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information technology [keywords]
- Organizational strategies for promoting patient and provider uptake of personal health records. [JOURNAL ARTICLE]
- J Am Med Inform Assoc 2014 Oct 17.
To investigate organizational strategies to promote personal health records (PHRs) adoption with a focus on patients with chronic disease.Using semi-structured interviews and a web-based survey, we sampled US health delivery organizations which had implemented PHRs for at least 12 months, were recognized as PHR innovators, and had scored highly in national patient satisfaction surveys. Respondents had lead positions for clinical information systems or high-risk population management. Using grounded theory approach, thematic categories were derived from interviews and coupled with data from the survey.Interviews were conducted with 30 informants from 16 identified organizations. Organizational strategies were directed towards raising patient awareness via multimedia communications, and provider acceptance and uptake. Strategies for providers were grouped into six main themes: organizational vision, governance and policies, work process redesign, staff training, information technology (IT) support, and monitoring and incentives. Successful organizations actively communicated their vision, engaged leaders at all levels, had clear governance, planning, and protocols, set targets, and celebrated achievement. The most effective strategy for patient uptake was through health professional encouragement. No specific outreach efforts targeted patients with chronic disease. Registration and PHR activity was routinely measured but without reference to a denominator population or high risk subpopulations.Successful PHR implementation represents a social change and operational project catalyzed by a technical solution. The key to clinician acceptance is making their work easier. However, organizations will likely not achieve the value they want from PHRs unless they target specific populations and monitor their uptake.
- Re-examining health IT policy: what will it take to derive value from our investment? [REVIEW]
- J Am Med Inform Assoc 2014 Oct 17.
Despite substantial investments in health information technology (HIT), the nation's goals of reducing cost and improving outcomes through HIT remain elusive. This period of transition, with new Office of National Coordinator for HIT leadership, upcoming Meaningful Use Stage III definitions, and increasing congressional oversight, is opportune to consider needed course corrections in HIT strategy. This article describes current problems and recommended changes in HIT policy, including approaches to usability, interoperability, and quality measurement. Recommendations refrain from interim measures, such as electronic health record adoption rates, and instead focus on measurable national value to benefit the economy, to reduce healthcare costs, and to improve clinical efficiency and care quality.
- Kinetic mechanism of Nicotiana tabacum myosin-11 defines a new type of a processive motor. [JOURNAL ARTICLE]
- FASEB J 2014 Oct 17.
The 175-kDa myosin-11 from Nicotiana tabacum (Nt(175kDa)myosin-11) is exceptional in its mechanical activity as it is the fastest known processive actin-based motor, moving 10 times faster than the structurally related class 5 myosins. Although this ability might be essential for long-range organelle transport within larger plant cells, the kinetic features underlying the fast processive movement of Nt(175kDa)myosin-11 still remain unexplored. To address this, we generated a single-headed motor domain construct and carried out a detailed kinetic analysis. The data demonstrate that Nt(175kDa)myosin-11 is a highduty ratio motor, which remains associated with actin most of its enzymatic cycle. However, different from other processive myosins that establish a high duty ratio on the basis of a rate-limiting ADP-release step, Nt(175kDa)myosin-11 achieves a high duty ratio by a prolonged duration of the ATP-induced isomerization of the actin-bound states and ADP release kinetics, both of which in terms of the corresponding time constants approach the total ATPase cycle time. Molecular modeling predicts that variations in the charge distribution of the actin binding interface might contribute to the thermodynamic fine-tuning of the kinetics of this myosin. Our study unravels a new type of a high duty ratio motor and provides important insights into the molecular mechanism of processive movement of higher plant myosins.-Diensthuber, R. P., Tominaga, M., Preller, M., Hartmann, F. K., Orii, H., Chizhov, I., Oiwa, K., Tsiavaliaris, G. Kinetic mechanism of Nicotiana tabacum myosin-11 defines a new type of a processive motor.
- Undergraduate psychiatry students' attitudes towards teaching methods at an Irish university. [JOURNAL ARTICLE]
- Ir J Med Sci 2014 Oct 18.
At University College Dublin, teaching in psychiatry includes clinical electives, lectures, small-group and problem-based teaching, consistent with international trends.To determine final-year psychiatry students' attitudes towards teaching methods.We distributed questionnaires to all final-year medical students in two classes (2008 and 2009), after final psychiatry examination (before results) and all of them participated (n = 111).Students' interest in psychiatry as a career increased during psychiatry teaching. Students rated objective structured clinical examination (OSCE) as the most useful element of teaching and examination. The most common learning style was "reflector"; the least common was "pragmatist". Two thirds believed teaching could be improved (increased patient contact) and 89 % reported that experience of psychiatry changed attitudes towards mental illness (increased understanding).Students' preference for OSCEs may reflect the closeness of OSCE as a form of learning to OSCE as a form of assessment: OSCEs both focus on specific clinical skills and help prepare for examinations. Future research could usefully examine the extent to which these findings are university-specific or instructor-dependent. Information on the consistency of various teaching, examination and modularisation methods would also be useful.
- ImmuCo: a database of gene co-expression in immune cells. [JOURNAL ARTICLE]
- Nucleic Acids Res 2014 Oct 17.
Current gene co-expression databases and correlation networks do not support cell-specific analysis. Gene co-expression and expression correlation are subtly different phenomena, although both are likely to be functionally significant. Here, we report a new database, ImmuCo (http://immuco.bjmu.edu.cn), which is a cell-specific database that contains information about gene co-expression in immune cells, identifying co-expression and correlation between any two genes. The strength of co-expression of queried genes is indicated by signal values and detection calls, whereas expression correlation and strength are reflected by Pearson correlation coefficients. A scatter plot of the signal values is provided to directly illustrate the extent of co-expression and correlation. In addition, the database allows the analysis of cell-specific gene expression profile across multiple experimental conditions and can generate a list of genes that are highly correlated with the queried genes. Currently, the database covers 18 human cell groups and 10 mouse cell groups, including 20 283 human genes and 20 963 mouse genes. More than 8.6 × 10(8) and 7.4 × 10(8) probe set combinations are provided for querying each human and mouse cell group, respectively. Sample applications support the distinctive advantages of the database.
- DEOP: a database on osmoprotectants and associated pathways. [JOURNAL ARTICLE]
- Database (Oxford) 2014.
Microorganisms are known to counteract salt stress through salt influx or by the accumulation of osmoprotectants (also called compatible solutes). Understanding the pathways that synthesize and/or breakdown these osmoprotectants is of interest to studies of crops halotolerance and to biotechnology applications that use microbes as cell factories for production of biomass or commercial chemicals. To facilitate the exploration of osmoprotectants, we have developed the first online resource, 'Dragon Explorer of Osmoprotection associated Pathways' (DEOP) that gathers and presents curated information about osmoprotectants, complemented by information about reactions and pathways that use or affect them. A combined total of 141 compounds were confirmed osmoprotectants, which were matched to 1883 reactions and 834 pathways. DEOP can also be used to map genes or microbial genomes to potential osmoprotection-associated pathways, and thus link genes and genomes to other associated osmoprotection information. Moreover, DEOP provides a text-mining utility to search deeper into the scientific literature for supporting evidence or for new associations of osmoprotectants to pathways, reactions, enzymes, genes or organisms. Two case studies are provided to demonstrate the usefulness of DEOP. The system can be accessed at. Database URL: http://www.cbrc.kaust.edu.sa/deop/
- Sequence assembly using next generation sequencing data-challenges and solutions. [JOURNAL ARTICLE]
- Sci China Life Sci 2014 Oct 17.
Sequence assembling is an important step for bioinformatics study. With the help of next generation sequencing (NGS) technology, high throughput DNA fragment (reads) can be randomly sampled from DNA or RNA molecular sequence. However, as the positions of reads being sampled are unknown, assembling process is required for combining overlapped reads to reconstruct the original DNA or RNA sequence. Compared with traditional Sanger sequencing methods, although the throughput of NGS reads increases, the read length is shorter and the error rate is higher. It introduces several problems in assembling. Moreover, paired-end reads instead of single-end reads can be sampled which contain more information. The existing assemblers cannot fully utilize this information and fails to assemble longer contigs. In this article, we will revisit the major problems of assembling NGS reads on genomic, transcriptomic, metagenomic and metatranscriptomic data. We will also describe our IDBA package for solving these problems. IDBA package has adopted several novel ideas in assembling, including using multiple k, local assembling and progressive depth removal. Compared with existence assemblers, IDBA has better performance on many simulated and real sequencing datasets.
- Prioritization of orphan disease-causing genes using topological feature and GO similarity between proteins in interaction networks. [JOURNAL ARTICLE]
- Sci China Life Sci 2014 Oct 17.
Identification of disease-causing genes among a large number of candidates is a fundamental challenge in human disease studies. However, it is still time-consuming and laborious to determine the real disease-causing genes by biological experiments. With the advances of the high-throughput techniques, a large number of protein-protein interactions have been produced. Therefore, to address this issue, several methods based on protein interaction network have been proposed. In this paper, we propose a shortest path-based algorithm, named SPranker, to prioritize disease-causing genes in protein interaction networks. Considering the fact that diseases with similar phenotypes are generally caused by functionally related genes, we further propose an improved algorithm SPGOranker by integrating the semantic similarity of GO annotations. SPGOranker not only considers the topological similarity between protein pairs in a protein interaction network but also takes their functional similarity into account. The proposed algorithms SPranker and SPGOranker were applied to 1598 known orphan disease-causing genes from 172 orphan diseases and compared with three state-of-the-art approaches, ICN, VS and RWR. The experimental results show that SPranker and SPGOranker outperform ICN, VS, and RWR for the prioritization of orphan disease-causing genes. Importantly, for the case study of severe combined immunodeficiency, SPranker and SPGOranker predict several novel causal genes.
- Histochemical analysis of heparan sulfate 3-o-sulfotransferase expression in mouse brain. [Journal Article]
- Methods Mol Biol 2015.:377-87.
In situ hybridization provides information for understanding the localization of gene expression in various tissues. The relative expression levels of mRNAs in a single cell can be sensitively visualized by this technique. Furthermore, since in situ hybridization is a histological technique, tissue structure is maintained after fixation, and it is possible to accurately identify cell types. We have examined the expression of heparan sulfate sulfotransferases by in situ hybridization to better understand the functions of heparan sulfate in the development of mouse nervous system. This chapter describes methods of in situ hybridization analyses using cRNA probes labeled with nonradioactive nucleotides.
- Informatics tools to advance the biology of glycosaminoglycans and proteoglycans. [Journal Article]
- Methods Mol Biol 2015.:271-87.
Glycomics researchers have identified the need for integrated database systems for collecting glycomics information in a consistent format. The goal is to create a resource for knowledge discovery and dissemination to wider research communities. This has the potential to extend the research community to include biologists, clinicians, chemists, and computer scientists. This chapter discusses the technology and approach needed to create integrated data resources to empower the broader community to leverage extant glycomics data. The focus is on glycosaminoglycan (GAGs) and proteoglycan research, but the approach can be generalized. The methods described span the development of glycomics standards from CarbBank to Glyco Connection Tables. The existence of integrated data sets provides a foundation for novel methods of analysis such as machine learning for knowledge discovery. The implications of predictive analysis are examined in relation to disease biomarker to expand the target audience of GAG and proteoglycan research.