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

Neurology

Contains reports on six research projects.United States Public Health Service (B-3055-4, B-3090-4, MH-06175-02)United States Navy, Office of Naval Research (Contract Nonr-1841(70))United States Air Force (AF49(638)-1313), administered by the Electronic Systems Laboratory, M. I. T

Lanthanide compounds containing a benzo-15-crown-5 derivatised [60]fullerene and the related [Tb(H2O)(3)(NO3)(2)(acac)]. C14H20O5 supramolecular adduct

Novel lanthanum(III), europium(III) and terbium(III) compounds of a benzo-15-crown-5 [60]fulleropyrrolidine were isolated in the solid state and characterised using vibrational (infrared and Raman) spectroscopy and by 13C CP MAS NMR for the lanthanum(III) compound. The photoluminescence properties were investigated for the europium(III) and terbium(III) compounds. The related [Tb(H2O)3(NO3)2(acac)] C14H20O5 [where acac ¼ acetylacetonate and C14H20O5 ¼ benzo-15-crown-5] supramolecular adduct was isolated using similar synthetic conditions, in the absence of [60]fullerene, and its crystal structure used as a model for the coordination sphere of the lanthanide [60]fullerene derivatives, with further supporting evidence given by photoluminescence measurements

Rule-based knowledge aggregation for large-scale protein sequence analysis of influenza A viruses

Background: The explosive growth of biological data provides opportunities for new statistical and comparative analyses of large information sets, such as alignments comprising tens of thousands of sequences. In such studies, sequence annotations frequently play an essential role, and reliable results depend on metadata quality. However, the semantic heterogeneity and annotation inconsistencies in biological databases greatly increase the complexity of aggregating and cleaning metadata. Manual curation of datasets, traditionally favoured by life scientists, is impractical for studies involving thousands of records. In this study, we investigate quality issues that affect major public databases, and quantify the effectiveness of an automated metadata extraction approach that combines structural and semantic rules. We applied this approach to more than 90,000 influenza A records, to annotate sequences with protein name, virus subtype, isolate, host, geographic origin, and year of isolation. Results: Over 40,000 annotated Influenza A protein sequences were collected by combining information from more than 90,000 documents from NCBI public databases. Metadata values were automatically extracted, aggregated and reconciled from several document fields by applying user-defined structural rules. For each property, values were recovered from ≥88.8% of records, with accuracy exceeding 96% in most cases. Because of semantic heterogeneity, each property required up to six different structural rules to be combined. Significant quality differences between databases were found: GenBank documents yield values more reliably than documents extracted from GenPept. Using a simple set of semantic rules and a reasoner, we reconstructed relationships between sequences from the same isolate, thus identifying 7640 isolates. Validation of isolate metadata against a simple ontology highlighted more than 400 inconsistencies, leading to over 3,000 property value corrections. Conclusion: To overcome the quality issues inherent in public databases, automated knowledge aggregation with embedded intelligence is needed for large-scale analyses. Our results show that user-controlled intuitive approaches, based on combination of simple rules, can reliably automate various curation tasks, reducing the need for manual corrections to approximately 5% of the records. Emerging semantic technologies possess desirable features to support today's knowledge aggregation tasks, with a potential to bring immediate benefits to this field

Structure in 6D and 4D N=1 supergravity theories from F-theory

We explore some aspects of 4D supergravity theories and F-theory vacua that are parallel to structures in the space of 6D theories. The spectrum and topological terms in 4D supergravity theories correspond to topological data of F-theory geometry, just as in six dimensions. In particular, topological axion-curvature squared couplings appear in 4D theories; these couplings are characterized by vectors in the dual to the lattice of axion shift symmetries associated with string charges. These terms are analogous to the Green-Schwarz terms of 6D supergravity theories, though in 4D the terms are not generally linked with anomalies. We outline the correspondence between F-theory topology and data of the corresponding 4D supergravity theories. The correspondence of geometry with structure in the low-energy action illuminates topological aspects of heterotic-F-theory duality in 4D as well as in 6D. The existence of an F-theory realization also places geometrical constraints on the 4D supergravity theory in the large-volume limit.Comment: 63 page

Contrasting impacts of heat stress on violent and nonviolent robbery in Beijing, China

Previous studies investigating the relation between heat stress and crime incidents often focus on violent crimes. In this study, the impacts of heat stress on two types of robbery (violent and nonviolent) in China are compared using crime statistics collected in Beijing and heat stress indices that consider the combined effects of temperature and humidity. The results indicate that the abrupt change in the trend of robbery rates is affected by the 2008 Beijing Olympic Games. The nonviolent robbery rates have a more pronounced seasonality and are better correlated with heat stress at daily scales, especially during the period from 2009 to 2014 when no trend exists. The results also demonstrate that both violent and nonviolent robbery rates significantly increase with heat stress in spring. The nonviolent robbery rates also significantly increase with heat stress in summer. The influence of heat stress on violent robbery rate is more complicated and nonlinear

Shotgun Lipidomics Identifies a Paired Rule for the Presence of Isomeric Ether Phospholipid Molecular Species

Ether phospholipids are abundant membrane constituents present in electrically active tissues (e.g., heart and the brain) that play important roles in cellular function. Alterations of ether phospholipid molecular species contents are associated with a number of genetic disorders and human diseases.Herein, the power of shotgun lipidomics, in combination with high mass accuracy/high resolution mass spectrometry, was explored to identify a paired rule for the presence of isomeric ether phospholipid molecular species in cellular lipidomes. The rule predicts that if an ether phospholipid A'-B is present in a lipidome, its isomeric counterpart B'-A is also present (where the ' represents an ether linkage). The biochemical basis of this rule results from the fact that the enzymes which participate in either the sequential oxidation of aliphatic alcohols to fatty acids, or the reduction of long chain fatty acids to aliphatic alcohols (metabolic precursors of ether lipid synthesis), are not entirely selective with respect to acyl chain length or degree of unsaturation. Moreover, the enzymatic selectivity for the incorporation of different aliphatic chains into the obligatory precursor of ether lipids (i.e., 1-O-alkyl-glycero-3-phosphate) is also limited.This intrinsic amplification of the number of lipid molecular species present in biological membranes predicted by this rule and demonstrated in this study greatly expands the number of ether lipid molecular species present in cellular lipidomes. Application of this rule to mass spectrometric analyses provides predictive clues to the presence of specific molecular species and greatly expands the number of identifiable and quantifiable ether lipid species present in biological samples. Through appropriate alterations in the database, use of the paired rule increases the number of identifiable metabolites in metabolic networks, thereby facilitating identification of biomarkers presaging disease states

Agreement between physicians and non-physician clinicians in starting antiretroviral therapy in rural Uganda

<p>Abstract</p> <p>Background</p> <p>The scarcity of physicians in sub-Saharan Africa – particularly in rural clinics staffed only by non-physician health workers – is constraining access to HIV treatment, as only they are legally allowed to start antiretroviral therapy in the HIV-positive patient. Here we present a pilot study from Uganda assessing agreement between non-physician clinicians (nurses and clinical officers) and physicians in their decisions as to whether to start therapy.</p> <p>Methods</p> <p>We conducted the study at 12 government antiretroviral therapy sites in three regions of Uganda, all of which had staff trained in delivery of antiretroviral therapy using the WHO Integrated Management of Adult and Adolescent Illness guidelines for chronic HIV care. We collected seven key variables to measure patient assessment and the decision as to whether to start antiretroviral therapy, the primary variable of interest being the Final Antiretroviral Therapy Recommendation. Patients saw either a clinical officer or nurse first, and then were screened identically by a blinded physician during the same clinic visit. We measured inter-rater agreement between the decisions of the non-physician health workers and physicians in the antiretroviral therapy assessment variables using simple and weighted Kappa analysis.</p> <p>Results</p> <p>Two hundred fifty-four patients were seen by a nurse and physician, while 267 were seen by a clinical officer and physician. The majority (> 50%) in each arm of the study were in World Health Organization Clinical Stages I and II and therefore not currently eligible for antiretroviral therapy according to national antiretroviral therapy guidelines. Nurses and clinical officers both showed moderate to almost perfect agreement with physicians in their Final Antiretroviral Therapy Recommendation (unweighted κ = 0.59 and κ = 0.91, respectively). Agreement was also substantial for nurses versus physicians for assigning World Health Organization Clinical Stage (weighted κ = 0.65), but moderate for clinical officers versus physicians (κ = 0.44).</p> <p>Conclusion</p> <p>Both nurses and clinical officers demonstrated strong agreement with physicians in deciding whether to initiate antiretroviral therapy in the HIV patient. This could lead to immediate benefits with respect to antiretroviral therapy scale-up and decentralization to rural areas in Uganda, as non-physician clinicians – particularly clinical officers – demonstrated the capacity to make correct clinical decisions to start antiretroviral therapy. These preliminary data warrant more detailed and multicountry investigation into decision-making of non-physician clinicians in the management of HIV disease with antiretroviral therapy, and should lead policy-makers to more carefully explore task-shifting as a shorter-term response to addressing the human resource crisis in HIV care and treatment.</p

Mitochondrial Associated Ubiquitin Fold Modifier-1 Mediated Protein Conjugation in Leishmania donovani

In this report, we demonstrate the existence of the ubiquitin fold modifier-1 (Ufm1) and its conjugation pathway in trypanosomatid parasite Leishmania donovani. LdUfm1 is activated by E1-like enzyme LdUba5. LdUfc1 (E2) specifically interacted with LdUfm1 and LdUba5 to conjugate LdUfm1 to proteinaceous targets. Mass spectrometry analysis revealed that LdUfm1 is conjugated to Leishmania protein targets that are associated with mitochondria. Immunofluorescence experiments showed that Leishmania Ufm1, Uba5 and Ufc1 are associated with the mitochondria. The demonstration that all the components of this system as well as the substrates are associated with mitochondrion suggests it may have physiological roles not yet described in any other organism. Overexpression of a non-conjugatable form of LdUfm1 and an active site mutant of LdUba5 resulted in reduced survival of Leishmania in the macrophage. Since mitochondrial activities are developmentally regulated in the life cycle of trypanosomatids, Ufm1 mediated modifications of mitochondrial proteins may be important in such regulation. Thus, Ufm1 conjugation pathway in Leishmania could be explored as a potential drug target in the control of Leishmaniasis

Mechanisms of Hearing Loss after Blast Injury to the Ear

Given the frequent use of improvised explosive devices (IEDs) around the world, the study of traumatic blast injuries is of increasing interest. The ear is the most common organ affected by blast injury because it is the bodyﾒs most sensitive pressure transducer. We fabricated a blast chamber to re-create blast profiles similar to that of IEDs and used it to develop a reproducible mouse model to study blast-induced hearing loss. The tympanic membrane was perforated in all mice after blast exposure and found to heal spontaneously. Micro-computed tomography demonstrated no evidence for middle ear or otic capsule injuries; however, the healed tympanic membrane was thickened. Auditory brainstem response and distortion product otoacoustic emission threshold shifts were found to be correlated with blast intensity. As well, these threshold shifts were larger than those found in control mice that underwent surgical perforation of their tympanic membranes, indicating cochlear trauma. Histological studies one week and three months after the blast demonstrated no disruption or damage to the intra-cochlear membranes. However, there was loss of outer hair cells (OHCs) within the basal turn of the cochlea and decreased spiral ganglion neurons (SGNs) and afferent nerve synapses. Using our mouse model that recapitulates human IED exposure, our results identify that the mechanisms underlying blast-induced hearing loss does not include gross membranous rupture as is commonly believed. Instead, there is both OHC and SGN loss that produce auditory dysfunction