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At least 127 records · Page 7Linked to original sources
PubMed2002

Assessing the applicability of GIS in a health and social care setting: planning services for informal carers in East Sussex, England.

Informal carers save the state's health and social care services billions of pounds each year. The stresses associated with caring have given rise to a number of short-term care services to provide respite to carers. The Carers (Recognition & Services) Act of 1995 identified formally for the first time, the important role that unpaid carers provide across the community in Britain. The planning of combined health and social care services such as short-term care is a less developed application of geographical information systems (GIS) and this paper examines awareness and application issues associated with the potential use of GIS to manage short-term care service planning for informal carers in East Sussex. The assessment of GIS awareness was carried out by using a semi-structured questionnaire approach and interviewing key local managers and planners across a number of agencies. GIS data was gathered from the agencies and developed within a GIS to build up a set of spatial databases of available services, location of users and additional geo-demographic and topographic information. The output from this system development was presented in turn at workshops with agencies associated with short-term care planning as well as users to help assess their perspectives on the potential use and value of GIS. A renewed emphasis on a planned approach to health care coupled with integrated/ joint working with social care creates a need for new approaches to planning. The feedback from planners and users, suggested that a number of key data elements attached to data-sharing may prove to be simultaneously progressive yet problematic, especially in the areas of ethics, confidentiality and informed consent. A critical response to the suitability of GIS as a tool to aid joint health and social care approaches is incorporated within a final summary.

Caregivers↗
PubMed2001

A comparison of microarray databases.

Microarray technology has become one of the most important functional genomics technologies. A proliferation of microarray databases has resulted. It can be difficult for researchers exploring this technology to know which bioinformatics systems best meet their requirements. In order to obtain a better understanding of the available systems, a survey and comparative analysis of microarray databases was undertaken. The survey included databases that are currently available, as well as databases that should become available in early 2001. Databases fall into three categories: (i) those that can be installed locally, (ii) those available for public data submission and (iii) those available for public query. Developers of microarray gene-expression databases were asked questions regarding the scope and availability of their database, its system requirements, its future compliance with MGED (Microarray Gene Expression Database) standards, and its associated analytical tools. Participants included AMAD (Stanford/Berkeley/UCSF), ArrayExpress (EBI), ChipDB (MIT/Whitehead), GeneX (NCGR), GeNet (Silicon Genetics), GeneDirector (BioDiscovery), GEO (NCBI), GXD (Jackson Laboratory), mAdb (NCI), maxdSQL (University of Manchester), NOMAD (UCSF), RAD (University of Pennsylvania) and SMD (Stanford University). Other database developers were contacted but data was not available at the time of manuscript preparation. Each database fulfils a different role, reflecting the widely varying needs of microarray users.

Animals↗
PubMed2001

A GIS planning model for urban oil spill management.

Oil spills in industrialized cities pose a significant threat to their urban water environment. The largest city in Canada, the city of Toronto, has an average 300-500 oil spills per year with an average total volume of about 160,000 L/year. About 45% of the spills was eventually cleaned up. Given the enormous amount of remaining oil entering into the fragile urban ecosystem, it is important to develop an effective pollution prevention and control plan for the city. A Geographic Information System (GIS) planning model has been developed to characterize oil spills and determine preventive and control measures available in the city. A database of oil spill records from 1988 to 1997 was compiled and geo-referenced. Attributes to each record such as spill volume, oil type, location, road type, sector, source, cleanup percentage, and environmental impacts were created. GIS layers of woodlots, wetlands, watercourses, Environmental Sensitive Areas, and Areas of Natural and Scientific Interest were obtained from the local Conservation Authority. By overlaying the spill characteristics with the GIS layers, evaluation of preventive and control solutions close to these environmental features was conducted. It was found that employee training and preventive maintenance should be improved as the principal cause of spills was attributed to human errors and equipment failure. Additionally, the cost of using oil separators at strategic spill locations was found to be $1.4 million. The GIS model provides an efficient planning tool for urban oil spill management. Additionally, the graphical capability of GIS allows users to integrate environmental features and spill characteristics in the management analysis.

Cities↗
PubMed2006

Gene expression omnibus: microarray data storage, submission, retrieval, and analysis.

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information archives and freely distributes high-throughput molecular abundance data, predominantly gene expression data generated by DNA microarray technology. The database has a flexible design that can handle diverse styles of both unprocessed and processed data in a Minimum Information About a Microarray Experiment-supportive infrastructure that promotes fully annotated submissions. GEO currently stores about a billion individual gene expression measurements, derived from over 100 organisms, submitted by over 1500 laboratories, addressing a wide range of biological phenomena. To maximize the utility of these data, several user-friendly web-based interfaces and applications have been implemented that enable effective exploration, query, and visualization of these data at the level of individual genes or entire studies. This chapter describes how data are stored, submission procedures, and mechanisms for data retrieval and query. GEO is publicly accessible at http://www.ncbi.nlm.nih.gov/projects/geo/.

Animals↗
PubMed2026

Integrative pan-cancer analysis of transferrin reveals context-dependent prognostic associations and links to immune and metabolic disease-related programs.

BACKGROUND: Iron metabolism is closely linked to tumor biology, yet the pan-cancer significance of transferrin (TF), the major circulating iron-transport protein, remains insufficiently defined. Although TF has been implicated in cancer-related processes, its prognostic relevance, immune associations, and broader disease-related transcriptional context have not been systematically characterized across tumor types. OBJECTIVE: This study aimed to perform an integrative pan-cancer analysis of TF to characterize its expression patterns, clinical associations, immune context, pathway features, and pharmacogenomic correlations, and to explore whether TF-related signals extend to selected metabolic and chronic organ injury settings. METHODS: We used multiple public databases, including The Cancer Genome Atlas (TCGA), Human Protein Atlas (HPA), Gene Expression Omnibus (GEO), and Cancer Cell Line Encyclopedia (CCLE), to integrate transcriptomic, proteomic, and clinical data across 33 tumor types and selected non-malignant conditions. TF expression was evaluated across normal tissues, tumors, and cell lines, followed by survival analysis, immune infiltration analysis, TMB/MSI and methylation assessment, pathway enrichment, and drug-response correlation. Independent GEO cohorts of non-alcoholic steatohepatitis (NASH), heart failure (HF), and liver cirrhosis (LC) were used for cross-disease extension. Selected findings were further explored in OA/PA-treated hepatocytes, 786-O renal carcinoma cells, and AC16 cardiomyocytes. RESULTS: TF showed pronounced tissue specificity and cancer-type-dependent dysregulation. Across pan-cancer cohorts, the most consistent adverse survival associations were observed in kidney renal clear cell carcinoma (KIRC) and stomach adenocarcinoma (STAD), where TF remained associated with overall survival (OS) in multivariable analyses. TF expression was also correlated with cancer-type-specific immune infiltration patterns and selected drug-response profiles. Across independent NASH, HF, and LC datasets, TF expression was elevated and TF-associated pathways partially overlapped with those observed in cancer. In vitro experiments provided preliminary support that TF modulation is associated with proliferative phenotypes in KIRC cells and stress- and metabolism-related phenotypes in hepatocyte and cardiomyocyte models. CONCLUSION: These findings support TF as a context-dependent biomarker candidate in cancer, with the most consistent prognostic relevance observed in KIRC and STAD. Rather than establishing a unified mechanism across diseases, this study provides an integrative framework suggesting that TF is associated with malignant behavior, immune context, and selected metabolic stress-related programs, and warrants further mechanistic investigation.

Iron metabolism↗
PubMed2026

Identification of Immune Response-Related Proteomic Biomarkers in Moyamoya Disease Using Serum Olink Proteomics.

Moyamoya disease, a rare chronic cerebrovascular disorder, requires invasive digital subtraction angiography (DSA) for diagnosis. This study employed high-throughput proteomics to identify plasma biomarkers for Moyamoya disease diagnosis. We conducted immunopanel analysis using the Olink platform to evaluate 92 immune-related proteins in plasma samples from 88 Moyamoya disease patients and 88 healthy controls. Key proteins were identified through differential expression analysis, GO, and KEGG enrichment analysis. A diagnostic model was constructed using LASSO regression, Boruta algorithm, and machine learning models including random forest and XGBoost. Validation of these proteins was performed using GEO external data sets, followed by prediction of potential therapeutic drugs and molecular docking validation through pharmacogenomic databases. A total of 44 differentially expressed proteins were identified through the Olink immunopanel, with 12 downregulated and 32 upregulated. GO and KEGG analyses revealed significant enrichment of these proteins in innate immune responses and signaling pathways such as NF-kB and MAPK. Through LASSO, random forest, and protein under-area analysis, four potential biomarkers for Moyamoya disease (MGMT, SIT1, PRDX1, TRAF2) were identified. A diagnostic model using these proteins showed the highest AUC value with the XGBoost model. Additionally, TRAF2 and PRDX1 exhibited significant expression differences in Moyamoya disease patients within the GEO data set. Our study revealed the immune landscape of Moyamoya disease, identified four biomarkers, and established a variety of diagnostic models.

Humans↗
PubMed2005

Geographic information system method for assessing chemo-diversity in medicinal plants.

The spatial distribution of wild germplasm of Podophyllum peltatum L. (American mayapple) has been analyzed using the Geographic Information System (GIS) with the objective to develop a method and a database for evaluation of biotic and abiotic factors influencing drug yield, and to map elite genotypes for propagation and improvement. The field assessment followed a standard procedure including geographical coordinates of each accession, leaf biomass randomly harvested, identification of associate species, collection of herbarium specimen, soil sample and digital pictures of the site. By overlaying morphological and chemical data with geomorphic information, a thematic map was created locating the podophyllotoxin-rich accessions and the uniqueness of each site was recorded for post-collection analysis. This work has enabled the establishment of a database of P. peltatum germplasm in Mississippi with drug yield linked to spatial locations for rational utilization of our natural resources. While this method integrates information of well-characterized diverse in situ P. peltatum germplasm, it might become a strategy for curators to reduce cost for establishing and maintaining ex situ collections since the genetic material is geo-referenced.

Databases, Factual↗
PubMed2004

Prognosis of environmental concentrations by geo-referenced and generic models: a comparison of GREAT-ER and EUSES exposure simulations for some consumer-product ingredients in the Itter.

The aim of this study was the comparison between predicted environmental concentrations (PEC) derived using a generic aspacial model, European Union System for the Evaluation of Substances (EUSES), and a geo-referenced model, the Geo-referenced Regional Environmental Assessment Tool for European Rivers (GREAT-ER). The PECs of some consumer-product ingredients (boron, LAS) and professional uses (EDTA, NTA and Triclosan) were calculated for the river catchment of the Itter, a small tributary to the river Rhine. The PEClocal and PECregional for the water compartment generated by EUSES (default scenario) were subsequently refined with data that realistically reflects the region of North Rhine-Westphalia (NRW scenario) and the Itter catchment (Itter scenario). The results of the three scenarios were then compared with the PECinitial and PECcatchment calculated by GREAT-ER, that was designed as a higher-tiered exposure assessment tool, and with concrete concentrations in the Itter, measured as 24-h composite samples. While the PECregional of all scenarios was close to the lower end of the measured concentrations, the geo-referenced PECs described equally well the real spacial situation. The measured environmental concentrations confirmed the built-in conservatism of the PEClocal calculations by EUSES showing for all investigated chemicals an unrealistically high PEClocal (default). The refinement in the more realistic scenarios could not provide a straight forward general improvement of the PEClocal. In conclusion, when the EUSES prognosis is refined using more detailed substance and regional specific data, it may provide a fairly accurate modelling especially of substances that are not eliminated in the environment. However, in the case of eliminable substances, it does not match the accuracy of higher-tiered geo-referenced exposure models like GREAT-ER.

Arylsulfonates↗
PubMed2005

Reconstructing recent human phylogenies with forensic STR loci: a statistical approach.

BACKGROUND: Forensic Short Tandem Repeat (STR) loci are effective for the purpose of individual identification, and other forensic applications. Most of these markers have high allelic variability and mutation rate because of which they have limited use in the phylogenetic reconstruction. In the present study, we have carried out a meta-analysis to explore the possibility of using only five STR loci (TPOX, FES, vWA, F13A and Tho1) to carry out phylogenetic assessment based on the allele frequency profile of 20 world population and north Indian Hindus analyzed in the present study. RESULTS: Phylogenetic analysis based on two different approaches - genetic distance and maximum likelihood along with statistical bootstrapping procedure involving 1000 replicates was carried out. The ensuing tree topologies and PC plots were further compared with those obtained in earlier phylogenetic investigations. The compiled database of 21 populations got segregated and finely resolved into three basal clusters with very high bootstrap values corresponding to three geo-ethnic groups of African, Orientals, and Caucasians. CONCLUSION: Based on this study we conclude that if appropriate and logistic statistical approaches are followed then even lesser number of forensic STR loci are powerful enough to reconstruct the recent human phylogenies despite of their relatively high mutation rates.

Forensic Anthropology↗
PubMed2006

Tuberculosis risks and socio-economic level: a case study of a city in the Brazilian south-east, 1998-2004.

OBJECTIVES: To explore tuberculosis (TB) risks in relation to potential determinants in the city of São José do Rio Preto, São Paulo State, Brazil; to analyse morbidity and mortality indicators in São José do Rio Preto, and to determine the relationship between the risk of TB and socio-economic level (SEL) using a geo-referenced information system (GIS) and the national census for 2000. METHOD: Standardised incidence rates and TB incidence and mortality rates were calculated. Socio-economic variables were determined using the statistical technique of principal component analysis. Data sources were the São Paulo State Data Analysis System (SEADE), the TB Notification Database (EPI-TB), the Information Department of the Brazilian Health Ministry (DATASUS), and the Brazilian Institute of Geography and Statistics (IBGE). New cases reported in 1998-1999 and 2003-2004 in the urban area of the city were geo-referenced and analysed. RESULTS: TB risk in the city is twice as high in areas of lower SEL than in areas with higher SEL. CONCLUSION: The identification of areas with different levels of risk enables the Municipal Health Department to propose innovative interventions to minimise the risk of disease at both individual and population level.

Brazil↗
PubMed2006

The GIS-based SafeAirView software for the concentration assessment of radioactive pollutants after an accidental release.

The European Commission Joint Research Centre (JRC) in Ispra (Italy) has long been running nuclear installations for research purposes. The Nuclear Decommissioning and Facilities Management Unit (NDFM) is responsible for the surveillance of radioactivity levels in nuclear emergency conditions. The NDFM Unit has commissioned the implementation of a specifically developed decision support system, which can be used for quick emergency evaluation in the case of hypothetical accident and for emergency exercises. The requisites were to be a user-friendly software, able to quickly calculate and display values of air and ground radioactive contamination in the complex area around JRC, following an accidental release of radioactive substances from a JRC nuclear research installation. The developed software, named "SafeAirView", is an advanced implementation of GIS technology applied to an existing MS-DOS mode dispersion model, SAFE_AIR (Simulation of Air pollution From Emissions_Above Inhomogeneous Regions). SAFE_AIR is a numerical model which simulates transport, diffusion, and deposition of airborne pollutants emitted in the low atmosphere above complex orography at both local and regional scale, under non-stationary and inhomogeneous emission and meteorological conditions. SafeAirView makes use of user-friendly MS-Windows type interface which drives the dispersion model by a sequential and continuous input-output process, allowing a real time simulation. The GIS environment allows a direct interaction with the territory elements in which the simulation takes place, using data for the JRC Ispra region represented in geo-referenced cartography. Furthermore it offers the possibility to relate concentrations with population distribution and other geo-referenced maps, in a geographic view. Output concentration and deposition patterns can be plotted and/or exported. In spite of the selected specific databases, the SafeAirView software architecture is a general structure, therefore the decision support system could be easily modified to be applied in a region different from the JRC one. Beside the description of SafeAirView, the present paper presents a statistical evaluation of the software, which has considered three well known tracer experiments: Copenhagen, Indianapolis and Kincaid. The data sets related to these experiments are all included in the so called Model Validation Kit.

Data Interpretation, Statistical↗
PubMed2026

Exploring the Mechanism of Zhigancao Decoction in the Treatment of Chronic Heart Failure via Modulation of Oxidative Stress.

BACKGROUND: Zhigancao decoction has shown therapeutic potential in the management of chronic heart failure (CHF); however, the molecular mechanisms underlying its pharmacological effects remain incompletely understood. This study aimed to investigate its potential mechanisms, with a particular focus on oxidative stress-related pathways. METHODS: The chemical profile of Zhigancao decoction was characterized by LC-MS/MS, and putative targets were predicted using SwissTargetPrediction. A protein-protein interaction (PPI) network was established using the STRING database and Cytoscape software, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Differentially expressed genes from two GEO datasets (GSE9128 and GSE84796) were integrated with reactive oxygen species (ROS)-related genes to identify candidate targets. Network pharmacology and molecular docking were subsequently performed to investigate compound-target interactions. RESULTS: A total of 66 chemical constituents and 818 putative targets were characterized and collected, respectively. Among these targets, MMP9 emerged as a central candidate associated with the therapeutic effects of Zhigancao decoction. GO and KEGG enrichment analyses demonstrated that the core targets were significantly enriched in oxidative stress-related pathways, inflammatory signaling cascades, and cell fate regulatory pathways. Computational deconvolution of bulk transcriptomic data suggested marked alterations in the estimated immune cell composition of the CHF microenvironment. Network pharmacology analysis further indicated that multiple chemical constituents of Zhigancao decoction converge on MMP9 and its associated pathways. Molecular docking analysis demonstrated favorable binding affinities between 10 representative compounds and MMP9, with binding energies below -7.0 kcal/mol. CONCLUSIONS: In silico predictions suggest that Zhigancao decoction may exert potential therapeutic effects against CHF through computationally predicted targeting of MMP9 and associated oxidative stress- and immune-related pathways. These computational findings provide a theoretical foundation for future experimental investigations into the mechanisms of Zhigancao decoction in CHF, though clinical application would require confirmation through rigorous in vivo and clinical studies.

Oxidative Stress↗
PubMed2005

In silico identification of breast cancer genes by combined multiple high throughput analyses.

Publicly available human genomic sequence data provide an unprecedented opportunity for researchers to decode the functionality of human genome. Such information is extremely valuable in cancer prevention diagnosis and treatment. Cancer Genome Anatomy Project (CGAP) and Gene Expression Omnibus (GEO) are two bioinformatic infrastructures for studying functional genomics. The goal of this study is to explore the feasibility of incorporating the Internet-available bioinformatic databases to discover human breast cancer-related genes. Several tools including the Gene Finder, Virtual Northern (vNorthern) and SAGE digital gene expression displayer (DGED) were used to analyze differential gene expression between benign and malignant breast tissues. A pilot study was performed using both EST and SAGE vNorthern to analyze the expression of a panel of known genes, including high abundance genes beta-actin and G3PDH, low abundance genes BRCA1 and p53, tissue-specific genes CEA and PSA and two breast cancer-related genes Her2/neu and MUC1. We found a high expression of beta-actin and G3PDH and a low expression of BRCA1 and p53 across different types of tissues as well as a tissue-specific expression of CEA in colon and PSA in prostate. A further analysis of 30 known breast cancer-related genes in breast cancer tissues by vNorthern demonstrated a high expression of oncogenes and low expression of tumor suppressor genes. An open-end analysis of two pools of breast cancer and benign breast tissue libraries by SAGE DGED produced 53 differentially expressed genes according to the screening criteria of a >five-fold difference and p<0.01. Further analysis by EST vNorthern and virtual microarray analysis reduced the candidate genes to six, with four down-regulated genes, ANXA1, CAV1, KRT5 and MMP7, and two up-regulated genes, ERBB2 and G1P3 in breast cancer. These findings were validated by a real-time RT-PCR analysis in eight paired human breast cancer tissue samples. We conclude that the combined multiple high throughput analyses is an effective data mining strategy in cancer gene identification. This approach may improve the usage of public available genomic data through strategic data mining of high throughput analysis.

Blotting, Northern↗
PubMed2000

Peri-implantation lethality in mice lacking the Sm motif-containing protein Lsm4.

Small nuclear ribonucleoproteins (snRNPs) are particles present only in eukaryotic cells. They are involved in a large variety of RNA maturation processes, most notably in pre-mRNA splicing. Several of the proteins typically found in snRNPs contain a sequence signature, the Sm domain, conserved from yeast to mammals. By using a promoter trap strategy to target actively transcribed loci in murine embryonic stem cells, a new murine gene encoding an Sm motif-containing protein was identified. Database searches revealed that it is the mouse orthologue of Lsm4p, a protein found in yeast and human cells and putatively associated with U6 snRNA. Introduction of the geo reporter gene cassette under the control of the murine Lsm4 (mLsm4) endogenous promoter showed that the gene was ubiquitously transcribed in embryonic and adult tissues. The insertion of the geo cassette disrupted the mLsm4 allele, and homozygosity for the mutation led to a recessive embryonic lethal phenotype. mLsm4-null zygotes survived to the blastocyst stages, implanted into the uterus, but died shortly thereafter. The early death of mLsm4p-null mice suggests that the role of mLsm4p in splicing is essential and cannot be compensated by other Lsm proteins.

Amino Acid Sequence↗
PubMed1998

Geochemistry of selenium.

Selenium (Se) is one of the most peculiar chemical elements in the geo- and biospheres. It partly resembles sulfur and tellurium; however, its behavior in the geosphere and its functions in the biosphere are very specific. Despite a relatively large database, its cycling in both the natural environment and in that modified by human activities requires further study. Selenium is rather concentrated in the geospheric cycle and is also bioconcentrated. The values of its accumulation ratios are: 5 for soil/sandstone, 2 for animal tissues/sandstone, and 5 for animal tissues/grain. For a specific plant/soil system, the bioconcentration factor for plants always has to be estimated because some plants can absorb extremely high concentrations of Se. Their ability to accumulate and tolerate high Se levels is related to different Se metabolisms. These plants play a significant role in geochemical prospecting and animal nutrition. This paper presents some geochemical observations toward a better understanding of the environmental properties of Se.

Chemical Phenomena↗
PubMed2003

TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.

TGICL is a pipeline for analysis of large Expressed Sequence Tags (EST) and mRNA databases in which the sequences are first clustered based on pairwise sequence similarity, and then assembled by individual clusters (optionally with quality values) to produce longer, more complete consensus sequences. The system can run on multi-CPU architectures including SMP and PVM.

Cluster Analysis↗
PubMed1998

Measuring access to primary medical care: some examples of the use of geographical information systems.

This paper explores the potential for geographical information system technology in defining some variables influencing the use of primary care medical services. Eighteen general practices in Scotland contributed to a study examining the accessibility of their services and their patients' use of the local Accident and Emergency Department. Geo-referencing of information was carried out through analysis of postcode data relating to practices and patients. This information was analyzed using ARC/INFO GIS software in conjunction with the ORACLE relational database and 1991 census information. The results demonstrate that GIS technology has an important role in defining and analyzing the use of health services by the population.

Data Collection↗