PADTUN - using semantic technologies in tunnel diagnosis and maintenance domain

YesA Decision Support System (DSS) in tunnelling domain deals with identifying pathologies based on disorders present in various tunnel portions and contextual factors affecting a tunnel. Another key area in diagnosing pathologies is to identify regions of interest (ROI). In practice, tunnel experts intuitively abstract regions of interest by selecting tunnel portions that are susceptible to the same types of pathologies with some distance approximation. This complex diagnosis process is often subjective and poorly scales across cases and transport structures. In this paper, we introduce PADTUN system, a working prototype of a DSS in tunnelling domain using semantic technologies. Ontologies are developed and used to capture tacit knowledge from tunnel experts. Tunnel inspection data are annotated with ontologies to take advantage of inferring capabilities offered by semantic technologies. In addition, an intelligent mechanism is developed to exploit abstraction and inference capabilities to identify ROI. PADTUN is developed in real-world settings offered by the NeTTUN EU Project and is applied in a tunnel diagnosis use case with Société Nationale des Chemins de Fer Français (SNCF), France. We show how the use of semantic technologies allows addressing the complex issues of pathology and ROI inferencing and matching experts’ expectations of decision support

Inspiratory muscle training reduces blood lactate concentration during volitional hyperpnoea

Although reduced blood lactate concentrations ([lac−]B) have been observed during whole-body exercise following inspiratory muscle training (IMT), it remains unknown whether the inspiratory muscles are the source of at least part of this reduction. To investigate this, we tested the hypothesis that IMT would attenuate the increase in [lac−]B caused by mimicking, at rest, the breathing pattern observed during high-intensity exercise. Twenty-two physically active males were matched for 85% maximal exercise minute ventilation (V˙Emax) and divided equally into an IMT or a control group. Prior to and following a 6 week intervention, participants performed 10 min of volitional hyperpnoea at the breathing pattern commensurate with 85% V˙Emax

NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR

Although the concepts of nonuniform sampling (NUS​​​​​​​) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge 4 decades ago (Bodenhausen and Ernst, 1981; Barna and Laue, 1987), it is only relatively recently that NUS has become more commonplace. Advantages of NUS include the ability to tailor experiments to reduce data collection time and to improve spectral quality, whether through detection of closely spaced peaks (i.e., “resolution”) or peaks of weak intensity (i.e., “sensitivity”). Wider adoption of these methods is the result of improvements in computational performance, a growing abundance and flexibility of software, support from NMR spectrometer vendors, and the increased data sampling demands imposed by higher magnetic fields. However, the identification of best practices still remains a significant and unmet challenge. Unlike the discrete Fourier transform, non-Fourier methods used to reconstruct spectra from NUS data are nonlinear, depend on the complexity and nature of the signals, and lack quantitative or formal theory describing their performance. Seemingly subtle algorithmic differences may lead to significant variabilities in spectral qualities and artifacts. A community-based critical assessment of NUS challenge problems has been initiated, called the “Nonuniform Sampling Contest” (NUScon), with the objective of determining best practices for processing and analyzing NUS experiments. We address this objective by constructing challenges from NMR experiments that we inject with synthetic signals, and we process these challenges using workflows submitted by the community. In the initial rounds of NUScon our aim is to establish objective criteria for evaluating the quality of spectral reconstructions. We present here a software package for performing the quantitative analyses, and we present the results from the first two rounds of NUScon. We discuss the challenges that remain and present a roadmap for continued community-driven development with the ultimate aim of providing best practices in this rapidly evolving field. The NUScon software package and all data from evaluating the challenge problems are hosted on the NMRbox platform

Chronic joint disease caused by persistent Chikungunya virus infection is controlled by the adaptive immune response

Chikungunya virus (CHIKV) is a reemerging mosquito-borne pathogen that causes incapacitating disease in humans characterized by intense joint pain that can persist for weeks, months, or even years. Although there is some evidence of persistent CHIKV infection in humans suffering from chronic rheumatologic disease symptoms, little is known about chronic disease pathogenesis, and no specific therapies exist for acute or chronic CHIKV disease. To investigate mechanisms of chronic CHIKV-induced disease, we utilized a mouse model and defined the duration of CHIKV infection in tissues and the associated histopathological changes. Although CHIKV RNA was readily detectable in a variety of tissues very early after infection, CHIKV RNA persisted specifically in joint-associated tissues for at least 16 weeks. Inoculation of Rag1(−/−) mice, which lack T and B cells, resulted in higher viral levels in a variety of tissues, suggesting that adaptive immunity controls the tissue specificity and persistence of CHIKV infection. The presence of CHIKV RNA in tissues of wild-type and Rag1(−/−) mice was associated with histopathological evidence of synovitis, arthritis, and tendonitis; thus, CHIKV-induced persistent arthritis is not mediated primarily by adaptive immune responses. Finally, we show that prophylactic administration of CHIKV-specific monoclonal antibodies prevented the establishment of CHIKV persistence, whereas therapeutic administration had tissue-specific efficacy. These findings suggest that chronic musculoskeletal tissue pathology is caused by persistent CHIKV infection and controlled by adaptive immune responses. Our results have significant implications for the development of strategies to mitigate the disease burden associated with CHIKV infection in humans

Large-Scale Selective Sweep among Segregation Distorter Chromosomes in African Populations of Drosophila melanogaster

Segregation Distorter (SD) is a selfish, coadapted gene complex on chromosome 2 of Drosophila melanogaster that strongly distorts Mendelian transmission; heterozygous SD/SD+ males sire almost exclusively SD-bearing progeny. Fifty years of genetic, molecular, and theory work have made SD one of the best-characterized meiotic drive systems, but surprisingly the details of its evolutionary origins and population dynamics remain unclear. Earlier analyses suggested that the SD system arose recently in the Mediterranean basin and then spread to a low, stable equilibrium frequency (1–5%) in most natural populations worldwide. In this report, we show, first, that SD chromosomes occur in populations in sub-Saharan Africa, the ancestral range of D. melanogaster, at a similarly low frequency (∼2%), providing evidence for the robustness of its equilibrium frequency but raising doubts about the Mediterranean-origins hypothesis. Second, our genetic analyses reveal two kinds of SD chromosomes in Africa: inversion-free SD chromosomes with little or no transmission advantage; and an African-endemic inversion-bearing SD chromosome, SD-Mal, with a perfect transmission advantage. Third, our population genetic analyses show that SD-Mal chromosomes swept across the African continent very recently, causing linkage disequilibrium and an absence of variability over 39% of the length of the second chromosome. Thus, despite a seemingly stable equilibrium frequency, SD chromosomes continue to evolve, to compete with one another, or evade suppressors in the genome

Adipose energy stores, physical work, and the metabolic syndrome: lessons from hummingbirds

Hummingbirds and other nectar-feeding, migratory birds possess unusual adaptive traits that offer important lessons concerning obesity, diabetes and the metabolic syndrome. Hummingbirds consume a high sugar diet and have fasting glucose levels that would be severely hyperglycemic in humans, yet these nectar-fed birds recover most glucose that is filtered into the urine. Hummingbirds accumulate over 40% body fat shortly before migrations in the spring and autumn. Despite hyperglycemia and seasonally elevated body fat, the birds are not known to become diabetic in the sense of developing polyuria (glucosuria), polydipsia and polyphagia. The tiny (3–4 g) Ruby-throated hummingbird has among the highest mass-specific metabolic rates known, and loses most of its stored fat in 20 h by flying up to 600 miles across the Gulf of Mexico. During the breeding season, it becomes lean and maintains an extremely accurate energy balance. In addition, hummingbirds can quickly enter torpor and reduce resting metabolic rates by 10-fold. Thus, hummingbirds are wonderful examples of the adaptive nature of fat tissue, and may offer lessons concerning prevention of metabolic syndrome in humans

Symptom increase following a functional capacity evaluation in patients with chronic low back pain:An explorative study of safety

Introduction: This study was performed to study intensity and duration of symptom increase following an FCE and to explore safety of an FCE. Methods: Included were 92 patients with chronic low back pain (CLBP), mean age 38.5 years, mean self-reported disability 12.5 (Roland Morris Disability Questionnaire). All patients underwent an FCE. Symptom increase was measured with a 2-item questionnaire. Operational definition for safety: no formal complaint filed and symptom increase to occur only temporarily. Results: No formal complaints were filed (n=92). In total, 54 patients returned the questionnaire (59%; 'responders'). Of the responders, 76% reported increased symptom intensity after an FCE, ranging from 'little increase' to 'severe increase'. Symptoms of all responders returned to pre-FCE level. Duration of symptom increase of the responders ranged from 1 day to 3 weeks. Symptom increase resided to pre-FCE level within 1 week in 93% of the responders. Symptom increase was weakly related to self-reported disability (r=0.38, p <0.05). Except for gender, differences between responders and non-responders were non-significant. Conclusion: A temporary increase in symptom intensity following an FCE is common. Within the operational definitions of safety used in this study, assessment of functional capacity of patients with CLBP appears safe

The action of a multidisciplinary team in the nutritional care of critically ill patients

Hospitalized patients may have special nutrient requirements imposed by a combination of malnutrition and enhanced utilization of nutrients resulting from the disease process. Nutritional support, mainly during critical stages of disease, should be provided safely and effectively. Several studies have evaluated the paper of a multidisciplinary team in the administration of a nutritional therapy. Individually, the majority of these studies are underpowered to evaluate an effect on the quality of nutritional care. With the objective to identify problems inherent to the supply of nutritional support to hospitalized patients and verify the impact of the actions of a multidisciplinary team on the quality of these procedures, we analysed articles that have been published between 1980 and 2004 about the role of the action of multidisciplinary teams in the care and nutritional outcome of hospitalized patients, especially those undergoing intensive care. The terms used for the search were: multidisciplinary team, nutritional support, parenteral nutrition, enteral feeding, critically ill, intensive care unit, critically ill child. Of 130 studies, intially identified, just 24 were selected, of which 14 compared the standard of nutritional therapy with and without the presence of a multidisciplinary team. The inadequate supply of nutrients, infection and metabolic complications and the excessive use of parenteral nutrition were the main problems detected in the supply of nutritional support to hospitalized patients. In the comparative studies, the presence of the multidisciplinary team improved the pattern of nutritional support, and reduced the incidence of complications and the costs.Pacientes hospitalizados podem ter necessidades nutricionais especiais em função da desnutrição e dos desequilíbrios metabólicos impostos pelas doenças. A terapia nutricional, principalmente nos estágios críticos das enfermidades, deve ser administrada de modo seguro e eficaz. Vários estudos têm avaliado o papel da equipe multidisciplinar na administração da terapia nutricional. Com o objetivo de identificar os problemas inerentes à administração da terapia nutricional em pacientes hospitalizados e verificar o impacto da atuação de uma equipe multidisciplinar na qualidade dos procedimentos, foi realizada uma revisão que analisou artigos publicados entre 1980 e 2004 sobre o papel da atuação de equipes multidisciplinares no cuidado e na evolução nutricional de pacientes hospitalizados, principalmente os que se encontravam sob cuidados intensivos. Os termos utilizados na pesquisa foram: multidisciplinary team, nutritional support, parente-ral nutrition, enteral feeding, critically ill, intensive care unit,critically ill child. Dos 130 estudos inicialmente identificados, foram selecionados 24, dos quais 14 compararam o padrão de terapia nutricional com e sem a presença da equipe multidisciplinar. Os principais problemas detectados na administração de terapia nutricional em pacientes hospitalizados foram a oferta inadequada de nutrientes, as complicações infecciosas e metabólicas e o uso excessivo de nutrição parenteral. Nos estudos comparativos, a presença da equipe multidisciplinar melhorou o padrão de oferta nutricional, reduziu a incidência de complicações e os custos.Universidade Federal de São Paulo (UNIFESP) Departamento de PediatriaHospital São Paulo Unidade de Cuidados Intensivos PediátricosHospital São Paulo Equipe Multidisciplinar de Terapia NutricionalUNIFESP, Depto. de PediatriaHospital São Paulo Unidade de Cuidados Intensivos PediátricosHospital São Paulo Equipe Multidisciplinar de Terapia NutricionalSciEL

Multi-Way Multi-Group Segregation and Diversity Indices

Background: How can we compute a segregation or diversity index from a three-way or multi-way contingency table, where each variable can take on an arbitrary finite number of values and where the index takes values between zero and one? Previous methods only exist for two-way contingency tables or dichotomous variables. A prototypical three-way case is the segregation index of a set of industries or departments given multiple explanatory variables of both sex and race. This can be further extended to other variables, such as disability, number of years of education, and former military service. Methodology/Principal Findings: We extend existing segregation indices based on Euclidean distance (square of coefficient of variation) and Boltzmann/Shannon/Theil index from two-way to multi-way contingency tables by including multiple summations. We provide several biological applications, such as indices for age polyethism and linkage disequilibrium. We also provide a new heuristic conceptualization of entropy-based indices. Higher order association measures are often independent of lower order ones, hence an overall segregation or diversity index should be the arithmetic mean of the normalized association measures at all orders. These methods are applicable when individuals selfidentify as multiple races or even multiple sexes and when individuals work part-time in multiple industries. Conclusions/Significance: The policy implications of this work are enormous, allowing people to rigorously test whethe

Accurate Strand-Specific Quantification of Viral RNA

The presence of full-length complements of viral genomic RNA is a hallmark of RNA virus replication within an infected cell. As such, methods for detecting and measuring specific strands of viral RNA in infected cells and tissues are important in the study of RNA viruses. Strand-specific quantitative real-time PCR (ssqPCR) assays are increasingly being used for this purpose, but the accuracy of these assays depends on the assumption that the amount of cDNA measured during the quantitative PCR (qPCR) step accurately reflects amounts of a specific viral RNA strand present in the RT reaction. To specifically test this assumption, we developed multiple ssqPCR assays for the positive-strand RNA virus o'nyong-nyong (ONNV) that were based upon the most prevalent ssqPCR assay design types in the literature. We then compared various parameters of the ONNV-specific assays. We found that an assay employing standard unmodified virus-specific primers failed to discern the difference between cDNAs generated from virus specific primers and those generated through false priming. Further, we were unable to accurately measure levels of ONNV (−) strand RNA with this assay when higher levels of cDNA generated from the (+) strand were present. Taken together, these results suggest that assays of this type do not accurately quantify levels of the anti-genomic strand present during RNA virus infectious cycles. However, an assay permitting the use of a tag-specific primer was able to distinguish cDNAs transcribed from ONNV (−) strand RNA from other cDNAs present, thus allowing accurate quantification of the anti-genomic strand. We also report the sensitivities of two different detection strategies and chemistries, SYBR® Green and DNA hydrolysis probes, used with our tagged ONNV-specific ssqPCR assays. Finally, we describe development, design and validation of ssqPCR assays for chikungunya virus (CHIKV), the recent cause of large outbreaks of disease in the Indian Ocean region