Bioinformatics advances in saliva diagnostics

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva diagnostics made possible by the Saliva Ontology and SDxMart

Factor structure and psychometric properties of the General Health Questionnaire (GHQ-12) among Ghanaian adolescents

Purpose: There is little information about the reliability and validity of the 12-item General Health Questionnaire (GHQ-12) in Ghana. This study sought to examine the reliability and factor structure of the GHQ-12 in Ghanaian adolescents. Method: sHigh school students (N = 770) completed the GHQ-12 and the Adolescent Stress Questionnaire (ASQ). Internal consistency, convergent validity and exploratory factor analysis were used. Results: A two factor structure, each with six items, was extracted. The total GHQ-12 had acceptable internal consistency and a generally high correlation with the ASQ subscales. Conclusion: The GHQ-12 can be used in Ghanaian samples, but more research is needed to confirm its factor structure

No entropy enigmas for N=4 dyons

We explain why multi-centered black hole configurations where at least one of the centers is a large black hole do not contribute to the indexed degeneracies in theories with N=4 supersymmetry. This is a consequence of the fact that such configurations, although supersymmetric, belong to long supermultiplets. As a result, there is no entropy enigma in N=4 theories, unlike in N=2 theories.Comment: 14 page

BKM Lie superalgebras from counting twisted CHL dyons

Following Sen[arXiv:0911.1563], we study the counting of (`twisted') BPS states that contribute to twisted helicity trace indices in four-dimensional CHL models with N=4 supersymmetry. The generating functions of half-BPS states, twisted as well as untwisted, are given in terms of multiplicative eta products with the Mathieu group, M_{24}, playing an important role. These multiplicative eta products enable us to construct Siegel modular forms that count twisted quarter-BPS states. The square-roots of these Siegel modular forms turn out be precisely a special class of Siegel modular forms, the dd-modular forms, that have been classified by Clery and Gritsenko[arXiv:0812.3962]. We show that each one of these dd-modular forms arise as the Weyl-Kac-Borcherds denominator formula of a rank-three Borcherds-Kac-Moody Lie superalgebra. The walls of the Weyl chamber are in one-to-one correspondence with the walls of marginal stability in the corresponding CHL model for twisted dyons as well as untwisted ones. This leads to a periodic table of BKM Lie superalgebras with properties that are consistent with physical expectations.Comment: LaTeX, 32 pages; (v2) matches published versio

BKM Lie superalgebra for the Z_5 orbifolded CHL string

We study the Z_5-orbifolding of the CHL string theory by explicitly constructing the modular form tilde{Phi}_2 generating the degeneracies of the 1/4-BPS states in the theory. Since the additive seed for the sum form is a weak Jacobi form in this case, a mismatch is found between the modular forms generated from the additive lift and the product form derived from threshold corrections. We also construct the BKM Lie superalgebra, tilde{G}_5, corresponding to the modular form tilde{Delta}_1 (Z) = tilde{Phi}_2 (Z)^{1/2} which happens to be a hyperbolic algebra. This is the first occurrence of a hyperbolic BKM Lie superalgebra. We also study the walls of marginal stability of this theory in detail, and extend the arithmetic structure found by Cheng and Dabholkar for the N=1,2,3 orbifoldings to the N=4,5 and 6 models, all of which have an infinite number of walls in the fundamental domain. We find that analogous to the Stern-Brocot tree, which generated the intercepts of the walls on the real line, the intercepts for the N >3 cases are generated by linear recurrence relations. Using the correspondence between the walls of marginal stability and the walls of the Weyl chamber of the corresponding BKM Lie superalgebra, we propose the Cartan matrices for the BKM Lie superalgebras corresponding to the N=5 and 6 models.Comment: 30 pages, 2 figure

Moving from evidence-based medicine to evidence-based health.

While evidence-based medicine (EBM) has advanced medical practice, the health care system has been inconsistent in translating EBM into improvements in health. Disparities in health and health care play out through patients' limited ability to incorporate the advances of EBM into their daily lives. Assisting patients to self-manage their chronic conditions and paying attention to unhealthy community factors could be added to EBM to create a broader paradigm of evidence-based health. A perspective of evidence-based health may encourage physicians to consider their role in upstream efforts to combat socially patterned chronic disease

PREDICT: a new UK prognostic model that predicts survival following surgery for invasive breast cancer.

INTRODUCTION: The aim of this study was to develop and validate a prognostication model to predict overall and breast cancer specific survival for women treated for early breast cancer in the UK. METHODS: Using the Eastern Cancer Registration and Information Centre (ECRIC) dataset, information was collated for 5,694 women who had surgery for invasive breast cancer in East Anglia from 1999 to 2003. Breast cancer mortality models for oestrogen receptor (ER) positive and ER negative tumours were derived from these data using Cox proportional hazards, adjusting for prognostic factors and mode of cancer detection (symptomatic versus screen-detected). An external dataset of 5,468 patients from the West Midlands Cancer Intelligence Unit (WMCIU) was used for validation. RESULTS: Differences in overall actual and predicted mortality were <1% at eight years for ECRIC (18.9% vs. 19.0%) and WMCIU (17.5% vs. 18.3%) with area under receiver-operator-characteristic curves (AUC) of 0.81 and 0.79 respectively. Differences in breast cancer specific actual and predicted mortality were <1% at eight years for ECRIC (12.9% vs. 13.5%) and <1.5% at eight years for WMCIU (12.2% vs. 13.6%) with AUC of 0.84 and 0.82 respectively. Model calibration was good for both ER positive and negative models although the ER positive model provided better discrimination (AUC 0.82) than ER negative (AUC 0.75). CONCLUSIONS: We have developed a prognostication model for early breast cancer based on UK cancer registry data that predicts breast cancer survival following surgery for invasive breast cancer and includes mode of detection for the first time. The model is well calibrated, provides a high degree of discrimination and has been validated in a second UK patient cohort.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Negative discriminant states in N=4 supersymmetric string theories

Single centered BPS black hole solutions exist only when the charge carried by the black hole has positive discriminant. On the other hand the exact dyon spectrum in heterotic string theory compactified on T^6 is known to contain states with negative discriminant. We show that all of these negative discriminant states can be accounted for as two centered black holes. Thus after the contribution to the index from the two centered black holes is subtracted from the total microscopic index, the index for states with negative discriminant vanishes even for finite values of charges, in agreement with the results from the black hole side. Bound state metamorphosis -- which requires us to identify certain apparently different two centered configurations according to a specific set of rules -- plays a crucial role in this analysis. We also generalize these results to a class of CHL string theories.Comment: LaTeX file, 32 pages; v2: reference added; v3: added new section 3.

Homozygosity for a missense mutation in the 67 kDa isoform of glutamate decarboxylase in a family with autosomal recessive spastic cerebral palsy: parallels with Stiff-Person Syndrome and other movement disorders

Background Cerebral palsy (CP) is an heterogeneous group of neurological disorders of movement and/or posture, with an estimated incidence of 1 in 1000 live births. Non-progressive forms of symmetrical, spastic CP have been identified, which show a Mendelian autosomal recessive pattern of inheritance. We recently described the mapping of a recessive spastic CP locus to a 5 cM chromosomal region located at 2q24-31.1, in rare consanguineous families. Methods Here we present data that refine this locus to a 0.5 cM region, flanked by the microsatellite markers D2S2345 and D2S326. The minimal region contains the candidate gene GAD1, which encodes a glutamate decarboxylase isoform (GAD67), involved in conversion of the amino acid and excitatory neurotransmitter glutamate to the inhibitory neurotransmitter γ-aminobutyric acid (GABA). Results A novel amino acid mis-sense mutation in GAD67 was detected, which segregated with CP in affected individuals. Conclusions This result is interesting because auto-antibodies to GAD67 and the more widely studied GAD65 homologue encoded by the GAD2 gene, are described in patients with Stiff-Person Syndrome (SPS), epilepsy, cerebellar ataxia and Batten disease. Further investigation seems merited of the possibility that variation in the GAD1 sequence, potentially affecting glutamate/GABA ratios, may underlie this form of spastic CP, given the presence of anti-GAD antibodies in SPS and the recognised excitotoxicity of glutamate in various contexts