Building sparse large margin classifiers

This paper presents an approach to build Sparse Large Margin Classifiers (SLMC) by adding one more constraint to the standard Support Vector Machine (SVM) training problem. The added constraint explicitly controls the sparseness of the classifier and an approach is provided to solve the formulated problem. When considering the dual of this problem, it can be seen that building an SLMC is equivalent to constructing an SVM with a modified kernel function. Further analysis of this kernel function indicates that the proposed approach essentially finds a discriminating subspace that can be spanned by a small number of vectors, and in this subspace different classes of data are linearly well separated. Experimental results over several classification benchmarks show that in most cases the proposed approach outperforms the state-of-art sparse learning algorithms. 1

Influence of noise on the inference of dynamic Bayesian networks from short time series

Abstract — In this paper we investigate the influence of external noise on the inference of network structures. The purpose of our simulations is to gain insights in the experimental design of microarray experiments to infer, e.g., transcription regulatory networks from microarray experiments. Here external noise means, that the dynamics of the system under investigation, e.g., temporal changes of mRNA concentration, is affected by measurement errors. Additionally to external noise another problem occurs in the context of microarray experiments. Practically, it is not possible to monitor the mRNA concentration over an arbitrary long time period as demanded by the statistical methods used to learn the underlying network structure. For this reason, we use only short time series to make our simulations more biologically plausible

Cloning, expression and characterization of endo-β-1,4-mannanase from aspergillus fumigatus in aspergillus sojae and pichia pastoris

To be utilized in biomass conversion, including ethanol production and galactosylated oligosaccharide synthesis, namely prebiotics, the gene of extracellular endo-β-1,4-mannanase (EC 32.1.78) of Aspergillus fumigatus IMI 385708 (formerly known as Thermomyces lanuginosus IMI 158749) was expressed first in Aspergillus sojae and then in Pichia pastoris under the control of the glyceraldehyde triphosphate dehydrogenase (gpdA) and the alcohol oxidase (AOX1) promoters, respectively. The highest production of mannanase (352 U mL -1)in A. sojae was observed after 6 days of cultivation. In P. pastoris, the highest mannanase production was observed 10 h after induction with methanol (61 U mL-1). The fold increase in mannanase production was estimated as ∼12-fold and ∼2-fold in A. sojae and P. pastoris, respectively, when compared with A. fumigatus. Both recombinant enzymes showed molecular mass of about 60 kDa and similar specific activities (∼350 U mg-1 protein). Temperature optima were at 60°C and 45°C, and maximum activity was at pH 4.5 and 5.2 for A. sojae and P. pastoris, respectively. The enzyme from P. pastoris was more stable retaining most of the activity up to 50°C, whereas the enzyme from A. sojae rapidly lost activity above 40°C

The role of T2-weighted images in assessing the grade of extraprostatic extension of the prostate carcinoma

Purpose Extraprostatic extension (EPE) is an unfavorable prognostic factor and the grade of EPE is also shown to be correlated with the prognosis of prostate cancer. The current study assessed the value of prostate magnetic resonance imaging (MRI) in measuring the radial distance (RD) of EPE and the role of T2 WI signs in predicting the grade of EPE. Materials and methods A total of 110 patients who underwent prostate MRI before radical prostatectomy are enrolled in this retrospective study. Eighty-four patients have organ confined disease and the remaining twenty-six patients have EPE all verified by histopathology. Prostate MRI examinations were conducted with 3T MRI scanner and phased array coil with the following sequences: T2 WI, T1 WI, DCE, DWI with ADC mapping, and high b-value at b = 1500 s/mm(2). The likelihood of EPE with 5-point Likert scale was assigned, several MRI features were extracted for each dominant tumor identified by using T2 WI. Tumors with Likert scales 4-5 were evaluated further to obtain MRI-based RD. The relationship between pathological and MRI-determined RD was tested. Univariate and multivariate logistic regression models were developed to detect the grade of pathological EPE. The inputs were among the 2 clinical parameters and 4 MRI features. Results There is a moderate correlation between pathological RD and MRI-determined RD (rho = 0.45, P < 0.01). In univariate and multivariate models, MRI features and clinical parameters possess varying significance levels (univariate models; P = 0.048-0.788, multivariate models; P = 0.173-0.769). Multivariate models perform better than the univariate models by offering fair to good performances (AUC = 0.69-0.85). The multivariate model that employs the MRI features offers better performance than the model employs clinical parameters (AUC = 0.81 versus 0.69). Conclusion Co-existence of T2 WI signs provide higher diagnostic value even than clinical parameters in predicting the grade of EPE. Combined use of clinical parameters and MRI features deliver slightly superior performance than MRI features alone

Pneumococcal Meningitis in 18 Year-Old Young Pregnant Woman

Community acquired bacterial meningitis is associated with high morbidity and mortality, and the most common bacterial pathogen is Streptococcus pneumoniae. Few case reports and two small case series of pneumococcal meningitis during pregnancy have been reported in the literature. This is the first case report of pneumococcal meningitis in an 18 year-old pregnant woman from Turkey. She was admitted to our emergency department at 33rd week of gestation with the complaints of fever, nausea, vomiting and sudden onset of confusion. The diagnosis of acute bacterial meningitis was made according to the findings of lumbar puncture. Empirical treatment with ceftriaxone (2 x 2 g/day) and vancomycin (4 x 500 mg/day) were started immediately. Caesarean section was performed on the sixth day of hospitalization (34th week of gestation) because of the premature rupture of membrane. Both mother and the infant survived without any sequela. Successful results for both mother and infant can be achieved with early diagnosis and appropriate treatment in cases of pneumococcal meningitis during pregnancy

Vancomycin Resistant Enterococcus Outbreak in a University Hospital: Investigation of Risk Factors

Introduction: In this study, independent risk factors for the acquisition of vancomycin resistant enterococcus (VRE) were investigated prospectively between September 2011 and March 2012 in a nosocomial VRE outbreak at a university hospital. Materials and Methods: After the detection of a VRE strain from wound culture sample of an inpatient in September 2011, a VRE outbreak was assumed in the hospital, and VRE surveillance was performed both at high-risk and VRE detected clinics. For the detection of gastrointestinal system (GIS) VRE colonization, weekly rectal swab specimens were taken from the hospitalized patients and when considering an infection, blood, urine and wound specimens were sent to the microbiology laboratory for each patient. The patients whom rectal swab and/or clinical specimens yielded VRE were accepted as VRE positive. Determining vancomycin resistance genotype among the VRE strains were done with multiplex polymerase chain reaction technique (GenExpert®, USA) by using the special test kits (Xpert®, USA). Results: During the seven-month of VRE outbreak, a total of 74 VRE positive patients, 6 (8.1%) of whom infected by a VRE in seven different clinics were determined. These 74 VRE positive patients and 1136 patients who were accepted as VRE negative (all were hospitalized in the same clinical wards) by the surveillance cultures were divided into two groups for comparing patient characteristics. A multivariate logistic regression analysis showed sulbactam-ampicillin [Odds ratio (OR) 3.18, 95% confi dence interval (95% CI) 1.70-5.97; p< 0.001], vancomycin (OR 5.16, 95% CI 1.92-13.9; p= 0.001), piperacillin/tazobactam (OR 4.09, 95% CI 1.85-9.45; p= 0.001), carbapenems (imipenem, meropenem) (OR 2.43, 95% CI 2.03-10.1; p< 0.001) and amikacin (OR 7.4, 95% CI 2.71-20.19; p< 0.001) use, all were detected as independent risk factors for VRE positivity. Further, diabetes mellitus (OR 2.44, 95% CI 1.31-4.53; p= 0.005), abdominal surgical operation (OR 2.49, 95% CI 1.18-5.29; p= 0.017), and the application of a nasogastric feeding tube (OR 0.31, 95% CI 0.13- 0.75; p= 0.01) were also determined as independent risk factors for VRE-acquisition. Seventy-three out (98.6%) of 74 VRE strains were both vancomycin [minimum inhibitor concantration (MIC) > 16 μg/mL)] and teicoplanin (MIC > 16 μg/mL) resistant (vanA genotype) Enterococcus faecium. Conclusion: The use of parenteral form of broad spectrum antibiotics and underlying diseases like diabetes and nasogastric tube applications, all increase nosocomial VRE risk