Gene Expression based Survival Prediction for Cancer Patients: A Topic Modeling Approach

Cancer is one of the leading cause of death, worldwide. Many believe that genomic data will enable us to better predict the survival time of these patients, which will lead to better, more personalized treatment options and patient care. As standard survival prediction models have a hard time coping with the high-dimensionality of such gene expression (GE) data, many projects use some dimensionality reduction techniques to overcome this hurdle. We introduce a novel methodology, inspired by topic modeling from the natural language domain, to derive expressive features from the high-dimensional GE data. There, a document is represented as a mixture over a relatively small number of topics, where each topic corresponds to a distribution over the words; here, to accommodate the heterogeneity of a patient's cancer, we represent each patient (~document) as a mixture over cancer-topics, where each cancer-topic is a mixture over GE values (~words). This required some extensions to the standard LDA model eg: to accommodate the "real-valued" expression values - leading to our novel "discretized" Latent Dirichlet Allocation (dLDA) procedure. We initially focus on the METABRIC dataset, which describes breast cancer patients using the r=49,576 GE values, from microarrays. Our results show that our approach provides survival estimates that are more accurate than standard models, in terms of the standard Concordance measure. We then validate this approach by running it on the Pan-kidney (KIPAN) dataset, over r=15,529 GE values - here using the mRNAseq modality - and find that it again achieves excellent results. In both cases, we also show that the resulting model is calibrated, using the recent "D-calibrated" measure. These successes, in two different cancer types and expression modalities, demonstrates the generality, and the effectiveness, of this approach

Mechanics-Based Modeling Approach for Rapid Prediction of Low Velocity Impact Damage in Composite Laminates

A mechanics-based modeling approach is developed to rapidly predict damage in polymer matrix composites resulting from a low velocity impact event. The approach is incorporated into a computer code that provides an efficient means to assess the damage resistance for a range of material systems, layup configurations, and impact scenarios. It is envisioned that the developed approach will aid in early design and analysis of composite structures where sizing and layup decisions must be made, and evaluating the feasibility of a large number of laminate configurations using numerical approaches such as finite element analysis (FEA) is prohibitively expensive. Therefore, the goal of the modeling approach is to predict the impact damage size given the laminate configuration and impact scenario. This information can then be used to determine the residual strength of the material. To be useful in such a context, the tool is designed to run quickly (<2 minutes) to allow a large number of design cases to be investigated. The results presented demonstrate that the model is capable of efficiently predicting low velocity impact damage size, shape, and location within an acceptable accuracy suitable for preliminary design and analysis of composite structures

Сучасний стан гончарства Гуцульщини та Покуття (за матеріалами керамологічної експедиції Інституту керамології – відділення Інституту народознавства НАН України та Національного музею-заповідника українського гончарства в Опішному)

6–17 червня 2007 року співробітниками Національного музею-заповідника українського гончарства в Опішному та науковцями Інституту керамології було проведено керамологічну експедицію до таких гончарних осередків Івано-Франківської області: Косів, Коломия, Кути, Пистинь

Inverse Method for Estimation of Composite Kink-Band Toughness from Open-Hole Compression Strength Data

Fiber-reinforced polymer matrix composite materials can fail by kink-band propagation mechanism when subjected to in-plane compressive loading. This mode of failure is especially prevalent in compressive loading of laminates with holes, cut-outs, or impact damage. Most of the successful models for predicting compressive strength of such laminates require fracture toughness associated with kink-band propagation under in-plane compression. However, this property is difficult to measure experimentally, limiting the use of such models in design practice. In this paper an inverse method is proposed to estimate the kink-band toughness of the laminate from its open-hole compression strength data, which is an easier property to measure experimentally. Furthermore, a scaling relationship is proposed to estimate kink-band toughness for other laminate configurations of the same material

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions

Babesia microti, a tick-transmitted, intraerythrocytic protozoan parasite circulating mainly among small mammals, is the primary cause of human babesiosis. While most cases are transmitted by Ixodes ticks, the disease may also be transmitted through blood transfusion and perinatally. A comprehensive analysis of genome composition, genetic diversity, and gene expression profiling of seven B. microti isolates revealed that genetic variation in isolates from the Northeast United States is almost exclusively associated with genes encoding the surface proteome and secretome of the parasite. Furthermore, we found that polymorphism is restricted to a small number of genes, which are highly expressed during infection. In order to identify pathogen-encoded factors involved in host-parasite interactions, we screened a proteome array comprised of 174 B. microti proteins, including several predicted members of the parasite secretome. Using this immuno-proteomic approach we identified several novel antigens that trigger strong host immune responses during the onset of infection. The genomic and immunological data presented herein provide the first insights into the determinants of B. microti interaction with its mammalian hosts and their relevance for understanding the selective pressures acting on parasite evolution

Toward optimal implementation of cancer prevention and control programs in public health: A study protocol on mis-implementation

Abstract Background Much of the cancer burden in the USA is preventable, through application of existing knowledge. State-level funders and public health practitioners are in ideal positions to affect programs and policies related to cancer control. Mis-implementation refers to ending effective programs and policies prematurely or continuing ineffective ones. Greater attention to mis-implementation should lead to use of effective interventions and more efficient expenditure of resources, which in the long term, will lead to more positive cancer outcomes. Methods This is a three-phase study that takes a comprehensive approach, leading to the elucidation of tactics for addressing mis-implementation. Phase 1: We assess the extent to which mis-implementation is occurring among state cancer control programs in public health. This initial phase will involve a survey of 800 practitioners representing all states. The programs represented will span the full continuum of cancer control, from primary prevention to survivorship. Phase 2: Using data from phase 1 to identify organizations in which mis-implementation is particularly high or low, the team will conduct eight comparative case studies to get a richer understanding of mis-implementation and to understand contextual differences. These case studies will highlight lessons learned about mis-implementation and identify hypothesized drivers. Phase 3: Agent-based modeling will be used to identify dynamic interactions between individual capacity, organizational capacity, use of evidence, funding, and external factors driving mis-implementation. The team will then translate and disseminate findings from phases 1 to 3 to practitioners and practice-related stakeholders to support the reduction of mis-implementation. Discussion This study is innovative and significant because it will (1) be the first to refine and further develop reliable and valid measures of mis-implementation of public health programs; (2) bring together a strong, transdisciplinary team with significant expertise in practice-based research; (3) use agent-based modeling to address cancer control implementation; and (4) use a participatory, evidence-based, stakeholder-driven approach that will identify key leverage points for addressing mis-implementation among state public health programs. This research is expected to provide replicable computational simulation models that can identify leverage points and public health system dynamics to reduce mis-implementation in cancer control and may be of interest to other health areas

Role of spin-orbit coupling on the spin triplet pairing in Na_{x}CoO_{2}yH_{2}O I: d-vector under zero magnetic field

The d-vector in possibile spin triplet superconductor Na_{x}CoO_{2}yH_{2}O is microscopically investigated on the basis of the multi-orbital Hubbard model including the atomic spin-orbit coupling. As a result of the perturbation theory, we obtain the stable spin triplet superconductivity where the p-wave and f-wave states can be stabilized. If we neglect the spin-orbit coupling, superconducting state has 6-fold (3-fold) degeneracy in the p-wave (f-wave) state. This degeneracy is lifted by the spin-orbit coupling. We determine the d-vector within the linearlized Dyson-Gorkov equation. It is shown that the d-vector is always along the plane when the pairing symmetry is p-wave, while it depends on the parameters in case of the f-wave state. The lifting of degeneracy is significant in the p-wave state while it is very small in the f-wave state. This is because the first order term with respect to the spin-orbit coupling is effective in the former case, while it is ineffective in the latter case. The consistency of these results with NMR and \muSR measurements are discussed.Comment: To appear in J. Phys. Soc. Jpn. 74 (2005) No.

Detection of human papillomavirus in laryngeal squamous cell carcinoma: systematic review and meta-analysis

Background: Recent studies have reported a human papillomavirus (HPV) prevalence of 20% to 30% in laryngeal squamous cell carcinoma (LSCC), although clinical data on HPV involvement remain largely inconsistent, ascribed by some to differences in HPV detection methods or in geographic origin of the studies. Objective To perform a systematic review and formal meta-analysis of the literature reporting on HPV detection in LSCC. Methods Literature was searched from January 1964 until March 2015. The effect size was calculated as event rates (95% confidence interval [CI]), with homogeneity testing using Cochran's Q and I2 statistics. Meta-regression was used to test the impact of study-level covariates (HPV detection method, geographic origin) on effect size. Potential publication bias was estimated using funnel plot symmetry. Results One hundred seventy nine studies were eligible, comprising a sample size of 7,347 LSCCs from different geographic regions. Altogether, 1,830 (25%) cases tested HPV-positive considering all methods, with effect size of 0.269 (95% CI: 0.242 to 0.297; random-effects model). In meta-analysis stratified by the 1) HPV detection technique and 2) geographic study origin, the between-study heterogeneity was significant only for geographic origin (P = .0001). In meta-regression, the HPV detection method (P = .876) or geographic origin (P = .234) were not significant study-level covariates. Some evidence for publication bias was found only for studies from North America and those using non–polymerase chain reaction methods, with a marginal effect on adjusted point estimates for both. Conclusions Variability in HPV detection rates in LSCC is explained by geographic origin of study but not by HPV detection method. However, they were not significant study-level covariates in formal meta-regression

Progressive age-associated activation of JNK associates with conduction disruption in the aged atrium.

Connexin43 (Cx43) is critical for maintaining electrical conduction across atrial muscle. During progressive aging cardiac conduction slows and becomes susceptible to disruption, predisposing to arrhythmias. Changes in Cx43 protein expression, or its phosphorylation status, can instigate changes in the conduction of the cardiac action potential. Our study investigated whether increased levels of activated c-jun N-terminal kinase (JNK) is the mechanism responsible for the decline of Cx43 protein and intercellular communication during progressive aging. We examined right atrial muscle from guinea pigs between 1 day and 38 months of age. The area of the intercalated disc increased with age concurrent with a 75% decline in total C43 protein expression and spatial re-organisation of the remaining protein. An age-dependent increase in activated-JNK correlated with a rise in phosphorylated Cx43. The data also correlated with slowing of the action potential conduction velocity across the right atria from 0.38±0.01 m/s at 1 month of age to 0.30±0.01 m/s at 38 months of age. The JNK activator anisomycin increased levels of activated JNK in myocytes and reduced Cx43 protein expression paralleling the aging effect The JNK inhibitor SP600125, was found to eradicate almost all trace of Cx43 protein from the intercalating discs. We conclude that in vivo activation of JNK increases with age leading to the loss of Cx43 protein from atrial myocytes. This progressive loss results in impaired conduction and is likely to contribute to the increasing risk of atrial arrhythmias with advancing age

Replica Rényi wormholes and generalised modular entropy in JT gravity

We consider the problem of computing semi-classical Rényi entropies of CFTon AdS2 backgrounds in JT gravity with nongravitating baths, for general replica number n. Away from the n =1 limit, the backreaction of the CFT twist fields on the geometry is nontrivial. For one twist field insertion and general n, we show that the quantum extremal surface (QES) condition involves extremisation of the generalised modular entropy, consistent with Dong’s generalisation of the Ryu-Takayanagi formula for general n. For multiple QES we describe replica wormhole geometries using the theory of Fuchsian uniformisation, explicitly working out the analytically tractable case of the n“2 double trumpet wormhole geometry. We determine the off-shell dependence of the gravitational action on the QES locations andboundary map. In a factorisation limit, corresponding to late times, we are able to relate this action functional to area terms given by the value of the JT dilaton at the (off-shell) QES locations, with computable corrections. Applied to the two-sided eternal black hole, we find the n-dependent Page times for Rényi enropies in the high temperature limit