A 2.3-Day Periodic Variability in the Apparently Single Wolf-Rayet Star WR 134: Collapsed Companion or Rotational Modulation?

We present the results of an intensive campaign of spectroscopic and photometric monitoring of the peculiar Wolf-Rayet star WR 134 from 1989 to 1997. This unprecedentedly large data set allows us to confirm unambiguously the existence of a coherent 2.25 +/- 0.05 day periodicity in the line-profile changes of He II 4686, although the global pattern of variability is different from one epoch to another. This period is only marginally detected in the photometric data set. Assuming the 2.25 day periodic variability to be induced by orbital motion of a collapsed companion, we develop a simple model aiming at investigating (i) the effect of this strongly ionizing, accreting companion on the Wolf-Rayet wind structure, and (ii) the expected emergent X-ray luminosity. We argue that the predicted and observed X-ray fluxes can only be matched if the accretion on the collapsed star is significantly inhibited. Additionally, we performed simulations of line-profile variations caused by the orbital revolution of a localized, strongly ionized wind cavity surrounding the X-ray source. A reasonable fit is achieved between the observed and modeled phase-dependent line profiles of He II 4686. However, the derived size of the photoionized zone substantially exceeds our expectations, given the observed low-level X-ray flux. Alternatively, we explore rotational modulation of a persistent, largely anisotropic outflow as the origin of the observed cyclical variability. Although qualitative, this hypothesis leads to greater consistency with the observations.Comment: 34 pages, 16 figures. Accepted by the Astrophysical Journa

Clustering cliques for graph-based summarization of the biomedical research literature

BACKGROUND: Graph-based notions are increasingly used in biomedical data mining and knowledge discovery tasks. In this paper, we present a clique-clustering method to automatically summarize graphs of semantic predications produced from PubMed citations (titles and abstracts). RESULTS: SemRep is used to extract semantic predications from the citations returned by a PubMed search. Cliques were identified from frequently occurring predications with highly connected arguments filtered by degree centrality. Themes contained in the summary were identified with a hierarchical clustering algorithm based on common arguments shared among cliques. The validity of the clusters in the summaries produced was compared to the Silhouette-generated baseline for cohesion, separation and overall validity. The theme labels were also compared to a reference standard produced with major MeSH headings. CONCLUSIONS: For 11 topics in the testing data set, the overall validity of clusters from the system summary was 10% better than the baseline (43% versus 33%). While compared to the reference standard from MeSH headings, the results for recall, precision and F-score were 0.64, 0.65, and 0.65 respectively

Autophagy and Exosomes in the Aged Retinal Pigment Epithelium: Possible Relevance to Drusen Formation and Age-Related Macular Degeneration

Age-related macular degeneration (AMD) is a major cause of loss of central vision in the elderly. The formation of drusen, an extracellular, amorphous deposit of material on Bruch's membrane in the macula of the retina, occurs early in the course of the disease. Although some of the molecular components of drusen are known, there is no understanding of the cell biology that leads to the formation of drusen. We have previously demonstrated increased mitochondrial DNA (mtDNA) damage and decreased DNA repair enzyme capabilities in the rodent RPE/choroid with age. In this study, we found that drusen in AMD donor eyes contain markers for autophagy and exosomes. Furthermore, these markers are also found in the region of Bruch's membrane in old mice. By in vitro modeling increased mtDNA damage induced by rotenone, an inhibitor of mitochondrial complex I, in the RPE, we found that the phagocytic activity was not altered but that there were: 1) increased autophagic markers, 2) decreased lysosomal activity, 3) increased exocytotic activity and 4) release of chemoattractants. Exosomes released by the stressed RPE are coated with complement and can bind complement factor H, mutations of which are associated with AMD. We speculate that increased autophagy and the release of intracellular proteins via exosomes by the aged RPE may contribute to the formation of drusen. Molecular and cellular changes in the old RPE may underlie susceptibility to genetic mutations that are found in AMD patients and may be associated with the pathogenesis of AMD in the elderly

Constructing a semantic predication gold standard from the biomedical literature

<p>Abstract</p> <p>Background</p> <p>Semantic relations increasingly underpin biomedical text mining and knowledge discovery applications. The success of such practical applications crucially depends on the quality of extracted relations, which can be assessed against a gold standard reference. Most such references in biomedical text mining focus on narrow subdomains and adopt different semantic representations, rendering them difficult to use for benchmarking independently developed relation extraction systems. In this article, we present a multi-phase gold standard annotation study, in which we annotated 500 sentences randomly selected from MEDLINE abstracts on a wide range of biomedical topics with 1371 semantic predications. The UMLS Metathesaurus served as the main source for conceptual information and the UMLS Semantic Network for relational information. We measured interannotator agreement and analyzed the annotations closely to identify some of the challenges in annotating biomedical text with relations based on an ontology or a terminology.</p> <p>Results</p> <p>We obtain fair to moderate interannotator agreement in the practice phase (0.378-0.475). With improved guidelines and additional semantic equivalence criteria, the agreement increases by 12% (0.415 to 0.536) in the main annotation phase. In addition, we find that agreement increases to 0.688 when the agreement calculation is limited to those predications that are based only on the explicitly provided UMLS concepts and relations.</p> <p>Conclusions</p> <p>While interannotator agreement in the practice phase confirms that conceptual annotation is a challenging task, the increasing agreement in the main annotation phase points out that an acceptable level of agreement can be achieved in multiple iterations, by setting stricter guidelines and establishing semantic equivalence criteria. Mapping text to ontological concepts emerges as the main challenge in conceptual annotation. Annotating predications involving biomolecular entities and processes is particularly challenging. While the resulting gold standard is mainly intended to serve as a test collection for our semantic interpreter, we believe that the lessons learned are applicable generally.</p

Assessing non-Mendelian inheritance in inherited axonopathies

PURPOSE: Inherited axonopathies (IA) are rare, clinically and genetically heterogeneous diseases that lead to length-dependent degeneration of the long axons in central (hereditary spastic paraplegia [HSP]) and peripheral (Charcot–Marie–Tooth type 2 [CMT2]) nervous systems. Mendelian high-penetrance alleles in over 100 different genes have been shown to cause IA; however, about 50% of IA cases do not receive a genetic diagnosis. A more comprehensive spectrum of causative genes and alleles is warranted, including causative and risk alleles, as well as oligogenic multilocus inheritance. METHODS: Through international collaboration, IA exome studies are beginning to be sufficiently powered to perform a pilot rare variant burden analysis. After extensive quality control, our cohort contained 343 CMT cases, 515 HSP cases, and 935 non-neurological controls. We assessed the cumulative mutational burden across disease genes, explored the evidence for multilocus inheritance, and performed an exome-wide rare variant burden analysis. RESULTS: We replicated the previously described mutational burden in a much larger cohort of CMT cases, and observed the same effect in HSP cases. We identified a preliminary risk allele for CMT in the EXOC4 gene (p value= 6.9 × 10-6, odds ratio [OR] = 2.1) and explored the possibility of multilocus inheritance in IA. CONCLUSION: Our results support the continuing emergence of complex inheritance mechanisms in historically Mendelian disorders

Comprehensive Optical Strain Sensing Through the Use of Colloidal Quantum Dots

The adaptation of colloidal quantum dots loaded within a polymer for use in nondestructive testing can be used as an optical strain gauge due to the nanomaterial’s strain sensing properties. In this paper, we utilized InP/ZnS colloidal quantum dots loaded within a polymer matrix applied onto the surface of a dog-bone foil pre-coated with an epoxy. By employing an empirical formula and a calibration factor, there is a propinquity between both the calculated optical strain and mechanical stress-strain reference data. Fluctuations are observed which may be due to both additional strain responses not seen by the mechanical data and quantum dot blinking. These results and methods show applied use of this novel optical non-destructive testing technique for a variety of structures, especially for structures which operate in harsh environments