Exploiting Conceptual Modeling for Searching Genomic Metadata: A Quantitative and Qualitative Empirical Study

Providing a common data model for the metadata of several heterogenous genomic data sources is hard, as they do not share any standard or agreed practice for metadata description. Two years ago we managed to discover a subset of common metadata present in most sources and to organize it as a smart genomic conceptual model (GCM); the model has been instrumental to our efforts in the development of a major software pipeline for data integration. More recently, we developed a user-friendly search interface, based on a simplified version of GCM. In this paper, we report our evaluation of the effectiveness of this new user interface. Specifically, we present the results of a compendious empirical study to answer the research question: How much is such a simple interface well-understood by a standard user? The target of this study is a mixed population, composed by biologists, bioinformaticians and computer scientists. The result of our empirical study shows that the users were successful in producing search queries starting from their natural language description, as they did it with good accuracy and small error rate. The study also shows that most users were generally satisfied; it provides indications on how to improve our search system and how to continue our effort in integration of genomic sources. We are consequently adapting the user interface, that will be soon opened to public use

Hypoxia Alters Cell Cycle Regulatory Protein Expression and Induces Premature Maturation of Oligodendrocyte Precursor Cells

Periventricular white matter injury (PWMI) is a common form of brain injury sustained by preterm infants. A major factor that predisposes to PWMI is hypoxia. Because oligodendrocytes (OLs) are responsible for myelination of axons, abnormal OL development or function may affect brain myelination. At present our understanding of the influences of hypoxia on OL development is limited. To examine isolated effects of hypoxia on OLs, we examined the influences of hypoxia on OL development in vitro.Cultures of oligodendrocyte precursor cells (OPCs) were prepared from mixed glial cultures and were 99% pure. OPCs were maintained at 21% O(2) or hypoxia (1% or 4% O(2)) for up to 7 days. We observed that 1% O(2) lead to an increase in the proportion of myelin basic protein (MBP)-positive OLs after 1 week in culture, and a decrease in the proportion of platelet-derived growth factor receptor alpha (PDGFRalpha)-positive cells suggesting premature OL maturation. Increased expression of the cell cycle regulatory proteins p27(Kip1) and phospho-cdc2, which play a role in OL differentiation, was seen as well.These results show that hypoxia interferes with the normal process of OL differentiation by inducing premature OPC maturation

Discussing life expectancy with surgical patients: Do patients want to know and how should this information be delivered?

<p>Abstract</p> <p>Background</p> <p>Predicted patient life expectancy (LE) and survival probability (SP), based on a patient's medical history, are important components of surgical decision-making and informed consent. The objective of this study was to assess patients' interpretation of and desire to know information relating to LE, in addition to establishing the most effective format for discussion.</p> <p>Methods</p> <p>A cross sectional survey of 120 patients (mean age = 68.7 years, range 50–90 years), recruited from general urological and surgical outpatient clinics in one District General and one Teaching hospital in Southwest England (UK) was conducted. Patients were included irrespective of their current diagnosis or associated comorbidity. Hypothetical patient case scenarios were used to assess patients' desire to know LE and SP, in addition to their preferred presentation format.</p> <p>Results</p> <p>58% of patients expressed a desire to know their LE and SP, if it were possible to calculate, with 36% not wishing to know either. Patients preferred a combination of numerical and pictorial formats in discussing LE and SP, with numerical, verbal and pictorial formats alone least preferred. 71% patients ranked the survival curve as either their first or second most preferred graph, with 76% rating facial figures their least preferred. No statistically significant difference was noted between sexes or educational backgrounds.</p> <p>Conclusion</p> <p>A proportion of patients seem unwilling to discuss their LE and SP. This may relate to their current diagnosis, level of associated comorbidity or degree of understanding. However it is feasible that by providing this information in a range of presentation formats, greater engagement in the shared decision-making process can be encouraged.</p

Three-dimensional coherent X-ray diffraction imaging of a ceramic nanofoam: determination of structural deformation mechanisms

Ultra-low density polymers, metals, and ceramic nanofoams are valued for their high strength-to-weight ratio, high surface area and insulating properties ascribed to their structural geometry. We obtain the labrynthine internal structure of a tantalum oxide nanofoam by X-ray diffractive imaging. Finite element analysis from the structure reveals mechanical properties consistent with bulk samples and with a diffusion limited cluster aggregation model, while excess mass on the nodes discounts the dangling fragments hypothesis of percolation theory.Comment: 8 pages, 5 figures, 30 reference

D3-D7 Quark-Gluon Plasmas at Finite Baryon Density

We present the string dual to SU(Nc) N=4 SYM, coupled to Nf massless fundamental flavors, at finite temperature and baryon density. The solution is determined by two dimensionless parameters, both depending on the 't Hooft coupling $\lambda_h$ at the scale set by the temperature T: $\epsilon_h\sim\lambda_h Nf/Nc$, weighting the backreaction of the flavor fields and $\tilde\delta\sim\lambda_h^{-1/2}nb/(Nf T^3)$, where $nb$ is the baryon density. For small values of these two parameters the solution is given analytically up to second order. We study the thermodynamics of the system in the canonical and grand-canonical ensembles. We then analyze the energy loss of partons moving through the plasma, computing the jet quenching parameter and studying its dependence on the baryon density. Finally, we analyze certain "optical" properties of the plasma. The whole setup is generalized to non abelian strongly coupled plasmas engineered on D3-D7 systems with D3-branes placed at the tip of a generic singular Calabi-Yau cone. In all the cases, fundamental matter fields are introduced by means of homogeneously smeared D7-branes and the flavor symmetry group is thus a product of abelian factors.Comment: 27 pages; v2: 29 pages, 1 (new) figure, new section 4.4 on optical properties, references, comments added; v3: eq. (3.19), comments and a reference adde

Interneuron Development Is Disrupted in Preterm Brains With Diffuse White Matter Injury: Observations in Mouse and Human

Preterm brain injury, occurring in approximately 30% of infants born <32 weeks gestational age, is associated with an increased risk of neurodevelopmental disorders, such as autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD). The mechanism of gray matter injury in preterm born children is unclear and likely to be multifactorial; however, inflammation, a high predictor of poor outcome in preterm infants, has been associated with disrupted interneuron maturation in a number of animal models. Interneurons are important for regulating normal brain development, and disruption in interneuron development, and the downstream effects of this, has been implicated in the etiology of neurodevelopmental disorders. Here, we utilize postmortem tissue from human preterm cases with or without diffuse white matter injury (WMI; PMA range: 23+2 to 28+1 for non-WMI group, 26+6 to 30+0 for WMI group, p = 0.002) and a model of inflammation-induced preterm diffuse white matter injury (i.p. IL-1β, b.d., 10 μg/kg/injection in male CD1 mice from P1–5). Data from human preterm infants show deficits in interneuron numbers in the cortex and delayed growth of neuronal arbors at this early stage of development. In the mouse, significant reduction in the number of parvalbumin-positive interneurons was observed from postnatal day (P) 10. This decrease in parvalbumin neuron number was largely rectified by P40, though there was a significantly smaller number of parvalbumin positive cells associated with perineuronal nets in the upper cortical layers. Together, these data suggest that inflammation in the preterm brain may be a contributor to injury of specific interneuron in the cortical gray matter. This may represent a potential target for postnatal therapy to reduce the incidence and/or severity of neurodevelopmental disorders in preterm infants

A Trp33Arg Mutation at Exon 1 of the MYH9 Gene in a Korean Patient with May-Hegglin Anomaly

In this report, we describe a Korean patient with May-Hegglin anomaly from a mutation of the MYH9 gene. The proband was a 21-year-old man with thrombocytopenia. He did not have a bleeding tendency. His neutrophil count was normal at 7490/mm3; however, the neutrophils contained abnormal basophilic inclusions in their cytoplasm. The platelet count was decreased at 15000/mm3 with giant platelets. Coagulation test results were not remarkable. Direct sequencing of MYH9 revealed that he was heterozygous for a mutation in exon 1, which was a 97T>A substitution mutation affecting codon 33, substituting tryptophan with arginine (Trp33Arg). Family study showed that both of his parents had normal phenotype and genotypes, indicating a de novo occurrence of the mutation in the proband

Peer education: The effects on knowledge of pregnancy related malaria and preventive practices in women of reproductive age in Edo State, Nigeria

<p>Abstract</p> <p>Background</p> <p>There is limited uptake of measures to prevent malaria by pregnant women in Nigeria which is often related to the lack of knowledge on Malaria in Pregnancy (MIP) and its effects on mother and foetus. This study, explored peer to peer education as a tool in raising knowledge of MIP among women of child bearing age.</p> <p>Methods</p> <p>1105 women of child bearing age were interviewed in their households using a structured questionnaire about their knowledge of malaria in general, MIP and use of preventive measures. Thereafter, a peer education campaign was launched to raise the level of knowledge in the community. The interviews were repeated after the campaign and the responses between the pre- and post-intervention were compared.</p> <p>Results</p> <p>In the pre-assessment women on average answered 64.8% of the question on malaria and its possibility to prevent malaria correctly. The peer education campaign had a significant impact in raising the level of knowledge among the women; after the campaign the respondents answered on average 73.8% of the questions correctly. Stratified analysis on pre and post assessment scores for malaria in general (68.8 & 72.9%) and MIP (61.7 & 76.3%) showed also significant increase. Uptake of bed nets was reported to be low: 11.6%</p> <p>Conclusion</p> <p>Peer education led to a significant increase in knowledge of malaria and its prevention but we could not asses its influence on the use of preventive measures.</p