A Novel Variable Selection Method for Classification with Application to Single Nucleotide Polymorphism Data

Introduction and Aims: In recent years, there has been a growing interest in studying genetic data so as to answer specific medical questions; for example, indicative biomarkers that can accurately predict (classify) outcomes (e.g. healthy and disease or different categories of patients’ response to treatment). In genome-wide data analysis, a typical procedure is to use a variable selection approach, often univariable, where the primary aim is to select the most important genetic variants, particularly Single Nucleotide Polymorphisms (SNPs), associated with an outcome of interest. This thesis proposes a novel variable selection method by considering the multivariate nature of the genetic data. The aim of this thesis is threefold: (i) to develop a quantitative variable selection method for classification which can be used in the multivariate setting, computationally inexpensive and easy to understand and to apply, (ii) to propose a multi-step approach that selects SNPs and evaluates the classification performance of the resulting models in a cross-validation framework, and (iii) to jointly model the longitudinal clinical and SNP data for classification using the Standard and New Antiepileptic Drugs (SANAD) dataset. Methods: A literature search was conducted to study the different approaches of variable selection and their relationship with classification performance. A novel variable selection method, tSNR within a logistic regression framework was developed to select the most informative SNPs. In addition, a multi-step framework that involved univariable and multivariable selection in a cross-validation setting was proposed. Then, the filter metric tSNR and the multi-step framework were assessed using simulated datasets. The methods were further examined using an epilepsy pharmacogenomics dataset (EpiPGX) in which the phenotype of interest is the remission from seizures status after receiving first well-tolerated antiepileptic drugs (AEDs). A second epilepsy dataset from the SANAD trial was used as the validation dataset. Within the SANAD dataset, the longitudinal clinical and SNP data were jointly modelled using a longitudinal discriminant analysis (LoDA) approach with multivariate generalised linear mixed model (MGLMM). The classification performance was measured by calculating the probability of correct classification (PCC) and area under the receiver operating characteristic (ROC) curve (AUC), sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV). Results: The literature review suggested the need for variable selection methods, which could potentially aid better classification accuracy. In the simulation study, the univariable tSNR ranking was able to capture the causal SNPs in the top ten ranked SNPs. In addition, within the proposed framework, the results using simulated datasets suggested that the classification performance using SNPs selected by cumulative tSNR (multivariate) are better than the SNPs based on univariable tSNR ranking. The results were further confirmed using the real clinical datasets. The addition of SNP data to the longitudinal model based on clinical data improved the mean prediction time at which patients who will not achieve remission from seizures within five years of commencing treatment are identified. However, it did not provide an improvement to the classification performance. Conclusions: The developed approach using a tSNR filter metric proved to be effective in ranking and selecting subset of SNPs that are associated with the outcome of interest. The SNPs selected by tSNR were shown to give good classification accuracy. Also, by jointly modelling the longitudinal clinical data and SNP data (selected using tSNR) in a longitudinal model the prediction time at which patients can be classified was improved

Ramond-Ramond Cohomology and O(D,D) T-duality

In the name of supersymmetric double field theory, superstring effective actions can be reformulated into simple forms. They feature a pair of vielbeins corresponding to the same spacetime metric, and hence enjoy double local Lorentz symmetries. In a manifestly covariant manner --with regard to O(D,D) T-duality, diffeomorphism, B-field gauge symmetry and the pair of local Lorentz symmetries-- we incorporate R-R potentials into double field theory. We take them as a single object which is in a bi-fundamental spinorial representation of the double Lorentz groups. We identify cohomological structure relevant to the field strength. A priori, the R-R sector as well as all the fermions are O(D,D) singlet. Yet, gauge fixing the two vielbeins equal to each other modifies the O(D,D) transformation rule to call for a compensating local Lorentz rotation, such that the R-R potential may turn into an O(D,D) spinor and T-duality can flip the chirality exchanging type IIA and IIB supergravities.Comment: 1+37 pages, no figure; Structure reorganized, References added, To appear in JHEP. cf. Gong Show of Strings 2012 (http://wwwth.mpp.mpg.de/members/strings/strings2012/strings_files/program/Talks/Thursday/Gongshow/Lee.pdf

Validity and reliability of Arabic version of the ID Pain screening questionnaire in the assessment of neuropathic pain

Diagnosis of neuropathic pain (NP) can be challenging. The ID Pain (ID-P) questionnaire, a screening tool for NP, has been used widely both in the original version and translated forms. The aim of this study was to develop an Arabic version of ID-P and assess its validity and reliability in detecting neuropathic pain. The original ID-P was translated in Arabic language and administered to the study population. Reliability of the Arabic version was evaluated by percentage observed agreement, and Cohen’s kappa; and validity by sensitivity, specificity, correctly classified, and receiver operating characteristic (ROC) curve. Physician diagnosis was considered as the gold standard for comparing the diagnostic accuracy. The study included 375 adult patients (153 [40.8%] with NP; 222 [59.2%] with nociceptive pain). Overall observed percentage agreement and Cohen’s kappa were >90% and >0.80, respectively. Median (range) score of ID-P scale was 3 (2–4) and 1 (0–2) in the NP group and NocP group, respectively (p<0.001). Area under the ROC curve was 0.808 (95% CI, 0.764–0.851). For the cut-off value of ≥2, sensitivity was 84.3%, specificity was 66.7%, and correct classification was 73.9%. Thus, the Arabic version of ID-P showed moderate reliability and validity as a pain assessment tool. This article presents the psychometric properties of the Arabic version of ID Pain questionnaire. This Arabic version may serve as a simple yet important screening tool, and help in appropriate management of neuropathic pain, specifically in primary care centers in the Kingdom of Saudi Arabia

Regular Khat (Catha edulis) chewing is associated with elevated diastolic blood pressure among adults in Butajira, Ethiopia: A comparative study

<p>Abstract</p> <p>Background</p> <p>Fresh leaves and buds of the Khat plant (<it>Catha edulis</it>) contain Cathinone, an amphetamine like alkaloid responsible for its pharmacological action. Chewing of Khat has been associated with a transient rise in blood pressure and heart rate in experimental studies. Few studies examined the effect of regular or frequent Khat chewing on blood pressure at the population level. This study was conducted to examine the association of regular Khat chewing with blood pressure among adults.</p> <p>Methods</p> <p>We compared systolic and diastolic blood pressure of adults 35-65 years of age who reported regular chewing of Khat during the preceding five years to those who never chewed Khat during the same period. Study participants were recruited from purposively selected urban and rural villages of Butajira District in Ethiopia. The comparative groups, chewers (334) and non-chewers (330), were identified from among the general population through a house-to-house visit using a screening questionnaire. They were frequency-matched for sex and age within a five-year range. Data were collected through structured interviews and physical measurements including blood pressure, weight and height.</p> <p>Results</p> <p>The prevalence of hypertension was significantly higher among Khat chewers (13.4%) than non-chewers (10.7%), odds ratio (OR) = 1.66 (95% confidence interval (CI) 1.05, 3.13). A considerably high proportion of chewers (29.9%) than non-chewers (20.6%) had sub-optimal diastolic blood pressure (> 80 mmHg). The mean (sd) diastolic blood pressure was significantly higher among Khat chewers [75.0 (11.6)] than non-chewers [72.9 (11.7)], P < 0.05. Similarly, Khat chewers had significantly higher mean (sd) heart rate [76.3 (11.5)] than non-chewers [73.9 (12.6)], P < 0.05. There was no significant difference in mean systolic blood pressure between the two groups.</p> <p>Conclusion</p> <p>Regular chewing of Khat is associated with elevated mean diastolic blood pressure, which is consistent with the peripheral vasoconstrictor effect of Cathinone. Regular Khat chewing may have sustained effects on the cardiovascular system that can contribute to elevated blood pressure at the population level.</p

Comparison of glucose tolerance in renal transplant recipients and hemodialysis patients

BACKGROUND: Impaired glucose tolerance is a risk factor for atherosclerosis in hemodialysis patients and renal transplant recipients. METHODS: To check the relationship of impaired glucose tolerance with the other atherosclerotic risk factors, fasting blood sugar and the standard two hour glucose tolerance test, serum tryglyceride, serum cholesterol, cyclosporine through level (in renal tranpslant recipients) and hemoglobin A1C were measured in 55 stable renal transplant recipients, 55 hemodialysis patients and 55 healthy controls with similar demographic characteristics. Patients with diabetes mellitus and propranolol consumers were excluded. The mean age and female to male ratio were 39 +/- 7 years and 23/22, respectively. RESULTS: Four of the renal transplant recipients and twelve of the hemodialysis patients had impaired glucose tolerance. Significant linear correlation was observed with body mass index and IGT only in hemodialysis patients (r = 0.4, p = 0.05). Glucose tolerance also had a significant correlation with triglyceride levels (217.2 +/- 55 mg/dl in hemodialysis patients vs. 214.3 +/- 13 mg/dl in renal transplant recipients and 100.2 +/- 18 mg/dl in control groups, p = 0.001). The glucose tolerance had significant relationship with higher serum cholesterol levels only in the renal transplant recipients (269.7 +/- 54 in renal transplant recipients vs. 199.2 +/- 36.6 mg/dl in hemodialysis and 190.5 +/- 34 mg/dl in control groups, p = 0.0001). In the renal transplant recipients, a linear correlation was observed with glucose tolerance and both the serum cyclosporine level (r = 0.9, p = 0.001) and the hemoglobin A1C concentration (6.2 +/- 0.9 g/dl). The later correlation was also observed in the hemodialysis patients (6.4 +/- 0.7 g/dl; r = 67, p = 0.001). CONCLUSIONS: We conclude that although fasting blood sugar is normal in non-diabetic renal transplant and hemodialysis patients, impaired glucose tolerance could be associated with the other atherosclerotic risk factors

PKCβ Facilitates Leukemogenesis in Chronic Lymphocytic Leukaemia by Promoting Constitutive BCR-Mediated Signalling

B cell antigen receptor (BCR) signalling competence is critical for the pathogenesis of chronic lymphocytic leukaemia (CLL). Defining key proteins that facilitate these networks aid in the identification of targets for therapeutic exploitation. We previously demonstrated that reduced PKCα function in mouse hematopoietic stem/progenitor cells (HPSCs) resulted in PKCβII upregulation and generation of a poor-prognostic CLL-like disease. Here, prkcb knockdown in HSPCs leads to reduced survival of PKCα-KR-expressing CLL-like cells, concurrent with reduced expression of the leukemic markers CD5 and CD23. SP1 promotes elevated expression of prkcb in PKCα-KR expressing cells enabling leukemogenesis. Global gene analysis revealed an upregulation of genes associated with B cell activation in PKCα-KR expressing cells, coincident with upregulation of PKCβII: supported by activation of key signalling hubs proximal to the BCR and elevated proliferation. Ibrutinib (BTK inhibitor) or enzastaurin (PKCβII inhibitor) treatment of PKCα-KR expressing cells and primary CLL cells showed similar patterns of Akt/mTOR pathway inhibition, supporting the role for PKCβII in maintaining proliferative signals in our CLL mouse model. Ibrutinib or enzastaurin treatment also reduced PKCα-KR-CLL cell migration towards CXCL12. Overall, we demonstrate that PKCβ expression facilitates leukemogenesis and identify that BCR-mediated signalling is a key driver of CLL development in the PKCα-KR model.</jats:p