Compositional Satisfiability Solving in Separation Logic

We introduce a novel decision procedure to the satisfiability problem in array separation logic combined with general inductively defined predicates and arithmetic. Our proposal differentiates itself from existing works by solving satisfiability through compositional reasoning. First, following Fermat’s method of infinite descent, it infers for every inductive definition a “base” that precisely characterises the satisfiability. It then utilises the base to derive such a base for any formula where these inductive predicates reside in. Especially, we identify an expressive decidable fragment for the compositionality. We have implemented the proposal in a tool and evaluated it over challenging problems. The experimental results show that the compositional satisfiability solving is efficient and our tool is effective and efficient when compared with existing solvers

Epileptogenic potential of mefloquine chemoprophylaxis: a pathogenic hypothesis

<p>Abstract</p> <p>Background</p> <p>Mefloquine has historically been considered safe and well-tolerated for long-term malaria chemoprophylaxis, but prescribing it requires careful attention in order to rule out contraindications to its use. Contraindications include a history of certain neurological conditions that might increase the risk of seizure and other adverse events. The precise pathophysiological mechanism by which mefloquine might predispose those with such a history to seizure remains unclear.</p> <p>Presentation of the hypothesis</p> <p>Studies have demonstrated that mefloquine at doses consistent with chemoprophylaxis accumulates at high levels in brain tissue, which results in altered neuronal calcium homeostasis, altered gap-junction functioning, and contributes to neuronal cell death. This paper reviews the scientific evidence associating mefloquine with alterations in neuronal function, and it suggests the novel hypothesis that among those with the prevalent EPM1 mutation, inherited and mefloquine-induced impairments in neuronal physiologic safeguards might increase risk of GABAergic seizure during mefloquine chemoprophylaxis.</p> <p>Testing and implications of the hypothesis</p> <p>Consistent with case reports of tonic-clonic seizures occurring during mefloquine chemoprophylaxis among those with family histories of epilepsy, it is proposed here that a new contraindication to mefloquine use be recognized for people with EPM1 mutation and for those with a personal history of myoclonus or ataxia, or a family history of degenerative neurologic disorder consistent with EPM1. Recommendations and directions for future research are presented.</p

High prevalence of vitamin D insufficiency and its association with obesity and metabolic syndrome among Malay adults in Kuala Lumpur, Malaysia

Background: Vitamin D status, as indicated by 25-hydroxyvitamin D is inversely associated with adiposity, glucose homeostasis, lipid profiles, and blood pressure along with its classic role in calcium homeostasis and bone metabolism. It is also shown to be inversely associated with metabolic syndrome and cardiovascular diseases in western populations. However, evidence from the Asian population is limited. Therefore, we aim to study the prevalence of vitamin D insufficiency (< 50 nmol/L) and the association of 25-hydroxyvitamin D with metabolic risk factors among an existing Malay cohort in Kuala Lumpur. Methods: This is an analytical cross sectional study. A total of 380 subjects were sampled and their vitamins D status (25-hydroxyvitamin D), fasting blood glucose, full lipid profile were assessed using venous blood. Systolic and diastolic blood pressure, weight, height and waist circumference were measured following standard protocols. Socio-demographic data such as sex, age, smoking status etc were also collected. Data was analysed using t-test, chi-square test, General Linear Model and multiple logistic regression. Results: Females made up 58 of the sample. The mean age of respondents was 48.5 (SD 5.2) years. Females had significantly lower mean Vitamin D levels (36.2; 95 CI: 34.5, 38.0 nmol/L) compared to males (56.2; 95 CI: 53.2, 59.2 nmol/L). Approximately 41 and 87 of males and females respectively had insufficient (< 50 nmol/L) levels of 25-hydroxyvitamin D (p < 0.001). The prevalence of Metabolic Syndrome for the whole sample was 38.4 (95 CI: 33.5, 43.3). In the multivariate model (adjusted for age, sex, abdominal obesity, HDL-cholesterol, diastolic blood pressure), insufficient Vitamin D status was significantly associated with 1-year age increments (OR: 0.93; 95 CI: 0.88, 0.98), being female (OR: 8.68; 95 CI: 5.08, 14.83) and abdominal obesity (OR: 2.57; 95 CI: 1.51, 4.39). Respondents with insufficient vitamin D were found to have higher odds of having Metabolic Syndrome (OR: 1.73; 95 CI: 1.02, 2.92) after adjusting for age and sex. Conclusions: Our results highlight the high prevalence of vitamin D insufficiency among Malay adults in Kuala Lumpur. Vitamin D insufficiency is independently associated with younger age, female sex and greater abdominal obesity. Vitamin D insufficiency is also associated with Metabolic Syndrome

Phenotype Recognition with Combined Features and Random Subspace Classifier Ensemble

<p>Abstract</p> <p>Background</p> <p>Automated, image based high-content screening is a fundamental tool for discovery in biological science. Modern robotic fluorescence microscopes are able to capture thousands of images from massively parallel experiments such as RNA interference (RNAi) or small-molecule screens. As such, efficient computational methods are required for automatic cellular phenotype identification capable of dealing with large image data sets. In this paper we investigated an efficient method for the extraction of quantitative features from images by combining second order statistics, or Haralick features, with curvelet transform. A random subspace based classifier ensemble with multiple layer perceptron (MLP) as the base classifier was then exploited for classification. Haralick features estimate image properties related to second-order statistics based on the grey level co-occurrence matrix (GLCM), which has been extensively used for various image processing applications. The curvelet transform has a more sparse representation of the image than wavelet, thus offering a description with higher time frequency resolution and high degree of directionality and anisotropy, which is particularly appropriate for many images rich with edges and curves. A combined feature description from Haralick feature and curvelet transform can further increase the accuracy of classification by taking their complementary information. We then investigate the applicability of the random subspace (RS) ensemble method for phenotype classification based on microscopy images. A base classifier is trained with a RS sampled subset of the original feature set and the ensemble assigns a class label by majority voting.</p> <p>Results</p> <p>Experimental results on the phenotype recognition from three benchmarking image sets including HeLa, CHO and RNAi show the effectiveness of the proposed approach. The combined feature is better than any individual one in the classification accuracy. The ensemble model produces better classification performance compared to the component neural networks trained. For the three images sets HeLa, CHO and RNAi, the Random Subspace Ensembles offers the classification rates 91.20%, 98.86% and 91.03% respectively, which compares sharply with the published result 84%, 93% and 82% from a multi-purpose image classifier WND-CHARM which applied wavelet transforms and other feature extraction methods. We investigated the problem of estimation of ensemble parameters and found that satisfactory performance improvement could be brought by a relative medium dimensionality of feature subsets and small ensemble size.</p> <p>Conclusions</p> <p>The characteristics of curvelet transform of being multiscale and multidirectional suit the description of microscopy images very well. It is empirically demonstrated that the curvelet-based feature is clearly preferred to wavelet-based feature for bioimage descriptions. The random subspace ensemble of MLPs is much better than a number of commonly applied multi-class classifiers in the investigated application of phenotype recognition.</p

PTSD, depression and anxiety among former abductees in Northern Uganda

<p>Abstract</p> <p>Background</p> <p>The population in Northern Uganda has been exposed to extreme levels of traumatic stress and thousands abducted forcibly became rebel combatants.</p> <p>Methods</p> <p>Using structured interviews, the prevalence and severity of posttraumatic stress disorder (PTSD), depression and anxiety was assessed in 72 former abducted adults, 62 of them being former child soldiers.</p> <p>Results</p> <p>As retrospective reports of exposure to traumatic stress increased, anxiety and PTSD occurrence increased (r = .45). 49% of respondents were diagnosed with PTSD, 70% presented with symptoms of depression, and 59% with those of anxiety. In a multiple linear regression analysis four factors could best explain the development of PTSD symptoms: male respondents (sex) living in an IDP-Camp (location) with a kinship murdered in the war (family members killed in the war) and having experienced a high number of traumatic events (number of traumatic events) were more likely to develop symptoms of PTSD than others. In disagreement to a simple dose-response-effect though, we also observed a negative correlation between the time spent with the rebels and the PTSD symptom level.</p> <p>Conclusions</p> <p>Former abductees continue to suffer from severe mental ill-health. Adaptation to the living condition of rebels, however, may lower trauma-related mental suffering.</p

Activation and modulation of antiviral and apoptotic genes in pigs infected with classical swine fever viruses of high, moderate or low virulence

The immune response to CSFV and the strategies of this virus to evade and suppress the pigs’ immune system are still poorly understood. Therefore, we investigated the transcriptional response in the tonsils, median retropharyngeal lymph node (MRLN), and spleen of pigs infected with CSFV strains of similar origin with high, moderate, and low virulence. Using a porcine spleen/intestinal cDNA microarray, expression levels in RNA pools prepared from infected tissue at 3 dpi (three pigs per virus strain) were compared to levels in pools prepared from uninfected homologue tissues (nine pigs). A total of 44 genes were found to be differentially expressed. The genes were functionally clustered in six groups: innate and adaptive immune response, interferon-regulated genes, apoptosis, ubiquitin-mediated proteolysis, oxidative phosphorylation and cytoskeleton. Significant up-regulation of three IFN-γ-induced genes in the MRLNs of pigs infected with the low virulence strain was the only clear qualitative difference in gene expression observed between the strains with high, moderate and low virulence. Real-time PCR analysis of four response genes in all individual samples largely confirmed the microarray data at 3 dpi. Additional PCR analysis of infected tonsil, MRLN, and spleen samples collected at 7 and 10 dpi indicated that the strong induction of expression of the antiviral response genes chemokine CXCL10 and 2′–5′ oligoadenylate synthetase 2, and of the TNF-related apoptosis-inducing ligand (TRAIL) gene at 3 dpi, decreased to lower levels at 7 and 10 dpi. For the highly and moderately virulent strains, this decrease in antiviral and apoptotic gene expression coincided with higher levels of virus in these immune tissues

Ab Initio Identification of Novel Regulatory Elements in the Genome of Trypanosoma brucei by Bayesian Inference on Sequence Segmentation

Background: The rapid increase in the availability of genome information has created considerable demand for both comparative and ab initio predictive bioinformatic analyses. The biology laid bare in the genomes of many organisms is often novel, presenting new challenges for bioinformatic interrogation. A paradigm for this is the collected genomes of the kinetoplastid parasites, a group which includes Trypanosoma brucei the causative agent of human African trypanosomiasis. These genomes, though outwardly simple in organisation and gene content, have historically challenged many theories for gene expression regulation in eukaryotes. Methodology/Principle Findings: Here we utilise a Bayesian approach to identify local changes in nucleotide composition in the genome of T. brucei. We show that there are several elements which are found at the starts and ends of multicopy gene arrays and that there are compositional elements that are common to all intergenic regions. We also show that there is a composition-inversion element that occurs at the position of the trans-splice site. Conclusions/Significance: The nature of the elements discovered reinforces the hypothesis that context dependant RN

Interventions aimed at increasing research use in nursing: a systematic review

<p>Abstract</p> <p>Background</p> <p>There has been considerable interest recently in developing and evaluating interventions to increase research use by clinicians. However, most work has focused on medical practices; and nursing is not well represented in existing systematic reviews. The purpose of this article is to report findings from a systematic review of interventions aimed at increasing research use in nursing.</p> <p>Objective</p> <p>To assess the evidence on interventions aimed at increasing research use in nursing.</p> <p>Methods</p> <p>A systematic review of research use in nursing was conducted using databases (Medline, CINAHL, Healthstar, ERIC, Cochrane Central Register of Controlled Trials, and Psychinfo), grey literature, ancestry searching (Cochrane Database of Systematic Reviews), key informants, and manual searching of journals. Randomized controlled trials and controlled before- and after-studies were included if they included nurses, if the intervention was explicitly aimed at increasing research use or evidence-based practice, and if there was an explicit outcome to research use. Methodological quality was assessed using pre-existing tools. Data on interventions and outcomes were extracted and categorized using a pre-established taxonomy.</p> <p>Results</p> <p>Over 8,000 titles were screened. Three randomized controlled trials and one controlled before- and after-study met the inclusion criteria. The methodological quality of included studies was generally low. Three investigators evaluated single interventions. The most common intervention was education. Investigators measured research use using a combination of surveys (three studies) and compliance with guidelines (one study). Researcher-led educational meetings were ineffective in two studies. Educational meetings led by a local opinion leader (one study) and the formation of multidisciplinary committees (one study) were both effective at increasing research use.</p> <p>Conclusion</p> <p>Little is known about how to increase research use in nursing, and the evidence to support or refute specific interventions is inconclusive. To advance the field, we recommend that investigators: (1) use theoretically informed interventions to increase research use, (2) measure research use longitudinally using theoretically informed and psychometrically sound measures of research use, as well as, measuring patient outcomes relevant to the intervention, and (3) use more robust and methodologically sound study designs to evaluate interventions. If investigators aim to establish a link between using research and improved patient outcomes they must first identify those interventions that are effective at increasing research use.</p