HI-Tree: Mining High Influence Patterns Using External and Internal Utility Values

We propose an efficient algorithm, called HI-Tree, for mining high influence patterns for an incremental dataset. In traditional pattern mining, one would find the complete set of patterns and then apply a post-pruning step to it. The size of the complete mining results is typically prohibitively large, despite the fact that only a small percentage of high utility patterns are interesting. Thus it is inefficient to wait for the mining algorithm to complete and then apply feature selection to post-process the large number of resulting patterns. Instead of generating the complete set of frequent patterns we are able to directly mine patterns with high utility values in an incremental manner. In this paper we propose a novel utility measure called an influence factor using the concepts of external utility and internal utility of an item. The influence factor for an item takes into consideration its connectivity with its neighborhood as well as its importance within a transaction. The measure is especially useful in problem domains utilizing network or interaction characteristics amongst items such as in a social network or web click-stream data. We compared our technique against state of the art incremental mining techniques and show that our technique has better rule generation and runtime performance

Mitochondrial DNA Copy Number Is Associated with Breast Cancer Risk

Mitochondrial DNA (mtDNA) copy number in peripheral blood is associated with increased risk of several cancers. However, data from prospective studies on mtDNA copy number and breast cancer risk are lacking. We evaluated the association between mtDNA copy number in peripheral blood and breast cancer risk in a nested case-control study of 183 breast cancer cases with pre-diagnostic blood samples and 529 individually matched controls among participants of the Singapore Chinese Health Study. The mtDNA copy number was measured using real time PCR. Conditional logistic regression analyses showed that there was an overall positive association between mtDNA copy number and breast cancer risk (Ptrend = 0.01). The elevated risk for higher mtDNA copy numbers was primarily seen for women with <3 years between blood draw and cancer diagnosis; ORs (95% CIs) for 2nd, 3rd, 4th, and 5th quintile of mtDNA copy number were 1.52 (0.61, 3.82), 2.52 (1.03, 6.12), 3.12 (1.31, 7.43), and 3.06 (1.25, 7.47), respectively, compared with the 1st quintile (Ptrend = 0.004). There was no association between mtDNA copy number and breast cancer risk among women who donated a blood sample ≥3 years before breast cancer diagnosis (Ptrend = 0.41). This study supports a prospective association between increased mtDNA copy number and breast cancer risk that is dependent on the time interval between blood collection and breast cancer diagnosis. Future studies are warranted to confirm these findings and to elucidate the biological role of mtDNA copy number in breast cancer risk. © 2013 Thyagarajan et al

Role of Esrrg in the Fibrate-Mediated Regulation of Lipid Metabolism Genes in Human ApoA-I Transgenic Mice

We have used a new ApoA-I transgenic mouse model to identify by global gene expression profiling, candidate genes that affect lipid and lipoprotein metabolism in response to fenofibrate treatment. Multilevel bioinformatical analysis and stringent selection criteria (2-fold change, 0% false discovery rate) identified 267 significantly changed genes involved in several molecular pathways. The fenofibrate-treated group did not have significantly altered levels of hepatic human APOA-I mRNA and plasma ApoA-I compared with the control group. However, the treatment increased cholesterol levels to 1.95-fold mainly due to the increase in high-density lipoprotein (HDL) cholesterol. The observed changes in HDL are associated with the upregulation of genes involved in phospholipid biosynthesis and lipid hydrolysis, as well as phospholipid transfer protein. Significant upregulation was observed in genes involved in fatty acid transport and β-oxidation, but not in those of fatty acid and cholesterol biosynthesis, Krebs cycle and gluconeogenesis. Fenofibrate changed significantly the expression of seven transcription factors. The estrogen receptor-related gamma gene was upregulated 2.36-fold and had a significant positive correlation with genes of lipid and lipoprotein metabolism and mitochondrial functions, indicating an important role of this orphan receptor in mediating the fenofibrate-induced activation of a specific subset of its target genes.National Institutes of Health (HL48739 and HL68216); European Union (LSHM-CT-2006-0376331, LSHG-CT-2006-037277); the Biomedical Research Foundation of the Academy of Athens; the Hellenic Cardiological Society; the John F Kostopoulos Foundatio

Rectal Transmission of Transmitted/Founder HIV-1 Is Efficiently Prevented by Topical 1% Tenofovir in BLT Humanized Mice

Rectal microbicides are being developed to prevent new HIV infections in both men and women. We focused our in vivo preclinical efficacy study on rectally-applied tenofovir. BLT humanized mice (n = 43) were rectally inoculated with either the primary isolate HIV-1(JRCSF) or the MSM-derived transmitted/founder (T/F) virus HIV-1(THRO) within 30 minutes following treatment with topical 1% tenofovir or vehicle. Under our experimental conditions, in the absence of drug treatment we observed 50% and 60% rectal transmission by HIV-1(JRCSF) and HIV-1(THRO), respectively. Topical tenofovir reduced rectal transmission to 8% (1/12; log rank p = 0.03) for HIV-1(JRCSF) and 0% (0/6; log rank p = 0.02) for HIV-1(THRO). This is the first demonstration that any human T/F HIV-1 rectally infects humanized mice and that transmission of the T/F virus can be efficiently blocked by rectally applied 1% tenofovir. These results obtained in BLT mice, along with recent ex vivo, Phase 1 trial and non-human primate reports, provide a critically important step forward in the development of tenofovir-based rectal microbicides

Enriching for correct prediction of biological processes using a combination of diverse classifiers

<p>Abstract</p> <p>Background</p> <p>Machine learning models (classifiers) for classifying genes to biological processes each have their own unique characteristics in what genes can be classified and to what biological processes. No single learning model is qualitatively superior to any other model and overall precision for each model tends to be low. The classification results for each classifier can be complementary and synergistic suggesting the benefit of a combination of algorithms, but often the prediction probability outputs of various learning models are neither comparable nor compatible for combining. A means to compare outputs regardless of the model and data used and combine the results into an improved comprehensive model is needed.</p> <p>Results</p> <p>Gene expression patterns from NCI's panel of 60 cell lines were used to train a Random Forest, a Support Vector Machine and a Neural Network model, plus two over-sampled models for classifying genes to biological processes. Each model produced unique characteristics in the classification results. We introduce the Precision Index measure (PIN) from the maximum posterior probability that allows assessing, comparing and combining multiple classifiers. The class specific precision measure (PIC) is introduced and used to select a subset of predictions across all classes and all classifiers with high precision. We developed a single classifier that combines the PINs from these five models in prediction and found that the PIN Combined Classifier (PINCom) significantly increased the number of correctly predicted genes over any single classifier. The PINCom applied to test genes that were not used in training also showed substantial improvement over any single model.</p> <p>Conclusions</p> <p>This paper introduces novel and effective ways of assessing predictions by their precision and recall plus a method that combines several machine learning models and capitalizes on synergy and complementation in class selection, resulting in higher precision and recall. Different machine learning models yielded incongruent results each of which were successfully combined into one superior model using the PIN measure we developed. Validation of the boosted predictions for gene functions showed the genes to be accurately predicted.</p

TRAIL receptor I (DR4) polymorphisms C626G and A683C are associated with an increased risk for hepatocellular carcinoma (HCC) in HCV-infected patients

<p>Abstract</p> <p>Background</p> <p>Tumour surveillance via induction of TRAIL-mediated apoptosis is a key mechanism, how the immune system prevents malignancy. To determine if gene variants in the TRAIL receptor I (<it>DR4</it>) gene affect the risk of hepatitis C virus (HCV)-induced liver cancer (HCC), we analysed <it>DR4 </it>mutations C626G (rs20575) and A683C (rs20576) in HCV-infected patients with and without HCC.</p> <p>Methods</p> <p>Frequencies of <it>DR4 </it>gene polymorphisms were determined by LightSNiP assays in 159 and 234 HCV-infected patients with HCC and without HCC, respectively. 359 healthy controls served as reference population.</p> <p>Results</p> <p>Distribution of C626G and A683C genotypes were not significantly different between healthy controls and HCV-positive patients without HCC. <it>DR4 </it>variants 626C and 683A occurred at increased frequencies in patients with HCC. The risk of HCC was linked to carriage of the 626C allele and the homozygous 683AA genotype, and the simultaneous presence of the two risk variants was confirmed as independent HCC risk factor by Cox regression analysis (Odds ratio 1.975, 95% CI 1.205-3.236; p = 0.007). Furthermore HCV viral loads were significantly increased in patients who simultaneously carried both genetic risk factors (2.69 ± 0.36 × 10⁶ IU/ml vs. 1.81 ± 0.23 × 10⁶ IU/ml, p = 0.049).</p> <p>Conclusions</p> <p>The increased prevalence of patients with a 626C allele and the homozygous 683AA genotype in HCV-infected patients with HCC suggests that these genetic variants are a risk factor for HCC in chronic hepatitis C.</p

Comparative Study Of The Influence Of Natural Convection On Directional Solidification Of Al-3.5 Wt% Ni And Al-7 Wt% Si Alloys

We present numerical simulations of thermosolutal convection for directional solidification of Al-3.5 wt% Ni and Al-7 wt% Si. Numerical results predict that fragmentation of dendrite arms resulting from dissolution could be favored in Al-7 wt% Si, but not in Al-3.5 wt% Ni. Corresponding experiments are in qualitative agreement with the numerical predictions. Distinguishing the two fragmentation mechanisms, namely dissolution and remelting, is critical during experiments on earth, when fluid flow is dominant. (C) 2007 COSPAR. Published by Elsevier Ltd. All rights reserved

Phosphorus removal from eutrophic waters with an aluminium hybrid nanocomposite

An excess of phosphorus (P) is the most common cause of eutrophication of freshwater bodies. Thus, it is imperative to reduce the concentration of P to prevent harmful algal blooms. Moreover, recovery of P has been gaining importance because its natural source will be exhausted in the near future. Therefore, the present work investigated the removal and recovery of phosphate from water using a newly developed hybrid nanocomposite containing aluminium nanoparticles (HPN). The HPN-Pr removes 0.80 ± 0.01 mg P/g in a pH interval between 2.0 and 6.5. The adsorption mechanism was described by a Freundlich adsorption model. The material presented good selectivity for phosphate and can be regenerated using an HCl dilute solution. The factors that contribute most to the attractiveness of HPN-Pr as a phosphate sorbent are its moderate removal capacity, feasible production at industrial scale, reuse after regeneration and recovery of phosphate.The authors acknowledge the Foundation for Science and Technology (FCT) Project SFRH/BD/39085/2007 for the financial support

Conditions for the Evolution of Gene Clusters in Bacterial Genomes

Genes encoding proteins in a common pathway are often found near each other along bacterial chromosomes. Several explanations have been proposed to account for the evolution of these structures. For instance, natural selection may directly favour gene clusters through a variety of mechanisms, such as increased efficiency of coregulation. An alternative and controversial hypothesis is the selfish operon model, which asserts that clustered arrangements of genes are more easily transferred to other species, thus improving the prospects for survival of the cluster. According to another hypothesis (the persistence model), genes that are in close proximity are less likely to be disrupted by deletions. Here we develop computational models to study the conditions under which gene clusters can evolve and persist. First, we examine the selfish operon model by re-implementing the simulation and running it under a wide range of conditions. Second, we introduce and study a Moran process in which there is natural selection for gene clustering and rearrangement occurs by genome inversion events. Finally, we develop and study a model that includes selection and inversion, which tracks the occurrence and fixation of rearrangements. Surprisingly, gene clusters fail to evolve under a wide range of conditions. Factors that promote the evolution of gene clusters include a low number of genes in the pathway, a high population size, and in the case of the selfish operon model, a high horizontal transfer rate. The computational analysis here has shown that the evolution of gene clusters can occur under both direct and indirect selection as long as certain conditions hold. Under these conditions the selfish operon model is still viable as an explanation for the evolution of gene clusters

Patient-physician mistrust and violence against physicians in Guangdong Province, China: a qualitative study.

OBJECTIVE: To better understand the origins, manifestations and current policy responses to patient-physician mistrust in China. DESIGN: Qualitative study using in-depth interviews focused on personal experiences of patient-physician mistrust and trust. SETTING: Guangdong Province, China. PARTICIPANTS: One hundred and sixty patients, patient family members, physicians, nurses and hospital administrators at seven hospitals varying in type, geography and stages of achieving goals of health reform. These interviews included purposive selection of individuals who had experienced both trustful and mistrustful patient-physician relationships. RESULTS: One of the most prominent forces driving patient-physician mistrust was a patient perception of injustice within the medical sphere, related to profit mongering, knowledge imbalances and physician conflicts of interest. Individual physicians, departments and hospitals were explicitly incentivised to generate revenue without evaluation of caregiving. Physicians did not receive training in negotiating medical disputes or humanistic principles that underpin caregiving. Patient-physician mistrust precipitated medical disputes leading to the following outcomes: non-resolution with patient resentment towards physicians; violent resolution such as physical and verbal attacks against physicians; and non-violent resolution such as hospital-mediated dispute resolution. Policy responses to violence included increased hospital security forces, which inadvertently fuelled mistrust. Instead of encouraging communication that facilitated resolution, medical disputes sometimes ignited a vicious cycle leading to mob violence. However, patient-physician interactions at one hospital that has implemented a primary care model embodying health reform goals showed improved patient-physician trust. CONCLUSIONS: The blind pursuit of financial profits at a systems level has eroded patient-physician trust in China. Restructuring incentives, reforming medical education and promoting caregiving are pathways towards restoring trust. Assessing and valuing the quality of caregiving is essential for transitioning away from entrenched profit-focused models. Moral, in addition to regulatory and legal, responses are urgently needed to restore trust