Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit.

BACKGROUND: Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. RESULTS: Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. CONCLUSION: Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers

Geographic disparity in premature mortality in Ontario, 1992–1996

BACKGROUND: Standardized mortality ratios are used to identify geographic areas with higher or lower mortality than expected. This article examines geographic disparity in premature mortality in Ontario, Canada, at three geographic levels of population and considers factors that may underlie variations in premature mortality across geographic areas. All-cause, sex and disease chapter specific premature mortality were analyzed at the regional, district and public health unit level to determine the extent of geographic variation. Standardized mortality ratios for persons aged 0–74 years were calculated to identify geographic areas with significantly higher or lower premature mortality than expected, using Ontario death rates as the basis for the calculation of expected deaths in the local population. Data are also presented from the household component of the 1996/97 National Population Health Survey and from the 1996 Statistics Canada Census. RESULTS: Results showed approximately 20% higher than expected all-cause premature mortality for males and females in the North region. However, disparity in all-cause premature mortality in Ontario was most pronounced at the public health unit level, ranging from 20% lower than expected to 30% higher than expected. Premature mortality disparities were largely influenced by neoplasms, circulatory diseases, injuries and poisoning, respiratory diseases and digestive diseases, which accounted for more than 80% of all premature deaths. Premature mortality disparities were also more pronounced for disease chapter specific mortality. CONCLUSION: Geographic disparities in premature mortality are clearly greater at the small area level. Geographic disparities in premature mortality undoubtedly reflect the underlying distribution of population health determinants such as health related behaviours, social, economic and environmental influences

The relationship between erectile dysfunction, sexual self efficacy and the dark triad

Erectile dysfunction (ED) is the lack, or loss of ability to achieve or maintain an erection and is a commonly reported sexual dysfunction in healthcare. Whilst research has centred on the dark triad, personality, and sexuality; associations between dark triad traits, and sexual dysfunction appear scarce. This study aimed to establish whether there was a relationship between the dark triad traits, sexual self-efficacy (SSE) and ED. Sixty-four participants including 45 men with ED and 19 men without ED, aged between 18-60 years contributed to an online cross-sectional survey consisting of questionnaires measuring ED, the dark triad traits, SSE and demographic information. Results suggested a moderate to high positive correlation with narcissism and psychopathy traits on ED (aggravating effect) and a negative moderate to high correlation with Machiavellianism and SSE (protective effect) on ED. Both Machiavellianism, specifically subscale reputation and SSE were predictors of ED. This suggests that higher levels of SSE and Machiavellianism (reputation) were associated with lower levels of ED and narcissism and psychopathy were associated with higher levels of ED. However, until further research is conducted on a larger and diverse cohort, which examines the causal pathways SSE and the dark triad might have on ED, this remains inconclusive. Nevertheless, this area warrants further exploration, with a view to developing suitable assessment and intervention stratagem in psychosexual services to support ED

Evaluating the Effectiveness of Data Management Training: DataONE’s Survey Instrument

Effective management is a key component for preparing data to be retained for future long term access, use, and reuse by a broader community. Developing the skills to plan and perform data management tasks is important for individuals and institutions. Teaching data literacy skills may also help to mitigate the impact of data deluge and other effects of being overexposed to and overwhelmed by data. The process of learning how to manage data effectively for the entire research data lifecycle can be complex. There are often multiple stages involved within a lifecycle for managing data, and each stage may require specific knowledge, expertise, and resources. Additionally, although a range of organizations offers data management education and training resources, it can often be difficult to assess how effective the resources are for educating users to meet their data management requirements. In the case of Data Observation Network for Earth (DataONE), DataONE’s extensive collaboration with individuals and organizations has informed the development of multiple educational resources. Through these interactions, DataONE understands that the process of creating and maintaining educational materials that remain responsive to community needs is reliant on careful evaluations. Therefore, the impetus for a comprehensive, customizable Education EVAluation instrument (EEVA) is grounded in the need for tools to assess and improve current and future training and educational resources for research data management. In this paper, the authors outline and provide context for the background and motivations that led to creating EEVA for evaluating the effectiveness of data management educational resources. The paper details the process and results of the current version of EEVA. Finally, the paper highlights the key features, potential uses, and the next steps in order to improve future extensions and revisions of EEVA

Role of multicellular aggregates in biofilm formation

In traditional models of in vitro biofilm development, individual bacterial cells seed a surface, multiply, and mature into multicellular, three-dimensional structures. Much research has been devoted to elucidating the mechanisms governing the initial attachment of single cells to surfaces. However, in natural environments and during infection, bacterial cells tend to clump as multicellular aggregates, and biofilms can also slough off aggregates as a part of the dispersal process. This makes it likely that biofilms are often seeded by aggregates and single cells, yet how these aggregates impact biofilm initiation and development is not known. Here we use a combination of experimental and computational approaches to determine the relative fitness of single cells and preformed aggregates during early development of Pseudomonas aeruginosa biofilms. We find that the relative fitness of aggregates depends markedly on the density of surrounding single cells, i.e., the level of competition for growth resources. When competition between aggregates and single cells is low, an aggregate has a growth disadvantage because the aggregate interior has poor access to growth resources. However, if competition is high, aggregates exhibit higher fitness, because extending vertically above the surface gives cells at the top of aggregates better access to growth resources. Other advantages of seeding by aggregates, such as earlier switching to a biofilm-like phenotype and enhanced resilience toward antibiotics and immune response, may add to this ecological benefit. Our findings suggest that current models of biofilm formation should be reconsidered to incorporate the role of aggregates in biofilm initiation

Gas emissions and subsurface architecture of fault-controlled geothermal systems : a case study of the North Abaya geothermal area

Funding: W. Hutchison is funded by a UKRI Future Leaders Fellowship (MR/S033505/1). E.R.D. Ogilvie was supported by a St Andrews Research Internship Scheme (StARIS) grant from the University of St Andrews.East Africa hosts significant reserves of untapped geothermal energy. Exploration has focused on geologically young (<1 Ma) silicic calderas, yet there are many sites of geothermal potential where there is no clear link to an active volcano. The origin and architecture of these systems are poorly understood. Here, we combine remote sensing and field observations to investigate a fault-controlled geothermal play located north of Lake Abaya in the Main Ethiopian Rift. Soil gas CO2 and temperature surveys were used to examine permeable pathways and showed elevated values along a ∼110 m high fault, which marks the western edge of the Abaya graben. Ground temperatures are particularly elevated where multiple intersecting faults form a wedged horst structure. This illustrates that both deep penetrating graben bounding faults and near-surface fault intersections control the ascent of hydrothermal fluids and gases. Total CO2 emissions along the graben fault are ∼300 t d−1; a value comparable to the total CO2 emission from silicic caldera volcanoes. Fumarole gases show δ13C of −6.4‰ to −3.8‰ and air-corrected 3He/4He values of 3.84–4.11 RA, indicating a magmatic source originating from an admixture of upper mantle and crustal helium. Although our model of the North Abaya geothermal system requires a deep intrusive heat source, we find no ground deformation evidence for volcanic unrest or recent volcanism along the graben fault. This represents a key advantage over the active silicic calderas that typically host these resources and suggests that fault-controlled geothermal systems offer viable prospects for geothermal exploration.Publisher PDFPeer reviewe

Key actions for a sustainable chemicals policy

Chemicals policies have spawned a wide range of regulations aimed at limiting damage to the environment and human health. Most instruments are reactive and fragmented. We propose a simple underpinning philosophy, “Do no harm”, to ensure a more sustainable, safe “chemical environment” for the future

Optimizing Nervous System-Specific Gene Targeting with Cre Driver Lines: Prevalence of Germline Recombination and Influencing Factors.

The Cre-loxP system is invaluable for spatial and temporal control of gene knockout, knockin, and reporter expression in the mouse nervous system. However, we report varying probabilities of unexpected germline recombination in distinct Cre driver lines designed for nervous system-specific recombination. Selective maternal or paternal germline recombination is showcased with sample Cre lines. Collated data reveal germline recombination in over half of 64 commonly used Cre driver lines, in most cases with a parental sex bias related to Cre expression in sperm or oocytes. Slight differences among Cre driver lines utilizing common transcriptional control elements affect germline recombination rates. Specific target loci demonstrated differential recombination; thus, reporters are not reliable proxies for another locus of interest. Similar principles apply to other recombinase systems and other genetically targeted organisms. We hereby draw attention to the prevalence of germline recombination and provide guidelines to inform future research for the neuroscience and broader molecular genetics communities