Data Capture Project at the Royal Botanic Garden Edinburgh

Botanic gardens, with their large holdings of living plants collected from around the world, are important guardians of plant biodiversity, but acquiring and curating these genetic resources is enormously expensive. For these reasons it is crucial that botanic gardens document and curate their collections in order to gain the greatest benefit from the plants in their care. Great priority is given to making detailed field notes and the process of documentation is often continued during the plants formative years when being propagated. However, for the large majority of plants this process often stops once the material is planted in its final garden location. The Data Capture Project at the Royal Botanic Garden Edinburgh is an attempt to document specific aspects of the plant collections so that the information captured can be of use to the research community even after the plants have died

A portable device for nucleic acid quantification powered by sunlight, a flame or electricity.

A decentralized approach to diagnostics can decrease the time to treatment of infectious diseases in resource-limited settings. Yet most modern diagnostic tools require stable electricity and are not portable. Here, we describe a portable device for isothermal nucleic-acid quantification that can operate with power from electricity, sunlight or a flame, and that can store heat from intermittent energy sources, for operation when electrical power is not available or reliable. We deployed the device in two Ugandan health clinics, where it successfully operated through multiple power outages, with equivalent performance when powered via sunlight or electricity. A direct comparison between the portable device and commercial qPCR (quantitative polymerase chain reaction) machines for samples from 71 Ugandan patients (29 of which were tested in Uganda) for the presence of Kaposi's sarcoma-associated herpesvirus DNA showed 94% agreement, with the four discordant samples having the lowest concentration of the herpesvirus DNA. The device's flexibility in power supply provides a needed solution for on-field diagnostics

Rehearsal: A Configuration Verification Tool for Puppet

Large-scale data centers and cloud computing have turned system configuration into a challenging problem. Several widely-publicized outages have been blamed not on software bugs, but on configuration bugs. To cope, thousands of organizations use system configuration languages to manage their computing infrastructure. Of these, Puppet is the most widely used with thousands of paying customers and many more open-source users. The heart of Puppet is a domain-specific language that describes the state of a system. Puppet already performs some basic static checks, but they only prevent a narrow range of errors. Furthermore, testing is ineffective because many errors are only triggered under specific machine states that are difficult to predict and reproduce. With several examples, we show that a key problem with Puppet is that configurations can be non-deterministic. This paper presents Rehearsal, a verification tool for Puppet configurations. Rehearsal implements a sound, complete, and scalable determinacy analysis for Puppet. To develop it, we (1) present a formal semantics for Puppet, (2) use several analyses to shrink our models to a tractable size, and (3) frame determinism-checking as decidable formulas for an SMT solver. Rehearsal then leverages the determinacy analysis to check other important properties, such as idempotency. Finally, we apply Rehearsal to several real-world Puppet configurations.Comment: In proceedings of ACM SIGPLAN Conference on Programming Language Design and Implementation (PLDI) 201

Vitamin D: beyond bone.

In recent years, vitamin D has been received increased attention due to the resurgence of vitamin D deficiency and rickets in developed countries and the identification of extraskeletal effects of vitamin D, suggesting unexpected benefits of vitamin D in health and disease, beyond bone health. The possibility of extraskeletal effects of vitamin D was first noted with the discovery of the vitamin D receptor (VDR) in tissues and cells that are not involved in maintaining mineral homeostasis and bone health, including skin, placenta, pancreas, breast, prostate and colon cancer cells, and activated T cells. However, the biological significance of the expression of the VDR in different tissues is not fully understood, and the role of vitamin D in extraskeletal health has been a matter of debate. This report summarizes recent research on the roles for vitamin D in cancer, immunity and autoimmune diseases, cardiovascular and respiratory health, pregnancy, obesity, erythropoiesis, diabetes, muscle function, and aging

Youth, caregiver, and prescriber experiences of antipsychotic-related weight gain

Objectives. To explore the lived experience of youth, caregivers, and prescribers with antipsychotic medications. Design. We conducted a qualitative interpretive phenomenology study. Youth aged 11 to 25 with recent experience taking antipsychotics, the caregivers of youth taking antipsychotics, and the prescribers of antipsychotics were recruited. Subjects. Eighteen youth, 10 caregivers (parents), and 11 prescribers participated. Results. Eleven of 18 youth, six of ten parents, and all prescribers discussed antipsychotic-related weight gain. Participants were attuned to the numeric weight changes usually measured in pounds. Significant discussions occurred around weight changes in the context of body image, adherence and persistence, managing weight increases, and metabolic effects. These concepts were often inextricably linked but maintained the significance as separate issues. Participants discussed tradeoffs regarding the perceived benefits and risks of weight gain, often with uncertainty and inadequate information regarding the short- and long-term consequences. Conclusion. Antipsychotic-related weight gain in youth influences body image and weight management strategies and impacts treatment courses with respect to adherence and persistence. In our study, the experience of monitoring for weight and metabolic changes was primarily reactive in nature. Participants expressed ambiguity regarding the short- and long-term consequences of weight and metabolic changes

Improved Chondrogenic Differentiation of rAAV SOX9-Modified Human MSCs Seeded in Fibrin-Polyurethane Scaffolds in a Hydrodynamic Environment

The repair of focal articular cartilage defects remains a problem. Combining gene therapy with tissue engineering approaches using bone marrow-derived mesenchymal stem cells (MSCs) may allow the development of improved options for cartilage repair. Here, we examined whether a three-dimensional fibrin-polyurethane scaffold provides a favorable environment for the effective chondrogenic differentiation of human MSCs (hMSCs) overexpressing the cartilage-specific SOX9 transcription factor via recombinant adeno-associated virus (rAAV) -mediated gene transfer cultured in a hydrodynamic environment in vitro. Sustained SOX9 expression was noted in the constructs for at least 21 days, the longest time point evaluated. Such spatially defined SOX9 overexpression enhanced proliferative, metabolic, and chondrogenic activities compared with control (reporter lacZ gene transfer) treatment. Of further note, administration of the SOX9 vector was also capable of delaying premature hypertrophic and osteogenic differentiation in the constructs. This enhancement of chondrogenesis by spatially defined overexpression of human SOX9 demonstrate the potential benefits of using rAAV-modified hMSCs seeded in fibrin-polyurethane scaffolds as a promising approach for implantation in focal cartilage lesions to improve cartilage repair

The Hubble Deep Field South Flanking Fields

As part of the Hubble Deep Field South program, a set of shorter 2-orbit observations were obtained of the area adjacent to the deep fields. The WFPC2 flanking fields cover a contiguous solid angle of 48 square arcminutes. Parallel observations with the STIS and NICMOS instruments produce a patchwork of additional fields with optical and near-infrared (1.6 micron) response. Deeper parallel exposures with WFPC2 and NICMOS were obtained when STIS observed the NICMOS deep field. These deeper fields are offset from the rest, and an extended low surface brightness object is visible in the deeper WFPC2 flanking field. In this data paper, which serves as an archival record of the project, we discuss the observations and data reduction, and present SExtractor source catalogs and number counts derived from the data. Number counts are broadly consistent with previous surveys from both ground and space. Among other things, these flanking field observations are useful for defining slit masks for spectroscopic follow-up over a wider area around the deep fields, for studying large-scale structure that extends beyond the deep fields, for future supernova searches, and for number counts and morphological studies, but their ultimate utility will be defined by the astronomical community.Comment: 46 pages, 15 figures. Images and full catalogs available via the HDF-S at http://www.stsci.edu/ftp/science/hdfsouth/hdfs.html at present. The paper is accepted for the February 2003 Astronomical Journal. Full versions of the catalogs will also be available on-line from AJ after publicatio

The International Bathymetric Chart of the Arctic Ocean (IBCAO) Version 3.0

[1] The International Bathymetric Chart of the Arctic Ocean (IBCAO) released its first gridded bathymetric compilation in 1999. The IBCAO bathymetric portrayals have since supported a wide range of Arctic science activities, for example, by providing constraint for ocean circulation models and the means to define and formulate hypotheses about the geologic origin of Arctic undersea features. IBCAO Version 3.0 represents the largest improvement since 1999 taking advantage of new data sets collected by the circum-Arctic nations, opportunistic data collected from fishing vessels, data acquired from US Navy submarines and from research ships of various nations. Built using an improved gridding algorithm, this new grid is on a 500 meter spacing, revealing much greater details of the Arctic seafloor than IBCAO Version 1.0 (2.5 km) and Version 2.0 (2.0 km). The area covered by multibeam surveys has increased from ∼6% in Version 2.0 to ∼11% in Version 3.0

Accessibility, sustainability, excellence: How to expand access to research publications. Executive summary

This article is a summary, by the authors, of a 140-page report prepared in 2012 by the UK Working Group on Expanding Access to Published Research Findings, chaired by British sociologist and academic administrator Janet Finch, DBE. The Working Group was charged with recommending how to develop a model that would be effective and sustainable over time, for expanding access to the published fi ndings of research. The whole report, which can be accessed at http://www.researchinfonet.org/wp-content/uploads/2012/06/Finch-Group-report-FINAL-VERSION.pdf [http://tinyurl.com/d2lxqks], has been published under a Creative Commons License Attribution 3.0 Unported. This is the fi rst of a series of Perspectives articles devoted to the Open Access Initiative that will be published in INTERNATIONAL MICROBIOLOGY. Our journal already published an Editorial on the topic in 2004 (Guerrero R & Piqueras M, Int Microbiol 7:157-161), and strongly supports open access. [Int Microbiol 2013; 16(2):125-132