of 1919 hospitalized patients and 27 (9.6%) of 280 controls. Children had the highest frequency of HRV detections (hospitalized: <1 year: 29%, 1-4 year: 29%, ≥ 65 years: 9%; controls: <1 year: 24%, 1-4 year: 14%, ≥ 65 years: 2.8%). Enrollment adjusted hospitalized HRV detection rates were highest among persons aged <1 year (1038/100,000 persons/year), 1-4 years (457), and ≥ 65 years (71). All three HRV species were identified, HRV-A was the most common species in most age groups including children aged <1 year (61%) and all adult age groups. HRV-C was the most common species in the 1-4 year (51%) and 5-19 year age groups (54%). Compared to controls, hospitalized adults (≥ 19 years) and children were more likely to have HRV detections (odds ratio [OR]: 4.8, 95% confidence interval [CI]: 1.5, 15.8; OR: 2.0, CI: 1.2, 3.3, respectively) and hospitalized children were more likely to have HRV-A (OR 1.7, CI: 0.8, 3.5) or HVR-C (OR 2.7, CI: 1.2, 5.9) detection. CONCLUSIONS: HRV rates were high among hospitalized children and the elderly but asymptomatic children also had substantial HRV detection. HRV (all species), and HRV-A and HRV-C detections were epidemiologically-associated with hospitalized illness. Treatment or prevention modalities effective against HRV could reduce hospitalizations due to HRV in Thailand