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At least 1,531 records · Page 85Linked to original sources
PubMed2003

Connecting sequence and biology in the laboratory mouse.

The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research grouphave generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These data provide a valuable foundation for genomic research. The challenges for the informatics community are how to integrate these data with the ever-expanding knowledge about the roles of genes and gene products in biological processes, and how to provide useful views to the scientific community. Public resources, such as the National Center for Biotechnology Information (NCBI; http://www.ncbi.nih.gov), and model organism databases, such as the Mouse Genome Informatics database (MGI; http://www.informatics.jax.org), maintain the primary data and provide connections between sequence and biology. In this paper, we describe how the partnership of MGI and NCBI LocusLink contributes to the integration of sequence and biology, especially in the context of the large-scale genome and transcriptome data now available for the laboratory mouse. In particular, we describe the methods and results of integration of 60,770 FANTOM2 mouse cDNAs with gene records in the databases of MGI and LocusLink.

Animals↗
PubMed1999

The bridge between administrative and clinical information system.

On one side, physicians are asked to record administrative information, such as activity measurement, case-mix of their specialty, billing, for statistical, legal or reimbursement purposes; and on the other side, they need to gather detailed information about their own patients in terms of clinical evolution, for the day-to-day care of the patients or for clinical research purposes. Many other actors are also involved with these processes, both on the administrative side, such as registration officers, administrators and on the clinical side, nurses and other care providers. Applications have been developed within hospital information systems for capturing and disseminating information according to these specific actors and dedicated purposes. But more and more appears the need to integrate these data for insuring the coherence of information and avoiding redundancy of data capture. How to conciliate these objectives? We describe the Geneva's approach for integrating the administrative and the clinical systems.

Data Collection↗
PubMed1996

Transcriptional analysis of the candidate region for incontinentia pigmenti (IP2) in Xq28.

The hereditary form of incontinentia pigmenti (IP2) is a rare disorder characterized by abnormalities of the tissues and organs derived from the ectoderm and neuroectoderm and has been linked to Xq28 distal to the factor VIII gene (F8C). Four YAC clones covering the 1.1-Mb candidate region at the telomere of Xq28 were subjected to direct cDNA selection and Alu long-range PCR. The products of both methods were subsequently used to isolate 154 cosmid clones that were assembled into five cosmid contigs. This first-generation cosmid map covered the region almost entirely and was used as a basis for constructing a transcript map that was in turn integrated with the physical YAC and cosmid maps. To isolate specifically coding sequences, exon trapping and cDNA selection methods were combined. Exon trapping was carried out on YAC Alu-PCR products, YAC Alu long-range PCR products, and on pools of cosmids. The region-specific enriched cDNA library was then screened by using the exon trap products as complex probes. To ensure a more complete analysis, the products from cDNA selection experiments were also used to screen conventional oligo(dT) primed cDNA libraries. Twenty overlapping cDNA contigs were assembled and computer analyses were performed to identify EST hits, open reading frames, protein motifs, and protein sequence homologies. Five of the cDNA contigs corresponded to known sequences such as the factor VIII, c6.1A, and c6.1B. genes, and both distal copies of the factor VIII intron 22 repeat sequence. Expression patterns of the 15 new cDNA contigs were analyzed by Northern blot and RT-PCR studies and these data were integrated with expression data obtained from known EST sequences. Although a more detailed analysis of this 1.1-Mb region with respect to the structure and function of the genes will only ultimately be possible by a global sequencing approach, an analysis of all novel transcripts as candidate genes for incontinentia pigmenti is already in progress.

Adult↗
PubMed2001

Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae.

Genomic and proteomic approaches can provide hypotheses concerning function for the large number of genes predicted from genome sequences. Because of the artificial nature of the assays, however, the information from these high-throughput approaches should be considered with caution. Although it is possible that more meaningful hypotheses could be formulated by integrating the data from various functional genomic and proteomic projects, it has yet to be seen to what extent the data can be correlated and how such integration can be achieved. We developed a 'transcriptome-interactome correlation mapping' strategy to compare the interactions between proteins encoded by genes that belong to common expression-profiling clusters with those between proteins encoded by genes that belong to different clusters. Using this strategy with currently available data sets for Saccharomyces cerevisiae, we provide the first global evidence that genes with similar expression profiles are more likely to encode interacting proteins. We show how this correlation between transcriptome and interactome data can be used to improve the quality of hypotheses based on the information from both approaches. The strategy described here may help to integrate other functional genomic and proteomic data, both in yeast and in higher organisms.

Fungal Proteins↗
PubMed2003

Integrating spatially referenced social and biophysical data to explore landholder responses to dryland salinity in Australia.

Researchers attempting to integrate socio-economic data in watershed planning often draw on nationally collected census data. However, there are critical limitations to the usefulness of this type of data for decision makers operating at the watershed scale. In this paper we demonstrate the relevance of spatially referenced socio-economic data collected using mail surveys to random selections of rural landholders. The issue explored was dryland salinity management in two large watersheds in the Murray-Darling Basin of south-eastern Australia. Contrary to the assumptions underlying public policy in Australia, but consistent with the literature on farmer knowledge, comparisons of expert maps and landholder identified salinity sites suggested that landholders in these watersheds had excellent knowledge of the current extent of salinity on their property. Our research also suggested that salinity education was a sound investment by governments. At the same time, the expert maps failed to predict half of the saline affected sites identified by landholders. Accurately mapping the extent of salinity would seem a first step in addressing this nationally significant land degradation issue.

Australia↗
PubMed2002

The MPEG-4 standard and electronic reporting for mobile, multimedia patient records.

Electronic reporting and transfer of confidential patient data to the electronic patient record using Internet-related and wireless technologies can pose threats to the security and integrity of data. The MPEG-4 (Moving Pictures Experts Group-Version 4) standard can enable the seamless integration of text, digitized images and video sequences, and the necessary data security protocols for mobile access to and transfer of patient information. This standard will improve the quality of the electronic patient record as well as the reliability of authentication of reports. Applying the standard for patient reporting will also improve ways for authorized users to interact with patient records. Easier access to mobile multimedia patient records will assist clinicians in documenting patient episodes in a more timely and synchronous manner. This will result in better communication between health-care team members by allowing them to stay linked and interactive even when separated by distances in a telemedicine environment.

Computer Security↗
PubMed2003

Drug induced nightmares--an etiology based review.

OBJECTIVE: Recent clinical trials have included patient complaints of nightmares as a category of reportable medication side effects. This study integrates that data into current experimental and theoretical research of drug effects that may alter dreaming and nightmares. The objective is to provide a clinical and theoretical framework useful in categorizing the potential and reported drug effects on nightmares. METHODOLOGY: This study reviews case reports and clinical trials that have reported nightmares or alterations in dreaming occurring secondary to medication usage. These data are analysed as to the probability of the drug/nightmare association, and integrated into current electrophysiological and neurochemical theories of dreaming and nightmares. RESULTS: Pharmacological agents affecting the neurotransmitters norepinephrine, serotonin and dopamine are clearly associated with patient reports of nightmares. Agents affecting immunological response to infectious disease are likely to induce nightmares in some patients. A possible association exists between reports of nightmares and agents affecting the neurotransmitters acetylcholine, GABA and histamine, as well as for some anesthetics, antipsychotics and antiepileptic agents. CONCLUSION: By utilizing our current experimental and theoretical knowledge base, the potential etiology of a majority of reported drug effects on nightmares can be classified. These data support current neurochemical theories of dreaming, as well as suggesting that the biochemical basis for dreaming and nightmare induction may be more complex than generally suggested.

Causality↗
PubMed1995

A 6-Mb yeast artificial chromosome contig and long-range physical map encompassing the region on chromosome 12q15 frequently rearranged in a variety of benign solid tumors.

Cytogenetic analysis of a variety of benign solid tumors, among which uterine leiomyoma, lipoma, pleomorphic salivary gland adenoma, and pulmonary chondroid hamartoma, has indicated that these tumors often display chromosome breakpoints in region q13-q15 of chromosome 12. In previous studies, we have reported that these breakpoints map between locus D12S8 and the CHOP gene, the latter of which has been shown to be consistently rearranged in myxoid liposarcomas with t(12;16)(q13;p11). Here, we report directional chromosome walking studies starting from D12S8 and resulting in the construction of a YAC contig of about 6 Mb. This YAC contig, whose orientation on chromosome 12 was determined by double-color fluorescence in situ hybridization (FISH) analysis, has at least double coverage and consists of 75 overlapping YAC clones, all isolated from CEPH YAC libraries. Their insert sizes were estimated by contour-clamped homogeneous electric field (CHEF) gel electrophoresis. Chromosomal localization and chimerism of the YACs were investigated by FISH analysis. Chimerism of YAC clones was independently determined by restriction mapping. On the basis of YAC end-derived DNA markers and sequence-tagged sites (STSs), with an average spacing of approximately 70 kb, as well as restriction enzyme analysis, a long-range physical map was established for the 6-Mb DNA region of chromosome 12 covered by the YAC contig. Within the YAC contig, the relative positions of various known genes, an expressed sequence-tagged site, and a number of CEPH/Généthon polymorphic markers were determined. The latter data allow full integration of our mapping data with those obtained by CEPH/Généthon as well as those reported at the Second International Workshop on Human Chromosome 12 Mapping. Finally, this YAC contig constitutes the basis for the contstruction of a transcriptional map of this region and is likely to facilitate identification of genes involved in the formation of various benign solid tumor types.

Adenoma↗
PubMed1989

The maize En-1/Spm element transposes in potato.

The maize transposable element En-1 has been introduced into a diploid potato line via transformation with Agrobacterium tumefaciens. The element is transcriptionally active in potato. Numerous En specific RNAs are observed, including a 6 kb transcript characteristic of an active En-1 element in maize. In contrast to maize, where the 6.0 kb transcript is hardly detectable, this transcript is very abundant in the transgenic potato. Transposition of En-1 in the potato clone was analysed by Southern blot hybridization and confirmed by molecular isolation of En-1 excision and integration events. Sequence data of excision and integration sites revealed footprints and target site duplications similar to the ones described for En-1 in maize.

Blotting, Southern↗
PubMed1987

Hormonal regulation of mouse mammary tumor growth.

In view of reports that human breast cancer cells secrete growth factors that can replace estradiol in sustaining tumor growth [1], we have investigated whether hormone independent (HI) GR mouse mammary tumors can sustain growth of estrogen-depleted hormone dependent (HD) tumors. HD GR mammary tumor TSl 106 was grafted subcutaneously in the right flank of estrone plus progesterone treated castrated (020 X GR)F1 mice. After 2 weeks the estrone treatment was stopped and the mice received 50, 100 or 150 mg HI GR mammary tumor TSl 104 in the left flank. However, the regression of the HD tumor due to estrone depletion was not prevented or retarded by the HI grafts. In other experiments we investigated integrations of mouse mammary tumor virus (MMTV) proviral DNA in the DNA of GR mammary tumors. We could demonstrate the presence of two cell populations in tumor TSl 96, both HD but differing in MMTV DNA integration events. Our data indicate that exogenous integrations of MMTV proviruses can take place in mouse mammary tumor DNA without loss of hormone dependency of the tumors. Like in GR/Mtv-2+ mice, mammary tumor transplants differing in MMTV proviral integrations are also observed in 020/Mtv-2+ mice.

Animals↗
PubMed2006

Expression and genomic profiling of colorectal cancer.

Colorectal cancer still represents a paradigm for the elucidation of the cellular, genetic and molecular mechanisms that underly solid tumor initiation, progression to malignancy, and metastasis to distal organ sites. The relative ease with which pathological specimens can be obtained by either surgery or endoscopy from different stages of tumor progression has facilitated the application of omics technologies to allow the genome-wide analysis both at the RNA (gene expression) and DNA (aneuploidy) levels. Here, we have reviewed the multiplicity of studies appeared to date in the scientific literature on the expression and genomic analysis of colorectal cancer, and attempted an integration of the profiling data generated and made available in the public domain. This approach is likely to pinpoint specific chromosomal loci and the corresponding genes which (i) play rate-limiting roles in colorectal cancer, (ii) represent putative diagnostic and prognostic markers for the accurate prediction of clinical outcome and response to treatment, and (iii) encompass potential therapeutic targets. Moreover, cross-species data mining and integration of the human colorectal cancer profiles with those obtained from mouse models of intestinal tumorigenesis will even more contribute to the elucidation of highly conserved pathways and cellular functions underlying malignancy in the GI tract. Notwithstanding the above promises, tumor heterogeneity, limited cohort sizes, and methodological differences among experimental and bioinformatic approaches still poses main obstacles towards the optimal utilization and integration of omics profiles.

Adenoma↗
PubMed2005

Patterns of care, outcomes, and direct health plan costs of antiepileptic therapy: a pharmacoeconomic analysis of the available carbamazepine formulations.

BACKGROUND: Although generic formulations of immediate-release carbamazepine (IR-CBZ) are available, extended-release delivery systems may offer important advantages, including the convenience of less-frequent administration and smaller peak-to-trough serum carbamazepine (CBZ) fluctuations. OBJECTIVE: The aim of this study was to compare the patterns of pharmacotherapy, rates of adverse events, and the utilization costs among patients treated with the available CBZ formulations (ie, generic and branded IR-CBZ, and extended-release CBZ (ER-CBZ) capsules [Carbatrol, Shire US Inc., Wayne, Pennsylvania] and tablets [Tegretol-XR, Novartis Pharmaccuticals Corporation, East Hanover, New Jersey]). METHODS: Data were retrieved from the PharMetrics patient-centric database (which contains integrated claims data for almost 36 million unique patients from 61 US health plans) for patients who were diagnosed with epilepsy and initiated CBZ between July 1999 and June 2001. Patient demographic and clinical characteristics, adverse events, discontinuations, CBZ therapy switches, and utilization and costs for related care subsequent to treatment initiation were recorded. Annual rates of adverse events and discontinuations were calculated, and the risks of these events were compared across treatment groups. RESULTS: Data were gathered for 1737 patients. The branded CBZ group was demographically and clinically different than the other groups (ie, migraine and cerebral palsy prevalence) and therefore was excluded from event-risk analyses. Results of the proportional hazards regression analysis indicated that Tegretol-XR patients were more likely to experience common central nervous system (CNS)-related adverse events relative to Carbatrol (hazard ratio, 1.67; P = 0.043). A lower percentage of subjects switched off ER-CBZ relative to IR-CBZ (Carbatrol, 5.2%; Tegretol-XR, 5.7%; generic IR-CBZ, 13.0%; branded IR-CBZ, 16.7%). Differences in mean payments for epilepsy-related health care services at 1 year among Carbatrol, Tegretol-XR, and branded or generic CBZ did not reach statistical significance. CONCLUSIONS: Among the available CBZ formulations, Carbatrol was associated with a lower incidence of common CNS adverse events. ER-CBZ formulations were also associated with reduced likelihood of therapy discontinuation or switching CBZ medications, relative to patients taking generic IR-CBZ, in this retrospective data analysis.

Adolescent↗
PubMed2005

The contribution of forensic science to crime analysis and investigation: forensic intelligence.

The debate in forensic science concentrates on issues such as standardisation, accreditation and de-contextualisation, in a legal and economical context, in order to ensure the scientific objectivity and efficiency that must guide the process of collecting, analysing, interpreting and reporting forensic evidence. At the same time, it is recognised that forensic case data is still poorly integrated into the investigation and the crime analysis process, despite evidence of its great potential in various situations and studies. A change of attitude is needed in order to accept an extended role for forensic science that goes beyond the production of evidence for the court. To stimulate and guide this development, a long-term intensive modelling activity of the investigative and crime analysis process that crosses the boundaries of different disciplines has been initiated. A framework that fully integrates forensic case data shows through examples the capital accumulated that may be put to use systematically.

Crime↗
PubMed1983

The relationship between developments in self-and peer perception during adolescence.

The hypothesis that self-perceptions would be more advanced developmentally than peer perceptions was assessed. The sample consisted of 80 males between 15 and 18 years of age. A structured interview was employed to obtain descriptions of self and a best friend. These data were coded into systems defining the constructs of differentiation, abstraction, and integration. The study's hypothesis was supported. A developmental model was presented to integrate the data on self and social cognition.

Adolescent↗
PubMed1997

Automated entry of hospital infection surveillance data.

OBJECTIVE: To assess the accuracy of an automated data entry system employing optical scanning technology and to provide an analysis of its costs as compared to manual data entry. DESIGN: The accuracy and cost of automated data entry of 100 surgical-wound infection surveillance questionnaires was compared to manual entry. SETTING: The Surgical Directorate, The Royal Hospitals, Belfast, Northern Ireland. RESULTS: The use of optical scanning technology greatly improved the speed and accuracy of data entry. The time spent by the keyboard operator on data entry was reduced substantially. For each surgical-wound infection questionnaire automatically processed, there was a saving in clerical time equivalent to $0.63. The automated data entry process resulted in a 22-fold productivity increase compared to manual data entry with validation. After validation, an error rate of < 0.2 errors per 1,000 responses was detected in automatically entered data compared to a rate of 12.4 errors per 1,000 responses for manually entered data. The automated system, including validation, provided a seven-fold productivity increase compared to "quick-and-dirty" manual data entry without validation. CONCLUSION: Hospital information technology systems may achieve total integration of data management, but realistically this would appear to be very much in the future. Until then, in view of the accuracy and substantial savings in time and money, we recommend the use of automated data entry technology. This system would be especially useful where data are transported from outlying hospitals to a central receiving center for collation and analysis.

Cost-Benefit Analysis↗
PubMed2006

EMBL Nucleotide Sequence Database: developments in 2005.

The EMBL Nucleotide Sequence Database (www.ebi.ac.uk/embl) at the EMBL European Bioinformatics Institute, UK, offers a comprehensive set of publicly available nucleotide sequence and annotation, freely accessible to all. Maintained in collaboration with partners DDBJ and GenBank, coverage includes whole genome sequencing project data, directly submitted sequence, sequence recorded in support of patent applications and much more. The database continues to offer submission tools, data retrieval facilities and user support. In 2005, the volume of data offered has continued to grow exponentially. In addition to the newly presented data, the database encompasses a range of new data types generated by novel technologies, offers enhanced presentation and searchability of the data and has greater integration with other data resources offered at the EBI and elsewhere. In stride with these developing data types, the database has continued to develop submission and retrieval tools to maximise the information content of submitted data and to offer the simplest possible submission routes for data producers. New developments, the submission process, data retrieval and access to support are presented in this paper, along with links to sources of further information.

Animals↗
PubMed2006

Developments in CORG: a gene-centric comparative genomics resource.

The CORG resource (Comparative Regulatory Genomics, http://corg.eb.tuebingen.mpg.de) provides extensive cross-species comparisons of promoter regions in particular and whole gene loci in general. Pairwise as well as multiple alignments of 10 vertebrate species form the key component of CORG. We implemented a rapid alignment approach based on weight matrix motif anchors to ensure efficient computation and biologically informative alignments. All CORG workbench components have been enhanced towards more flexibility and interactivity. Reference sequence based data presentation and analysis was put into the well-known and modular Generic Genome Browser framework. Herein, various plugins facilitate online data analysis and integration with static conservation data. Main emphasis was put on the design of a new JAVA WebStart application for comparative data display. Flexible data import and export options for standard formats complete the provided services.

Animals↗
PubMedDate not supplied

Security aspects of electronic data interchange between a state health department and a hospital emergency department.

Electronic emergency department reporting provides the potential for enhancing local and state surveillance capabilities for a wide variety of syndromes and reportable conditions. The task of protecting data confidentiality and integrity while developing electronic data interchange between a hospital emergency department and a state public health department proved more complex than expected. This case study reports on the significant challenges that had to be resolved to accomplish this goal; these included application restrictions and incompatibilities, technical malfunctions, changing standards, and insufficient dedicated resources. One of the key administrative challenges was that of coordinating project security with enterprise security. The original project has evolved into an ongoing pilot, with the health department currently receiving secure data from the emergency department at four-hour intervals. Currently, planning is underway to add more emergency departments to the project.

Computer Communication Networks↗