Complete genome sequence of the Pseudomonas aeruginosa bacteriophage phiIBB-PAA2

Pseudomonas aeruginosa phage phiIBB-PAA2 is a broad-host-range virus isolated from raw hospital sewage (Porto, Portugal). This phage has a terminally redundant (183 bp), 45,344-bp double-stranded DNA (dsDNA) genome encoding 66 coding sequences (CDSs) and 3 tRNAs. It belongs to the family Podoviridae and the genus Luz24likevirus.D.P.P. and S.S. acknowledge the financial support from the Portuguese Foundation for Science and Technology (FCT) through the grants SFRH/BD/764407/2011 and SFRH/BPD/48803/2008. This work was supported by the FEDER fund through the COMPETE program and through the National fund of FCT in the scope of the project PTDC/EBB-BIO/114760/2009 (FCOMP-01-0124-FEDER-014759)

A primary screen of the bovine genome for quantitative trait loci affecting some growth traits of Japanese Black calves.

A primary genomic screen for quantitative trait loci (QTL) affecting growth traits was performed by genotyping 99 and 85 microsatellite markers on 18 and 19 progeny from 2 Japanese Black sires. Traits analyzed were birth weight, weaning weight, yearling weight and average daily gain from birth to weaning. Data were analyzed by generating an F-statistic profile computed at 1-cM intervals for each chromosome by the regression of phenotype on the conditional probability of receiving the allele from the sire. Each sire family was analyzed separately as the markers differed. Data were adjusted for the effects of sex of calf and parity of dam. There was evidence for a QTL of the first sire affecting yearling weight, weaning weight and average daily gain in chromosomes A, B and C. Some putative QTL at or just below the threshold were also detected. Results provided and represented a portion of research work being conducted to identify and characterize QTL affecting growth and body shape traits of Japanese Black calves

Characterization of inter-seasonal climatic variability through dry-season rice productivity in the north-west region of Bangladesh

Inter-annual climatic variability in Bangladesh is significant and the probability of occurrence of extreme episodic/ climatic events has increased in the last couple of decades and thus threatening food security. Impact of inter-seasonal climatic va riability on Boro rice (dry season) yield in north-western parts of Bangladesh was analyzed using the historic weather datasets for 1971 to 2010 and MAKESENS model. Boro rice yield increased from 1980 onwards and the growth rate picked up with time. Inter-annual and inter-seasonal climatic variability was noticed through maximum and minimum temperatures, rainfall and sunshine hours. In general, temperatures and rainfall showed increasing trends but sunshine hours were decreasing gradually during the study period. Growth rates in average annual maximum, minimum and mean air temperatures were 0.001, 0.016 and 0.009°C year-1, respectively. On regional scale, Boro-rice seasonal maximum temperature was decreasing by 0.013°C year-1 but minimum and mean temperatures were increasing by 0.024 and 0.006°C year-1, respectively. Annual average sunshine hours in the study location were in decreasing trend by 0.027 hr year-1, but reduction in seasonal sunshine hours was 0.035 hr year-1. Inter-seasonal climatic variability was characterized through the Boro-rice yields in four test regions of north-west region of Bangladesh. Trend line equations were evolved for assessing the impact of climatic variations on Bororice yield. If maximum temperature changes by 1oC, Boro rice yield could be increased by 0.13 t ha-1, but it would reduce by 0.34 t ha-1 with one degree rise in minimum temperature. If sunshine hour decreases by 1 hr, Boro rice yield would decrease by 0.70 t ha-1 in study locations. Combined effects of maximum and minimum temperatures and sunshine hours showed significant influence on grain yields of Boro rice. These imply that temperature tolerant and solar radiation use-efficient rice varieties need to be bred for combating climate change impact in Bangladesh. There is a need to identify optimum sowing/transplanting window for the region, choice of suitable cultivars/ideo-types, and adoption of appropriate water and nutrients management strategies and adoption of appropriate resource conservation technologies for sustainable Boro rice production in Bangladesh

Fixing Collinearity Instability Using Principal Component and Ridge Regression Analyses in the Relationship Between Body Measurements and Body Weight in Japanese Black Cattle

Monthly measurements of withers height (WHT), hip height (HIPHT), body length (BL), chest width (CHWD), shoulder width (SHWD), chest depth (CHDP), hip width (HIPWD), lumbar vertebrae width (LUVWD), thurl width (THWD), pin bone width (PINWD), rump length (RUMPLN), cannon circumference (CANNCIR) and chest circumference (CHCIR) from birth to yearling age, were utilised in principal component and ridge regression analyses to study their relationship with body weight in Japanese Black cattle with an objective of fixing the problem of collinearity instability. The data comprised of a total of 10,543 records on calves born between 1937 and 2002 within the same herd under the same management. Simple pair wise correlation coefficients between the body measurements revealed positive, highly significant (P<0.001) values of 0.98 between WHT and HIPHT, HIPWD and LUVWD, while the lowest correlation of 0.50 was between CHDP and SHWD. Severe collinearity problems as portrayed by variance inflation factors (VIF) above 10 were evident in all body measurements ranging from 11.25 in PINWD to 46.94 in LUVWD except for SHWD (1.80), CHDP (3.70), CHWD (7.11) and CANNCIR (7.33). Principal component and ridge regression analyses allowed the derivation of new and more stable regression coefficients that overcame the problem of collinearity. Of all the body measurements studied, hip height was shown to be the least important for predicting the body weight of Japanese Black cattle, while SHWD and CHWD were the most important

Biomechanical evolution of the Tkachev on uneven bars in female gymnastics

The development of joint kinematics and kinetics is fundamental to the successful performance of complex flight skills in gymnastics bar routines. Biomechanical understanding of these skills can provide coaches and scientists with key information to make training safe and effective. The Tkachev is a complex and popular gymnastics skill with many different variations. Recently, a new version has been performed, which has become popular with elite female performers. This study examined the key biomechanical characteristics of this skill and contrasted these to the earlier versions reported. Elite female gymnasts (n = 5) were recorded and manually digitised using twin video cameras (50 Hz) at the 2007 World Gymnastics Championships. Three-dimensional (3D) DLT was used to reconstruct the real world coordinates. Individualised inertia characteristics were calculated and used to determine mass centre kinematics. Inverse dynamics analysis was used to calculate joint kinetics at the hips and shoulders from the known values at the toes. The results of this study showed an increased flight time and rotational capacity during the aerial phase for the toe-on Tkachev, as well as a more simple movement pattern and joint kinetic demand with single power impulses at the hips and shoulders compared with previous versions. The key finding of this study was that the toe-on version appeared to be less physically demanding than that the inward and outward techniques, and provide the opportunity to perform more complex aerial phase body positions. These results can help coaches to physically prepare their gymnasts and biomechanists in terms of understanding the demands of these skills

Description and process evaluation of pharmacists’ interventions in a pharmacist-led information technology-enabled multicentre cluster randomised controlled trial for reducing medication errors in general practice (PINCER trial)

Objective To undertake a process evaluation of pharmacists' recommendations arising in the context of a complex IT-enabled pharmacist-delivered randomised controlled trial (PINCER trial) to reduce the risk of hazardous medicines management in general practices. Methods PINCER pharmacists manually recorded patients’ demographics, details of interventions recommended, actions undertaken by practice staff and time taken to manage individual cases of hazardous medicines management. Data were coded and double entered into SPSS v15, and then summarised using percentages for categorical data (with 95% CI) and, as appropriate, means (SD) or medians (IQR) for continuous data. Key findings Pharmacists spent a median of 20 minutes (IQR 10, 30) reviewing medical records, recommending interventions and completing actions in each case of hazardous medicines management. Pharmacists judged 72% (95%CI 70, 74) (1463/2026) of cases of hazardous medicines management to be clinically relevant. Pharmacists recommended 2105 interventions in 74% (95%CI 73, 76) (1516/2038) of cases and 1685 actions were taken in 61% (95%CI 59, 63) (1246/2038) of cases; 66% (95%CI 64, 68) (1383/2105) of interventions recommended by pharmacists were completed and 5% (95%CI 4, 6) (104/2105) of recommendations were accepted by general practitioners (GPs), but not completed at the end of the pharmacists’ placement; the remaining recommendations were rejected or considered not relevant by GPs. Conclusions The outcome measures were used to target pharmacist activity in general practice towards patients at risk from hazardous medicines management. Recommendations from trained PINCER pharmacists were found to be broadly acceptable to GPs and led to ameliorative action in the majority of cases. It seems likely that the approach used by the PINCER pharmacists could be employed by other practice pharmacists following appropriate training

Outbreak of Middle East Respiratory Syndrome at Tertiary Care Hospital, Jeddah, Saudi Arabia, 2014

During March–May 2014, a Middle East respiratory syndrome (MERS) outbreak occurred in Jeddah, Saudi Arabia, that included many persons who worked or received medical treatment at King Fahd General Hospital. We investigated 78 persons who had laboratory-confirmed MERS during March 2–May 10 and documented contact at this hospital. The 78 persons with MERS comprised 53 patients, 16 healthcare workers, and 9 visitors. Among the 53 patients, the most probable sites of acquisition were the emergency department (22 patients), inpatient areas (17), dialysis unit (11), and outpatient areas (3). Infection control deficiencies included limited separation of suspected MERS patients, patient crowding, and inconsistent use of infection control precautions; aggressive improvements in these deficiencies preceded a decline in cases. MERS coronavirus transmission probably was multifocal, occurring in multiple hospital settings. Continued vigilance and strict application of infection control precautions are necessary to prevent future MERS outbreaks

A novel pathway producing dimethylsulphide in bacteria is widespread in soil environments

The volatile compound dimethylsulphide (DMS) is important in climate regulation, the sulphur cycle and signalling to higher organisms. Microbial catabolism of the marine osmolyte dimethylsulphoniopropionate (DMSP) is thought to be the major biological process generating DMS. Here we report the discovery and characterisation of the first gene for DMSP-independent DMS production in any bacterium. This gene, mddA, encodes a methyltransferase that methylates methanethiol (MeSH) and generates DMS. MddA functions in many taxonomically diverse bacteria including sediment-dwelling pseudomonads, nitrogen-fixing bradyrhizobia and cyanobacteria, and mycobacteria, including the pathogen Mycobacterium tuberculosis. The mddA gene is present in metagenomes from varied environments, being particularly abundant in soil environments, where it is predicted to occur in up to 76% of bacteria. This novel pathway may significantly contribute to global DMS emissions, especially in terrestrial environments, and could represent a shift from the notion that DMSP is the only significant precursor of DMS

Toward Human-Carnivore Coexistence: Understanding Tolerance for Tigers in Bangladesh

Fostering local community tolerance for endangered carnivores, such as tigers (Panthera tigris), is a core component of many conservation strategies. Identification of antecedents of tolerance will facilitate the development of effective tolerance-building conservation action and secure local community support for, and involvement in, conservation initiatives. We use a stated preference approach for measuring tolerance, based on the ‘Wildlife Stakeholder Acceptance Capacity’ concept, to explore villagers’ tolerance levels for tigers in the Bangladesh Sundarbans, an area where, at the time of the research, human-tiger conflict was severe. We apply structural equation modeling to test an a priori defined theoretical model of tolerance and identify the experiential and psychological basis of tolerance in this community. Our results indicate that beliefs about tigers and about the perceived current tiger population trend are predictors of tolerance for tigers. Positive beliefs about tigers and a belief that the tiger population is not currently increasing are both associated with greater stated tolerance for the species. Contrary to commonly-held notions, negative experiences with tigers do not directly affect tolerance levels; instead, their effect is mediated by villagers’ beliefs about tigers and risk perceptions concerning human-tiger conflict incidents. These findings highlight a need to explore and understand the socio-psychological factors that encourage tolerance towards endangered species. Our research also demonstrates the applicability of this approach to tolerance research to a wide range of socio-economic and cultural contexts and reveals its capacity to enhance carnivore conservation efforts worldwide