User interface development and software environments : the Chiron-1 system

User interface development systems for software environments have to cope with the broad, extensible and dynamic character of such environments, must support internal and external integration, and should enable various software development strategies. The Chiron-1 system adapts and extends key ideas from current research in user interface development systems to address the particular demands of software environments. Important Chiron-1 concepts are: separation of concerns, dynamism, and open architecture. We discuss the requirements on such user interface development systems, present the Chiron-1 architecture and a scenario of its usage, detail the concepts it embodies, and report on its design and prototype implementation

Perceived stigma of patients undergoing treatment with cannabis-based medicinal products

Cannabis-based medicinal products (CBMPs) are prescribed with increasing frequency. This study aimed to investigate the perceived stigma attached to patients prescribed CBMPs in the UK to establish its prevalence. A qualitative survey was developed by an expert multidisciplinary group and data were collected via Qualtrics. In total, 2319 patients on CBMP therapy were invited to take part in this study. 450 (19.4%) participants completed the questionnaire. In total, 81.3% (n = 366), 76.9% (n = 346), and 61.3% (n = 276) of participants reported feeling very comfortable or comfortable telling friends, family, and medical professionals, respectively, about their treatment. Participants thought that friends (n = 372; 82.7%) and family (n = 339; 75.3%) were very approving or somewhat approving of their CBMP prescription. However, participants thought that only 37.8% (n = 170) of healthcare professionals and 32.9% (n = 148) of society in general were very approving or somewhat approving of their CBMP prescription. 57.1% (n = 257), 55.3% (n = 249), and 40.2% (n = 181) of participants were afraid of what the police or criminal justice system, other government agencies, and healthcare professionals might think about their treatment. This study highlights those patients treated with CBMPs experience a high prevalence of perceived stigma from many corners of society. Future work should be undertaken to explore strategies to reduce perceived stigma at an individual and community level to avoid discrimination of patients, likely increasing appropriate access

Pair Creation and an X-ray Free Electron Laser

Using a quantum kinetic equation coupled to Maxwell's equation we study the possibility that focused beams at proposed X-ray free electron laser facilities can generate electric field strengths large enough to cause spontaneous electron-positron pair production from the QED vacuum. Our approach yields the time and momentum dependence of the single particle distribution function. Under conditions reckoned achievable at planned facilities, repeated cycles of particle creation and annihilation take place in tune with the laser frequency. However, the peak particle number density is insensitive to this frequency and one can anticipate the production of a few hundred particle pairs per laser period. Field-current feedback and quantum statistical effects are small and can be neglected in this application of non-equilibrium quantum mean field theory.Comment: 4 pages, LaTeX2

NCBI GEO: mining millions of expression profiles—database and tools

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest fully public repository for high-throughput molecular abundance data, primarily gene expression data. The database has a flexible and open design that allows the submission, storage and retrieval of many data types. These data include microarray-based experiments measuring the abundance of mRNA, genomic DNA and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. GEO currently holds over 30 000 submissions representing approximately half a billion individual molecular abundance measurements, for over 100 organisms. Here, we describe recent database developments that facilitate effective mining and visualization of these data. Features are provided to examine data from both experiment- and gene-centric perspectives using user-friendly Web-based interfaces accessible to those without computational or microarray-related analytical expertise. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo

Target Selection for the SDSS-IV APOGEE-2 Survey

APOGEE-2 is a high-resolution, near-infrared spectroscopic survey observing roughly 300,000 stars across the entire sky. It is the successor to APOGEE and is part of the Sloan Digital Sky Survey IV (SDSS-IV). APOGEE-2 is expanding upon APOGEE's goals of addressing critical questions of stellar astrophysics, stellar populations, and Galactic chemodynamical evolution using (1) an enhanced set of target types and (2) a second spectrograph at Las Campanas Observatory in Chile. APOGEE-2 is targeting red giant branch (RGB) and red clump (RC) stars, RR Lyrae, low-mass dwarf stars, young stellar objects, and numerous other Milky Way and Local Group sources across the entire sky from both hemispheres. In this paper, we describe the APOGEE-2 observational design, target selection catalogs and algorithms, and the targeting-related documentation included in the SDSS data releases.Comment: 19 pages, 6 figures. Accepted to A

NCBI Peptidome: a new repository for mass spectrometry proteomics data

Peptidome is a public repository that archives and freely distributes tandem mass spectrometry peptide and protein identification data generated by the scientific community. Data from all stages of a mass spectrometry experiment are captured, including original mass spectra files, experimental metadata and conclusion-level results. The submission process is facilitated through acceptance of data in commonly used open formats, and all submissions undergo syntactic validation and curation in an effort to uphold data integrity and quality. Peptidome is not restricted to specific organisms, instruments or experiment types; data from any tandem mass spectrometry experiment from any species are accepted. In addition to data storage, web-based interfaces are available to help users query, browse and explore individual peptides, proteins or entire Samples and Studies. Results are integrated and linked with other NCBI resources to ensure dissemination of the information beyond the mass spectroscopy proteomics community. Peptidome is freely accessible at http://www.ncbi.nlm.nih.gov/peptidome

NCBI GEO: archive for high-throughput functional genomic data

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest public repository for high-throughput gene expression data. Additionally, GEO hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. These data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. The database has a flexible infrastructure that can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as ‘Minimum Information About a Microarray Experiment’ (MIAME). In addition to serving as a centralized data storage hub, GEO offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/

A computerized biomechanical model--Development of and use in studying gross body actions

Gross body actions involved in heavy industry, e.g. lifting and carrying materials, are often the cause of injury to the musculoskeletal system. A computer model is developed which treats the human body as a series of seven links from which reactive forces and torques are computed at each articulation during various simulated materials handling tasks. In addition, an analysis of shearing and compressing forces at the lower lumbar spine is included. The assumptions of the present model are presented, along with a discussion of future models.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/32890/1/0000269.pd

Maternal iron deficiency perturbs embryonic cardiovascular development in mice.

Congenital heart disease (CHD) is the most common class of human birth defects, with a prevalence of 0.9% of births. However, two-thirds of cases have an unknown cause, and many of these are thought to be caused by in utero exposure to environmental teratogens. Here we identify a potential teratogen causing CHD in mice: maternal iron deficiency (ID). We show that maternal ID in mice causes severe cardiovascular defects in the offspring. These defects likely arise from increased retinoic acid signalling in ID embryos. The defects can be prevented by iron administration in early pregnancy. It has also been proposed that teratogen exposure may potentiate the effects of genetic predisposition to CHD through gene-environment interaction. Here we show that maternal ID increases the severity of heart and craniofacial defects in a mouse model of Down syndrome. It will be important to understand if the effects of maternal ID seen here in mice may have clinical implications for women

NCBI GEO: archive for functional genomics data sets—10 years on

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20 000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/