In-Depth Performance Evaluation of PFP and ESG Sequence-Based Function Prediction Methods in CAFA 2011 Experiment

Background Many Automatic Function Prediction (AFP) methods were developed to cope with an increasing growth of the number of gene sequences that are available from high throughput sequencing experiments. To support the development of AFP methods, it is essential to have community wide experiments for evaluating performance of existing AFP methods. Critical Assessment of Function Annotation (CAFA) is one such community experiment. The meeting of CAFA was held as a Special Interest Group (SIG) meeting at the Intelligent Systems in Molecular Biology (ISMB) conference in 2011. Here, we perform a detailed analysis of two sequence-based function prediction methods, PFP and ESG, which were developed in our lab, using the predictions submitted to CAFA. Results We evaluate PFP and ESG using four different measures in comparison with BLAST, Prior, and GOtcha. In addition to the predictions submitted to CAFA, we further investigate performance of a different scoring function to rank order predictions by PFP as well as PFP/ESG predictions enriched with Priors that simply adds frequently occurring Gene Ontology terms as a part of predictions. Prediction accuracies of each method were also evaluated separately for different functional categories. Successful and unsuccessful predictions by PFP and ESG are also discussed in comparison with BLAST. Conclusion The in-depth analysis discussed here will complement the overall assessment by the CAFA organizers. Since PFP and ESG are based on sequence database search results, our analyses are not only useful for PFP and ESG users but will also shed light on the relationship of the sequence similarity space and functions that can be inferred from the sequences

Uterine Rupture in a Primigravida with Mullerian Anomaly at 27 Weeks Gestation

Mullerian anomalies are rare and are often associated with infertility, chronic pelvic pain and pregnancy  wastage. This is a case report of a primigravida at 27 weeks gestation, who presented in shock. Intra- operatively, a mullerian anomaly with a ruptured left horn was found and excised. She made remarkable  recovery and was discharged home. Uterine anomalies should be ruled out in the evaluation of pregnancy  wastage. When present, management should be individualized based on the clinical history, presentation, anatomical aberration and the patient’s future fertility desire

Premature ovarian failure in twins: case report

Premature ovarian failure (POF)is a serious life-changing condition that affects young women, remains an enigma and the researchers’ challenge. POF, premature ovarian insufficiency (POI), premature menopause, premature dysfunction (POD), or hypergonadotropic hypogonadism is one of the most perplexing disorders with aheterogeneous origin. Infertility, social and psychological stress are common consequences of this entity. This paper presents a rare condition where both twins had presented with POF

Community Knowledge and Perceptions on National School-Based De-Worming Programme

Objectives: To determine the community level of knowledge, attitude and perception of soil transmitted helminthes and the national school-based de-worming programme in selected villages of Busia County in Kenya. Design: A cross-sectional survey. Setting: Busia and Bunyala districts in Busia County. Subjects: A total of 384 participants were studied. Main outcome measures: Socio-demographic characteristics, then knowledge, causes and effects of Soil Transmitted Infections on health and education, prevention strategies, knowledge of national school-based de-worming programming, implementing strategies of the programme, benefits of the programme, community satisfaction and health seeking behaviour. Results: Eating the uncooked food as a cause for soil transmitted infections constituted 27.16% (63) followed by 16.38% (38) not using latrines, 15.95% (37) eating left over foods, 12.93% (30) eating cold food, 10.78% (25) eating not well cooked pork, 9.48% (22) eating contaminated soil, and 7.33% (17) changing of diet. One head teacher interviewed stated that “One can be able to notice if his/her child has worm infection if the child eats without getting satisfied, eating all the time and yet his belly is big.”Community Health Extension Worker in the FGD stated that: “During floods seasons most of the areas in Budalangi become flooded and all latrines are filled with water and the excreta start overflowing. Most of the residents don’t have shoes especially the children and therefore they are prone to the worm infection.”99.57% of the parents were aware of the national school based de-worming programme of which (92%) learnt about the programme after their children were de-wormed in their various schools. Seventy five percent (174) were satisfied about the programme; 65.1% (151) and 10.3% indicated that the programme improves the children’s health and student’s school performance respectively. Conclusion: Most of the parents do not have adequate knowledge on worms, their causes and signs and symptoms of the intestinal worms. Low educational levels and poverty levels also contribute to the lack of awareness on intestinal worms and putting the prevention measures across the board. The study also found out that the community perception towards the de-worming programme was good because the de-worming programme improved the children’s health and performance in education

Magnetic and Dielectric Properties in Multiferroic Cu3Mo2O9 under High Magnetic Fields

The magnetic and dielectric properties under high magnetic fields are studied in the single crystal of Cu3Mo2O9. This multiferroic compound has distorted tetrahedral spin chains. The effects of the quasi-one dimensionality and the geometrical spin frustration are expected to appear simultaneously. We measure the magnetoelectric current and the differential magnetization under the pulsed magnetic field up to 74 T. We also measure the electric polarization versus the electric field curve/loop under the static field up to 23 T. Dielectric properties change at the magnetic fields where the magnetization jumps are observed in the magnetization curve. Moreover, the magnetization plateaus are found at high magnetic fields.Comment: 6 pages, 3 figures, in press in JPS Conf. Proc. as a part of SCES2013 Proceeding

Helium, Oxygen, Proton, and Electron (HOPE) Mass Spectrometer for the Radiation Belt Storm Probes Mission

The HOPE mass spectrometer of the Radiation Belt Storm Probes (RBSP) mission (renamed the Van Allen Probes) is designed to measure the in situ plasma ion and electron fluxes over 4π sr at each RBSP spacecraft within the terrestrial radiation belts. The scientific goal is to understand the underlying physical processes that govern the radiation belt structure and dynamics. Spectral measurements for both ions and electrons are acquired over 1 eV to 50 keV in 36 log-spaced steps at an energy resolution ΔE FWHM/E≈15 %. The dominant ion species (H+, He+, and O+) of the magnetosphere are identified using foil-based time-of-flight (TOF) mass spectrometry with channel electron multiplier (CEM) detectors. Angular measurements are derived using five polar pixels coplanar with the spacecraft spin axis, and up to 16 azimuthal bins are acquired for each polar pixel over time as the spacecraft spins. Ion and electron measurements are acquired on alternate spacecraft spins. HOPE incorporates several new methods to minimize and monitor the background induced by penetrating particles in the harsh environment of the radiation belts. The absolute efficiencies of detection are continuously monitored, enabling precise, quantitative measurements of electron and ion fluxes and ion species abundances throughout the mission. We describe the engineering approaches for plasma measurements in the radiation belts and present summaries of HOPE measurement strategy and performance

Reduction of myocardial infarction by postischemic administration of the calpain inhibitor A-705253 in comparison to the Na(+)/H(+) exchange inhibitor Cariporide (R) in isolated perfused rabbit hearts

The calpain inhibitor A-705253 and the Na(+)/H(+) exchange inhibitor Cariporide (R) were studied in isolated perfused rabbit hearts subjected to 60 min occlusion of the ramus interventricularis of the left coronary artery (below the origin of the first diagonal branch), followed by 120 min of reperfusion. The inhibitors were added to the perfusion fluid solely or in combination at the beginning of reperfusion. Hemodynamic monitoring and biochemical analysis of perfusion fluid from the coronary outflow were performed. Myocardial infarct size and area at risk (transiently not perfused myocardium) were determined from left ventricular slices after a special staining procedure with Evans blue and 2,3,5-triphenyltetrazolium chloride. The infarcted area (dead myocardium) was 72.7 +/- 4.0% of the area at risk in untreated controls, but was significantly smaller in the presence of the inhibitors. The largest effect was observed with 10(-6) M A-705253, which reduced the infarcted area to 49.2 +/- 4.1% of the area at risk, corresponding to a reduction of 33.6%. Cariporide (R) at 10(-6) M reduced the infarct size to the same extent. The combination of both inhibitors, however, did not further improve cardioprotection. No significant difference was observed between the experimental groups in coronary perfusion, left ventricular pressure, heart rate, or in the release of lactate dehydrogenase and creatine kinase from heart muscle