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PubMed2000

NMRLAB-Advanced NMR data processing in matlab

NMRLAB is a toolbox for NMR data processing in MATLAB (The Mathworks). MATLAB is a matrix-oriented high-level programming environment which gives access to fast algorithms for a large number of numerical tasks on many common computer platforms. To take advantage of fast matrix operations in MATLAB most processing commands in NMRLAB have been vectorized. Data processing can be achieved either by scripts or by a user-friendly command structure. An interface to WaveLab enables spectral denoising employing wavelet transforms. The use of wavelet denoising is demonstrated for one- and two-dimensional data. Copyright 2000 Academic Press.

Journal Article↗

PubMed1996

Computational combinatorial ligand design: application to human alpha-thrombin.

A new method is presented for computer-aided ligand design by combinatorial selection of fragments that bind favorably to a macromolecular target of known three-dimensional structure. Firstly, the multiple-copy simultaneous-search procedure (MCSS) is used to exhaustively search for optimal positions and orientations of functional groups on the surface of the macromolecule (enzyme or receptor fragment). The MCSS minima are then sorted according to an approximated binding free energy, whose solvation component is expressed as a sum of separate electrostatic and nonpolar contributions. The electrostatic solvation energy is calculated by the numerical solution of the linearized Poisson-Boltzmann equation, while the nonpolar contribution to the binding free energy is assumed to be proportional to the loss in solvent-accessible surface area. The program developed for computational combinatorial ligand design (CCLD) allows the fast and automatic generation of a multitude of highly diverse compounds, by connecting in a combinatorial fashion the functional groups in their minimized positions. The fragments are linked as two atoms may be either fused, or connected by a covalent bond or a small linker unit. To avoid the combinatorial explosion problem, pruning of the growing ligand is performed according to the average value of the approximated binding free energy of its fragments. The method is illustrated here by constructing candidate ligands for the active site of human alpha-thrombin. The MCSS minima with favorable binding free energy reproduce the interaction patterns of known inhibitors. Starting from these fragments, CCLD generates a set of compounds that are closely related to high-affinity thrombin inhibitors. In addition, putative ligands with novel binding motifs are suggested. Probable implications of the MCSS-CCLD approach for the evolving scenario of drug discovery are discussed.

Binding Sites↗

PubMed1988

Youth suicide in California: a comparative study of perceived causes and interventions.

Comparative survey data were obtained from five sample groups of respondents composed of young people 12 to 20 years of age, parents of young people within this age range, and respondents to psychological autopsies of decreased youth. The findings revealed that family dysfunction, intrapersonal psychopathology and distress, problems with interpersonal relationships, and drug and alcohol abuse were most frequently mentioned by the respondents as the major causes of youth suicide. In terms of solutions, the availability of social support from family and friends and access to formal intervention programs for troubled adolescents were seen as the most effective measures that could be taken to stop young people from intentionally hurting themselves.

Achievement↗

PubMed1997

Consumer empowerment in mental health organizations: concept, benefits, and impediments.

This article proposes a framework for promoting consumer empowerment in mental health organizations. Consumer empowerment involves consumer participation in organizational decision-making, program development and evaluation, access to resources, and opportunities for consumers to develop and run services as well as to maintain personal dignity and integrity. The benefits include increased service innovation, responsiveness to changes in the market place, accountability, as well as the enhancement of quality of care, the protection of consumer rights, among others.

Community Participation↗

PubMed2004

Public evaluation of open space in Illinois: citizen support for natural area acquisition.

Numerous studies have indicated a broad-based support for open space preservation and protection. Research also has characterized the public values and rationale that underlie the widespread support for open space. In recognition of the widespread public support for open space, various levels of government have implemented programs to provide public access to open space. There are many different types of open space, ranging from golf courses, ball parks, wildlife areas, and prairies, to name a few. This paper addresses questions related to the types of open space that should be prioritized by planners and natural resource managers. The results of this study are based on a stratified random sample of 5000 households in Illinois that were sent a questionnaire related to their support for various types of open space. Through a comparatively simple action grid analysis, the open space types that should be prioritized for public access include forest areas, stream corridors, wildlife habitat, and lakes/ponds. These were the open space types rated of the highest importance, yet were also the open space types rated the lowest in respondent satisfaction. This kind of analysis does not require the technical expertise of other options for land-use prioritizations (e.g., conjoint analysis, contingent valuation), yet provides important policy directives for planners. Although open space funds often allow for purchase of developed sites such as golf courses, ball parks, and community parks, this study indicates that undeveloped (or nature-based) open space lands are most needed in Illinois.

Adult↗

PubMed2004

Multiple spindles and cellularization during microsporogenesis in an artificially induced tetraploid accession of Brachiaria ruziziensis (Gramineae).

The genus Brachiaria is characterized by a majority of polyploid accessions--mainly tetraploid--and apomictic reproduction. Sexuality is found among diploids. To overcome incompatibility barriers, accessions with the same ploidy level are necessarily used in hybridization. Thus, sexual diploid accessions were tetraploidized to be used as female genitors. This paper reports microsporogenesis in an artificially induced tetraploid accession of Brachiaria ruziziensis. Chromosome pairing at diakinesis ranged from univalents to tetravalents, with predominance of bivalents. Irregular chromosome segregation was frequent in both meiotic divisions. During the first division, multiple spindles showing different arrangements were recorded. The spindle position determined the plane of first cytokinesis and the number of chromosomes determined the size of the cell. Meiotic products were characterized by polyads with spores of different sizes. Pollen sterility was estimated at 61.38%. The limitations of using this accession in the breeding program are discussed.

Brachiaria↗

PubMed2005

Web based Health Education, E-learning, for weight management.

Obesity is a major health problem across the United States and becoming a progressive world wide problem. An overweight person could access the weight management program and develop a personalized weight reduction plan. The customer enters specific data to personalize the program and in the future an artificial intelligence program can evaluate customer behavior and adjust accordingly. This is an on-line program with class room support, offered as back up when desired by the patient.

Education, Distance↗

PubMed1993

Animated visualization of a high resolution color three dimensional digital computer model of the whole human head.

The interactive visualization of animated images through a computerized three dimensional (3D) full color model of an unstained cadaveric human head is presented. Serial full color images were taken of the blockface of a cryomicrotomed frozen human head every 200 microns. From this series of images a three dimensional digital model with a resultant pixel resolution of 200 microns3 was created on a UNIX workstation. Using this database, resampled images were computed along orthogonal axes and written sequentially to a write-once-read-many times (WORM) videodisc unit. Playback of this customized videodisc dataset provides animations of the digitally reconstructed slices and 3D reconstructed surface models. An interactive interface to the animated sequences is provided through a PC based tutorial package. This tutorial program is able to access videodisc frames to display animations and labeled still images in a software window to illustrate various neuroanatomic topics. The technique of animation as applied to this high resolution 3D model provides insight into complex spatial relationships and has great potential in research and as a teaching tool in the neurosciences.

Brain↗

PubMed1984

Methods for comparing sequence data such as restriction endonuclease maps or nucleotide sequences of viral nucleic acid molecules.

Maps of restriction endonuclease sites in the DNA genomes of orthopoxviruses were compared by computer classification methods. Data from such maps were recorded as qualitative binary information, and gave closely similar dendrograms when different dissimilarity measures and sorting strategies were used for the computations. A method for calculating dendrograms from small data sets, by 'hand', is described in detail to assist those who do not have access to suitable computer programs. The same calculation strategy gave useful classifications of partial nucleotide and amino acid sequences of orthomyxovirus haemagglutinins.

Animals↗

PubMed1989

SMILE--shaded molecular imaging on low-cost equipment.

The SMILE program runs under MS-DOS on IBM PC AT-compatible computers equipped with the SM640 or the PG640 Matrox graphic board. The program allows real-time three-dimensional (3D) animation and modeling of several isolated molecules that can be built from scratch, manipulated interactively and compared by superimposition. SMILE enables users to compute atomic partial charges, molecular surface area, molecular volume, electrostatic and nonbonded potential energies. PLUTO, ORTEP, and MMP2 input files are set up automatically. The program also provides simple access to crystal packing by real-time animation of the unit cell contents, interactive inspection of the relevant stereochemical parameters and fragment manipulation within the unit cell. SMILE animates stereo views and produces beautiful shaded 3D images (8 colors, 32 shades each) of molecules in many different styles--stick, ball-and-stick, CPK (space filling), and transparent CPK with backbone.

Computer Graphics↗

PubMed1992

Nutrition education for cardiovascular disease prevention among low income populations--description and pilot evaluation of a physician-based model.

Low income Americans are at greatest risk for coronary heart disease but have least access to health promotion programs for life style modification. Primary care physicians may represent one of the few sources of preventive care available to the poor. However, the majority of physicians feel unprepared to help patients achieve dietary change, and few existing nutrition intervention programs address the special needs of low literacy populations. The Food for Heart Program was developed to facilitate dietary counseling experienced by primary care physicians who care for low literacy patients and to overcome barriers to behavior change faced by patients. The program consists of three components: (1) a validated dietary risk assessment that rapidly identifies atherogenic eating habits and requires no nutritional expertise to administer or interpret, (2) a structured diet treatment program that is culturally specific for a southern patient population and links practical behavior change recommendations with results of the diet assessment, and (3) a system for monitoring and reinforcement that prompts physicians to review progress, reinforce prior messages, and reward positive change. Behavior change theory is used to guide the intervention and readability of the material has been assessed at the 5-6th grade level. An evaluation study of the Food for Heart Program suggests that it has a positive impact on physician counseling and that patients are responding favorably to these efforts.

Cardiovascular Diseases↗

PubMed2005

COMPARE/Radiology, an interactive Web-based radiology teaching program evaluation of user response.

RATIONALE AND OBJECTIVES: The aim of this study is to assess user benefits of COMPARE/Radiology, a highly interactive World Wide Web-based training program for radiology, as perceived by its users. MATERIALS AND METHODS: COMPARE/Radiology (http://www.idr.med.uni-erlangen.de/compare.htm), an interactive training program based on 244 teaching cases, was created by the authors and made publicly available on the Internet. An anonymous survey was conducted among users to investigate the composition of the program's user base and assess the acceptance of the training program. In parallel, Web access data were collected and analyzed using descriptive statistics. RESULTS: The group of responding users (n = 1370) consisted of 201 preclinical medical students (14.7%), 314 clinical medical students (22.9%), 359 residents in radiology (26.2%), and 205 users of other professions (14.9%). A majority of respondents (1230; 89%) rated the interactivity of COMPARE/Radiology as good or excellent. Many respondents use COMPARE/Radiology for self-study (971; 70%) and for teaching others (600; 43%). Web access statistics show an increase in number of site visits from 1248 in December 2002 to 4651 in April 2004. CONCLUSION: Users appreciate the benefits of COMPARE/Radiology. The interactive instructional design was rated positively by responding users. The popularity of the site is growing, evidenced by the number of network accesses during the observation period.

Computer-Assisted Instruction↗

PubMed2025

Genetic architecture and analysis practices of circulating metabolites in the NHLBI Trans-Omics for Precision Medicine Program.

Circulating metabolite levels partly reflect the state of human health and diseases and can be impacted by genetic determinants. Hundreds of loci associated with circulating metabolites have been identified; however, most findings focus on predominantly European ancestry or single-study analyses. Leveraging the rich metabolomics resources generated by the National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) Program, we harmonized and accessibly cataloged 1,729 circulating metabolites among 25,058 ancestrally diverse samples. From our comparison of multiple methods, we provided a set of reasonable strategies for outlier and imputation handling to process metabolite data and show that inverse normalization by study and half-minimum imputation provide mostly similar results for pooled or meta-analysis. Following the practical analysis framework, we further performed a genome-wide association analysis on 1,135 selected metabolites using whole-genome sequencing data from 16,359 individuals passing the quality-control filters and discovered 1,775 independent loci associated with 667 metabolites. Among 160 unreported locus-metabolite pairs, we identified associations with loci locating within previously implicated metabolite-associated genes, as well as associations with loci locating in genes such as GAB3 and VSIG4 (located on the X chromosome) that may play a role in metabolic regulation. In the sex-stratified analysis, we revealed 85 independent locus-metabolite pairs with evidence of sexual dimorphism, which were located in well-known metabolic genes such as FADS2, D2HGDH, SUGP1, and UGT2B17, strongly supporting the importance of exploring sex difference in the human metabolome. Taken together, our study depicted the genetic contribution to circulating metabolite levels, providing additional insight into the understanding of human health.

Humans↗

PubMed2005

Endoscopic therapy of lower gastrointestinal cancer.

Since the 1960's, endoscopy has revolutionised the practice of gastroenterology. Although initially diagnostic, endoscopy is now playing an increasingly therapeutic role. There are many reasons to believe that therapeutic endoscopy will shape the practice of gastroenterology further in the future. Only a few years ago we relied on low-resolution fibreoptic endoscopes. Nowadays even standard equipment allows the mucosa to be scrutinised in great detail. Dedicated training in endoscopy together with attention to quality indicators such as polyp detection and caecal intubation rates will ensure that fewer early gastrointestinal cancers are missed in the future. Open access endoscopy and screening programs are being introduced in many Western countries which will also lead to more lesions being detected in their early stages. This chapter discusses the main issues surrounding the endoscopic therapy of lower gastrointestinal cancers.

Colon↗

PubMed2005

Beyond the physical examination: the nurse practitioner's role in adolescent risk reduction and resiliency building in a school-based health center.

School-based health centers in high schools provide a unique setting in which to deliver risk-reduction and resilience-building services to adolescents. The traditional health care system operating in the United States focuses on the treatment of illness and disease rather than on preventing problems originating from health risk behaviors. Nurse practitioners can promote healthy behavior in adolescents through linkages to parents, schools, and community organizations; by conducting individual risk assessments; and by providing health education and access to creative health programs that build resilience and promote protective factors. With a focus on wellness, nurse practitioners as advanced practice nurses and specialists in disease prevention and health promotion can establish students' health priorities in the context of the primary health care they deliver on a daily basis.

Adolescent↗

PubMed2005

Cycling in and out of treatment; participation in methadone treatment in NSW, 1990-2002.

BACKGROUND: There are few descriptions of patterns of long-term participation in methadone treatment. There has been progressive expansion of methadone maintenance treatment (MMT) in Australia in the last 15 years, and by international standards Australia has a high participation rate in MMT, and has accumulated extensive data on participation. AIM: (1) To analyse predictors of retention in treatment (a proxy measure of treatment effectiveness) in three cohorts of people entering public and private methadone treatment, in 1990, 1995, and 2000 in the state of New South Wales (NSW), and to compare retention rates with those reported from recent clinical trials; and (2) to describe the pattern of participation in subsequent treatment and predictors of re-entry. METHOD: Sequential first admissions to MMT for the month of February during 1990, 1995, and 2000, were identified from the NSW Health database. Initial treatment setting (public or private) was identified. Pattern of subsequent participation in treatment of all subjects was also extracted. Descriptive statistics were generated, and predictors of retention in treatment and re-entry to treatment were analysed. RESULTS: The sample comprised 342 subjects commencing in private and 135 in public settings. Retention did not differ between settings. At 6 months, 51% in the current study were retained, compared to 48% in pooled clinical trials from Australia. There was a significant cohort effect; at 3 months retention was significantly better in the 1990 cohort, but by 12 months, differences between the year-cohorts were not statistically significant. Most people who left treatment dropped out; two-thirds subsequently re-entered MMT, often having multiple episodes. Participation in non-continuous treatment was around 45% for the 5 years after first entering treatment. Using multiple logistic regression, the significant predictors of re-entry to treatment were age, and duration of first treatment episode; specifically, older people and those with >12 months continuous treatment were significantly less likely to re-enter. CONCLUSION: Retention in treatment in practice, across a range of settings, appears comparable to treatment delivered in clinical trials. Participants cycle in and out of treatment, and this recycling appears to have increased as the program has expanded and access to treatment has increased.

Adult↗

PubMed2005

T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles.

Terminal restriction fragment length polymorphism (tRFLP) is a potentially high-throughput method for the analysis of complex microbial communities. Comparison of multiple tRFLP profiles to identify shared and unique components of microbial communities however, is done manually, which is both time consuming and error prone. This paper describes a freely accessible web-based program, T-Align (http://inismor.ucd.ie/~talign/), which addresses this problem. Initially replicate profiles are compared and used to generate a single consensus profile containing only terminal restriction fragments that occur in all replicate profiles. Subsequently consensus profiles representing different communities are compared to produce a list showing whether a terminal restriction fragment (TRF) is present in a particular sample and its relative fluorescence intensity. The use of T-Align thus allows rapid comparison of numerous tRFLP profiles. T-Align is demonstrated by alignment of tRFLP profiles generated from bacterioplankton communities collected from the Irish and Celtic Seas in November 2000. Ubiquitous TRFs and site-specific TRFs were identified using T-Align.

Bacteria↗

PubMed2005

An evidence-based estimate of the appropriate rate of utilization of radiotherapy for cancer of the cervix.

PURPOSE: Current estimates of the proportion of cancer patients who will require radiotherapy (RT) are based almost entirely on expert opinion. The objective of this study was to calculate the proportion of incident cases of cervical cancer that should receive RT by application of an evidence-based approach. METHODS AND MATERIALS: A systematic review of the literature was done to identify indications for RT for cervical cancer and to ascertain the level of evidence that supported each indication. A survey of Canadian gynecologic oncologists and radiation oncologists who treat cervical cancer was done to determine the level of acceptance of each indication among doctors who practice in the field. An epidemiologic approach was then used to estimate the incidence of each indication for RT in a typical North American population of patients with cervical cancer. RESULTS: The systematic review of the literature identified 29 different indications for RT for cervical cancer. The majority of the 75 experts who responded to the mail survey stated that they "usually" or "always" recommended RT in all but one of the clinical situations that were identified as indications for RT on the basis of the systematic review. The analysis of epidemiologic data revealed that, in a typical North American population, 65.4% +/- 2.5% of cervical cancer cases will develop one or more indications for RT at some point in the course of the illness, 63.4% +/- 2.3% will develop indications for RT as part of their initial management, and 2.0% +/- 0.9% will develop indications for RT for progressive or recurrent disease. The effects of variations in case mix on the need for RT was examined by sensitivity analysis, which suggested that the maximum plausible range for the appropriate rate of utilization of RT was 54.3% to 67.9%. The proportion of cases that required RT was stage dependent: 10.6% +/- 1.2% in Stage IA, 74.9% +/- 1.3% in Stage IB, 100% in Stages II and III, and 97.2% +/- 1.1% in Stage IV. CONCLUSIONS: This evidence-based estimate of the appropriate rate of use of RT for cervical cancer adds to the growing pool of knowledge about the need for RT that will ultimately provide a rational basis for long-term planning for RT programs and for auditing access to RT in the general population.

Canada↗