Farm management factors associated with bulk tank total bacterial count in Irish dairy herds during 2006/07

Research has shown that total bacterial count (TBC), which is the bacterial growth per ml of milk over a fixed period of time, can be decreased by good hygiene and farm management practices. The objective of the current study was to quantify the associations between herd management factors and bulk tank TBC in Irish spring calving, grass-based dairy herds. The relationship between bulk tank TBC and farm management and infrastructure was examined using data from 400 randomly selected Irish dairy farms where the basal diet was grazed grass. Herd management factors associated with bulk tank TBC were identified using linear models with herd annual total bacterial score (i.e., arithmetic mean of the natural logarithm of bulk tank TBC) included as the dependent variable. All herd management factors were individually analysed in a separate regression model, that included an adjustment for geographical location of the farm. A multiple stepwise regression model was subsequently developed. Median bulk tank TBC for the sample herds was 18,483 cells/ml ranging from 10,441 to 130,458 cells/ml. Results from the multivariate analysis indicated that the following management practices were associated with low TBC; use of heated water in the milking parlour; participation in a milk recording scheme; and tail clipping of cows at a frequency greater than once per year. Increased level of hygiene of the parlour and cubicles were also associated with lower TBC. Herd management factors associated with bulk tank TBC in Irish grazing herds were generally in agreement with most previous studies from confinement systems of milk production

The ASSIST Study - The BD Odon Device for assisted vaginal birth: a safety and feasibility study.

BACKGROUND: Assisted vaginal birth is a vital health intervention that can result in better outcomes for mothers and their babies when complications arise in the second stage of labour. Unfortunately, instruments for assisted vaginal birth (forceps and ventouse) are often not utilised in settings where there is most clinical need, resulting in maternal and neonatal morbidity and mortality which could have been prevented. The BD Odon Device is a new device for assisted vaginal birth that may be able to address this unmet need. However, before dissemination, the device requires evaluation in robust clinical trials. A feasibility study to investigate the clinical impact, safety, and acceptability of the BD Odon Device for assisted vaginal birth is therefore planned. This will provide further information on acceptability, recruitment, and the outcome data required to design a future randomised controlled trial of the BD Odon Device versus Kiwi ventouse. METHODS: Forty women who require an assisted vaginal birth for a recognised clinical indication will have the birth assisted with the BD Odon Device. The primary outcome is successful vaginal birth completed with the BD Odon Device. Secondary clinical outcomes include maternal and neonatal outcomes, and maternal and practitioner satisfaction. Safety data will be reviewed following every birth. DISCUSSION: A future randomised controlled trial of the BD Odon Device versus the current standard instrument (the Kiwi ventouse) is planned. The findings of the ASSIST Study will inform the randomised controlled trial design. TRIAL REGISTRATION: ISRCTN, ISRCTN10203171 . Prospectively registered on 27 July 2018

Automatically extracting functionally equivalent proteins from SwissProt

In summary, FOSTA provides an automated analysis of annotations in UniProtKB/Swiss-Prot to enable groups of proteins already annotated as functionally equivalent, to be extracted. Our results demonstrate that the vast majority of UniProtKB/Swiss-Prot functional annotations are of high quality, and that FOSTA can interpret annotations successfully. Where FOSTA is not successful, we are able to highlight inconsistencies in UniProtKB/Swiss-Prot annotation. Most of these would have presented equal difficulties for manual interpretation of annotations. We discuss limitations and possible future extensions to FOSTA, and recommend changes to the UniProtKB/Swiss-Prot format, which would facilitate text-mining of UniProtKB/Swiss-Prot

Long-term halocarbon observations from a coastal and an inland site in Sabah, Malaysian Borneo

Abstract. Short-lived halocarbons are believed to have important sources in the tropics, where rapid vertical transport could provide a significant source to the stratosphere. In this study, quasi-continuous measurements of short-lived halocarbons are reported for two tropical sites in Sabah (Malaysian Borneo), one coastal and one inland (rainforest). We present the observations for C2Cl4, CHBr3, CH2Br2* (actually ~80% CH2Br2 and ~20% CHBrCl2) and CH3I from November 2008 to January 2010 made using our μDirac gas chromatographs with electron capture detection (GC-ECD). We focus on the first 15 months of observations, showing over one annual cycle for each compound and therefore adding significantly to the few limited-duration observational studies that have been conducted thus far in southeast Asia. The main feature in the C2Cl4 behaviour at both sites is its annual cycle, with the winter months being influenced by northerly flow with higher concentrations, typical of the Northern Hemisphere, and with the summer months influenced by southerly flow and lower concentrations representative of the Southern Hemisphere. No such clear annual cycle is seen for CHBr3, CH2Br2* or CH3I. The baseline values for CHBr3 and CH2Br2* are similar at the coastal (overall median: CHBr3 1.7 ppt, CH2Br2* 1.4 ppt) and inland sites (CHBr3 1.6 ppt, CH2Br2* 1.1 ppt), but periods with elevated values are seen at the coast (overall 95th percentile: CHBr3 4.4 ppt, CH2Br2ast 1.9 ppt), presumably resulting from the stronger influence of coastal emissions. Overall median bromine values from [CHBr3 × 3] + [CH2Br2* × 2] are 8.0 ppt at the coast and 6.8 ppt inland. The median values reported here are largely consistent with other limited tropical data and imply that southeast Asia generally is not, as has been suggested, a hot spot for emissions of these compounds. These baseline values are consistent with the most recent emissions found for southeast Asia using the p-TOMCAT (Toulouse Off-line Model of Chemistry And Transport) model. CH3I, which is only observed at the coastal site, is the shortest-lived compound measured in this study, and the observed atmospheric variations reflect this, with high variability throughout the study period. This work was supported by a NERC consortium grant to the OP3 team, by NCAS, by the European Commission through the SCOUT-O3 project (505390-GOCE-CF2004) and by NERC western Pacific grant number NE/F020341/1 and NERC CAST grant number NE/J006246/1. L. M. O’Brien and M. J. Ashfold thank NERC for research studentships. A. D. Robinson acknowledges NERC for their support through small grant project NE/D008085/1. N. R. P. Harris is supported by a NERC Advanced Research Fellowship. We thank the Sabah Foundation, Danum Valley Field Centre and the Royal Society (Glen Reynolds) for field site support. The research leading to these results has received funding from the European Union’s Seventh Framework Programme FP7/2007–2013 under grant agreement no. 226224 – SHIVA. We thank David Oram and Stephen Humphrey at UEA for their assistance in checking the calibration of our Aculife cylinder in May 2009. This is paper number 626 of the Royal Society’s South East Asian Rainforest Research Programme.This is the final published version. It first appeared at http://www.atmos-chem-phys.net/14/8369/2014/acp-14-8369-2014.html

Delivery of chlamydia screening to young women requesting emergency hormonal contraception at pharmacies in Manchester, UK: a prospective study

<p>Abstract</p> <p>Background</p> <p>More women are requesting Emergency Hormonal Contraception (EHC) at pharmacies where screening for <it>Chlamydia trachomatis </it>is not routinely offered. The objective of this study was to assess the uptake of free postal chlamydia screening by women under 25 years who requested EHC at pharmacies in Manchester, UK.</p> <p>Methods</p> <p>Six Primary Care Trusts (PCTs) that had contracted with pharmacies to provide free EHC, requested the largest EHC providers (≥ 40 doses annually) to also offer these clients a coded chlamydia home testing kit. Pharmacies kept records of the ages and numbers of women who accepted or refused chlamydia kits. Women sent urine samples directly to the laboratory for testing and positive cases were notified. Audit data on EHC coverage was obtained from PCTs to assess the proportion of clients eligible for screening and to verify the uptake rate.</p> <p>Results</p> <p>33 pharmacies participated. Audit data for 131 pharmacy months indicated that only 24.8% (675/2718) of women provided EHC were also offered chlamydia screening. Based on tracking forms provided by pharmacies for the whole of the study, 1348/2904 EHC clients (46.4%) who had been offered screening accepted a screening kit. 264 (17.6%) of those who accepted a kit returned a sample, of whom 24 (9.1%) were chlamydia-positive. There was an increase in chlamydia positivity with age (OR: 1.2 per year; 1.04 to 1.44; p = 0.015).</p> <p>Conclusion</p> <p>Chlamydia screening for EHC pharmacy clients is warranted but failure of pharmacists to target all EHC clients represented a missed opportunity for treating a well defined high-risk group.</p

Patterns of atrophy in pathologically confirmed dementias: a voxelwise analysis

$\textbf{OBJECTIVE}$: Imaging is recommended to support the clinical diagnoses of dementias, yet imaging research studies rarely have pathological confirmation of disease. This study aims to characterise patterns of brain volume loss in six primary pathologies compared with controls and to each other. $\textbf{METHODS}$: One hundred and eighty-six patients with a clinical diagnosis of dementia and histopathological confirmation of underlying pathology, and 73 healthy controls were included in this study. Voxel-based morphometry, based on ante-mortem T1-weighted MRI, was used to identify cross-sectional group differences in brain volume. $\textbf{RESULTS}$: Early-onset and late-onset Alzheimer's disease exhibited different patterns of grey matter volume loss, with more extensive temporoparietal involvement in the early-onset group, and more focal medial temporal lobe loss in the late-onset group. The Presenilin-1 group had similar parietal involvement to the early-onset group with localised volume loss in the thalamus, medial temporal lobe and temporal neocortex. Lewy body pathology was associated with less extensive volume loss than the other pathologies, although precentral/postcentral gyri volume was reduced in comparison with other pathological groups. Tau and TDP43A pathologies demonstrated similar patterns of frontotemporal volume loss, although less extensive on the right in the 4-repeat-tau group, with greater parietal involvement in the TDP43A group. The TDP43C group demonstrated greater left anterior-temporal involvement. $\textbf{CONCLUSIONS}$: Pathologically distinct dementias exhibit characteristic patterns of regional volume loss compared with controls and other dementias. Voxelwise differences identified in these cohorts highlight imaging signatures that may aid in the differentiation of dementia subtypes during life. The results of this study are available for further examination via NeuroVault (http://neurovault.org/collections/ADHMHOPN/).The Dementia Research Centre is an Alzheimer’s Research UK coordinating centre. The authors acknowledge the support of Alzheimer’s Research UK (grant number ART-NCG2010B-2), the Medical Research Council (grant number MR/J014257/2), the NIHR Queen Square Dementia Biomedical Research Unit, UCL/H Biomedical Research Centre, the Leonard Wolfson Experimental Neurology Centre, the NIHR Newcastle Biomedical Research Unit in Lewy body dementia and the NIHR Cambridge Biomedical Research Unit in Dementia. LH is supported by funding from Alzheimer’s Research UK and a UCL Impact Studentship. NCF and JTOB hold NIHR Senior Investigator Awards. JMS acknowledges the support of the NIHR Queen Square Dementia BRU, the NIHR UCL/H Biomedical Research Centre, Wolfson Foundation, EPSRC (EP/J020990/1), MRC (CSUB19166), ARUK (ARUK-Network 2012–6-ICE; ARUK-PG2014-1946) and European Commission (H2020-PHC-2014-2015-666992)

Density of Healthcare Providers and Patient Outcomes: Evidence from a Nationally Representative Multi-Site HIV Treatment Program in Uganda

This study examined the association between density of healthcare providers and patient outcomes using a large nationally representative cohort of patients receiving combination antiretroviral therapy (cART) in Uganda.Objective: We examined the association between density of healthcare providers and patient outcomes using a large nationally representative cohort of patients receiving combination antiretroviral therapy (cART) in Uganda. Design: We obtained data from The AIDS Support Organization (TASO) in Uganda. Patients 18 years of age and older who initiated cART at TASO between 2004 and 2008 contributed to this analysis. The number of healthcare providers per 100 patients, the number of patients lost to follow-up per 100 person years and number of deaths per 100 person years were calculated. Spearman correlation was used to identify associations between patient loss to follow-up and mortality with the healthcare provider-patient ratios. Results: We found no significant associations between the number of patients lost to follow-up and physicians (p = 0.45), nurses (p = 0.93), clinical officers (p = 0.80), field officers (p = 0.56), and healthcare providers overall (p = 0.83). Similarly, no significant associations were observed between mortality and physicians (p = 0.65), nurses (p = 0.49), clinical officers (p = 0.73), field officers (p = 0.78), and healthcare providers overall (p = 0.73). Conclusions: Patient outcomes, as measured by loss to follow-up and mortality, were not significantly associated with the number of doctors, nurses, clinical officers, field officers, or healthcare providers overall. This may suggest that that other factors, such as the presence of volunteer patient supporters or broader political or socioeconomic influences, may be more closely associated with outcomes of care among patients on cART in Uganda

CA125/MUC16 Is Dispensable for Mouse Development and Reproduction

Cancer antigen 125 (CA125) is a blood biomarker that is routinely used to monitor the progression of human epithelial ovarian cancer (EOC) and is encoded by MUC16, a member of the mucin gene family. The biological function of CA125/MUC16 and its potential role in EOC are poorly understood. Here we report the targeted disruption of the of the Muc16 gene in the mouse. To generate Muc16 knockout mice, 6.0 kb was deleted that included the majority of exon 3 and a portion of intron 3 and replaced with a lacZ reporter cassette. Loss of Muc16 protein expression suggests that Muc16 homozygous mutant mice are null mutants. Muc16 homozygous mutant mice are viable, fertile, and develop normally. Histological analysis shows that Muc16 homozygous mutant tissues are normal. By the age of 1 year, Muc16 homozygous mutant mice appear normal. Downregulation of transcripts from another mucin gene (Muc1) was detected in the Muc16 homozygous mutant uterus. Lack of any prominent abnormal phenotype in these Muc16 knockout mice suggests that CA125/MUC16 is not required for normal development or reproduction. These knockout mice provide a unique platform for future studies to identify the role of CA125/MUC16 in organ homeostasis and ovarian cancer

Crystal Structures Reveal the Multi-Ligand Binding Mechanism of Staphylococcus aureus ClfB

Staphylococcus aureus (S. aureus) pathogenesis is a complex process involving a diverse array of extracellular and cell wall components. ClfB, an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules) family surface protein, described as a fibrinogen-binding clumping factor, is a key determinant of S. aureus nasal colonization, but the molecular basis for ClfB-ligand recognition remains unknown. In this study, we solved the crystal structures of apo-ClfB and its complexes with fibrinogen α (Fg α) and cytokeratin 10 (CK10) peptides. Structural comparison revealed a conserved glycine-serine-rich (GSR) ClfB binding motif (GSSGXGXXG) within the ligands, which was also found in other human proteins such as Engrailed protein, TCF20 and Dermokine proteins. Interaction between Dermokine and ClfB was confirmed by subsequent binding assays. The crystal structure of ClfB complexed with a 15-residue peptide derived from Dermokine revealed the same peptide binding mode of ClfB as identified in the crystal structures of ClfB-Fg α and ClfB-CK10. The results presented here highlight the multi-ligand binding property of ClfB, which is very distinct from other characterized MSCRAMMs to-date. The adherence of multiple peptides carrying the GSR motif into the same pocket in ClfB is reminiscent of MHC molecules. Our results provide a template for the identification of other molecules targeted by S. aureus during its colonization and infection. We propose that other MSCRAMMs like ClfA and SdrG also possess multi-ligand binding properties

On the Observability of Recurrent Nova Super-Remnants

The nova super-remnant (NSR) surrounding M 31N 2008-12a (12a), the annually erupting recurrent nova (RN), is the only known example of this phenomenon. As this structure has grown as a result of frequent eruptions from 12a, we might expect to see NSRs around other RNe; this would confirm the RN–NSR association and strengthen the connection between novae and type Ia supernovae (SN Ia) as NSRs centered on SN Ia provide a lasting, unequivocal signpost to the single degenerate progenitor type of that explosion. The only previous NSR simulation used identical eruptions from a static white dwarf (WD). In this Paper, we simulate the growth of NSRs alongside the natural growth/erosion of the central WD, within a range of environments, accretion rates, WD temperatures, and initial WD masses. The subsequent evolving eruptions create dynamic NSRs tens of parsecs in radius comprising a low-density cavity, bordered by a hot ejecta pile-up region, and surrounded by a cool high-density, thin, shell. Higher density environments restrict NSR size, as do higher accretion rates, whereas the WD temperature and initial mass have less impact. NSRs form around growing or eroding WDs, indicating that NSRs also exist around old novae with low-mass WDs. Observables such as X-ray and