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PubMed2003

CORG: a database for COmparative Regulatory Genomics.

Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a catalogue of conserved non-coding sequence blocks and provide the CORG-'COmparative Regulatory Genomics'-database. The data were computed based on statistically significant local suboptimal alignments of 15 kb regions upstream of the translation start sites of, currently, 10 793 pairs of orthologous genes. The resulting conserved non-coding blocks were annotated with EST matches for easier detection of non-coding mRNA and with hits to known transcription factor binding sites. CORG data are accessible from the ENSEMBL web site via a DAS service as well as a specially developed web service (http://corg.molgen.mpg.de) for query and interactive visualization of the conserved blocks and their annotation.

Animals↗

PubMed2003

The SNP Consortium website: past, present and future.

The SNP Consortium website (http://snp.cshl.org) has undergone many changes since its initial conception three years ago. The database back end has been changed from the venerable ACeDB to the more scalable MySQL engine. Users can access the data via gene or single nucleotide polymorphism (SNP) keyword searches and browse or dump SNP data to textfiles. A graphical genome browsing interface shows SNPs mapped onto the genome assembly in the context of externally available gene predictions and other features. SNP allele frequency and genotype data are available via FTP-download and on individual SNP report web pages. SNP linkage maps are available for download and for browsing in a comparative map viewer. All software components of the data coordinating center (DCC) website (http://snp.cshl.org) are open source.

Chromosome Mapping↗

PubMed2004

SledgeHMMER: a web server for batch searching the Pfam database.

The SledgeHMMER web server is intended for genome-scale searching of the Pfam database without having to install this database and the HMMER software locally. The server implements a parallelized version of hmmpfam, the program used for searching the Pfam HMM database. Pfam search results have been calculated for the entire Swiss-Prot and TrEmbl database sequences (approximately 1.2 million) on 256 processors of IA64-based teragrid machines. The Pfam database can be searched in local, glocal or merged mode, using either gathering or E-value thresholds. Query sequences are first matched against the pre-calculated entries to retrieve results, and those without matches are processed through a new search process. Results are emailed in a space-delimited tabular format upon completion of the search. While most other Pfam-searching web servers set a limit of one sequence per query, this server processes batch sequences with no limit on the number of input sequences. The web server and downloadable data are accessible from http://SledgeHmmer.sdsc.edu.

Algorithms↗

PubMed2005

BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser.

The growing amount of information resulting from the increasing number of publicly available genomes and experimental results thereof necessitates the development of comprehensive systems for data processing and analysis. In this paper, we describe the current state and latest developments of our BRIGEP bioinformatics software system consisting of three web-based applications: GenDB, EMMA and ProDB. These applications facilitate the processing and analysis of bacterial genome, transcriptome and proteome data and are actively used by numerous international groups. We are currently in the process of extensively interconnecting these applications. BRIGEP was developed in the Bioinformatics Resource Facility of the Center for Biotechnology at Bielefeld University and is freely available. A demo project with sample data and access to all three tools is available at https://www.cebitec.uni-bielefeld.de/groups/brf/software/brigep/. Code bundles for these and other tools developed in our group are accessible on our FTP server at ftp.cebitec.uni-bielefeld.de/pub/software/.

Bacterial Proteins↗

PubMed2006

pTARGET: a web server for predicting protein subcellular localization.

The pTARGET web server enables prediction of nine distinct protein subcellular localizations in eukaryotic non-plant species. Predictions are made using a new algorithm [C. Guda and S. Subramaniam (2005) pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics, 21, 3963-3969], which is primarily based on the occurrence patterns of location-specific protein functional domains in different subcellular locations. We have implemented a relational database, PreCalcDB, to store pre-computed prediction results for all eukaryotic non-plant protein sequences in the public domain that includes about 770,000 entries. Queries can be made by entering protein sequences or by uploading a file containing up to 5000 protein sequences in FASTA format. Prediction results for queries with matching entries in the PreCalcDB will be retrieved instantly; while for the missing ones new predictions will be computed and sent by email. Pre-computed predictions can also be downloaded for complete proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Mus musculus and Homo sapiens. The server, its documentation and the data are accessible from http://bioinformatics.albany.edu/~ptarget.

Algorithms↗

PubMed2007

Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de.

Functional glycomics, the scientific attempt to identify and assign functions to all glycan molecules synthesized by an organism, is an emerging field of science. In recent years, several databases have been started, all aiming to support deciphering the biological function of carbohydrates. However, diverse encoding and storage schemes are in use amongst these databases, significantly hampering the interchange of data. The mutual online access between the Bacterial Carbohydrate Structure DataBase (BCSDB) and the GLYCOSCIENCES.de portal, as a first reported attempt of a structure-based direct interconnection of two glyco-related databases is described. In this approach, users have to learn only one interface, will always have access to the latest data of both services, and will have the results of both searches presented in a consistent way. The establishment of this connection helped to find shortcomings and inconsistencies in the database design and functionality related to underlying data concepts and structural representations. For the maintenance of the databases, duplication of work can be easily avoided, and will hopefully lead to a better worldwide acceptance of both services within the community of glycoscienists. BCSDB is available at http://www.glyco.ac.ru/bcsdb/ and the GLYCOSCIENCES.de portal at http://www.glycosciences.de/.

Animals↗

PubMed2006

The mouse genome database (MGD): new features facilitating a model system.

The mouse genome database (MGD, http://www.informatics.jax.org/), the international community database for mouse, provides access to extensive integrated data on the genetics, genomics and biology of the laboratory mouse. The mouse is an excellent and unique animal surrogate for studying normal development and disease processes in humans. Thus, MGD's primary goals are to facilitate the use of mouse models for studying human disease and enable the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Core MGD data content includes gene characterization and functions, phenotype and disease model descriptions, DNA and protein sequence data, polymorphisms, gene mapping data and genome coordinates, and comparative gene data focused on mammals. Data are integrated from diverse sources, ranging from major resource centers to individual investigator laboratories and the scientific literature, using a combination of automated processes and expert human curation. MGD collaborates with the bioinformatics community on the development of data and semantic standards, and it incorporates key ontologies into the MGD annotation system, including the Gene Ontology (GO), the Mammalian Phenotype Ontology, and the Anatomical Dictionary for Mouse Development and the Adult Anatomy. MGD is the authoritative source for mouse nomenclature for genes, alleles, and mouse strains, and for GO annotations to mouse genes. MGD provides a unique platform for data mining and hypothesis generation where one can express complex queries simultaneously addressing phenotypic effects, biochemical function and process, sub-cellular location, expression, sequence, polymorphism and mapping data. Both web-based querying and computational access to data are provided. Recent improvements in MGD described here include the incorporation of single nucleotide polymorphism data and search tools, the addition of PIR gene superfamily classifications, phenotype data for NIH-acquired knockout mice, images for mouse phenotypic genotypes, new functional graph displays of GO annotations, and new orthology displays including sequence information and graphic displays.

Animals↗

PubMed2006

CSRDB: a small RNA integrated database and browser resource for cereals.

Plant small RNAs (smRNAs), which include microRNAs (miRNAs), short interfering RNAs (siRNAs) and trans-acting siRNAs (ta-siRNAs), are emerging as significant components of epigenetic processes and of gene networks involved in development and in homeostasis. Here we present a bioinformatics resource for cereal crops, the Cereal Small RNA Database (CSRDB), consisting of large-scale datasets of maize and rice smRNA sequences generated by high-throughput pyrosequencing. The smRNA sequences have been mapped to the rice genome and to the available maize genome sequence and these results are presented in two genome browser datasets using the Generic Genome Browser. Potential RNA targets for the smRNAs have been predicted and access to the resulting smRNA/RNA target pair dataset has been made available through a MySQL based relational database. Various ways to access the data are provided including links from the genome browser to the target database. Data linking and integration are the main focus for this interface, and internal as well as external links are present. The resource is available at http://sundarlab.ucdavis.edu/smrnas/ and will be updated as more sequences become available.

Databases, Nucleic Acid↗

PubMed1997

The use of mapping in public health and planning health services.

The availability of relatively inexpensive, user-friendly geographical information systems, with a steadily extending range of analytic and other facilities, provides a powerful tool for the analysis and display of the increasing number of health-related data sets, and for their greater accessibility. Relationships between several sets of variables can become immediately apparent from a map in a way that is much more difficult to comprehend from a table or description. It is also easy to define ad hoc areas, such as the area adjacent to a possible toxic point source or to a main road, in terms of unit postcodes and Census output areas, to determine standardized rates for mortality and hospital admissions. Apart from the geographical information system itself, the basic requirements are access to relevant data sets including Census data, and to the central postcode directory, which provides grid references for unit postcodes and permits matching of postcoded health events to Census output areas.

Catchment Area, Health↗

PubMed1996

Responses within nonfederal hospitals in Pennsylvania to the Americans with Disabilities Act of 1990.

BACKGROUND AND PURPOSE: This study described responses within nonfederal hospitals in Pennsylvania to the Americans With Disabilities Act of 1990 (ADA). SUBJECTS: The target population consisted of all 277 nonfederal hospitals licensed by the Pennsylvania Department of Health and Department of Public Welfare. METHODS: Questionnaires were mailed to the 270 chief administrators for the 277 hospitals. RESULTS: One hundred seventeen questionnaires (43.3%) were returned. More facilities had trained their managers regarding the ADA versus their nonmanagerial employees. Overall, 80.3% of the hospitals had an ADA committee or coordinator. Fifty-four percent of the respondents reported that job accommodations cost less than $500. Approximately 45% of the participants cited that the percentage of new construction costs spent to increase accessibility in their hospitals was less than 4.9%. More complaints and legal matters were received by facilities regarding the employment provisions of the ADA rather than the accessibility provisions. CONCLUSION AND DISCUSSION: The results suggest that hospitals need to monitor ADA-related expenses, more employee training is needed to ensure the ADA's success, and more representation is needed on hospital committees by rehabilitation personnel and individuals with disabilities.

Analysis of Variance↗

PubMed1999

Planning ahead: practical hints for designing ambulatory care facilities.

This article discusses a variety of topics that need to be addressed during the design of an ambulatory care facility, particularly those areas that need to be discussed at the beginning of the project. Topics include life safety/code issues involving building classification, employee safety, and accessibility; regulatory agencies; design issues including design sources, touring comparable facilities, room mock-ups, staff evaluation/wish list, setting standards, and determining responsibility; and medical equipment including planning and current trends. The time you spend planning ahead is time well spent.

Ambulatory Care Facilities↗

PubMed2003

Primary and metastatic cancer of the parotid: comparison of clinical behavior in 232 cases.

OBJECTIVES/HYPOTHESIS: Parotid malignancy may develop as a primary cancer of salivary tissue or by metastatic involvement of parotid lymph nodes. The aim of the study was to compare the clinical behavior of primary and metastatic parotid cancers by analyzing patterns of treatment failure and clinical outcomes. STUDY DESIGN: Retrospective review of clinical and pathologic data prospectively accessioned onto a computerized database. METHODS: A prospectively documented series of 232 parotidectomies carried out for treatment of cancer from 1988 to 1999 was reviewed. There were 177 male and 55 female patients with a median age of 65 years (age range, 17-97 y). Median follow-up time was 4 years. Pathological groups included 54 patients with primary parotid cancer, 101 with metastatic cutaneous squamous cell carcinoma, 69 with metastatic melanoma, and 8 with other metastatic cancers. RESULTS: Neck nodes were clinically positive in 12 patients with primary cancer, 24 patients with squamous cell carcinoma, 16 with melanoma, and 2 with other metastatic malignancies. Conservative parotidectomy, preserving the main trunk of the facial nerve, was performed in 185 patients, and 47 patients had a radical parotidectomy sacrificing the facial nerve. There were 54 therapeutic and 110 elective neck dissections. Adjuvant radiotherapy was given to 39 patients with primary cancer, 86 with squamous cell carcinoma, 50 with melanoma, and 8 in the other metastatic group (78% of the patients in the series). Local control rates at 5 years in the four groups were 86%, 75%, 94%, and 100%, respectively (P <.01). Survival rates at 5 years were 77%, 65%, 46%, and 56%, respectively (P <.01). CONCLUSIONS: The pattern of parotid malignancy is unique in Australia because of the high incidence of skin cancer, which can metastasize to the parotid gland. Metastatic cutaneous malignancy predominates. The pattern of failure and outcome varied depending on histological findings. Local failure occurred most often in metastatic squamous cell carcinoma, whereas patients with melanoma had the highest incidence of distant spread.

Adolescent↗

PubMedDate not supplied

Nursing information systems: applications in nursing curricula.

America's healthcare system is being transformed to meet a new set of priorities: cost-effectiveness, quality, and access. To meet these priorities, health practitioners of the 21st century will rely heavily on computer information systems to provide complete, easily accessed patient data. Incorporation of this technology in nursing programs will enhance the quality of the graduates who will then strengthen the availability of a qualified work force to employers.

Computer User Training↗

PubMed1999

Measuring quality in hospitals: is there a difference between for-profits and not-for-profits?

Health care professionals agree that by measuring quality, improvements can be made in care delivery. There are measurable differences between not-for-profit and for-profit hospitals, both in public perception and care outcomes. The ability by consumers, insurers and providers to easily access quality data will drive the health care industry to take a quality focus in their daily business. Quality providers with measurable results will gain a larger share of health care dollars and consumer trust. Physicians will choose to partner with the quality leaders and will refine their practices as part of the quality evolution.

Diagnosis-Related Groups↗

PubMed2002

The process to develop a meaningful community health assessment in New York State.

Conducting and producing a meaningful Community Health Assessment (CHA) is an important and essential public health service and a mandatory biennial activity for New York State's (NYS) Local Health Departments. The Assessment Initiative project has allowed the NYS Department of Health to better understand and identify strategies to strengthen CHAs and to develop training, education, and technical assistance programs. The Assessment Initiative project has benefited from participation, coordination, and sharing of resources and expertise with other community health improvement initiatives in NYS, including those that emphasize collaborative approaches to health improvement, workforce development, and expanding access to data.

Community Health Planning↗

PubMed2005

Prevention of mother-to-child transmission and voluntary counseling and testing programme data: what is their utility for HIV surveillance?

OBJECTIVE: Antenatal clinic (ANC)-based surveillance through unlinked anonymous testing (UAT) for HIV without informed consent provides solid long-term trend data in resource-constrained countries with generalized epidemics. The rapid expansion of the prevention of mother-to-child transmission (PMTCT) and voluntary counseling and testing (VCT) programmes prompts the question regarding their utility for HIV surveillance and their potential to replace UAT-based ANC surveillance. METHODS: Four presentations on the use of PMTCT or VCT data for HIV surveillance were presented at a recent international conference. The main findings are presented in this paper, and the operational and epidemiological aspects of using PMTCT or VCT data for surveillance are considered. RESULTS: VCT data in Uganda confirm the falling trend in HIV prevalence observed in ANC surveillance. Thailand, a country with nationwide PMTCT coverage and a very high acceptance of HIV testing, has replaced UAT data in favor of PMTCT data for surveillance. Studies from Botswana and Kenya showed that PMTCT-based HIV prevalences was similar, but the quality and availability of the PMTCT data varied. CONCLUSION: The strength of UAT lies in the absence of selection bias and the availability of individual data. Conversely, the quantity of VCT and PMTCT programme testing data often exceed those in UAT, but may be subject to bias due to self-selection or test refusal. When using VCT or PMTCT data for surveillance, investigators must consider these caveats, as well as their varying data quality, accessibility, and availability of individual records.

Adolescent↗

PubMed2003

Clinical and educational uses of handheld computers.

Handheld computers, also known as personal digital assistants (PDAs), are becoming an increasingly valuable aid to physicians at the point of care. We review the use of handheld computers and their impact in clinical practice and medical education. Clinicians commonly use PDAs to access patient data and as a clinical reference tool. In medical education, handheld computers are most frequently used to track patient encounters and procedures done during medical school rotations and residency training. This report describes some interesting applications for present and future use of PDAs in inpatient care and medical education. Physicians and educational programs not using PDAs may wish to consider incorporating this technology.

Computers, Handheld↗

PubMed2005

Relating connectional architecture to grey matter function using diffusion imaging.

Understanding brain function in terms of connectional architecture is a major goal of neuroimaging. However, direct investigation of the influence of brain circuitry on function has been hindered by the lack of a technique for exploring anatomical connectivity in the in vivo brain. Recent advances in magnetic resonance diffusion imaging have given scientists access to data relating to local white matter architecture and, for the first time, have raised the possibility of in vivo investigations into brain circuitry. This review investigates whether diffusion imaging may be used to identify regions of grey matter that are distinct in their connectional architecture, and whether these connectional differences are reflected either in local cytoarchitecture or in local grey matter function. Establishing a direct relationship between regional boundaries based on diffusion imaging and borders between regions that perform different functions would not only be of great significance when interpreting functional results, but would also provide a first step towards the validation of diffusion-based anatomical connectivity studies.

Brain↗