Signal peptide discrimination and cleavage site identification using SVM and NN.

About 15% of all proteins in a genome contain a signal peptide (SP) sequence, at the N-terminus, that targets the protein to intracellular secretory pathways. Once the protein is targeted correctly in the cell, the SP is cleaved, releasing the mature protein. Accurate prediction of the presence of these short amino-acid SP chains is crucial for modelling the topology of membrane proteins, since SP sequences can be confused with transmembrane domains due to similar composition of hydrophobic amino acids. This paper presents a cascaded Support Vector Machine (SVM)-Neural Network (NN) classification methodology for SP discrimination and cleavage site identification. The proposed method utilises a dual phase classification approach using SVM as a primary classifier to discriminate SP sequences from Non-SP. The methodology further employs NNs to predict the most suitable cleavage site candidates. In phase one, a SVM classification utilises hydrophobic propensities as a primary feature vector extraction using symmetric sliding window amino-acid sequence analysis for discrimination of SP and Non-SP. In phase two, a NN classification uses asymmetric sliding window sequence analysis for prediction of cleavage site identification. The proposed SVM-NN method was tested using Uni-Prot non-redundant datasets of eukaryotic and prokaryotic proteins with SP and Non-SP N-termini. Computer simulation results demonstrate an overall accuracy of 0.90 for SP and Non-SP discrimination based on Matthews Correlation Coefficient (MCC) tests using SVM. For SP cleavage site prediction, the overall accuracy is 91.5% based on cross-validation tests using the novel SVM-NN model.

Knowledge and practice of urethral catheterisation by newly qualified medical interns.

BACKGROUND: Urethral catheterisation is a procedure which is daily performed in clinical practice. Though, interns are expected to be proficient in this, the situation is always not so and complications have occurred due to inadequate knowledge of safe urethral catheterisation. AIMS AND OBJECTIVES: The study is intended to assess the knowledge and the practice of urethral catheterisation of prospective interns with a view of making suggestions for improvement in the teaching of this procedural skill to medical students and interns. METHODOLOGY: Questionnaires were administered to all prospective interns who had applied to do their compulsory one year internship in the University of Ilorin Teaching Hospital, Ilorin, Nigeria. The data were analysed using SPSS 11 statistical package. RESULTS: There were 96 respondents 65 (69.9%) of these were males. They graduated from 6 medical schools in Nigeria and 1 in the Sudan and they were aged between 23 and 36 years. They all had observed urethral catheterisation before while 92.5% have performed urethral catheterisation: 78.5 % under supervision and 14% under no supervision and 7 (7.5%) have not. Only 19.4% had good knowledge of the indications for urethral catheterisation and 53.9% had knowledge of appropriate list of materials for safe urethral catheterisation. Only 29.1% could describe well the steps of safe catheterisation and 31.2%.could list well the possible complications of catheterisation. Less than half had good knowledge of appropriate catheter sizes. CONCLUSION: Urethral catheterisation is yet to be well mastered by many newly qualified interns and improvement in the teaching of procedural skills in medical schools may likely improve the situation.

Effects of controlled blood cooling on hemodynamic stability and urea kinetics during high-efficiency hemodialysis.

Although the use of cooled dialysate during hemodialysis is associated with stabilization of intradialytic BP, the effects of blood cooling on hemodynamics and urea kinetics in high-efficiency hemodialysis have not been completely studied. In particular, the effects of blood cooling have not been elucidated in very short-time, high K/V dialysis treatments, in which postdialysis urea rebound is maximized. In theory, blood cooling could increase urea compartmentalization during treatment and decrease dialysis efficacy. Measurements of cardiovascular hemodynamics and urea kinetics were performed in 15 patients (56 studies) during dialysis, using a blood temperature monitor with control of dialysate temperature. Dialysate temperature was adjusted to either lower the core temperature or raise the core temperature by, respectively, producing negative heat-energy exchange (cooled dialysis) or keeping heat-energy exchange in the extracorporeal circuit neutral (thermoneutral dialysis) so that energy was not transferred to or from the patient. Each subject was studied on both protocols, thereby allowing each individual to act as his own control. In cooled dialysis, heat-energy exchange in the extracorporeal circuit was -266+/-15 kJ per treatment, and dialysate temperature averaged 35.7+/-0.02 degrees C. In thermoneutral dialysis, heat-energy exchange in the extracorporeal circuit averaged 5+/-31 kJ per treatment, and dialysate temperature averaged 37.1+/-0.02 degrees C. Dialysate cooling resulted in a reduction in mean body temperature compared with thermoneutral therapy (-0.22+/-0.04 versus +0.31+/-0.05 degrees C). Cooling resulted in a greater increase in peripheral vascular resistance index (+515+/-160 versus + 114+/-92 dyn.sec/cm5 per m2), an increase in mean arterial pressure (+4+/-3 versus -4+/-4 mmHg), a reduction in the maximum intradialytic fall in mean arterial pressure (-10+/-2 versus -18+/-3, mmHg), and a reduction in staff interventions for hypotension or dialytic symptoms (6 of 28 versus 12 of 28 studies). These differences occurred without differences in the change in blood volume (-14.3+/-1.8% versus -13.9+/-2.2%) or cardiac index (-0.4+/-0.1 versus -0.4+/-0.2, L/min per m2). Urea rebound (37+/-4% versus 38+/-3%) and effective Kt/V (1.29+/-0.05 versus 1.32+/-0.06) were not different between groups. Thus, body temperature cooling can be used to stabilize BP and reduce intradialytic events requiring staff intervention without compromising the efficacy of treatment in high-efficiency dialysis.