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At least 343 records · Page 19Linked to original sources
PubMed2005

Efficient retrieval of vegetation leaf area index and canopy clumping factor from satellite data to support pollutant deposition assessments.

Canopy leaf area index (LAI) is an important structural parameter of the vegetation controlling pollutant uptake by terrestrial ecosystems. This paper presents a computationally efficient algorithm for retrieval of vegetation LAI and canopy clumping factor from satellite data using observed Simple Ratios (SR) of near-infrared to red reflectance. The method employs numerical inversion of a physics-based analytical canopy radiative transfer model that simulates the bi-directional reflectance distribution function (BRDF). The algorithm is independent of ecosystem type. The method is applied to 1-km resolution AVHRR satellite images to retrieve a geo-referenced data set of monthly LAI values for the conterminous USA. Satellite-based LAI estimates are compared against independent ground LAI measurements over a range of ecosystem types. Verification results suggest that the new algorithm represents a viable approach to LAI retrieval at continental scale, and can facilitate spatially explicit studies of regional pollutant deposition and trace gas exchange.

Algorithms↗
PubMed2006

The role of cystatins in cells of the immune system.

The cystatins constitute a large group of evolutionary related proteins with diverse biological activities. Initially, they were characterized as inhibitors of lysosomal cysteine proteases - cathepsins. Cathepsins are involved in processing and presentation of antigens, as well as several pathological conditions such as inflammation and cancer. Recently, alternative functions of cystatins have been proposed: they also induce tumour necrosis factor and interleukin 10 synthesis and stimulate nitric oxide production. The aim of the present review was the analysis of data on cystatins from NCBI GEO database and the literature, and obtained in microarray and serial analysis of gene expression (SAGE) experiments. The expression of cystatins A, B, C, and F in macrophages, dendritic cells and natural killer cells of the immune system, during differentiation and activation is discussed.

Animals↗
PubMed2005

Analysis of 101 nuclear transcriptomes reveals 23 distinct regulons and their relationship to metabolism, chromosomal gene distribution and co-ordination of nuclear and plastid gene expression.

Post-endosymbiotic evolution of the proto-chloroplast was characterized by gene transfer to the nucleus. Hence, most chloroplast proteins are nuclear-encoded and the regulation of chloroplast functions includes nuclear transcriptional control. The expression profiles of 3292 nuclear Arabidopsis genes, most of them encoding chloroplast proteins, were determined from 101 different conditions and have been deposited at the GEO database (http://www.ncbi.nih.gov/geo/) under . The 1590 most-regulated genes fell into 23 distinct groups of co-regulated genes (regulons). Genes of some regulons are not evenly distributed among the five Arabidopsis chromosomes and pairs of adjacent, co-expressed genes exist. Except regulons 1 and 2, regulons are heterogeneous and consist of genes coding for proteins with different subcellular locations or contributing to several biochemical functions. This implies that different organelles and/or metabolic pathways are co-ordinated at the nuclear transcriptional level, and a prototype for this is regulon 12 which contains genes with functions in amino acid and carbohydrate metabolism, as well as genes associated with transport or transcription. The co-expression of nuclear genes coding for subunits of the photosystems or encoding proteins involved in the transcription/translation of plastome genes (particularly ribosome polypeptides) (regulons 1 and 2, respectively) implies the existence of a novel mechanism that co-ordinates plastid and nuclear gene expression and involves nuclear control of plastid ribosome abundance. The co-regulation of genes for photosystem and plastid ribosome proteins escapes a previously described general control of nuclear chloroplast proteins imposed by a transcriptional master switch, highlighting a mode of transcriptional regulation of photosynthesis which is different compared to other chloroplast functions. From the evolutionary standpoint, the results provided indicate that functional integration of the proto-chloroplast into the eukaryotic cell was associated with the establishment of different layers of nuclear transcriptional control.

Arabidopsis↗
PubMed2026

An oxidative stress - and immunotherapy-related six-gene signature defines immune subtypes and predicts prognosis and immunotherapy response in hepatocellular carcinoma.

BACKGROUND: Oxidative stress and the tumor immune microenvironment jointly shape hepatocellular carcinoma (HCC) progression and response to immunotherapy, yet integrated biomarkers linking these processes are lacking. METHODS: Transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets were used to identify oxidative stress- and immunotherapyrelated differentially expressed genes (OSIRDEGs). Functional enrichment, weighted gene co-expression network analysis (WGCNA) and LASSO-Cox regression were used to construct a prognostic signature. Consensus clustering, TIDE, CIBERSORT and ssGSEA characterized immune phenotypes. Somatic mutation, copy-number and drug-response data were integrated to assess genomic alterations and drug sensitivity. Expression of model genes was validated by qRT-PCR and western blotting in HCC cell lines. RESULTS: We identified 24 OSIRDEGs enriched in cell-cycle and mitotic pathways. WGCNA intersection yielded 18 module genes, from which a six-gene signature (BUB1B, CDKN2A, CENPE, HMMR, PTTG1, SPP1) was derived. The signature robustly stratified patients into high- and low-risk groups with significantly different progression-free and disease-free survival in both TCGA-LIHC and GSE14520. Based on signature expression, two molecular subtypes were defined, exhibiting distinct survival, immune landscapes and predicted immunotherapy responsiveness. Model genes harbored recurrent alterations and showed significant correlations with anticancer agents. All six genes were upregulated at mRNA and protein levels in metastatic HCC cell lines versus normal hepatocytes. CONCLUSIONS: We systematically explored the landscape of OSIRDEGs in HCC, and proposed a validated six-gene signature that refines prognostic stratification, delineates immunerelevant HCC subtypes and highlights candidate biomarkers for therapeutic selection and mechanistic investigation.

Humans↗
PubMed2006

Responses of 6500 households to arsenic mitigation in Araihazar, Bangladesh.

This study documents the response of 6500 rural households in a 25 km(2) area of Bangladesh to interventions intended to reduce their exposure to arsenic contained in well water. The interventions included public education, posting test results for arsenic on the wells, and installing 50 community wells. Sixty-five percent of respondents from the subset of 3410 unsafe wells changed their source of drinking water, often to new and untested wells. Only 15% of respondents from the subset of safe wells changed their source, indicating that health concerns motivated the changes. The geo-referenced data indicate that distance to the nearest safe well also influenced household responses.

Arsenic Poisoning↗
PubMed2006

Clustering of childhood cancer in the inner city of Tehran metropolitan area: a GIS-based analysis.

The aim of this study was both to map the childhood cancer incidence in the districts of Tehran metropolitan area and to explore possible clustering of cancer cases in the diverse environments of this area. All incidence cases of childhood cancers (age group under 15 years) belonging to the 22 districts of Tehran metropolis and occurring during the period of 1998 till 2002 were ascertained from three sources. Each case's place of residency was geo-referenced. The scan statistics cluster detecting technique was used to evaluate clustering of cases throughout Tehran. The overall incidence rate (IR) of childhood cancer was 176.3/1,000,000 children under 15 years of age. The lowest IR among both boys and girls was observed in district 22 (69.4/1,000,000) and the highest was observed in district 6 (242.09/1,000,000). The detection of clusters was performed for all cancer sites. All the cancer sites combined category showed clustering in the districts 7, 13, 8, 6, 3, 14, 12, 11, and 4. For this category, the clustering likelihood was marginally statistically significant (p-value=0.056), with an overall relative risk of 1.30. No statistically significant patterns of clustering were detected for other categories.

Adolescent↗
PubMed2004

Access and authorisation in a Glocal e-Health Policy context.

Challenges to the development of appropriate yet adaptable policy and tools for security of the individual patient electronic health record (EHR) are proving to be significant. Compounding this is the unique capability of e-health to transgress all existing geo-political and other barriers. Initiatives to develop and advance policy, standards, and tools in relation to EHR access control and authorisation management must address this capability. Currently policy development initiatives take place largely in an isolated manner. This jeopardises the potential of e-health because decisions made in one jurisdiction might hamper, even prevent, an e-health opportunity in another. This paper places access and authorisation issues in an overall policy context through describing current Canadian initiatives. The National Initiative for Telehealth (NIFTE) Guidelines project is developing a framework of national guidelines for telehealth. The Policy and Peer Permission (PPP) project is developing a unique tool that provides persistent protection of data. The new corporate body 'Infoway' is developing a pan-Canadian electronic health record solution. Finally, the Glocal e-Health Policy initiative is developing a tool with which to identify and describe the inter-relationships of e-health issues amongst policy levels, themes, and actors.

Access to Information↗
PubMed2006

Probabilistic study of well capture zones distribution at the Lauswiesen field site.

The delineation of well capture zones is of utmost environmental and engineering relevance as pumping wells are commonly used both for drinking water supply needs, where protection zones have to be defined, and for investigation and remediation of contaminated aquifers. We analyze the probabilistic nature of well capture zones within the well field located at the "Lauswiesen" experimental site. The test site is part of an alluvial heterogeneous aquifer located in the Neckar river valley, close to the city of Tübingen in South-West Germany. We explore the effect of different conceptual models of the structure of aquifer heterogeneities on the delineation of three-dimensional probabilistic well catchment and time-related capture zones, in the presence of migration of conservative solutes. The aquifer is modeled as a three-dimensional, doubly stochastic composite medium, where distributions of geo-materials and hydraulic properties are uncertain. We study the relative importance of uncertain facies geometry and uncertain hydraulic conductivity and porosity on predictions of catchment and solute time of travel to the pumping well by focusing on cases in which (1) the facies distribution is random, but the hydraulic properties of each material are fixed, and (2) both facies geometry and material properties vary stochastically. The problem is tackled within a conditional numerical Monte Carlo framework. Results are provided in terms of probabilistic demarcations of the three-dimensional well catchment and time-related capture zones. Our findings suggest that the uncertainty associated with the prediction of the location of the outer boundary of well catchment at the "Lauswiesen" site is significantly affected by the conceptual model adopted to incorporate the heterogeneous nature of the aquifer domain in a predictive framework. Taking into account randomness of both lithofacies distribution and materials hydraulic conductivity allows recognizing the existence of preferential flow paths that influence the extent of the well catchment and the solute travel time distribution at the site.

Computer Simulation↗
PubMed2005

Combined use of GIS and environmental indicators for assessment of chemical, physical and biological soil degradation in a Spanish Mediterranean region.

Soil is one of the main non-renewable natural resources in the world. In the Valencian Community (Mediterranean coast of Spain), it is especially important because agriculture and forest biomass exploitation are two of the main economic activities in the region. More than 44% of the total area is under agriculture and 52% is forested. The frequently arid or semi-arid climate with rainfall concentrated in few events, usually in the autumn and spring, scarcity of vegetation cover, and eroded and shallow soils in several areas lead to soil degradation processes. These processes, mainly water erosion and salinization, can be intense in many locations within the Valencian Community. Evaluation of soil degradation on a regional scale is important because degradation is incompatible with sustainable development. Policy makers involved in land use planning require tools to evaluate soil degradation so they can go on to develop measures aimed at protecting and conserving soils. In this study, a methodology to evaluate physical, chemical and biological soil degradation in a GIS-based approach was developed for the Valencian Community on a 1/200,000 scale. The information used in this study was obtained from two different sources: (i) a soil survey with more than 850 soil profiles sampled within the Valencian Community, and (ii) the environmental information implemented in the Geo-scientific map of the Valencian Community digitised on an Arc/Info GIS. Maps of physical, chemical and biological soil degradation in the Valencian Community on a 1/200,000 scale were obtained using the methodology devised. These maps can be used to make a cost-effective evaluation of soil degradation on a regional scale. Around 29% of the area corresponding to the Valencian Community is affected by high to very high physical soil degradation, 36% by high to very high biological degradation, and 6% by high to very high chemical degradation. It is, therefore, necessary to draw up legislation and to establish the policy framework for actions focused on preventing soil degradation and conserving its productive potential.

Agriculture↗
PubMed2006

Dynamic modeling of chemical fate and transport in multimedia environments at watershed scale-I: theoretical considerations and model implementation.

A geo-referenced environmental fate model was developed for analyzing unsteady-state dispersion and distribution of chemicals in multimedia environmental systems. Chemical transport processes were formulated in seven environmental compartments of air, canopy, surface soil, root-zone soil, vadose-zone soil, surface water, and sediment. The model assumed that the compartments were completely mixed and chemical equilibrium was established instantaneously between the sub-compartments within each compartment. A fugacity approach was utilized to formulate the mechanisms of diffusion, advection, physical interfacial transport, and transformation reactions. The governing equations of chemical mass balances in the environmental compartments were solved simultaneously to reflect the interactions between the compartments. A geographic information system (GIS) database and geospatial analysis were integrated into the chemical transport simulation to provide spatially explicit estimations of model parameters at watershed scale. Temporal variations of the environmental properties and source emissions were also considered in the parameter estimations. The outputs of the model included time-dependent chemical concentrations in each compartment and its sub-compartments, and inter-media mass fluxes between adjacent compartments at daily time steps.

Computer Simulation↗
PubMed2004

Environmental characterization and radio-ecological impacts of non-nuclear industries on the Red Sea coast.

The Red Sea is a deep semi-enclosed and narrow basin connected to the Indian Ocean by a narrow sill in the south and to the Suez Canal in the north. Oil industries in the Gulf of Suez, phosphate ore mining activities in Safaga-Quseir region and intensified navigation activities are non-nuclear pollution sources that could have serious radiological impacts on the marine environment and the coastal ecosystems of the Red Sea. It is essential to establish the radiological base-line data, which does not exist yet, and to investigate the present radio-ecological impact of the non-nuclear industries to preserve and protect the coastal environment of the Red Sea. Some natural and man-made radionuclides have been measured in shore sediment samples collected from the Egyptian coast of the Red Sea. The specific activities of 226Ra and 210Pb (238U) series, 232Th series, 40K and 137Cs (Bq/kg dry weight) were measured using gamma ray spectrometers based on hyper-pure germanium detectors. The specific activities of 210Po (210Pb) and uranium isotopes (238U, 235U and 234U) (Bq/kg dry weight) were measured using alpha spectrometers based on surface barrier (PIPS) detectors after radiochemical separation. The absorbed radiation dose rates in air (nGy/h) due to natural radionuclides in shore sediment and radium equivalent activity index (Bq/kg) were calculated. The specific activity ratios of 228Ra/226Ra, 210Pb/226Ra, 226Ra/238U and 234U/238U were calculated for evaluation of the geo-chemical behaviour of these radionuclides. The average specific activity of 226Ra (238U) series, 232Th series, 40K and 210Pb were 24.7, 31.4, 427.5 and 25.6 Bq/kg, respectively. The concentration of 137Cs in the sediment samples was less than the lower limit of detection. The Red Sea coast is an arid region with very low rainfall and the sediment is mainly composed of sand. The specific activity of 238U, 235U and 234U were 25.3, 2.9 and 25.0 Bq/kg. The average specific activity ratios of 226Ra/228Ra, 210Pb/226Ra and 234U/238U were 1.67, 1.22 and 1.0, respectively. The relationship between 226Ra/228Ra activity ratio and sample locations along the coastal shoreline indicates the increase of this ratio in the direction of the Shuqeir in the north and Safaga in the south where the oil exploration and phosphate mining activities are located. These activities may contribute a high flux of 226Ra. The concentration and distribution pattern of 226Ra in sediment can be used to trace the radiological impact of the non-nuclear industries on the Red Sea coast.

Egypt↗
PubMed2006

Characterisation of submarine groundwater discharge offshore south-eastern Sicily.

A complex approach in characterisation of submarine groundwater discharge (SGD) off south-eastern Sicily comprising applications of radioactive and non-radioactive tracers, direct seepage measurements, geophysical surveys and a numerical modelling is presented. SGD fluxes in the Donnalucata boat basin were estimated by direct seepage measurements to be from 4 to 12Ls(-1), which are comparable with the total SGD flux in the basin of 17Ls(-1) obtained from radon measurements. The integrated SGD flux over the Donnalucata coast estimated on the basis of Ra isotopes was around 60m(3)s(-1) per km of the coast. Spatial variations of SGD were observed in the Donnalucata boat basin, the average (222)Rn activity concentration in seawater varied from approximately 0.1kBqm(-3) to 3.7kBqm(-3) showing an inverse relationship with salinity. The continuous monitoring carried out at the site closest to the coast has revealed an inverse relationship of (222)Rn activity concentration on the tide. The (222)Rn concentrations in seawater varied from 2.3kBqm(-3) during high tides to 4.8kBqm(-3) during low tides, thus confirming an influence of the tide on submarine groundwater discharge. Stable isotopes (delta(2)H and delta(18)O) showed that SGD samples consist up to 50% of groundwater. Geo-electrical measurements showed a spatial variability of the salt/fresh water interface and its complex transformation in the coastal zone. The presented results imply that in the studied Donnalucata site there are at least two different sources of SGD, one superficial, represented by mixed fresh water and seawater, and the second one which originates in a deeper limestone aquifer.

Sicily↗
PubMed2006

Soil radioactivity and incidence of cancer in Nigeria.

The significance of exposure from natural radioactivity in soil and the potential risk for causing health detriment have not received adequate attention in Nigeria. Cancer has become a major cause of mortality in the recent times and now the public interest in the long-term effects of radiation on humans has assumed great prominence following the establishment of a nuclear regulatory body in Nigeria. This study is an effort to investigate a possible relationship between reported cancer incidence and external terrestrial radiation dose level across the six geo-political zones of the country. Data from the national cancer registries across the zones were compared with expected cancer incidences due to soil radioactivity based on the linear no-threshold model (LNT). A regression equation that best describe the reported cancer incidence and the expected cancer incidence was developed. It was observed that cancer cases attributable to radiation exposure due to soil radioactivity is low, constituting only between 1.3% and 9.2% of the total reported cases.

Background Radiation↗
PubMed2004

Studies of channel sediments contaminated with organics and heavy metals.

The paper discusses the geo-environmental studies carried out to revitalise a silted up channel in Guanabara Bay. A dredging operation has been planned to remove about 1.5 million cubic meters of contaminated sediment. Investigations were performed to characterise the sediment in terms of its physical and chemical properties and to evaluate the presence of heavy metals and organic compounds, particularly polycyclic aromatic hydrocarbons PAH. Finally, dredging and disposal schemes are briefly outlined based on measured contamination levels.

Brazil↗
PubMed2006

Equilibrium and kinetic studies for the sorption of 3-methoxybenzaldehyde on activated kaolinites.

The sorption of 3-methoxybenzaldehyde on activated kaolinites has been investigated at different temperatures. Two types of activation tests were performed. The sorption equilibrium was studied by sorption isotherms in the temperature range 303-333K for natural (untreated), thermally and acid activated kaolinites. It was shown that the isotherm shapes were not affected by temperature and activation types of kaolinite. The absorbance data at 312nm were fitted reasonably well with the Langmuir and Freundlich isotherm models and the model parameters were determined for different temperatures. Thermodynamic quantities such as Gibbs free energy (DeltaG), the enthalpy (DeltaH) and the entropy change of sorption (DeltaS) were determined for natural, thermally and acid activated kaolinites. It was shown that the sorption processes were an endothermic reactions, controlled by physical mechanisms and spontaneously. Adsorption capacity of acid activated kaolinite for 3-methoxybenzaldehyde was higher compared to that of natural and thermally activated kaolinites at various temperatures. The adsorption and desorption rate constants (k(a) and k(d)) were obtained separately by applying a geometric approach to the first order Langmuir model. This method provided good conformity between the K from Langmuir parameters and K(geo) (k(a)/k(d)) from geometric approach.

Adsorption↗
PubMed2025

Role of HLA-DRA-CREB3L4 regulatory axis in the pathogenesis of ovarian endometriosis: Inhibition of CREB3L4 expression by HLA-DRA increases the risk of disease.

BACKGROUND: Ovarian endometriosis is a common gynecological condition characterized by the abnormal growth of endometrial-like tissue in locations outside the uterus, and its development remains poorly understood. This study aims to investigate potential protein regulatory networks and assess their impact on disease risk using both protein quantitative trait locus (pQTL) analysis and Mendelian randomization (MR) techniques. METHODS: This study systematically integrates two major genome-wide pQTL databases, UKB-PPP and deCODE, to identify pQTL signals associated with ovarian endometriosis. Additionally, we utilized the GEO database to validate differences in protein expression. We conducted a Mendelian randomization analysis to further explore the regulatory relationships between proteins and their roles in disease development. RESULTS: After the Bonferroni correction, we identified 33 pQTL signals from UKB-PPP and 19 pQTL signals from deCODE. Among these, 8 signals from UKB-PPP and 3 signals from deCODE were validated based on expression differences. The mediation analysis results indicate that HLA-DRA significantly increases the risk of developing ovarian endometriosis by inhibiting the expression of CREB3L4 (with a mediation proportion of 13.99 %), and the direction of the mediation effect is consistent with the total effect. CONCLUSION: This study provides new insights that HLA-DRA downregulates the expression of CREB3L4, which may affect the risk of developing endometriosis. The results provide new evidence for understanding the genetic and molecular basis of ovarian endometriosis and establish a theoretical foundation for the development of future diagnostic markers and targeted treatment strategies.

Humans↗
PubMed2026

SLC1A5 and NUMA1 are potential regulators and therapeutic targets of ferroptosis in diffuse large B-cell lymphoma.

BACKGROUND: Ferroptosis, a form of regulated cell death driven by iron-dependent lipid peroxidation, has emerged as a potential therapeutic target in various cancers, including diffuse large B-cell lymphoma (DLBCL). This study aimed to identify and characterize ferroptosis-related panel genes with prognostic value in DLBCL. METHODS: Transcriptomic data from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were analyzed to identify differentially expressed genes (DEGs) in DLBCL samples. Gene set variation analysis (GSVA) and network topology analysis were performed to identify key ferroptosis-related genes. Lasso regression was utilized to construct a prognostic model based on the identified panel genes. In vitro experiments, including gene silencing, overexpression, and ferroptosis induction, were conducted to evaluate the functional roles of the identified genes, NUMA1 and SLC1A5, in DLBCL cells. RESULTS: A panel of ferroptosis-related genes with prognostic value, including NUMA1 and SLC1A5, was identified in DLBCL samples. Silencing SLC1A5 or overexpressing NUMA1 in DLBCL cells enhanced sensitivity to ferroptosis inducers, increased intracellular labile iron and lipid peroxidation levels, promoted mitochondrial damage, and modulated the expression of key ferroptosis markers. Furthermore, SLC1A5 silencing or NUMA1 overexpression augmented radiation-induced ferroptosis in DLBCL cells. CONCLUSION: NUMA1 and SLC1A5 are potential ferroptosis regulators and therapeutic targets in DLBCL. Silencing the ferroptosis-suppressive transporter SLC1A5 or restoring NUMA1 expression promotes lipid peroxidation and ferroptotic cell death, thereby sensitizing DLBCL cells to ferroptosis and enhancing radiosensitivity-providing a rationale for novel ferroptosis-based therapeutic strategies.

Humans↗
PubMed2003

Morpholino oligonucleotide-triggered knockdown reveals a role for maternal E-cadherin during early mouse development.

We report that gene silencing via intracytoplasmic microinjections of morpholino-modified antisense oligonucleotides is an effective and reproducible method to study both maternal and zygotic gene functions during early and late stages of mouse preimplantation development. The zygotic expression of the beta-geo transgene in the ROSA26 mouse strain could be inhibited until at least the early blastula stages. Thus morpholino-triggered gene inactivation appears to be a useful method to study the functional role of genes in preimplantation development. Using this approach, we have investigated a potential role of maternal expression of Cdh1, the gene encoding the cell-adhesion molecule E-cadherin. Inhibition of translation of maternal E-cadherin mRNA causes a developmental arrest at the two-cell stage. BrUTP incorporation assays indicated that this developmental defect cannot be explained by a general failure in transcriptional activity. This defect is reversible since E-cadherin mRNA can rescue the affected embryos, suggesting that a functional adhesion complex, present at the junction between blastomeres, is a prerequisite for the normal development of the mouse preimplantation embryo. Our study thus reveals a previously unanticipated role of maternal E-cadherin during early stages of mouse development.

Animals↗