Genetic Variation in Spatio-Temporal Confined USA300 Community-Associated MRSA Isolates: A Shift from Clonal Dispersion to Genetic Evolution?

NTRODUCTION: Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) are increasingly isolated, with USA300-0114 being the predominant clone in the USA. Comparative whole genome sequencing of USA300 isolates collected in 2002, 2003 and 2005 showed a limited number of single nucleotide polymorphisms and regions of difference. This suggests that USA300 has undergone rapid clonal expansion without great genomic diversification. However, whole genome comparison of CA-MRSA has been limited to isolates belonging to USA300. The aim of this study was to compare the genetic repertoire of different CA-MRSA clones with that of HA-MRSA from the USA and Europe through comparative genomic hybridization (CGH) to identify genetic clues that may explain the successful and rapid emergence of CA-MRSA. MATERIALS AND METHODS: Hierarchical clustering based on CGH of 48 MRSA isolates from the community and nosocomial infections from Europe and the USA revealed dispersed clustering of the 19 CA-MRSA isolates. This means that these 19 CA-MRSA isolates do not share a unique genetic make-up. Only the PVL genes were commonly present in all CA-MRSA isolates. However, 10 genes were variably present among 14 USA300 isolates. Most of these genes were present on mobile elements. CONCLUSION: The genetic variation present among the 14 USA300 isolates is remarkable considering the fact that the isolates were recovered within one month and originated from a confined geographic area, suggesting continuous evolution of this clone

Integrating Knowledge Graphs for Analysing Academia and Industry Dynamics

Academia and industry are constantly engaged in a joint effort for producing scientific knowledge that will shape the society of the future. Analysing the knowledge flow between them and understanding how they influence each other is a critical task for researchers, governments, funding bodies, investors, and companies. However, current corpora are unfit to support large-scale analysis of the knowledge flow between academia and industry since they lack of a good characterization of research topics and industrial sectors. In this short paper, we introduce the Academia/Industry DynAmics (AIDA) Knowledge Graph, which characterizes 14M papers and 8M patents according to the research topics drawn from the Computer Science Ontology. 4M papers and 5M patents are also classified according to the type of the author's affiliations (academy, industry, or collaborative) and 66 industrial sectors (e.g., automotive, financial, energy, electronics) obtained from DBpedia. AIDA was generated by an automatic pipeline that integrates several knowledge graphs and bibliographic corpora, including Microsoft Academic Graph, Dimensions, English DBpedia, the Computer Science Ontology, and the Global Research Identifier Database

Social epidemiology of the Mediterranean-dietary approaches to stop hypertension intervention for neurodegenerative delay (MIND) diet among early adolescents: the Adolescent Brain Cognitive Development Study

BackgroundThe purpose of our study was to understand the relationship between sociodemographic factors and adherence to the MIND (Mediterranean-DASH [Dietary Approaches to Stop Hypertension] Intervention for Neurodegenerative Delay) diet in a demographically diverse national population-based sample of 9-12-year-olds in the US.MethodsWe analyzed data from the Adolescent Brain and Cognitive Development (ABCD) Study (Year 1, N = 8333). Multivariable linear regression analysis was used to identify associations between MIND diet score and sociodemographic factors, including race/ethnicity, household income, parent education level, age, sex, and sexual minority status.ResultsCompared to White adolescents, Latino adolescents showed the greatest adherence to the MIND diet. Boys had lower adherence to the MIND diet than girls. Lower household income was associated with lower adherence to the MIND diet. Older age was associated with lower adherence to the MIND diet. Sexual minorities had a lower adherence to the MIND diet when compared to their heterosexual counterparts.DiscussionFemale sex, Latino ethnicity, Asian and Black race, high household income, heterosexual sexual orientation, and younger age were associated with higher adherence to the MIND diet. These sociodemographic differences can inform targeted screening and counseling for clinicians and public health organizations among diverse adolescent populations.Impact statementSociodemographic disparities in diet quality have been documented, but none have explored adherence to the MIND (Mediterranean-DASH [Dietary Approaches to Stop Hypertension] Intervention for Neurodegenerative Delay) diet in early adolescence. In this demographically diverse sample of 9-12-year-old early adolescents in the U.S., we found notable and nuanced sociodemographic disparities in adherence to the MIND diet. Sociodemographic factors associated with higher adherence to the MIND diet included female sex, Latino ethnicity, high household income, heterosexual sexual orientation, and younger age

ResearchFlow: Understanding the Knowledge Flow between Academia and Industry

Understanding, monitoring, and predicting the flow of knowledge between academia and industry is of critical importance for a variety of stakeholders, including governments, funding bodies, researchers, investors, and companies. To this purpose, we introduce ResearchFlow, an approach that integrates semantic technologies and machine learning to quantifying the diachronic behaviour of research topics across academia and industry. ResearchFlow exploits the novel Academia/Industry DynAmics (AIDA) Knowledge Graph in order to characterize each topic according to the frequency in time of the related i) publications from academia, ii) publications from industry, iii) patents from academia, and iv) patents from industry. This representation is then used to produce several analytics regarding the academia/industry knowledge flow and to forecast the impact of research topics on industry. We applied ResearchFlow to a dataset of 3.5M papers and 2M patents in Computer Science and highlighted several interesting patterns. We found that 89.8% of the topics first emerge in academic publications, which typically precede industrial publications by about 5.6 years and industrial patents by about 6.6 years. However this does not mean that academia always dictates the research agenda. In fact, our analysis also shows that industrial trends tend to influence academia more than academic trends affect industry. We evaluated ResearchFlow on the task of forecasting the impact of research topics on the industrial sector and found that its granular characterization of topics improves significantly the performance with respect to alternative solutions

Comparative risk judgements for oral health hazards among Norwegian adults: a cross sectional study

BACKGROUND: This study identified optimistic biases in health and oral health hazards, and explored whether comparative risk judgements for oral health hazards vary systematically with socio-economic characteristics and self-reported risk experience. METHODS: A simple random sample of 1,190 residents born in 1972 was drawn from the population resident in three counties of Norway. A total of 735 adults (51% women) completed postal questionnaires at home. RESULTS: Mean ratings of comparative risk judgements differed significantly (p < 0.001) from the mid point of the scales. T-values ranged from -13.1 and -12.1 for the perceived risk of being divorced and loosing all teeth to -8.2 and -7.8 (p < 0.001) for having gum disease and toothdecay. Multivariate analyses using General Linear Models, GLM, revealed gender differences in comparative risk judgements for gum disease, whereas social position varied systematically with risk judgements for tooth decay, gum disease and air pollution. The odds ratios for being comparatively optimistic with respect to having gum disease were 2.9, 1.9, 1.8 and 1.5 if being satisfied with dentition, having a favourable view of health situation, and having high and low involvement with health enhancing and health detrimental behaviour, respectively. CONCLUSION: Optimism in comparative judgements for health and oral health hazards was evident in young Norwegian adults. When judging their comparative susceptibility for oral health hazards, they consider personal health situation and risk behaviour experience

Should patients with abnormal liver function tests in primary care be tested for chronic viral hepatitis: cost minimisation analysis based on a comprehensively tested cohort

Background Liver function tests (LFTs) are ordered in large numbers in primary care, and the Birmingham and Lambeth Liver Evaluation Testing Strategies (BALLETS) study was set up to assess their usefulness in patients with no pre-existing or self-evident liver disease. All patients were tested for chronic viral hepatitis thereby providing an opportunity to compare various strategies for detection of this serious treatable disease. Methods This study uses data from the BALLETS cohort to compare various testing strategies for viral hepatitis in patients who had received an abnormal LFT result. The aim was to inform a strategy for identification of patients with chronic viral hepatitis. We used a cost-minimisation analysis to define a base case and then calculated the incremental cost per case detected to inform a strategy that could guide testing for chronic viral hepatitis. Results Of the 1,236 study patients with an abnormal LFT, 13 had chronic viral hepatitis (nine hepatitis B and four hepatitis C). The strategy advocated by the current guidelines (repeating the LFT with a view to testing for specific disease if it remained abnormal) was less efficient (more expensive per case detected) than a simple policy of testing all patients for viral hepatitis without repeating LFTs. A more selective strategy of viral testing all patients for viral hepatitis if they were born in countries where viral hepatitis was prevalent provided high efficiency with little loss of sensitivity. A notably high alanine aminotransferase (ALT) level (greater than twice the upper limit of normal) on the initial ALT test had high predictive value, but was insensitive, missing half the cases of viral infection. Conclusions Based on this analysis and on widely accepted clinical principles, a "fast and frugal" heuristic was produced to guide general practitioners with respect to diagnosing cases of viral hepatitis in asymptomatic patients with abnormal LFTs. It recommends testing all patients where a clear clinical indication of infection is present (e.g. evidence of intravenous drug use), followed by testing all patients who originated from countries where viral hepatitis is prevalent, and finally testing those who have a notably raised ALT level (more than twice the upper limit of normal). Patients not picked up by this efficient algorithm had a risk of chronic viral hepatitis that is lower than the general population

Stationary Black Holes: Uniqueness and Beyond

The spectrum of known black-hole solutions to the stationary Einstein equations has been steadily increasing, sometimes in unexpected ways. In particular, it has turned out that not all black-hole-equilibrium configurations are characterized by their mass, angular momentum and global charges. Moreover, the high degree of symmetry displayed by vacuum and electro-vacuum black-hole spacetimes ceases to exist in self-gravitating non-linear field theories. This text aims to review some developments in the subject and to discuss them in light of the uniqueness theorem for the Einstein-Maxwell system.Comment: Major update of the original version by Markus Heusler from 1998. Piotr T. Chru\'sciel and Jo\~ao Lopes Costa succeeded to this review's authorship. Significantly restructured and updated all sections; changes are too numerous to be usefully described here. The number of references increased from 186 to 32

A new nail with a locking blade for complex proximal humeral fractures

INTRODUCTION: The objective of this study was to assess the clinical outcome of displaced proximal humerus fracture treated with a new locking blade nail. MATERIALS AND METHODS: This prospective study included a series of 92 patients with acute fracture of the proximal humerus treated in one hospital level I trauma centre with locking blade nail between December 2010 and December 2013. According to the Neer classification, all fractures were two- to four-part fractures. Age adopted Constant score, DASH and visual analogue scores were used as outcome measures. RESULTS: A total of 92 patients were enrolled in the study. However, 29 patients were excluded due to loss to follow-up and death. Ultimately, 63 patients were available for final follow-up and data analysis. The mean duration of follow-up was 22 months (range 16–48 months). On average at 1 year, all fractures had united. The mean weighted Constant score was 84.2 % and the median disabilities of the arm, shoulder and hand (DASH) score was 26, the range of elevation was 115 and range of abduction was 97. The head shaft angle was 130, and pain visual analogue was 1.6. We found that 5 of the 63 patients (8 %) demonstrated complications. Two patients (3 %) displayed secondary displacement and require device removal. Two patients (3 %) had impingement due to prominent metal work, and one patient had a superficial wound infection which was treated with a course of antibiotics. CONCLUSION: Our study shows excellent results with new locking blade nail for displaced proximal humerus fractures. We think the locking blade nail offers stiff triangular fixation of the head fragment and support of the medial calcar region to prevent secondary varus collapse. LEVEL OF EVIDENCE: III

Characterizing genomic alterations in cancer by complementary functional associations.

Systematic efforts to sequence the cancer genome have identified large numbers of mutations and copy number alterations in human cancers. However, elucidating the functional consequences of these variants, and their interactions to drive or maintain oncogenic states, remains a challenge in cancer research. We developed REVEALER, a computational method that identifies combinations of mutually exclusive genomic alterations correlated with functional phenotypes, such as the activation or gene dependency of oncogenic pathways or sensitivity to a drug treatment. We used REVEALER to uncover complementary genomic alterations associated with the transcriptional activation of β-catenin and NRF2, MEK-inhibitor sensitivity, and KRAS dependency. REVEALER successfully identified both known and new associations, demonstrating the power of combining functional profiles with extensive characterization of genomic alterations in cancer genomes