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Biological Data (biological + data)
Selected AbstractsChemInform Abstract: Synthesis and Biological Data of 4-Amino-1-(2-chloro-2-phenylethyl)-1H-pyrazolo [3,4-b]pyridine-5-carboxylic Acid Ethyl Esters, a New Series of A1 -Adenosine Receptor (A1AR) Ligands.CHEMINFORM, Issue 5 2002Silvia Schenone Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Novel Pirinixic Acids as PPAR, Preferential Dual PPAR,/, AgonistsMOLECULAR INFORMATICS, Issue 5 2009Heiko Zettl Abstract Pirinixic acid is a moderate agonist of both the alpha and the gamma subtype of the peroxisome proliferator activated receptor (PPAR). Previously, we have shown that ,-alkyl substitution leads to balanced low micromolar-active dual agonists of PPAR, and PPAR,. Taking ,-hexyl pirinixic acid as a new scaffold, we further optimized PPAR activity by enlargement of the lipophilic backbone by substituting the 2,3-dimethylphenyl with biphenylic moieties. Such a substitution pattern had only minor impact on PPAR, activity but further increased PPAR, activity leading to nanomolar activities. Supporting docking studies proposed that the (R)-enantiomer should fit the PPAR, ligand-binding pocket better and thus be more active than the (S)-enantiomer. Single enantiomers of selected active analogues were then prepared by enantio-selective synthesis and enantio-selective preparative HPLC, respectively. Biological data for the distinct enantiomers fully corroborated the docking experiments and substantiate a stereochemical impact on PPAR activation. [source] Modeling multisystem biological risk in young adults: The Coronary Artery Risk Development in Young Adults StudyAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 4 2010Teresa Seeman Although much prior research has focused on identifying the roles of major regulatory systems in health risks, the concept of allostatic load (AL) focuses on the importance of a more multisystems view of health risks. How best to operationalize allostatic load, however, remains the subject of some debate. We sought to test a hypothesized metafactor model of allostatic load composed of a number of biological system factors, and to investigate model invariance across sex and ethnicity. Biological data from 782 men and women, aged 32,47, from the Oakland, CA and Chicago, IL sites of the Coronary Artery Risk Development in Young Adults Study (CARDIA) were collected as part of the Year 15exam in 2000. These include measures of blood pressure, metabolic parameters (glucose, insulin, lipid profiles, and waist circumference), markers of inflammation (interleukin-6, C-reactive protein, and fibrinogen), heart rate variability, sympathetic nervous system activity (12-hr urinary norepinephrine and epinephrine) and hypothalamic-pituitary-adrenal axis activity (diurnal salivary free cortisol). A "metafactor" model of AL as an aggregate measure of six underlying latent biological subfactors was found to fit the data, with the metafactor structure capturing 84% of variance of all pairwise associations among biological subsystems. There was little evidence of model variance across sex and/or ethnicity. These analyses extend work operationalizing AL as a multisystems index of biological dysregulation, providing initial support for a model of AL as a metaconstruct of inter-relationships among multiple biological regulatory systems, that varies little across sex or ethnicity. Am. J. Hum. Biol. 2010. © 2009 Wiley-Liss, Inc. [source] 2-Acylaminopyridin-4-ylimidazoles as p38 MAP Kinase Inhibitors: Design, Synthesis, and Biological and Metabolic EvaluationsCHEMMEDCHEM, Issue 11 2009Katharina Ziegler Dr. Abstract Targeting cytokines has become an important focus in the treatment of many inflammatory disorders. p38 MAP kinase (MAPK) is the key enzyme in regulating the biosynthesis and release of pro-inflammatory cytokines such as IL-1, and TNF,. Inhibition of p38 MAPK results in decreased expression of these cytokines. Tri- and tetrasubstituted pyridinylimidazoles are potent inhibitors of p38 MAPK. Substitution on the pyridinyl moiety allows the design of inhibitors that show increased selectivity and activity by targeting the enzyme's hydrophobic region,II. The objective of this study was to synthesize novel 1,2,4,5-tetrasubstituted imidazole derivates and to characterize them not only for their ability to inhibit p38 MAPK and modulate cytokine release in human whole blood, but also to evaluate their metabolic stability. Biological data and metabolic studies demonstrate that the introduction of a 2-acylamino function at C2 of the pyridine results in highly efficient and metabolically stable inhibitors relative to C2-alkylamino derivatives. A series of novel candidates was investigated for metabolic stability in human liver microsomes and in human whole blood. Additionally, metabolic S-oxidation was investigated, and possible metabolites were synthesized. [source] Single-cell gene profiling of planarian stem cells using fluorescent activated cell sorting and its "index sorting" function for stem cell researchDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 1 2010Tetsutaro Hayashi To achieve an integrated understanding of the stem cell system of planarians at both the cellular and molecular levels, we developed a new method by combining "fluorescent activated cell sorting (FACS) index sorting" analysis and single-cell reverse transcription,polymerase chain reaction (RT,PCR) to detect the gene expression and cell cycle state of stem cells simultaneously. Single cells were collected using FACS, and cDNAs of each cell were used for semi-quantitative RT,PCR. The results were plotted on the FACS sorting profile using the "index sorting" function, which enabled us to analyze the gene expression in combination with cell biological data (such as cell cycle phase) for each cell. Here we investigated the adult stem cells of planarians using this method and obtained findings suggesting that the stem cells might undergo commitment during S to G2/M phase. This method could be a powerful and straightforward tool for examining the stem cell biology of not only planarians but also other organisms, including vertebrates. [source] Aquatic macroinvertebrates in the altes land, an intensely used orchard region in Germany: Correlation between community structure and potential for pesticide exposureENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 12 2006Christoph Schäfers Abstract To assess the impact of pesticides on aquatic organisms under realistic worst-case conditions, a macroinvertebrate community of small ditches was sampled at 40 sites of the orchard region Altes Land near Hamburg, Germany. To differentiate between pesticide impact and other variables, the ditches selected for sampling were located at different distances along grassland, unused apple orchards, and orchards managed with integrated and/or organic crop protection methods. Samples of macroinvertebrates were taken on five dates over two years. In addition to biological data, water chemistry and structural parameters were measured. For each sampling site, a potential for exposure was calculated on the basis of the distance of the ditch to the nearest row of trees and the depth and width of the ditch. The neighborhood to either grassland or orchards turned out to have a larger impact on the macroinvertebrate community than the potential for exposure. Therefore, grassland sites were omitted from further evaluation. Remaining sites were grouped into low exposure (sites at unused orchards), medium exposure (distance of 3,5 m [track] between trees and ditch), and high exposure (trees close to the ditch, mean distance , 1.5 m). Principal response curves showed differences in community structure between the three exposure groups over time. Whereas for sites from the high exposure group significant differences from low exposure was observed in all seasons, significant differences between low and medium were observed only occasionally. Effects were less pronounced in samples taken at springtime before the starting pesticide applications, suggesting some community recovery. Species richness was negatively correlated to exposure potential. Isopoda, Eulamellibranchiata, and insects, especially Ephemeroptera, showed a high negative correlation with the potential for pesticide exposure, suggesting that these taxa are sensitive to the pesticide use in the orchards. [source] Methodology for the evaluation of cumulative episodic exposure to chemical stressors in aquatic risk assessment,ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 4 2000Michael G. Morton Abstract An ecological risk assessment method was developed to evaluate the magnitude, duration, and episodic nature of chemical stressors on aquatic communities. The percent of an ecosystem's species at risk from a designated chemical exposure scenario is generated. In effects assessment, probabilistic extrapolation methods are used to generate estimated safe concentrations (ESCs) for an ecosystem using laboratory toxicity test results. Fate and transport modeling is employed to generate temporal stressor concentration profiles. In risk characterization, area under the curve integration is performed on predicted exposure concentration profiles to calculate a cumulative exposure concentration (CEC) for the exposure event. A correction is made to account for the allowable exposure duration to the stressor ESC. Finally, the CEC is applied to the extrapolation model (curve) of the stressor to predict percent species at risk to the episodic exposure. The method may be used for either prospective or retrospective risk assessments. The results of a retrospective risk assessment performed on the Leadenwah Creek, South Carolina, USA, estuarine community are presented as a case study. The creek experienced periodic episodes of pesticide-contaminated agricultural runoff from 1986 through 1989. Although limited biological data were available for method validation, the risk estimates compared well with the Leadenwah Creek in situ bioassay results. [source] The influence of pelagic habitat selection and interspecific competition on productivity of juvenile walleye pollock (Theragra chalcogramma) and capelin (Mallotus villosus) in the Gulf of AlaskaFISHERIES OCEANOGRAPHY, Issue 4 2010ELIZABETH A. LOGERWELL Abstract Here we investigate processes affecting productivity of capelin and walleye pollock in the Gulf of Alaska. We examine pelagic habitat selection by comparing the distribution of juvenile fish and their prey with oceanographic properties and we evaluate the potential for interspecific competition by comparing diets and measures of foraging. The primary field study was conducted in Barnabus Trough, Kodiak Island, Alaska, during September 2005. The distribution of fish was assessed acoustically and trawls were used to collect individual fish for stomach content analyses. Physical and biological data were collected with conductivity,temperature,depth probes and zooplankton tows. Age-0 pollock were distributed in cool waters offshore of a mid-trough front, coincident with the distribution of euphausiids, their preferred prey. In contrast, capelin and their prey (copepods) were distributed throughout the trough. We observed that sympatric capelin (occurring with pollock) often had reduced foraging success compared to allopatric capelin (occurring alone). Results of a bioenergetic model also suggest that the exclusion of capelin from foraging on euphausiids can have negative consequences for capelin growth. [source] Modelling potential spawning habitat of sardine (Sardina pilchardus) and anchovy (Engraulis encrasicolus) in the Bay of BiscayFISHERIES OCEANOGRAPHY, Issue 1 2007BENJAMIN PLANQUE Abstract Large amplitude variations in recruitment of small pelagic fish result from interactions between a fluctuating environment and population dynamics processes such as spawning. The spatial extent and location of spawning, which is critical to the fate of eggs and larvae, can vary strongly from year to year, as a result of changing population structure and environmental conditions. Spawning habitat can be divided into ,potential spawning habitat', defined as habitat where the hydrographic conditions are suitable for spawning, ,realized spawning habitat', defined as habitat where spawning actually occurs, and ,successful spawning habitat', defined as habitat from where successful recruitment has resulted. Using biological data collected during the period 2000,2004, as well as hydrographic data, we investigate the role of environmental parameters in controlling the potential spawning habitat of anchovy and sardine in the Bay of Biscay. Anchovy potential spawning habitat appears to be primarily related to bottom temperature followed by surface temperature and mixed-layer depth, whilst surface and bottom salinity appear to play a lesser role. The possible influence of hydrographic factors on the spawning habitat of sardine seems less clear than for anchovy. Modelled relationships between anchovy and sardine spawning are used to predict potential spawning habitat from hydrodynamical simulations. The results show that the seasonal patterns in spawning are well reproduced by the model, indicating that hydrographic changes may explain a large fraction of spawning spatial dynamics. Such models may prove useful in the context of forecasting potential impacts of future environmental changes on sardine and anchovy reproductive strategy in the north-east Atlantic. [source] Using patch studies to link mesoscale patterns of feeding and growth in larval fish to environmental variabilityFISHERIES OCEANOGRAPHY, Issue 4 2002John F. Dower We present results from a series of three patch studies designed to examine links between environmental variability and mesoscale patterns of feeding and growth of larval radiated shanny (Ulvaria subbifurcata). We examine the effects of variability in temperature, turbulence and prey concentration on both the mean (i.e. population level) and the variance (i.e. individual level) of larval feeding and growth rates among the three bays. Although both gut fullness and growth rates differ significantly between bays, our results show only weak environmental influences. When larvae are pooled across bays (i.e. treated as independent observations), environmental factors generally explain <4% of the variability in gut fullness. When treated as daily mean residuals, however, temperature accounts for 41% of the variability in mean gut fullness, while both temperature and prey concentration also explain significant portions of the variance in gut fullness (38 and 43%, respectively). Between-bay differences in larval growth rates are consistent with patterns of temperature variation but not with patterns of prey availability. Studies relying on tracking a single patch of larvae typically suffer from having too few observations to detect significant relationships between feeding or growth and environmental variables. By following three patches we collected a larger number of observations. However, as we encountered only a limited range of environmental conditions it remains difficult to adequately assess the role of environmental factors. In part, this problem stems from the inability of fisheries oceanographers to track the recent environmental history of individual larvae on the same fine scales currently employed to collect biological data (e.g. guts and otoliths) on individuals. [source] The use of periphytic diatoms as a means of assessing impacts of point source inorganic nutrient pollution in south-eastern AustraliaFRESHWATER BIOLOGY, Issue 5 2006JOCELYN DELA-CRUZ Summary 1. Periphytic diatoms are used as indicators of water quality because their ecological tolerances or preferences to environmental variables are thought to be predictable. However, much of the present autecological information for periphytic diatoms has been derived from studies conducted in the northern hemisphere. In this present study we used periphytic diatoms to determine the impacts of inorganic nutrient pollution in a tidal river system in the temperate latitudes of south-east Australia. In so doing, we assess the suitability of the use of the ,northern hemisphere' ecological tolerance/preference data for periphytic diatoms. 2. Artificial substrates were used to collect periphytic diatoms at 35 sites, which were positioned along the riverbanks and the middle of the river at various distances upstream and downstream of the sewage outfall. The sampling design took into account tidal excursions and the observed sewage plume dynamics. Periphytic diatoms were collected during the austral winter month of August and the austral spring months of September and October. We deployed the artificial substrates for 4 weeks to allow the periphytic diatoms to recruit and colonise, before identifying and enumerating the assemblages. 3. Data analysis included two approaches: multivariate visualisations of combinations of environmental and biological data to investigate shifts in species structure of the periphytic diatom assemblage and multimetric indices based on ecological tolerance/preference data. 4. We found that the spatial patterns inferred from multivariate and multimetric analyses were consistent. Temporal variation in the composition of the periphytic diatom assemblage was greater than the spatial variation along horizontal sections of the river (in any one deployment) due mainly to shifts between winter and spring species. 5. Outfall effects were most apparent in winter, possibly because subsequent deployments were swamped by growth of spring periphytic diatoms. The outfall effects included a shift towards pollutant tolerant species and a reduction in the variability of the periphytic diatom assemblage across the river. 6. We conclude that the use of periphytic diatoms and associated ecological tolerance/preference data as a means of assessing impacts of point source inorganic nutrient pollution is effective. An understanding of river and sewage flow patterns is essential to the design of appropriate monitoring programmes and to the interpretation of results, especially as periphytic diatoms are sensitive to many environmental variables. [source] Application of pharmacokinetic modelling to the routine therapeutic drug monitoring of anticancer drugsFUNDAMENTAL & CLINICAL PHARMACOLOGY, Issue 4 2002Annick Rousseau Abstract Over the last 10 years, proofs of the clinical interest of therapeutic drug monitoring (TDM) of certain anticancer drugs have been established. Numerous studies have shown that TDM is an efficient tool for controlling the toxicity of therapeutic drugs, and a few trials have even demonstrated that it can improve their efficacy. This article critically reviews TDM tools based on pharmacokinetic modelling of anticancer drugs. The administered dose of anticancer drugs is sometimes adjusted individually using either a priori or a posteriori methods. The most frequent clinical application of a priori formulae concerns carboplatin and allows the computation of the first dose based on biometrical and biological data such as weight, age, gender, creatinine clearance and glomerular filtration rate. A posteriori methods use drug plasma concentrations to adjust the subsequent dose(s). Thus, nomograms allowing dose adjustment on the basis of blood concentration are routinely used for 5-fluorouracil given as long continuous infusions. Multilinear regression models have been developed, for example for etoposide, doxorubicin, carboplatin, cyclophosphamide and irinotecan, to predict a single exposure variable [such as area under concentration,time curve (AUC)] from a small number of plasma concentrations obtained at predetermined times after a standard dose. These models can only be applied by using the same dose and schedule as the original study. Bayesian estimation offers more flexibility in blood sampling times and, owing to its precision and to the amount of information provided, is the method of choice for ensuring that a given patient benefits from the desired systemic exposure. Unlike the other a posteriori methods, Bayesian estimation is based on population pharmacokinetic studies and can take into account the effects of different individual factors on the pharmacokinetics of the drug. Bayesian estimators have been used to determine maximum tolerated systemic exposure thresholds (e.g. for topotecan or teniposide) as well as for the routine monitoring of drugs characterized by a very high interindividual pharmacokinetic variability such as methotrexate or carboplatin. The development of these methods has contributed to improving cancer chemotherapy in terms of patient outcome and survival and should be pursued. [source] Trends and determinants of severe morbidity in HIV-infected patients: the ANRS CO3 Aquitaine Cohort, 2000,2004,HIV MEDICINE, Issue 8 2007F Bonnet Objective The aim of the study was to characterize the causes, trends and determinants of severe morbidity in a large cohort of HIV-infected patients between 2000 and 2004. Method Severe morbid events were defined as medical events associated with hospitalization or death. Epidemiological and biological data were recorded at the time of the morbid event. Trends were estimated using Poisson regression. Results Among 3863 individuals followed between 2000 and 2004, 1186 experienced one or more severe events, resulting in 1854 hospitalizations or deaths. The severe events recorded included bacterial infections (21%), AIDS events (20%), psychiatric events (10%), cardiovascular events (9%), digestive events including cirrhosis (7%), viral infections (6%) and non-AIDS cancers (5%). Between 2000 and 2004, the incidence rate of AIDS events decreased from 60 to 20 per 1000 person-years, that of bacterial infections decreased from 45 to 24 per 1000 person-years, and that of psychiatric events decreased from 26 to 14 per 1000 person-years (all P<0.01), whereas the incidences of cardiovascular events and of non-AIDS cancers remained stable at 14 and 10 per 1000 person-years, on average, respectively. Conclusion Severe morbidity has shifted from AIDS-related to non-AIDS-related events during the course of HIV infection in developed countries. Limiting endpoints to AIDS events and death is insufficient to describe HIV disease progression in the era of combination antiretroviral therapy. [source] Assessment of the Ecological Status of Streams in Two Carpathian SubregionsINTERNATIONAL REVIEW OF HYDROBIOLOGY, Issue 4-5 2007Il'ja Krno Abstract A multimetric assessment system was developed to determine the ecological status of two types of stream in the Carpathian ecoregion following the requirements of the WFD. The organic pollution gradient was defined using Canonical Correspondence Analysis. Classification based on physical, chemical and biological data divided the tested sites into two stream types with subsequent grouping into several ecological quality classes. From all the metrics tested, 17 for the East Carpathian streams and 15 for the West Carpathian streams, from seven metric categories, were included in the resulting multimetric index. Different kinds of response to degradation (linear, unimodal, exponential) were observed. The Saprobic index (Zelinka and Marvan), Rheoindex (Banning, with abundance classes) and Index of Biocenotic region, showed the best discriminatory ability for both stream types. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Factors Affecting Macroinvertebrate Richness and Diversity in Portuguese Streams: a Two-Scale AnalysisINTERNATIONAL REVIEW OF HYDROBIOLOGY, Issue 2 2004Manuel A. S. Graēa Abstract We analysed the spatial patterns in macroinvertebrate taxon richness and abundance at two scales: sampling unit and basin. We sampled 12 stream sites in three zones of Portugal, differing in climate geomorphology and water chemistry. At a sampling unit scale, substratum organic matter content, depth and the dominant size of substratum particles were correlated with numbers of taxa and individuals. We propose that the number of taxa at a small scale depends on the number of individuals, which in turn is the result of organic matter accumulation, hydrologic and substratum characteristics. The environmental parameters better explaining the large-scale biological data were temperature, minimum size of substratum particles and pH. Regardless of the relative importance of variable types and mechanisms regulating stream invertebrates along the climatic gradient, rivers from the North and Centre appeared to be richer in taxa than the typically Mediterranean streams in the South. [source] Water Framework Directive: ecological classification of Danish lakesJOURNAL OF APPLIED ECOLOGY, Issue 4 2005MARTIN SŲNDERGAARD Summary 1The European Water Framework Directive (WFD) requires that all European waterbodies are assigned to one of five ecological classes, based primarily on biological indicators, and that minimum good ecological quality is obtained by 2015. However, the directive provides only general guidance regarding indicator definitions and determination of boundaries between classes. 2We used chemical and biological data from 709 Danish lakes to investigate whether and how lake types respond differently to eutrophication. In the absence of well-defined reference conditions, lakes were grouped according to alkalinity and water depth, and the responses to eutrophication were ordered along a total phosphorus (TP) gradient to test the applicability of pre-defined boundaries. 3As a preliminary classification we suggest a TP-based classification into high, good, moderate, bad and poor ecological quality using 0,25, 25,50, 50,100, 100,200 and > 200 µg P L,1 boundaries for shallow lakes, and 0,12·5, 12·5,25, 25,50, 50,100 and > 100 µg P L,1 boundaries for deep lakes. Within each TP category, median values are used to define preliminary boundaries for the biological indicators. 4Most indicators responded strongly to increasing TP, but there were only minor differences between low and high alkalinity lakes and modest variations between deep and shallow lakes. The variability of indicators within a given TP range was, however, high, and for most indicators there was a considerable overlap between adjacent TP categories. Cyanophyte biomass, submerged macrophyte coverage, fish numbers and chlorophyll a were among the ,best' indicators, but their ability to separate different TP classes varied with TP. 5When using multiple indicators the risk that one or more indicators will indicate different ecological classes is high because of a high variability of all indicators within a specific TP class, and the ,one out , all out' principle in relation to indicators does not seem feasible. Alternatively a certain compliance level or a ,mean value' of the indicators can be used to define ecological classes. A precise ecological quality ratio (EQR) using values between 0 and 1 can be calculated based on the extent to which the total number of indicators meets the boundary conditions, as demonstrated from three Danish lakes. 6Synthesis and applications. The analysis of Danish lakes has identified a number of useful indicators for lake quality and has suggested a method for calculating an ecological quality ratio. However, it also demonstrates that the implementation of the Water Framework Directive faces several challenges: gradual rather than stepwise changes for all indicators, large variability of indicators within lake classes, and problems using the one out , all out principle for lake classification. [source] A Three-Dimensional Simulation of Age-Related Remodeling in Trabecular Bone,JOURNAL OF BONE AND MINERAL RESEARCH, Issue 4 2001J. C. Van Der Linden Abstract After peak bone mass has been reached, the bone remodeling process results in a decrease in bone mass and strength. The formation deficit, the deficit of bone formation compared with previous resorption, results in bone loss. Moreover, trabeculae disconnected by resorption cavities probably are not repaired. The contributions of these mechanisms to the total bone loss are unclear. To investigate these contributions and the concomitant changes in trabecular architecture and mechanical properties, we made a computer simulation model of bone remodeling using microcomputed tomography (micro-CT) scans of human vertebral trabecular bone specimens. Up to 50 years of physiological remodeling were simulated. Resorption cavities were created and refilled 3 months later. These cavities were not refilled completely, to simulate the formation deficit. Disconnected trabeculae were not repaired; loose fragments generated during the simulation were removed. Resorption depth, formation deficit, and remodeling space were based on biological data. The rate of bone loss varied between 0.3% and 1.1% per year. Stiffness anisotropy increased, and morphological anisotropy (mean intercept length [MIL]) was almost unaffected. Connectivity density increased or decreased, depending on the remodeling parameters. The formation deficit accounted for 69,95%, disconnected trabeculae for 1,21%, and loose fragments for 1,17% of the bone loss. Increasing formation deficit from 1.8% to 5.4% tripled bone loss but only doubled the decrease in stiffness. Increasing resorption depth from 28 to 56 ,m slightly increased bone loss but drastically decreased stiffness. Decreasing the formation deficit helps to prevent bone loss, but reducing resorption depth is more effective in preventing loss of mechanical stiffness. [source] Substituent electronic descriptors for fast QSAR/QSPRJOURNAL OF CHEMOMETRICS, Issue 3-4 2007Bahram Hemmateenejad Abstract Substituent electronic descriptors (SED), calculated by ab initio quantum chemical methods for radical substituents, were proposed as an efficient and simple to use descriptors for use in Quantitative structure-activity/property relationships (QSPR/QSAR) studies. Twenty five SED parameters were calculated for a set of simple substituents using orbital energies, local charges, and dipole moments. Calculation of these parameters for a substituent takes much lower time comparing with that for parent molecule. Different chemical and biological data were analyzed by the SED parameters and it was found that in addition to the simplicity and speed of calculations, models obtained by SED parameters have better or comparable efficiency in relative to existing models. Copyright © 2007 John Wiley & Sons, Ltd. [source] Biological mediators and periodontal regeneration: a review of enamel matrix proteins at the cellular and molecular levelsJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 2008Dieter D. Bosshardt Abstract Background: Despite a large body of clinical and histological data demonstrating beneficial effects of enamel matrix proteins (EMPs) for regenerative periodontal therapy, it is less clear how the available biological data can explain the mechanisms underlying the supportive effects of EMPs. Objective: To analyse all available biological data of EMPs at the cellular and molecular levels that are relevant in the context of periodontal wound healing and tissue formation. Methods: A stringent systematic approach was applied using the key words "enamel matrix proteins" OR "enamel matrix derivative" OR "emdogain" OR "amelogenin". The literature search was performed separately for epithelial cells, gingival fibroblasts, periodontal ligament cells, cementoblasts, osteogenic/chondrogenic/bone marrow cells, wound healing, and bacteria. Results: A total of 103 papers met the inclusion criteria. EMPs affect many different cell types. Overall, the available data show that EMPs have effects on: (1) cell attachment, spreading, and chemotaxis; (2) cell proliferation and survival; (3) expression of transcription factors; (4) expression of growth factors, cytokines, extracellular matrix constituents, and other macromolecules; and (5) expression of molecules involved in the regulation of bone remodelling. Conclusion: All together, the data analysis provides strong evidence for EMPs to support wound healing and new periodontal tissue formation. [source] Multiple classifier integration for the prediction of protein structural classesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2009Lei Chen Abstract Supervised classifiers, such as artificial neural network, partition trees, and support vector machines, are often used for the prediction and analysis of biological data. However, choosing an appropriate classifier is not straightforward because each classifier has its own strengths and weaknesses, and each biological dataset has its own characteristics. By integrating many classifiers together, people can avoid the dilemma of choosing an individual classifier out of many to achieve an optimized classification results (Rahman et al., Multiple Classifier Combination for Character Recognition: Revisiting the Majority Voting System and Its Variation, Springer, Berlin, 2002, 167,178). The classification algorithms come from Weka (Witten and Frank, Data Mining: Practical Machine Learning Tools and Techniques, Morgan Kaufmann, San Francisco, 2005) (a collection of software tools for machine learning algorithms). By integrating many predictors (classifiers) together through simple voting, the correct prediction (classification) rates are 65.21% and 65.63% for a basic training dataset and an independent test set, respectively. These results are better than any single machine learning algorithm collected in Weka when exactly the same data are used. Furthermore, we introduce an integration strategy which takes care of both classifier weightings and classifier redundancy. A feature selection strategy, called minimum redundancy maximum relevance (mRMR), is transferred into algorithm selection to deal with classifier redundancy in this research, and the weightings are based on the performance of each classifier. The best classification results are obtained when 11 algorithms are selected by mRMR method, and integrated together through majority votes with weightings. As a result, the prediction correct rates are 68.56% and 69.29% for the basic training dataset and the independent test dataset, respectively. The web-server is available at http://chemdata.shu.edu.cn/protein_st/. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] A spatial model of coexistence among three Banksia species along a topographic gradient in fire-prone shrublandsJOURNAL OF ECOLOGY, Issue 5 2002J. Groeneveld Summary 1A spatially explicit, rule-based model for three co-occurring Banksia species was developed to investigate coexistence mediating processes in a fire-prone shrubland in western Australia. Fecundity, recruitment, mortality and other biological data for two non-sprouting (B. hookeriana, B. prionotes) and one resprouting (B. attenuata) species were available from 15 years of empirical field studies. 2Without interspecific competition, each species could persist for a wide range of fire intervals (10 to > 20 years). The resprouting species performed better under shorter fire intervals (10,13 years), while both non-sprouting species were favoured by longer (15 to > 20 years) fire intervals. These results conform with those obtained from single-species, non-spatial population models. 3When interspecific competition for space was included in the model, all three species exhibited optima at shorter fire intervals and with a narrower range than in isolation. The three species did not co-occur under any fire regime. At intermediate fire frequencies (11,13 years), B. hookeriana excluded the other species, while for longer intervals between fires B. prionotes became dominant. 4The introduction of temporal (stochastic) variability in fire intervals (drawn from a normal distribution) failed to produce coexistence, unless spatial variability as a spatial ignition gradient was also included. The spatial arrangement of the non-sprouters observed in the field was then reproduced. 5Observed patterns of coexistence and spatial distributions of all species occurred when a spatial establishment gradient for the resprouter species was included in the model (individuals of B. attenuata are known to produce more seeds in swales than on dune crests and recruit seedlings here more frequently). 6Coexistence appears to be highly dependent upon the mean interfire period in combination with subtle gradients associated with fire propagation and recruitment conditions. Variation around the mean fire interval is less critical. When the system is modelled over a long time period (1500 years) coexistence is most strongly favoured for a narrow window of mean fire intervals (12,14 years). [source] The Human Ageing Genomic Resources: online databases and tools for biogerontologistsAGING CELL, Issue 1 2009Joćo Pedro De Magalhćes Summary Aging is a complex, challenging phenomenon that requires multiple, interdisciplinary approaches to unravel its puzzles. To assist basic research on aging, we developed the Human Ageing Genomic Resources (HAGR). This work provides an overview of the databases and tools in HAGR and describes how the gerontology research community can employ them. Several recent changes and improvements to HAGR are also presented. The two centrepieces in HAGR are GenAge and AnAge. GenAge is a gene database featuring genes associated with aging and longevity in model organisms, a curated database of genes potentially associated with human aging, and a list of genes tested for their association with human longevity. A myriad of biological data and information is included for hundreds of genes, making GenAge a reference for research that reflects our current understanding of the genetic basis of aging. GenAge can also serve as a platform for the systems biology of aging, and tools for the visualization of protein,protein interactions are also included. AnAge is a database of aging in animals, featuring over 4000 species, primarily assembled as a resource for comparative and evolutionary studies of aging. Longevity records, developmental and reproductive traits, taxonomic information, basic metabolic characteristics, and key observations related to aging are included in AnAge. Software is also available to aid researchers in the form of Perl modules to automate numerous tasks and as an SPSS script to analyse demographic mortality data. The HAGR are available online at http://genomics.senescence.info. [source] Individual Differences in Alcohol Drinking Frequency Are Associated With Electrophysiological Responses to Unexpected NonrewardsALCOHOLISM, Issue 4 2010Ingmar H. A. Franken Background:, It has been suggested that alcohol use is related to sensitivity of the reward system. Although there are several studies using self-reported measures supportive of this notion, objective biological data in humans on this issue are lacking. Aims:, This study is designed to test whether alcohol drinking frequency is associated with electrophysiological indices of reward processing. Materials and Methods:, In a passive gambling task, stimuli predicted the presence (reward) and absence (nonreward) of rewards resulting in P2 and medial frontal negativity (MFN) indices of reward processing. Forty-seven undergraduate students were asked about their habitual drinking frequency and the P2 and MFN to stimuli predicting reward were measured. Results:, Most importantly, the MFN to unpredicted nonrewards at the frontal midline (Fz) location correlated significantly with drinking frequency, with frequent drinkers showing larger MFN amplitudes. The results did not show a significant association between frequency and alcohol drinking and P2. Discussion:, Although several studies showing increased reward-sensitivity in addictive behaviors, the present results indicate that, in frequent alcohol drinkers, electrophysiological responsiveness is particularly activated by unpredicted nonrewards. In general, this may point to the involvement of the reward system in alcohol drinking frequency. Conclusion:, More specifically, the results demonstrate an increased vulnerability of high frequency drinkers to signals of (frustrative) nonrewards. [source] Analgesic and antiinflammatory activity of Cyclamen repandum S. et S.PHYTOTHERAPY RESEARCH, Issue 7 2007E. Speroni Abstract According to folk medicine some species belonging to the genus Cyclamen were used for their biological activities. Early investigation of the different species of the genus resulted in the isolation of triterpenic saponins. No phytochemical and biological data are available on C. repandum. As part of a series of phytochemical investigations for bioactive compounds from medicinal plants, Cyclamen repandum S. et S. was investigated. The present study sought to find the antiinflammatory and antinociceptive activities of C. repandum tubers in rats and mice. A preliminary screening was conducted with three different extracts in the tests used, particularly the paw edema and the writhing tests. Subsequently some saponins isolated from the ME extract, the more effective one, have been identified. This paper also describes the results of fractionation and bioassay guided chemical studies. Chemical investigation of the active extract afforded the isolation and characterization of six triterpenic saponins. The possible antiinflammatory and analgesic properties were investigated as the saponin content of the fractions allows to speculate on such aspect. Copyright © 2007 John Wiley & Sons, Ltd. [source] Discovering functions and revealing mechanisms at molecular level from biological networksPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 16 2007Shihua Zhang Abstract With the increasingly accumulated data from high-throughput technologies, study on biomolecular networks has become one of key focuses in systems biology and bioinformatics. In particular, various types of molecular networks (e.g., protein,protein interaction (PPI) network; gene regulatory network (GRN); metabolic network (MN); gene coexpression network (GCEN)) have been extensively investigated, and those studies demonstrate great potentials to discover basic functions and to reveal essential mechanisms for various biological phenomena, by understanding biological systems not at individual component level but at a system-wide level. Recent studies on networks have created very prolific researches on many aspects of living organisms. In this paper, we aim to review the recent developments on topics related to molecular networks in a comprehensive manner, with the special emphasis on the computational aspect. The contents of the survey cover global topological properties and local structural characteristics, network motifs, network comparison and query, detection of functional modules and network motifs, function prediction from network analysis, inferring molecular networks from biological data as well as representative databases and software tools. [source] Bridging proteomics and systems biology: What are the roads to be traveled?PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 16 2005Serhiy Souchelnytskyi Abstract The comprehensive study of proteomes has become an important part of attempts to uncover the systemic properties of biological systems. Proteomics provides data of a quality which increasingly fulfills strict requirements of systems biology for quantitative and qualitative information. Notably, proteomics can generate rich datasets that describe dynamic changes of proteomes. On the other hand, large-scale modeling requires the development of mathematic tools that are adequate for the processing of largely uncertain biological data. In this review, recent developments that pave the way for the integration of proteomics into systems biology are discussed. These developments include the standardization of data acquisition and presentation, the increased comprehensiveness of proteomics studies in description of functional status, localization and dynamics of proteins, and advanced modeling approaches. [source] Further analysis of the population history of ancient EgyptiansAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 2 2009Michael A. Schillaci Abstract The origins of state formation in ancient Egypt have been the focus of recent research utilizing biological data to test hypotheses regarding in situ development of local groups, or large-scale in-migration, possibly by an invading army. The primary goal of the present research is to further test these hypotheses. Our secondary goal is to compare different distance measures and assess how they might affect interpretation of population history. We analyze craniodental nonmetric data using several different measures of biological distance, as well as a method for estimating group diversity using multidimensional scaling of distance estimates. Patterns of biological variation and population relationships were interpreted in temporal and geographic contexts. The results of our analyses suggest that the formation of the ancient Egyptian state likely included a substantial in situ process, with some level of contribution by outside migrants probable. The higher level of population structure in Lower Egypt, relative to Upper Egypt, suggests that such influence and migration by outsiders may not have been widespread geographically. These findings support, but serve to refine further those obtained by the second author in a previous study. Moreover, our comparison of distance measures indicates that the choice of measure can influence identification and interpretation of the microevolutionary processes shaping population history, despite being strongly correlated with one another. Am J Phys Anthropol 2009. © 2009 Wiley-Liss, Inc. [source] Lung cancer: Progress in diagnosis, staging and therapyRESPIROLOGY, Issue 1 2010Stephen G. SPIRO ABSTRACT Lung cancer remains one of the greatest medical challenges with nearly 1.5 million new cases worldwide each year and a growing tobacco epidemic in the developing world. This review summarizes briefly the current status in growing areas of clinical research. The value of screening for early disease is not yet established and trials to see if mortality can be improved as a result are in progress. Better and more accurate staging will both streamline investigation and prove cost-effective once ultrasound-guided biopsy and aspiration of mediastinal nodes become universally accepted. This, allied to the new staging classification, will improve selection of cases for surgery, intensive multimodality therapy and for adjuvant treatment postoperatively. Much still needs to be done to refine staging as within a particular stage group, the outcome shows great variation. More information is needed on the genetic make-up in some groups of tumours and not just their size; that is, more biological data on tumour growth patterns are likely to be at least as discriminating. The place of the stem cell theory of tumorigenesis is also explored in this paper. Finally, targeted therapy for advanced non-small-cell lung cancer is highlighted as a development with early promise, but still much clarification is required, before it can be considered as a universal approach in late disease. [source] The promise of geometric morphometricsAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue S35 2002Joan T. Richtsmeier Abstract Nontraditional or geometric morphometric methods have found wide application in the biological sciences, especially in anthropology, a field with a strong history of measurement of biological form. Controversy has arisen over which method is the "best" for quantifying the morphological difference between forms and for making proper statistical statements about the detected differences. This paper explains that many of these arguments are superfluous to the real issues that need to be understood by those wishing to apply morphometric methods to biological data. Validity, the ability of a method to find the correct answer, is rarely discussed and often ignored. We explain why demonstration of validity is a necessary step in the evaluation of methods used in morphometrics. Focusing specifically on landmark data, we discuss the concepts of size and shape, and reiterate that since no unique definition of size exists, shape can only be recognized with reference to a chosen surrogate for size. We explain why only a limited class of information related to the morphology of an object can be known when landmark data are used. This observation has genuine consequences, as certain morphometric methods are based on models that require specific assumptions, some of which exceed what can be known from landmark data. We show that orientation of an object with reference to other objects in a sample can never be known, because this information is not included in landmark data. Consequently, a descriptor of form difference that contains information on orientation is flawed because that information does not arise from evidence within the data, but instead is a product of a chosen orientation scheme. To illustrate these points, we apply superimposition, deformation, and linear distance-based morphometric methods to the analysis of a simulated data set for which the true differences are known. This analysis demonstrates the relative efficacy of various methods to reveal the true difference between forms. Our discussion is intended to be fair, but it will be obvious to the reader that we favor a particular approach. Our bias comes from the realization that morphometric methods should operate with a definition of form and form difference consistent with the limited class of information that can be known from landmark data. Answers based on information that can be known from the data are of more use to biological inquiry than those based on unjustifiable assumptions. Yrbk Phys Anthropol 45:63,91, 2002. © 2002 Wiley-Liss, Inc. [source] Relationships between personality traits, seminal parameters and hormones in male infertilityANDROLOGIA, Issue 5 2002R. Conrad Summary. In this study we investigated the relationship between personality attitudes, psychopathological symptoms and biological parameters in male infertility. Eighty-four infertile men underwent a psychological and medical examination at our clinic. The psychological tests comprised the Symptom Checklist 90-R, the Toronto Alexithymia Scale and the NEO-Five Factor Inventory. Seminal parameters, gonadotrophins, sex steroids, cortisol and prolactin were analyzed to obtain biological data. Compared with questionnaires completed by normal populations those in the study group scored higher on the scales for ,conscientiousness', ,agreeableness', ,alexithymia' and ,somatization' and lower on the scale for ,neuroticism'. Regarding psychobiological correlations we found a negative correlation between seminal parameters and ,extraversion', ,anxiety' and ,psychoticism'. ,Alexithymia' was negatively correlated with stress hormones and ,conscientiousness' was correlated with sex steroids. The findings suggest above average social competence in the study group. The psychobiological correlations indicate a link between social-competence-related personality traits such as ,extraversion' and ,conscientiousness' and biological fertility characteristics. Implications of a higher alexithymia in infertile men, which is negatively correlated with stress hormones, are discussed. [source] | |||||||||||||||||||||||||