PiRaNhA: A server for the computational prediction of RNA-binding residues in protein sequences

The PiRaNhA web server is a publicly available online resource that automatically predicts the location of RNA-binding residues (RBRs) in protein sequences. The goal of functional annotation of sequences in the field of RNA binding is to provide predictions of high accuracy that require only small numbers of targeted mutations for verification. The PiRaNhA server uses a support vector machine (SVM), with position-specific scoring matrices, residue interface propensity, predicted residue accessibility and residue hydrophobicity as features. The server allows the submission of up to 10 protein sequences, and the predictions for each sequence are provided on a web page and via email. The prediction results are provided in sequence format with predicted RBRs highlighted, in text format with the SVM threshold score indicated and as a graph which enables users to quickly identify those residues above any specific SVM threshold. The graph effectively enables the increase or decrease of the false positive rate. When tested on a non-redundant data set of 42 protein sequences not used in training, the PiRaNhA server achieved an accuracy of 85%, specificity of 90% and a Matthews correlation coefficient of 0.41 and outperformed other publicly available servers. The PiRaNhA prediction server is freely available at http://www.bioinformatics.sussex.ac.uk/PIRANHA. © The Author(s) 2010. Published by Oxford University Press

Estimating the proportion of offenders supervised by probation trusts in England and Wales who are ex-Armed Forces

On 15 September 2010 Defence Analytical Services and Advice (DASA) published its estimate of the proportion of prisoners in England and Wales who are ex-Armed Forces. The study involved matching the personal details of adult prisoners (a snapshot taken on 06/11/09) against DASA’s Service leavers’ database. It was estimated that 3.5% of prisoners were veterans of the UK Regular Armed Forces. A similar matching exercise has now been undertaken to estimate the proportion of those being supervised by Probation Trusts in England and Wales who are ex-Armed Forces

Estimating the proportion of prisoners in England and Wales who are ex-Armed Forces - further analysis

On 25 January 2010 Defence Analytical Services and Advice (DASA) published its initial estimate of the proportion of prisoners in England and Wales who are ex-Armed Forces. The study involved matching the personaldetails of adult prisoners against DASA’s Service leavers database. The initial report published on 25 January 2010 reported that 2,207 records of Service leavers matched against the 81,071 prisoner records supplied by the Ministry of Justice (MoJ) (a snapshot taken on 06/11/09). From this it was estimated that 2.7% (rounded up to 3%) of prisoners were veterans of the UK Regular Armed Forces. The initial report committed the Ministry of Defence to three areas of further analysis. These three components are described in detail in this report which is divided into the following sections:Section A: Revising the estimate of the proportion of prisoners in England and Wales who are ex-Armed Forces.Section B: Describing the characteristics of the prisoners in England and Wales who were identified as ex-Armed Forces.Section C: Comparing the proportion of ex-Armed Forcesidentified as being in prison with the proportion of the general population in prison, overall and by offence group

NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules

Similarities in the 3D patterns of RNA base interactions or arrangements can provide insights into their functions and roles in stabilization of the RNA 3D structure. Nucleic Acids Search for Substructures and Motifs (NASSAM) is a graph theoretical program that can search for 3D patterns of base arrangements by representing the bases as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. The input files for NASSAM are PDB formatted 3D coordinates. This web server can be used to identify matches of base arrangement patterns in a query structure to annotated patterns that have been reported in the literature or that have possible functional and structural stabilization implications. The NASSAM program is freely accessible without any login requirement at http://mfrlab.org/grafss/nassam/

Genital warts and cervical neoplasia: an epidemiological study.

Cervical carcinoma and cervical intra-epithelial neoplasia (CIN) are likely to be associated with all sexually transmitted diseases (STDs). To help discover which (if any) of the recognised STDs might actually cause these conditions, a key question is whether one particular such association is much stronger than the others. The present study is therefore only of women newly attending an STD clinic, and compares the prevalences of cytological abnormalities of the cervix among 415 women attending with genital warts, 135 with genital herpes, and 458 with trichomoniasis or gonorrhoea. Significantly more genital wart patients (8.1%) than trichomoniasis or gonorrhoea patients (1.9%) showed dyskaryotic changes (adjusted relative risk (RR) = 5.8 with 95% limits 2.5-13.5) at, or a few months before, first attendance, while no excess whatever was seen in women with genital herpes. Moreover, half the women had a subsequent smear (at an average of 3-4 years after first attendance) and, although the diagnosis at first attendance was not related to the onset rate of dyskaryotic changes observed in these subsequent smears, it was related to the onset rate of grade III cervical intra-epithelial neoplasia (CIN III), which was found in 7 previous genital wart patients, in 2 previous trichomonas patients, but in 0 previous genital herpes patients. Thus, our findings suggest that herpes is not directly relevant to dyskaryotic change, but that one or more of the human papilloma viruses that cause genital warts may be

Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis

Low-oxygen (hypoxia) stress associated with natural phenomena such as waterlogging, results in widespread transcriptome changes and a metabolic switch from aerobic respiration to anaerobic fermentation. High-throughput sequencing of small RNA libraries obtained from hypoxia-treated and control root tissue identified a total of 65 unique microRNA (miRNA) sequences from 46 families, and 14 trans-acting small interfering RNA (tasiRNA) from three families. Hypoxia resulted in changes to the abundance of 46 miRNAs from 19 families, and all three tasiRNA families. Chemical inhibition of mitochondrial respiration caused similar changes in expression in a majority of the hypoxia-responsive small RNAs analysed. Our data indicate that miRNAs and tasiRNAs play a role in gene regulation and possibly developmental responses to hypoxia, and that a major signal for these responses is likely to be dependent on mitochondrial function

Migratory bird hunting activity and harvest during the 1999 and 2000 hunting seasons Final Report April 2006

National surveys of waterfowl, dove, band-tailed pigeon (Columba fasciata), American woodcock (Scolopax minor), common snipe (Gallinago gallinago), rail, gallinule, and American coot (Fulica americana) hunters were conducted during the 1999 and 2000 migratory bird hunting seasons. About 1.3 million waterfowl hunters harvested 16,188,300 (±3%) ducks and 3,455,700 (±5%) geese in 1999, and a similar number of waterfowl hunters harvested 15,966,200 (±4%) ducks and 3,716,000 (±7%) geese in 2000. Mallard (Anas platyrhynchos), gadwall (A. strepera), green-winged teal (A. crecca), wood duck (Aix sponsa), and blue-winged teal (A. discors) were the most-harvested duck species, and Canada goose (Branta canadensis) was the predominant goose species in the harvest. About 1.2 million dove hunters harvested 24,437,300 (±4%) mourning doves (Zenaida macroura) in 1999 and 26,295,300 (±4%) in 2000. Woodcock hunters numbered about 170,600 in 1999 and 154,500 in 2000, and they harvested 444,800 (±20%) birds in 1999 and 390,900 (±20%) in 2000. Among the lesser-hunted species, about 40,200 people hunted snipe in 1999 (29,200 in 2000), and they harvested 276,500 (±56%) and 86,400 (±52%) snipe in 1999 and 2000, respectively; rail hunters (11,900 in 1999 and 6,900 in 2000) harvested 31,600 (±41%) rails in 1999 and 15,300 (±56%) rails in 2000; about 4,000 hunters harvested 32,900 (±74%) gallinules in 1999 and 20,900 (±70%) in 2000; and about 40,000 coot hunters harvested 236,000 (±26%) coots in 1999 and 335,000 (±45%) in 2000