NamesforLife Semantic Resolution Services for the Life Sciences

A major challenge in bioinformatics, life sciences, and medicine is using correct and informative names. While this sounds simple enough, many different naming conventions exist in the life sciences and medicine that may be either complementary or competitive with other naming conventions. For a variety of reasons, proper names are not always used, leading to an accumulated semantic ambiguity that readers of the literature and end users of databases are left to resolve on their own. This ambiguity is a growing problem and the biocuration community is aware of its consequences. 

To assist those confronted with ambiguous names (which not only includes researchers but clinicians, manufacturers, patent attorneys, and others who use biological data in their routine work), we developed a generalizable semantic model that represents names, concepts, and exemplars (representations of biological entities) as distinct objects. By identifying each object with a Digital Object Identifier (DOI) it becomes possible to place forward-pointing links in the published literature, in databases, and vector graphics that can be used as part of a mechanism for resolving ambiguities, thereby “future proofing” a nomenclature or terminology. A full implementation of the N4L model for the _Bacteria_ and _Archaea_ was released in April, 2010. The system is professionally curated and represents a Tier III resource in Parkhill’s view of bioinformatic services. A variety of tools and web services have been developed for readers, publishers, and others (N4L Guide, N4L Autotagger, N4L Semantic Search, N4L Taxonomic Abstracts) and we are incorporating other taxonomies into the N4L data model, as well as adding additional phenotypic, genotypic, and genomic information to the existing exemplars to add greater value to end users

Co-Transport of Polycyclic Aromatic Hydrocarbons by Motile Microorganisms Leads to Enhanced Mass Transfer under Diffusive Conditions.

The environmental chemodynamics of hydrophobic organic chemicals (HOCs) are often rate-limited by diffusion in stagnant boundary layers. This study investigated whether motile microorganisms can act as microbial carriers that enhance mass transfer of HOCs through diffusive boundary layers. A new experimental system was developed that allows (1) generation of concentration gradients of HOCs under the microscope, (2) exposure and direct observation of microorganisms in such gradients, and (3) quantification of HOC mass transfer. Silicone O-rings were integrated into a Dunn chemotaxis chamber to serve as sink and source for polycyclic aromatic hydrocarbons (PAHs). This resulted in stable concentration gradients in water (>24 h). Adding the model organism <i>Tetrahymena pyriformis</i> to the experimental system enhanced PAH mass transfer up to hundred-fold (benzo­[a]­pyrene). Increasing mass transfer enhancement with hydrophobicity indicated PAH co-transport with the motile organisms. Fluorescence microscopy confirmed such transport. The effective diffusivity of <i>T. pyriformis</i>, determined by video imaging microscopy, was found to exceed molecular diffusivities of the PAHs up to four-fold. Cell-bound PAH fractions were determined to range from 28% (naphthalene) to 92% (pyrene). Motile microorganisms can therefore function as effective carriers for HOCs under diffusive conditions and might significantly enhance mobility and availability of HOCs

Entrepreneurship, Windfall Gains and Financial Constraints: The Case of Germany

In this paper we investigate the link between entrepreneurship and financial constraints. We develop a dynamic partial equilibrium model of an individual utility maximization that predicts that the person is more likely to start her business when financial constraints are eased. We test this hypothesis using German Socio-Economic Panel data covering the periods 2000{2002 and measure release from financial constraints by windfall gains. The estimates confirm that the individual has higher propensity to start her business when she gets windfall gains. Furthermore, there are stronger effects for persons that have sufficient, but not very high levels of income and abilities

Intimate strangers: perspectives on female converts to Islam in Britain

This article explores the relationships between female converts to Islam in Britain and their close friends and family. It pays attention to the perspectives of converts but focuses on the reactions of their intimates to the conversion. We argue that converts become ‘intimate strangers’ through conversion—estranged on the level of understanding and belief but intimate on the emotional plane. This strangeness is symbolised by the Orientalist stereotypes associated with the converts. At the same time, friends and family shun engagement with the conversion itself, thus keeping alive the stereotypes and precluding understanding. In refusing to engage with matters of belief even within the intimate space of the family, secularism’s orthodox private/public divide gets busted where religiosity, instead, becomes an issue between the (individual) private and the (family) public. Lacking reciprocity and with no access to the inner depths of the people they are closest to, the liberal rhetoric of friends and family about personal choice and equal acceptance of all paths amounts to bigotry and turns out to be painful for both the converts and their intimates.Arts and Humanities Research Council, Prince Alwaleed Bin Talal Centre of Islamic Studie

Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer.

To identify common alleles associated with different histotypes of epithelial ovarian cancer (EOC), we pooled data from multiple genome-wide genotyping projects totaling 25,509 EOC cases and 40,941 controls. We identified nine new susceptibility loci for different EOC histotypes: six for serous EOC histotypes (3q28, 4q32.3, 8q21.11, 10q24.33, 18q11.2 and 22q12.1), two for mucinous EOC (3q22.3 and 9q31.1) and one for endometrioid EOC (5q12.3). We then performed meta-analysis on the results for high-grade serous ovarian cancer with the results from analysis of 31,448 BRCA1 and BRCA2 mutation carriers, including 3,887 mutation carriers with EOC. This identified three additional susceptibility loci at 2q13, 8q24.1 and 12q24.31. Integrated analyses of genes and regulatory biofeatures at each locus predicted candidate susceptibility genes, including OBFC1, a new candidate susceptibility gene for low-grade and borderline serous EOC

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10-8, HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10-8, HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4×10-8, HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific associat

Decline in subarachnoid haemorrhage volumes associated with the first wave of the COVID-19 pandemic

BACKGROUND: During the COVID-19 pandemic, decreased volumes of stroke admissions and mechanical thrombectomy were reported. The study\u27s objective was to examine whether subarachnoid haemorrhage (SAH) hospitalisations and ruptured aneurysm coiling interventions demonstrated similar declines. METHODS: We conducted a cross-sectional, retrospective, observational study across 6 continents, 37 countries and 140 comprehensive stroke centres. Patients with the diagnosis of SAH, aneurysmal SAH, ruptured aneurysm coiling interventions and COVID-19 were identified by prospective aneurysm databases or by International Classification of Diseases, 10th Revision, codes. The 3-month cumulative volume, monthly volumes for SAH hospitalisations and ruptured aneurysm coiling procedures were compared for the period before (1 year and immediately before) and during the pandemic, defined as 1 March-31 May 2020. The prior 1-year control period (1 March-31 May 2019) was obtained to account for seasonal variation. FINDINGS: There was a significant decline in SAH hospitalisations, with 2044 admissions in the 3 months immediately before and 1585 admissions during the pandemic, representing a relative decline of 22.5% (95% CI -24.3% to -20.7%, p\u3c0.0001). Embolisation of ruptured aneurysms declined with 1170-1035 procedures, respectively, representing an 11.5% (95%CI -13.5% to -9.8%, p=0.002) relative drop. Subgroup analysis was noted for aneurysmal SAH hospitalisation decline from 834 to 626 hospitalisations, a 24.9% relative decline (95% CI -28.0% to -22.1%, p\u3c0.0001). A relative increase in ruptured aneurysm coiling was noted in low coiling volume hospitals of 41.1% (95% CI 32.3% to 50.6%, p=0.008) despite a decrease in SAH admissions in this tertile. INTERPRETATION: There was a relative decrease in the volume of SAH hospitalisations, aneurysmal SAH hospitalisations and ruptured aneurysm embolisations during the COVID-19 pandemic. These findings in SAH are consistent with a decrease in other emergencies, such as stroke and myocardial infarction