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Sample records for factor xa-binding site

  1. Characterization of a human coagulation factor Xa-binding site on Viperidae snake venom phospholipases A2 by affinity binding studies and molecular bioinformatics

    Directory of Open Access Journals (Sweden)

    Gowda Veerabasappa T

    2007-12-01

    Full Text Available Abstract Background The snake venom group IIA secreted phospholipases A2 (SVPLA2, present in the Viperidae snake family exhibit a wide range of toxic and pharmacological effects. They exert their different functions by catalyzing the hydrolysis of phospholipids (PL at the membrane/water interface and by highly specific direct binding to: (i presynaptic membrane-bound or intracellular receptors; (ii natural PLA2-inhibitors from snake serum; and (iii coagulation factors present in human blood. Results Using surface plasmon resonance (SPR protein-protein interaction measurements and an in vitro biological test of inhibition of prothrombinase activity, we identify a number of Viperidae venom SVPLA2s that inhibit blood coagulation through direct binding to human blood coagulation factor Xa (FXa via a non-catalytic, PL-independent mechanism. We classify the SVPLA2s in four groups, depending on the strength of their binding. Molecular electrostatic potentials calculated at the surface of 3D homology-modeling models show a correlation with inhibition of prothrombinase activity. In addition, molecular docking simulations between SVPLA2 and FXa guided by the experimental data identify the potential FXa binding site on the SVPLA2s. This site is composed of the following regions: helices A and B, the Ca2+ loop, the helix C-β-wing loop, and the C-terminal fragment. Some of the SVPLA2 binding site residues belong also to the interfacial binding site (IBS. The interface in FXa involves both, the light and heavy chains. Conclusion We have experimentally identified several strong FXa-binding SVPLA2s that disrupt the function of the coagulation cascade by interacting with FXa by the non-catalytic PL-independent mechanism. By theoretical methods we mapped the interaction sites on both, the SVPLA2s and FXa. Our findings may lead to the design of novel, non-competitive FXa inhibitors.

  2. Adaptive evolution of transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Berg Johannes

    2004-10-01

    Full Text Available Abstract Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection. Results We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background mutation rate, the selection coefficient, and the effective population size. Conclusions The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.

  3. Comparison of Transcription Factor Binding Site Models

    KAUST Repository

    Bhuyan, Sharifulislam

    2012-05-01

    Modeling of transcription factor binding sites (TFBSs) and TFBS prediction on genomic sequences are important steps to elucidate transcription regulatory mechanism. Dependency of transcription regulation on a great number of factors such as chemical specificity, molecular structure, genomic and epigenetic characteristics, long distance interaction, makes this a challenging problem. Different experimental procedures generate evidence that DNA-binding domains of transcription factors show considerable DNA sequence specificity. Probabilistic modeling of TFBSs has been moderately successful in identifying patterns from a family of sequences. In this study, we compare performances of different probabilistic models and try to estimate their efficacy over experimental TFBSs data. We build a pipeline to calculate sensitivity and specificity from aligned TFBS sequences for several probabilistic models, such as Markov chains, hidden Markov models, Bayesian networks. Our work, containing relevant statistics and evaluation for the models, can help researchers to choose the most appropriate model for the problem at hand.

  4. Risk factors for surgical site infections following clean orthopaedic ...

    African Journals Online (AJOL)

    Risk factors for surgical site infections following clean orthopaedic operations. ... the host and environmental risk factors for surgical site infections following clean ... Materials and Methods: Consecutive patients who satisfied the inclusion ...

  5. Nuclear power plant site evaluation using site population-meterology factor

    International Nuclear Information System (INIS)

    Rho, B.H.; Kang, C.H.

    1982-01-01

    In this paper, as a site evaluation technique, SPNF(Site Population Neteorology Factor) which is modified from SPF(Site Population Factor) of the USNRC model, is defined from site population and meteorology data in order to consider the radiological impacts to the population at large from the atmospheric dispersion of the radioactive effluents released during routine plant operation as well as accidental conditions. The SPMF model proved its propriety from the comparison of SPMF and SPF for Kori site. The relative suitability of Korean sites to the U.S. sites have been also examined using SPF. (Author)

  6. Siting factors for the Swedish deep repository for spent fuel

    International Nuclear Information System (INIS)

    Stroem, A.; Ericsson, Lars O.; Svemar, C.; Almen, K.E.; Andersson, Johan

    1998-01-01

    A project entitled Siting factors and criteria for site evaluation was initiated at the SKB in 1997. The project comprises an important part of the work of siting and site selection that is being pursued within SKB. The purpose of the project is to create a logical structure for the continued siting work, and its results should also be able to be used to assist in evaluating sites. The project will thereby also provide a means - in accordance with the Government's decision regarding Research Programme 95 - to obtain more detailed and quantified siting factors and criteria than those previously presented in the supplement to Research Programme 92. The overall goals of the project are to identify and quantify requirements and preferences regarding the properties of the rock and the soil from the perspectives of long-term safety, performance and planning and design of the rock works, and to identify siting factors and criteria. The latter should be able to be used to determine whether requirements and preferences are satisfied, both when screening sites for site investigation and after completed site investigation. Presented requirements, preferences, factors and criteria must be acceptable to national and municipal authorities or others with influence over the siting work. To start with, requirements and preferences regarding the performance of the rock in a deep repository have been clarified. These requirements and preferences are based on many years of experience of safety assessments and construction analyses within SKB. What is new here is the structuring that has been done, where a classification is made into different geoscientific disciplines, and the formalism that has been developed for the concepts requirements, preferences and performance. This is a prerequisite for a consistent and hopefully comprehensive set of requirements from a functional perspective. Work has continued on siting factors with reference to a coming site investigation programme. A

  7. Magnitude and factors associated with post-cesarean surgical site ...

    African Journals Online (AJOL)

    Magnitude and factors associated with post-cesarean surgical site infection at Hawassa University Teaching and referral hospital, southern Ethiopia: a ... the hospital. Thus, it should be averted by implementing infection prevention techniques.

  8. Empirical Site Amplification Factors Incorporating Soil Nonlinearity in Taiwan

    Science.gov (United States)

    Kuo, C. H.; Chung, C. H.; Che-Min, L.; Huang, J. Y.; Wen, K. L.

    2017-12-01

    Characteristics of site amplifications caused by both crustal and subduction earthquakes are important in Taiwan. For example, seismic waves were amplified and led to significant building damages in the Taipei Basin by the 1986 Hualien offshore (subduction interface) and the 1999 Chi-Chi earthquakes (crustal), for which the epicentral distances were about 100 km. To understand local site amplifications in Taiwan, empirical site amplification factors for horizontal ground motions are studied using recently constructed strong motion and site databases for the free-field TSMIP stations in Taiwan. Records of large magnitude earthquakes of ML larger than six from 1994 to 2014 were selected for this study. Site amplification factors at site conditions with Vs30 of 120 m/s to 1500 m/s and base accelerations up to 0.7g were inferred from intensity ratios of station pairs within specific distances. The reference site condition is assumed as Vs30 of 760 m/s (B/C boundary). Preliminary results indicate: 1. Soil nonlinearity is more obviously at short periods (PGA, Sa0.3) than long periods (PGV, Sa1.0). 2. Soil nonlinearity is significant for stations belong to site classes of B, C, D, and E in Taiwan. 3. Effect of station-pair distance is seen at short periods (PGA and Sa0.3). 4. No significant different is found in site amplifications of crustal and subduction earthquakes. The result could be a reference for the Fa and Fv in Taiwan's building code.

  9. Accident Causal Factors on the Building Construction Sites: A Review

    Directory of Open Access Journals (Sweden)

    Opeyemi Samuel Williams

    2018-01-01

    Full Text Available The concerns for cost, quality and timely delivery of projects have been in existence from time immemorial, whereas the passion for these should be extended to safe execution of site works by the construction participants, as safety of life is very paramount. However, high level of commitment that is essential for the safe execution of site works has become a taboo. Hence, a plethora of accidents takes place on the site ranging from falls from height, contact with working tools, vehicle-related, slip and trip, collapse, exposure to harmful substances, to lifting and handling object accidents. It is pertinent to know that, responsibility for accidents on site cuts across all project participants (clients, consultants, contractors, workers, as well as the construction site environment. Recognition of the construction participants and site environmental factors as agents of accident is the focus of this research. Through extensive review of literature, a copious number of factors were identified and subsequently grouped under five factors as client-related, consultant-related, contractor-related, construction workers-related, and construction site-related. However, there has been a dearth of research in the grouping of accident contributing factors. The identification and understanding of these factors will go a long way in mitigating construction accidents, coupled with proven measures taken in positively addressing them. Efforts to prevent these causative factors include inter alia elimination of hazards from design, effective safety management, adequate planning of activities and employment of seasoned professionals by the client. The contractors are to embark on staff safety auditing, set up safety committees, conduct regular training for staff, use innovative technology, uphold housekeeping and report accident occurrence, while strict adherence to safety regulations must be adopted by all construction operatives.

  10. FACTORS PREDICTING CONSUMERS' ASSESSMENT OF ADVERTISEMENTS ON SOCIAL NETWORKING SITES

    OpenAIRE

    Hossam Deraz; Gabriel Baffour Awuah; Desalegn Abraha Gebrekidan

    2015-01-01

    Marketers act on social networking sites (SNSs) in order to be more efficient in merchandising their products and/or services. Even so, the scope of the published studies regarding the assessment of advertisements on social networking sites (SNAs) is limited. Consequently, the present study aimed to consider credibility and interactivity, in addition to information, entertainment and irritation values, as main factors for consumers’ assessment of SNAs, as perceived by SNSs’ users. An analysis...

  11. Dispersion factors - tables and diagrams for the Karlsruhe site

    International Nuclear Information System (INIS)

    Papadopoulos, D.; Baer, M.; Honcu, S.

    1984-02-01

    Dispersion experiments were performed at the Nuclear Research Center for the Karlsruhe site. The evaluation of these experiments allowed to determine the parameters of lateral or vertical atmospheric dispersions. This report is a compilation of tables and diagrams showing the dispersion factors calculated with the help of the dispersion parameters. These dispersion factors are valid for the Karlsruhe site. They have been normalized to 1 m/s wind speed and to 1 g/s (or 1 Bq/s) source strength. (orig.) [de

  12. [Risk factors related to surgical site infection in elective surgery].

    Science.gov (United States)

    Angeles-Garay, Ulises; Morales-Márquez, Lucy Isabel; Sandoval-Balanzarios, Miguel Antonio; Velázquez-García, José Arturo; Maldonado-Torres, Lulia; Méndez-Cano, Andrea Fernanda

    2014-01-01

    The risk factors for surgical site infections in surgery should be measured and monitored from admission to 30 days after the surgical procedure, because 30% of Surgical Site Infection is detected when the patient was discharged. Calculate the Relative Risk of associated factors to surgical site infections in adult with elective surgery. Patients were classified according to the surgery contamination degree; patient with surgery clean was defined as no exposed and patient with clean-contaminated or contaminated surgery was defined exposed. Risk factors for infection were classified as: inherent to the patient, pre-operative, intra-operative and post-operative. Statistical analysis; we realized Student t or Mann-Whitney U, chi square for Relative Risk (RR) and multivariate analysis by Cox proportional hazards. Were monitored up to 30 days after surgery 403 patients (59.8% women), 35 (8.7%) developed surgical site infections. The factors associated in multivariate analysis were: smoking, RR of 3.21, underweight 3.4 hand washing unsuitable techniques 4.61, transfusion during the procedure 3.22, contaminated surgery 60, and intensive care stay 8 to 14 days 11.64, permanence of 1 to 3 days 2.4 and use of catheter 1 to 3 days 2.27. To avoid all risk factors is almost impossible; therefore close monitoring of elective surgery patients can prevent infectious complications.

  13. Incorporating evolution of transcription factor binding sites into ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    Identifying transcription factor binding sites (TFBSs) is essential to elucidate ... alignments with parts annotated as gap lessly aligned TFBSs (pair-profile hits) are generated. Moreover, the pair- profile related parameters are derived in a sound statistical framework. ... Much research has gone into the study of the evolution of.

  14. Structural Fingerprints of Transcription Factor Binding Site Regions

    Directory of Open Access Journals (Sweden)

    Peter Willett

    2009-03-01

    Full Text Available Fourier transforms are a powerful tool in the prediction of DNA sequence properties, such as the presence/absence of codons. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers. In this work we apply Fourier techniques to the analysis of the structural properties of human chromosomes 21 and 22 and also to three sets of transcription factor binding sites within these chromosomes. We find that, for a given structural property, the structural property power spectra of chromosomes 21 and 22 are strikingly similar. We find common peaks in their power spectra for both Sp1 and p53 transcription factor binding sites. We use the power spectra as a structural fingerprint and perform similarity searching in order to find transcription factor binding site regions. This approach provides a new strategy for searching the genome data for information. Although it is difficult to understand the relationship between specific functional properties and the set of structural parameters in our database, our structural fingerprints nevertheless provide a useful tool for searching for function information in sequence data. The power spectrum fingerprints provide a simple, fast method for comparing a set of functional sequences, in this case transcription factor binding site regions, with the sequences of whole chromosomes. On its own, the power spectrum fingerprint does not find all transcription factor binding sites in a chromosome, but the results presented here show that in combination with other approaches, this technique will improve the chances of identifying functional sequences hidden in genomic data.

  15. Transcription factor binding sites prediction based on modified nucleosomes.

    Directory of Open Access Journals (Sweden)

    Mohammad Talebzadeh

    Full Text Available In computational methods, position weight matrices (PWMs are commonly applied for transcription factor binding site (TFBS prediction. Although these matrices are more accurate than simple consensus sequences to predict actual binding sites, they usually produce a large number of false positive (FP predictions and so are impoverished sources of information. Several studies have employed additional sources of information such as sequence conservation or the vicinity to transcription start sites to distinguish true binding regions from random ones. Recently, the spatial distribution of modified nucleosomes has been shown to be associated with different promoter architectures. These aligned patterns can facilitate DNA accessibility for transcription factors. We hypothesize that using data from these aligned and periodic patterns can improve the performance of binding region prediction. In this study, we propose two effective features, "modified nucleosomes neighboring" and "modified nucleosomes occupancy", to decrease FP in binding site discovery. Based on these features, we designed a logistic regression classifier which estimates the probability of a region as a TFBS. Our model learned each feature based on Sp1 binding sites on Chromosome 1 and was tested on the other chromosomes in human CD4+T cells. In this work, we investigated 21 histone modifications and found that only 8 out of 21 marks are strongly correlated with transcription factor binding regions. To prove that these features are not specific to Sp1, we combined the logistic regression classifier with the PWM, and created a new model to search TFBSs on the genome. We tested the model using transcription factors MAZ, PU.1 and ELF1 and compared the results to those using only the PWM. The results show that our model can predict Transcription factor binding regions more successfully. The relative simplicity of the model and capability of integrating other features make it a superior method

  16. Geoscientific evaluation factors and criteria for siting and site evaluation. Progress report

    International Nuclear Information System (INIS)

    Stroem, A.; Ericsson, Lars O.; Svemar, C.; Almen, K.E.; Andersson, Johan

    1999-03-01

    The purposes of the present report are to: present the work that has been done to identify the parameters that need to be determined in a geoscientific site investigation and that serve as the basis for the work with geoscientific evaluation factors; give a progress report from the project that was initiated in 1997 named Siting Factors and Criteria for Site Evaluation, with an emphasis on definitions, outline and structure for the execution of the work; present geoscientific requirements on function both general and in detail in the form of an example for the discipline rock mechanics; present geoscientific evaluation factors associated with different stages in the siting work in the form of an example for the discipline hydrogeochemical composition; present plans for further work as regards criteria for site evaluation in different siting stages. The project is under way, and this is to be regarded as a progress report since e.g. criteria for site evaluation will be presented at a later date. The long-term performance and safety of the deep repository must always be evaluated by means of an integrated safety assessment. The work with factors and criteria can never take the place of such an assessment, but can provide guidance regarding its outcome. Requirements and preferences regarding the function of the rock in the deep repository have been clarified in this progress report. What is new here is the structuring that has been carried out, with a classification into different geoscientific disciplines, and the formalism that has been given to the terms requirement, preference and function. Based on fundamental safety and construction functions, requirements on function have been specified for the disciplines geology, thermal properties, hydro-geology, rock mechanics, chemistry and transport properties. Furthermore, function analyses have been identified by means of which it is possible to concretize requirements on function and which geoscientific parameters are

  17. Geoscientific evaluation factors and criteria for siting and site evaluation. Progress report

    Energy Technology Data Exchange (ETDEWEB)

    Stroem, A.; Ericsson, Lars O.; Svemar, C. [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden); Almen, K.E. [KEA GEO-konsult AB (Sweden); Andersson, Johan [Golder Grundteknik KB (Sweden)

    1999-03-01

    The purposes of the present report are to: present the work that has been done to identify the parameters that need to be determined in a geoscientific site investigation and that serve as the basis for the work with geoscientific evaluation factors; give a progress report from the project that was initiated in 1997 named Siting Factors and Criteria for Site Evaluation, with an emphasis on definitions, outline and structure for the execution of the work; present geoscientific requirements on function both general and in detail in the form of an example for the discipline rock mechanics; present geoscientific evaluation factors associated with different stages in the siting work in the form of an example for the discipline hydrogeochemical composition; present plans for further work as regards criteria for site evaluation in different siting stages. The project is under way, and this is to be regarded as a progress report since e.g. criteria for site evaluation will be presented at a later date. The long-term performance and safety of the deep repository must always be evaluated by means of an integrated safety assessment. The work with factors and criteria can never take the place of such an assessment, but can provide guidance regarding its outcome. Requirements and preferences regarding the function of the rock in the deep repository have been clarified in this progress report. What is new here is the structuring that has been carried out, with a classification into different geoscientific disciplines, and the formalism that has been given to the terms requirement, preference and function. Based on fundamental safety and construction functions, requirements on function have been specified for the disciplines geology, thermal properties, hydro-geology, rock mechanics, chemistry and transport properties. Furthermore, function analyses have been identified by means of which it is possible to concretize requirements on function and which geoscientific parameters are

  18. Factors Enabling Information Propagation in a Social Network Site

    DEFF Research Database (Denmark)

    Magnani, Matteo; Montesi, Danilo; Rossi, Luca

    2013-01-01

    A relevant feature of Social Network Sites is their ability to propagate units of information and create large distributed conversations. This phenomenon is particularly relevant because of the speed of information propagation, which is known to be much faster than within traditional media......, and because of the very large amount of people that can potentially be exposed to information items. While many general formal models of network propagation have been developed in different research fields, in this chapter we present the result of an empirical study on a Large Social Database (LSD) aimed...... at measuring specific socio-technical factors enabling information spreading in Social Network Sites....

  19. A systems biology approach to transcription factor binding site prediction.

    Directory of Open Access Journals (Sweden)

    Xiang Zhou

    2010-03-01

    Full Text Available The elucidation of mammalian transcriptional regulatory networks holds great promise for both basic and translational research and remains one the greatest challenges to systems biology. Recent reverse engineering methods deduce regulatory interactions from large-scale mRNA expression profiles and cross-species conserved regulatory regions in DNA. Technical challenges faced by these methods include distinguishing between direct and indirect interactions, associating transcription regulators with predicted transcription factor binding sites (TFBSs, identifying non-linearly conserved binding sites across species, and providing realistic accuracy estimates.We address these challenges by closely integrating proven methods for regulatory network reverse engineering from mRNA expression data, linearly and non-linearly conserved regulatory region discovery, and TFBS evaluation and discovery. Using an extensive test set of high-likelihood interactions, which we collected in order to provide realistic prediction-accuracy estimates, we show that a careful integration of these methods leads to significant improvements in prediction accuracy. To verify our methods, we biochemically validated TFBS predictions made for both transcription factors (TFs and co-factors; we validated binding site predictions made using a known E2F1 DNA-binding motif on E2F1 predicted promoter targets, known E2F1 and JUND motifs on JUND predicted promoter targets, and a de novo discovered motif for BCL6 on BCL6 predicted promoter targets. Finally, to demonstrate accuracy of prediction using an external dataset, we showed that sites matching predicted motifs for ZNF263 are significantly enriched in recent ZNF263 ChIP-seq data.Using an integrative framework, we were able to address technical challenges faced by state of the art network reverse engineering methods, leading to significant improvement in direct-interaction detection and TFBS-discovery accuracy. We estimated the accuracy

  20. Effects of cytosine methylation on transcription factor binding sites

    KAUST Repository

    Medvedeva, Yulia A

    2014-03-26

    Background: DNA methylation in promoters is closely linked to downstream gene repression. However, whether DNA methylation is a cause or a consequence of gene repression remains an open question. If it is a cause, then DNA methylation may affect the affinity of transcription factors (TFs) for their binding sites (TFBSs). If it is a consequence, then gene repression caused by chromatin modification may be stabilized by DNA methylation. Until now, these two possibilities have been supported only by non-systematic evidence and they have not been tested on a wide range of TFs. An average promoter methylation is usually used in studies, whereas recent results suggested that methylation of individual cytosines can also be important.Results: We found that the methylation profiles of 16.6% of cytosines and the expression profiles of neighboring transcriptional start sites (TSSs) were significantly negatively correlated. We called the CpGs corresponding to such cytosines " traffic lights" We observed a strong selection against CpG " traffic lights" within TFBSs. The negative selection was stronger for transcriptional repressors as compared with transcriptional activators or multifunctional TFs as well as for core TFBS positions as compared with flanking TFBS positions.Conclusions: Our results indicate that direct and selective methylation of certain TFBS that prevents TF binding is restricted to special cases and cannot be considered as a general regulatory mechanism of transcription. 2013 Medvedeva et al.; licensee BioMed Central Ltd.

  1. Atrial natriuretic factor binding sites in experimental congestive heart failure

    International Nuclear Information System (INIS)

    Bianchi, C.; Thibault, G.; Wrobel-Konrad, E.; De Lean, A.; Genest, J.; Cantin, M.

    1989-01-01

    A quantitative in vitro autoradiographic study was performed on the aorta, renal glomeruli, and adrenal cortex of cardiomyopathic hamsters in various stages of heart failure and correlated, in some instances, with in vivo autoradiography. The results indicate virtually no correlation between the degree of congestive heart failure and the density of 125I-labeled atrial natriuretic factor [(Ser99, Tyr126)ANF] binding sites (Bmax) in the tissues examined. Whereas the Bmax was increased in the thoracic aorta in moderate and severe heart failure, there were no significant changes in the zona glomerulosa. The renal glomeruli Bmax was lower in mild and moderate heart failure compared with control and severe heart failure. The proportion of ANF B- and C-receptors was also evaluated in sections of the aorta, adrenal, and kidney of control and cardiomyopathic hamsters with severe heart failure. (Arg102, Cys121)ANF [des-(Gln113, Ser114, Gly115, Leu116, Gly117) NH2] (C-ANF) at 10(-6) M displaced approximately 505 of (Ser99, Tyr126)125I-ANF bound in the aorta and renal glomeruli and approximately 20% in the adrenal zona glomerulosa in both series of animals. These results suggest that ANF may exert a buffering effect on the vasoconstriction of heart failure and to a certain extent may inhibit aldosterone secretion. The impairment of renal sodium excretion does not appear to be related to glomerular ANF binding sites at any stage of the disease

  2. Identifying Key Factors Relevant for Base Camp Siting

    Science.gov (United States)

    2017-12-01

    centers. 3.2.6.3 Religious and historical sites Respecting sacred sites helps build rapport with the host nation. 3.2.6.4 Local infrastructure...churches, mosques, national libraries, hospitals, cemeteries, historical ruins, religious sites, cultural areas, and other protected sites...controlled and protected wells. • Electricity: town engineer • Academic: government and religious leaders • Trash: private business (local

  3. Mutations and binding sites of human transcription factors

    KAUST Repository

    Kamanu, Frederick Kinyua

    2012-06-01

    Mutations in any genome may lead to phenotype characteristics that determine ability of an individual to cope with adaptation to environmental challenges. In studies of human biology, among the most interesting ones are phenotype characteristics that determine responses to drug treatments, response to infections, or predisposition to specific inherited diseases. Most of the research in this field has been focused on the studies of mutation effects on the final gene products, peptides, and their alterations. Considerably less attention was given to the mutations that may affect regulatory mechanism(s) of gene expression, although these may also affect the phenotype characteristics. In this study we make a pilot analysis of mutations observed in the regulatory regions of 24,667 human RefSeq genes. Our study reveals that out of eight studied mutation types, insertions are the only one that in a statistically significant manner alters predicted transcription factor binding sites (TFBSs). We also find that 25 families of TFBSs have been altered by mutations in a statistically significant manner in the promoter regions we considered. Moreover, we find that the related transcription factors are, for example, prominent in processes related to intracellular signaling; cell fate; morphogenesis of organs and epithelium; development of urogenital system, epithelium, and tube; neuron fate commitment. Our study highlights the significance of studying mutations within the genes regulatory regions and opens way for further detailed investigations on this topic, particularly on the downstream affected pathways. 2012 Kamanu, Medvedeva, Schaefer, Jankovic, Archer and Bajic.

  4. Prediction of nucleosome positioning based on transcription factor binding sites.

    Directory of Open Access Journals (Sweden)

    Xianfu Yi

    Full Text Available BACKGROUND: The DNA of all eukaryotic organisms is packaged into nucleosomes, the basic repeating units of chromatin. The nucleosome consists of a histone octamer around which a DNA core is wrapped and the linker histone H1, which is associated with linker DNA. By altering the accessibility of DNA sequences, the nucleosome has profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is of great importance for the study of genomic control mechanisms. Transcription factors (TFs have been suggested to play a role in nucleosome positioning in vivo. PRINCIPAL FINDINGS: Here, the minimum redundancy maximum relevance (mRMR feature selection algorithm, the nearest neighbor algorithm (NNA, and the incremental feature selection (IFS method were used to identify the most important TFs that either favor or inhibit nucleosome positioning by analyzing the numbers of transcription factor binding sites (TFBSs in 53,021 nucleosomal DNA sequences and 50,299 linker DNA sequences. A total of nine important families of TFs were extracted from 35 families, and the overall prediction accuracy was 87.4% as evaluated by the jackknife cross-validation test. CONCLUSIONS: Our results are consistent with the notion that TFs are more likely to bind linker DNA sequences than the sequences in the nucleosomes. In addition, our results imply that there may be some TFs that are important for nucleosome positioning but that play an insignificant role in discriminating nucleosome-forming DNA sequences from nucleosome-inhibiting DNA sequences. The hypothesis that TFs play a role in nucleosome positioning is, thus, confirmed by the results of this study.

  5. Standard protocol for evaluation of environmental transfer factors around NPP sites

    International Nuclear Information System (INIS)

    Hegde, A.G.; Verma, P.C.; Rao, D.D.

    2009-01-01

    This document presents the standard procedures for evaluation of site specific environmental transfer factors around NPP sites. The scope of this document is to provide standard protocol to be followed for evaluation of environmental transfer factors around NPP sites. The studies on transfer factors are being carried out at various NPP sites under DAE-BRNS projects for evaluation of site specific transfer factors for radionuclides released from power plants. This document contains a common methodology in terms of sampling, processing, measurements and analysis of elemental/radionuclides, while keeping the site specific requirements also in place. (author)

  6. Risk Factors for Surgical Site Infections in Dermatological Surgery

    Directory of Open Access Journals (Sweden)

    Xiaomeng Liu

    2017-11-01

    Full Text Available Current literature on risk factors for surgical site infection (SSI in dermatological surgery in the absence of antibiotic prophylaxis is limited. The aim of this study was to retrospectively evaluate patients presenting for dermatological surgery. A total of 1,977 procedures were reviewed. SSI was clinically suspected in 79 (4.0% patients and confirmed by culture in 38 (1.9%. Using the strictest definition of SSI (clinical symptoms with positive culture significantly higher risk of SSI was found for location on the ear (odds ratio (OR 6.03, 95% confidence interval (95% CI 2.12–17.15, larger defects (OR 1.08 per cm2 increase, 95% CI 1.03–1.14, closure with flaps (OR 6.35, 95% CI 1.33–30.28 and secondary intention (OR 3.01, 95% CI 1.11–8.13. These characteristics were also associated with higher risk of clinically suspected SSI regardless of culture results with slightly lower ORs. In conclusion, the risk of acquiring a SSI is increased in surgeries performed on the ear, in larger wounds and in defects closed with flaps or healed by secondary intention.

  7. Protective actions as a factor in power reactor siting

    Energy Technology Data Exchange (ETDEWEB)

    Gant, K.S.; Schweitzer, M.

    1984-06-01

    This report examines the relationship between a power reactor site and the ease of implementing protective actions (emergency measures a serious accident). Limiting populating density around a reactor lowers the number of people at risk but cannot assure that all protective actions are possible for those who reside near the reactor. While some protective measures can always be taken (i.e., expedient respiratory protection, sheltering) the ability to evacuate the area or find adequate shelter may depend on the characteristics of the area near the reactor site. Generic siting restrictions designed to identify and eliminate these site-specific constraints would be difficult to formulate. The authors suggest identifying possible impediments to protective actions at a proposed reactor site and addressing these problems in the emergency plans. 66 references, 6 figures, 8 tables.

  8. Protective actions as a factor in power reactor siting

    International Nuclear Information System (INIS)

    Gant, K.S.; Schweitzer, M.

    1984-06-01

    This report examines the relationship between a power reactor site and the ease of implementing protective actions (emergency measures a serious accident). Limiting populating density around a reactor lowers the number of people at risk but cannot assure that all protective actions are possible for those who reside near the reactor. While some protective measures can always be taken (i.e., expedient respiratory protection, sheltering) the ability to evacuate the area or find adequate shelter may depend on the characteristics of the area near the reactor site. Generic siting restrictions designed to identify and eliminate these site-specific constraints would be difficult to formulate. The authors suggest identifying possible impediments to protective actions at a proposed reactor site and addressing these problems in the emergency plans. 66 references, 6 figures, 8 tables

  9. Geographic factors related to site suitability of low-level waste disposal

    International Nuclear Information System (INIS)

    Zittel, H.E.

    1981-01-01

    A number of factors related to the site suitability of low-level waste disposal sites are discussed. The factors are a combination of those which might be considered environmental and those dealing with site criteria. Among the factors covered are: possible population criteria, alternative site selection, transportation criteria and community involvement considerations. All these factors are discussed in a manner based on the premise that the technology exists to carry out low-level waste disposal in a manner such that public health and safety can be insured. The conclusion of the discussion is that problems encountered in siting low-level waste facilities will be largely societal and political in nature

  10. Surgical Site Infection Rate and Risk Factors among Obstetric Cases ...

    African Journals Online (AJOL)

    2009-04-01

    Among surgical patients in obstetrics, Surgical Site Infections were the most ... for delivery from April 1, 2009 to March 31, 2010 in obstetric ward of the Hospital. ... applying improved surgical techniques and improving infection prevention ...

  11. Deriving amplification factors from simple site parameters using generalized regression neural networks: implications for relevant site proxies

    Science.gov (United States)

    Boudghene Stambouli, Ahmed; Zendagui, Djawad; Bard, Pierre-Yves; Derras, Boumédiène

    2017-07-01

    Most modern seismic codes account for site effects using an amplification factor (AF) that modifies the rock acceleration response spectra in relation to a "site condition proxy," i.e., a parameter related to the velocity profile at the site under consideration. Therefore, for practical purposes, it is interesting to identify the site parameters that best control the frequency-dependent shape of the AF. The goal of the present study is to provide a quantitative assessment of the performance of various site condition proxies to predict the main AF features, including the often used short- and mid-period amplification factors, Fa and Fv, proposed by Borcherdt (in Earthq Spectra 10:617-653, 1994). In this context, the linear, viscoelastic responses of a set of 858 actual soil columns from Japan, the USA, and Europe are computed for a set of 14 real accelerograms with varying frequency contents. The correlation between the corresponding site-specific average amplification factors and several site proxies (considered alone or as multiple combinations) is analyzed using the generalized regression neural network (GRNN). The performance of each site proxy combination is assessed through the variance reduction with respect to the initial amplification factor variability of the 858 profiles. Both the whole period range and specific short- and mid-period ranges associated with the Borcherdt factors Fa and Fv are considered. The actual amplification factor of an arbitrary soil profile is found to be satisfactorily approximated with a limited number of site proxies (4-6). As the usual code practice implies a lower number of site proxies (generally one, sometimes two), a sensitivity analysis is conducted to identify the "best performing" site parameters. The best one is the overall velocity contrast between underlying bedrock and minimum velocity in the soil column. Because these are the most difficult and expensive parameters to measure, especially for thick deposits, other

  12. Using TESS to predict transcription factor binding sites in DNA sequence.

    Science.gov (United States)

    Schug, Jonathan

    2008-03-01

    This unit describes how to use the Transcription Element Search System (TESS). This Web site predicts transcription factor binding sites (TFBS) in DNA sequence using two different kinds of models of sites, strings and positional weight matrices. The binding of transcription factors to DNA is a major part of the control of gene expression. Transcription factors exhibit sequence-specific binding; they form stronger bonds to some DNA sequences than to others. Identification of a good binding site in the promoter for a gene suggests the possibility that the corresponding factor may play a role in the regulation of that gene. However, the sequences transcription factors recognize are typically short and allow for some amount of mismatch. Because of this, binding sites for a factor can typically be found at random every few hundred to a thousand base pairs. TESS has features to help sort through and evaluate the significance of predicted sites.

  13. Identification of Site Selection Factors in the U.S. Franchise Restaurant Industry: An Exploratory Study

    OpenAIRE

    Park, Kunsoon

    2002-01-01

    The purpose of this study was to identify and rank the importance of the site selection factors that influence the U.S. franchise restaurant industry as well as rank the confidence level of the experts. To identify the site selection factors, this study sought assistance and support from restaurant professionals. The Delphi technique was used to elicit the opinions of a panel of experts regarding the site selection factors. The panel was composed of restaurant professionals of restaurant c...

  14. Reassessment of selected factors affecting siting of Nuclear Power Plants

    Energy Technology Data Exchange (ETDEWEB)

    Davis, R.E.; Hanson, A.L.; Mubayi, V.; Nourbakhsh, H.P.

    1997-02-01

    Brookhaven National Laboratory has performed a series of probabilistic consequence assessment calculations for nuclear reactor siting. This study takes into account recent insights into severe accident source terms and examines consequences in a risk based format consistent with the quantitative health objectives (QHOs) of the NRC`s Safety Goal Policy. Simplified severe accident source terms developed in this study are based on the risk insights of NUREG-1150. The results of the study indicate that both the quantity of radioactivity released in a severe accident as well as the likelihood of a release are lower than those predicted in earlier studies. The accident risks using the simplified source terms are examined at a series of generic plant sites, that vary in population distribution, meteorological conditions, and exclusion area boundary distances. Sensitivity calculations are performed to evaluate the effects of emergency protective action assumptions on the risk of prompt fatality and latent cancers fatality, and population relocation. The study finds that based on the new source terms the prompt and latent fatality risks at all generic sites meet the QHOs of the NRC`s Safety Goal Policy by margins ranging from one to more than three orders of magnitude. 4 refs., 17 figs., 24 tabs.

  15. Geographic factors related to site suitability of low-level waste disposal

    Science.gov (United States)

    Zittel, H. E.

    Factors related to the site suitability of low level waste disposal sites are discussed including those which might be considered environmental and those dealing with site criteria. Possible population criteria, alternative site selection, transportation criteria, and community involvement are considered. All these factors are based on the premise that the technology exists to carry out low level waste disposal in a manner such that public health and safety can be insured. It is concluded that problems encountered in siting low level waste facilities are largely societal and political in nature.

  16. Evaluation of disposal site geochemical performance using a containment factor

    International Nuclear Information System (INIS)

    Lerman, A.; Domenico, P.A.; Bartlett, J.W.

    1988-01-01

    The containment factor is a measure of retention by geologic setting of wastes released from a repository. The factor is alternatively defined either in terms of several measurable hydrological and geochemical parameters, or in terms of amounts of waste components that may be released to the geologic setting and, subsequently, to the environment. Containment factors for individual waste components in a given geologic setting are functions of groundwater to rock volume ratios, sorption or exchange characteristics of the rocks, and containment time to groundwater travel time ratios. For high-level radioactive wastes, containment factors based on the NRC and EPA limit values for cumulative releases from waste and to the environment provide a measure of the geochemical performance of the geologic setting in tuff, basalt, and salt. The containment factor values for individual nuclides from high-level wastes indicate that for some of the nuclides containment may be achieved by groundwater travel time along. For other nuclides, additional performance functions need to be allocated to geochemical retention by such processes as sorption, ion-exchange or precipitation

  17. Toward a regional power plant siting method: AEC-Maryland regional siting factors study, FY 1974 progress report

    International Nuclear Information System (INIS)

    Yaffee, S.L.; Miller, C.A.

    1974-11-01

    The ''AEC-Maryland Regional Siting Factors Study'' examines the process of siting in a regional context. It is developing an analysis method to delineate candidate areas for siting of several power plant technology packages, including both fossil-fueled and nuclear options. Tools that are being used include simulation modeling, economic and demographic forecasting, spatial analysis, and computer graphics and numerical manipulation. The approach will describe the trade-offs incurred if a power plant is located in one candidate area rather than in another. In FY 1974, a suitability analysis method was developed which uses engineering and environmental parameters to define a level of environmental cost incurred if a segment of land is used to site a specific technology package. (U.S.)

  18. Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively.

    Science.gov (United States)

    Clifford, Jacob; Adami, Christoph

    2015-09-02

    Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein-DNA interactions at the sequence level is through position weight matrices (PWMs) that estimate the joint probability of a DNA binding site sequence by assuming positional independence within the DNA sequence. Here we construct conditional PWMs that depend on the motif signatures in the flanking DNA sequence, by conditioning known binding site loci on the presence or absence of additional binding sites in the flanking sequence of each site's locus. Pooling known sites with similar flanking sequence patterns allows for the estimation of the conditional distribution function over the binding site sequences. We apply our model to the Dorsal transcription factor binding sites active in patterning the Dorsal-Ventral axis of Drosophila development. We find that those binding sites that cooperate with nearby Twist sites on average contain about 0.5 bits of information about the presence of Twist transcription factor binding sites in the flanking sequence. We also find that Dorsal binding site detectors conditioned on flanking sequence information make better predictions about what is a Dorsal site relative to background DNA than detection without information about flanking sequence features.

  19. Factors for Successful Use of Social Networking Sites in Higher Education

    Directory of Open Access Journals (Sweden)

    L Schlenkrich

    2012-09-01

    Full Text Available Social networking sites are extremely popular online destinations that offer users easy ways to build and maintain relationships with each other, and to disseminate information in an activity referred to as social networking. Students, lecturers, teachers, parents and businesses, in increasing numbers, use tools available on social networking sites to communicate with each other in a fast and cost-effective manner. The use of social networking sites to support educational initiatives has received much attention. However, the full potential of social network sites has yet to be achieved as users continue to strive for optimal ways of using these sites, as well as battle to overcome the negative characteristics (for example, privacy, security, governance, user behaviour, information quality of these sites. This paper proposes factors for successful use of social networking sites in higher educational institutions. These success factors need to be adopted by users in order to develop the positive aspects of social networking, while at the same time mitigating the negative characteristics. An initial set of factors for successful use of social networking sites, as well as measures to test successful use of social networking sites were derived from the literature. These factors were tested by means of an online survey of students at a university, the results of which informed the final factors for successful use of social networking sites. The factors enable users to overcome the negative characteristics associated with social networking sites. If used successfully, social networking sites can offer lecturers and students a useful tool with which to develop their relationship and contribute to their learning experience.

  20. Preliminary geologic site selection factors for the National Waste Terminal Storage Program

    International Nuclear Information System (INIS)

    1977-06-01

    The geologic considerations and the associated factors that have to be addressed in the selection of repository sites in deep geologic formations are listed and described. In addition a description is given of the information necessary to assess the geologic factors. The methods of obtaining this information are described. An illustration is given of a general approach of how the geologic factors could be applied and integrated to assess the acceptability of candidate sites. No consideration is given to a detailed description of the application of integration of the geologic factors. The criteria associated with each factor that will be used are not defined

  1. Risk factors for delayed healing at the free anterolateral thigh flap donor site

    Directory of Open Access Journals (Sweden)

    Yoshiro Abe

    2018-01-01

    Full Text Available Background The free anterolateral thigh (ALT flap has been widely used for various kinds of reconstructions. However, delayed healing at the donor site occasionally occurs due to wound dehiscence or the partial loss of grafted skin at the donor site. The aim of the present study was to identify reliable predictive factors for delayed healing at the donor site after the harvest of a free ALT flap. Methods This study included 52 patients who underwent reconstructive procedures using free ALT flaps. The delayed healing group included patients with wounds at the donor site that had not healed over 3 weeks after surgery, and the normal healing group included patients who showed wound healing within 3 weeks after surgery. Multivariate logistic regression models were created to identify the risk factors for delayed healing at the ALT flap donor site. Results Among the 52 patients, 24 (46.2% showed delayed healing at the donor site, and 6 patients required additional operative treatment. A high preoperative body mass index (BMI, smoking, and skin grafting were found to be significantly associated with delayed healing at the ALT donor site. Of the 37 patients who underwent skin grafting, 23 (62% experienced delayed healing at the donor site. Conclusions A high preoperative BMI, smoking, and skin grafting were risk factors for delayed healing at the free ALT donor site. Skin grafting at the ALT donor site should be avoided in patients with a high BMI or a habit of smoking.

  2. Site specific transfer factor studies for Kaiga region

    International Nuclear Information System (INIS)

    Karunakara, N.

    2012-01-01

    The Radioecology Laboratory of University Science Instrumentation Centre, Mangalore University is engaged in frontline research studies on different aspects of environmental radioactivity and radiation protection for the last 20 years. Extensive studies have been carried out on radiation levels, radionuclides distribution, and transfer of radionuclides through terrestrial, aquatic and atmospheric pathways in the environment of West Coast of India including the Kaiga nuclear power plant. The baseline studies on radioactivity levels around Kaiga region was carried out well before the nuclear power plant became operational and the data generated under these studies are considered to be highly valuable for future impact assessments. The nuclear power plant became operational in the year 1999 and since then this laboratory is involved in radiological impact assessment studies around the nuclear power plant. Detailed Kaiga specific studies are now ongoing to estimate the transfer factors and transfer coefficients for radionuclides for different pathways, such as, (i) soil to rice (ii) soil to different types of vegetables (iii) water/sediment to fish (iv) soil to grass (v) grass to cow milk and (vi) milk to child. For these studies, rice and vegetable fields were developed very close to the nuclear power plant in Kaiga to study the transfer of radionuclides. The water required for this field was drawn from coolant water discharge canal of the power plant. Rice and different types of vegetables were grown in the experimental fields in different seasons of the year and the uptake of radionuclides was studied. For a comparative study, rice and vegetables were also collected from the fields of farmers of nearby villages and analysed. The transfer of artificial radionuclides through pathway involving cow milk was also studied in detail. A grass field was developed and cows were adopted specifically for this study. The cows were allowed to graze freely in this grass field

  3. Influence of economic factor and site milestones on the salience of environmental issues at Department of Energy sites

    International Nuclear Information System (INIS)

    O'Connor, S.; Yin, J.

    1997-01-01

    The change in the US Department of Energy's (DOE) mission from nuclear weapons production to remediation and restoration of its installations, in 1989, challenged all citizens around the nation's weapons complex to get involved in DOE's environmental management decision-making process. The purpose of this study is to determine whether, and to what extent, economic factors and site milestones influence the rise and fall of environmental issues and participation. One might believe that citizen participation would be influenced by economic conditions, particularly with the down-sizing that occurred at many DOE sites. Another factor that might influence salience of environmental issues is the occurrence of crucial events, or site milestones. Important events occurring at DOE installations are well publicized by local and national media, and citizens' interest and opinions are influenced by media. In this study, the authors use the number of comments expressed by the public and Indian tribes as a measure of public involvement and salience of issues. Their study, using multiple regression analysis, examined the relationships between the number of comments expressed and the economic conditions as indicated by monthly unemployment rates, and the relationship between the number of comments expressed and the occurrence of crucial site events or milestones

  4. Factors affecting the frequency and amount of social networking site use: Motivations, perceptions, and privacy concerns

    OpenAIRE

    Cha, Jiyoung

    2010-01-01

    The purpose of this study is to explore the factors that affect the use of social networking Web sites. In doing so, this investigation focuses on two dimensions of social networking site use frequency (i.e., how often people use social networking sites) and amount (i.e., how much time people spend on social networks). Integrating the technology acceptance model with uses and gratification and other consumer characteristics, this study found that interpersonal utility, perceived ease of use, ...

  5. CONREAL web server: identification and visualization of conserved transcription factor binding sites

    NARCIS (Netherlands)

    Berezikov, E.; Guryev, V.; Cuppen, E.

    2005-01-01

    The use of orthologous sequences and phylogenetic footprinting approaches have become popular for the recognition of conserved and potentially functional sequences. Several algorithms have been developed for the identification of conserved transcription factor binding sites (TFBSs), which are

  6. The influence of site factors on nitrogen mineralization in forest soils ...

    African Journals Online (AJOL)

    The influence of site factors on nitrogen mineralization in forest soils of the ... on N mineralization, as well as the effect of N mineralization on forest productivity. ... of the natural log of mean annual temperature, geological substrate and total N ...

  7. Why Do You Adopt Social Networking Sites? Investigating the Driving Factors through Structural Equation Modelling

    Science.gov (United States)

    Jan, Muhammad Tahir

    2017-01-01

    Purpose: The purpose of this paper is to investigate those factors that are associated with the adoption of social networking sites from the perspective of Muslim users residing in Malaysia. Design/methodology/approach: A complete self-administered questionnaire was collected from 223 Muslim users of social networking sites in Malaysia. Both…

  8. Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites.

    Directory of Open Access Journals (Sweden)

    Amy L Bauer

    2010-11-01

    Full Text Available An important step in understanding gene regulation is to identify the DNA binding sites recognized by each transcription factor (TF. Conventional approaches to prediction of TF binding sites involve the definition of consensus sequences or position-specific weight matrices and rely on statistical analysis of DNA sequences of known binding sites. Here, we present a method called SiteSleuth in which DNA structure prediction, computational chemistry, and machine learning are applied to develop models for TF binding sites. In this approach, binary classifiers are trained to discriminate between true and false binding sites based on the sequence-specific chemical and structural features of DNA. These features are determined via molecular dynamics calculations in which we consider each base in different local neighborhoods. For each of 54 TFs in Escherichia coli, for which at least five DNA binding sites are documented in RegulonDB, the TF binding sites and portions of the non-coding genome sequence are mapped to feature vectors and used in training. According to cross-validation analysis and a comparison of computational predictions against ChIP-chip data available for the TF Fis, SiteSleuth outperforms three conventional approaches: Match, MATRIX SEARCH, and the method of Berg and von Hippel. SiteSleuth also outperforms QPMEME, a method similar to SiteSleuth in that it involves a learning algorithm. The main advantage of SiteSleuth is a lower false positive rate.

  9. A Study of Factors Influencing Consumer Adoption of Group-Buying Sites in Malaysia

    OpenAIRE

    Bohara, Shilpa

    2011-01-01

    Group-buying sites have been the biggest internet phenomena in the recent B2C ecommerce industry. This new development has led to this research’s main objective of identifying factors that influence consumers’ intention to purchase from groupbuying sites, particularly in Malaysia. Using the extended Technology Acceptance Model, the five factors measured against consumers’ behavioral intent to transact are perceived knowledge, perceived benefits of price promotion, personal innovativeness, soc...

  10. Radiological bioconcentration factors for aquatic, terrestrial, and wetland ecosystems at the Savannah River Site

    International Nuclear Information System (INIS)

    Cummins, C.L.

    1994-09-01

    As a result of operations at the Savannah River Site (SRS), over 50 radionuclides have been released to the atmosphere and to onsite streams and seepage basins. Now, many of these radionuclides are available to aquatic and/or terrestrial organisms for uptake and cycling through the food chain. Knowledge about the uptake and cycling of these radionuclides is now crucial in evaluating waste management and clean-up alternatives for the site. Numerous studies have been conducted at the SRS over the past forty years to study the uptake and distribution of radionuclides in the Savannah River Site environment. In many instances, bioconcentration factors have been calculated to quantify the uptake of a radionuclide by an organism from the surrounding medium (i.e., soil or water). In the past, it has been common practice to use bioconcentration factors from the literature because site-specific data were not readily available. However, because of the variability of bioconcentration factors due to experimental or environmental conditions, site-specific data should be used when available. This report compiles and summarizes site-specific bioconcentration factors for selected radionuclides released at the Savannah River Site (SRS). An extensive literature search yielded site-specific bioconcentration factors for cesium, strontium, cobalt, plutonium, americium, curium, and tritium. These eight radionuclides have been the primary radionuclides studied at SRS because of their long half lives or because they are major contributors to radiological dose from exposure. For most radionuclides, it was determined that the site-specific bioconcentration factors were higher than those reported in literature. This report also summarizes some conditions that affect radionuclide bioavailability to and bioconcentration by aquatic and terrestrial organisms

  11. Impact of personality traits and demographic factors on relationship to deal sites

    DEFF Research Database (Denmark)

    Sudzina, Frantisek; Pavlicek, Antonin

    2017-01-01

    There is an increasing body of research about deal sites. But there is still exists a gap when it comes to factors influencing potential or existing users of deal sites. The aim of this paper is to investigate impact of gender, city of origin, and personality traits on relationship to deal sites....... Big Five Inventory framework is used for personality traits. The research was conducted in the Czech Republic. With regards to the findings, city of origin has a significant effect, and openness to experience a borderline significant effect on the relationship to deal sites....

  12. Risk factors for acute surgical site infections after lumbar surgery: a retrospective study.

    Science.gov (United States)

    Lai, Qi; Song, Quanwei; Guo, Runsheng; Bi, Haidi; Liu, Xuqiang; Yu, Xiaolong; Zhu, Jianghao; Dai, Min; Zhang, Bin

    2017-07-19

    Currently, many scholars are concerned about the treatment of postoperative infection; however, few have completed multivariate analyses to determine factors that contribute to the risk of infection. Therefore, we conducted a multivariate analysis of a retrospectively collected database to analyze the risk factors for acute surgical site infection following lumbar surgery, including fracture fixation, lumbar fusion, and minimally invasive lumbar surgery. We retrospectively reviewed data from patients who underwent lumbar surgery between 2014 and 2016, including lumbar fusion, internal fracture fixation, and minimally invasive surgery in our hospital's spinal surgery unit. Patient demographics, procedures, and wound infection rates were analyzed using descriptive statistics, and risk factors were analyzed using logistic regression analyses. Twenty-six patients (2.81%) experienced acute surgical site infection following lumbar surgery in our study. The patients' mean body mass index, smoking history, operative time, blood loss, draining time, and drainage volume in the acute surgical site infection group were significantly different from those in the non-acute surgical site infection group (p operative type in the acute surgical site infection group were significantly different than those in the non-acute surgical site infection group (p operative type, operative time, blood loss, and drainage time were independent predictors of acute surgical site infection following lumbar surgery. In order to reduce the risk of infection following lumbar surgery, patients should be evaluated for the risk factors noted above.

  13. Position specific variation in the rate of evolution intranscription factor binding sites

    Energy Technology Data Exchange (ETDEWEB)

    Moses, Alan M.; Chiang, Derek Y.; Kellis, Manolis; Lander, EricS.; Eisen, Michael B.

    2003-08-28

    The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental and computational methods have been developed to characterize transcription factor binding sites, they remain difficult to identify. Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution. Here we analyze the genome sequences of the budding yeasts Saccharomyces cerevisiae, S. bayanus, S. paradoxus and S. mikataeto study the evolution of transcription factor binding sites. As expected, we find that both experimentally characterized and computationally predicted binding sites evolve slower than surrounding sequence, consistent with the hypothesis that they are under purifying selection. We also observe position-specific variation in the rate of evolution within binding sites. We find that the position-specific rate of evolution is positively correlated with degeneracy among binding sites within S. cerevisiae. We test theoretical predictions for the rate of evolution at positions where the base frequencies deviate from background due to purifying selection and find reasonable agreement with the observed rates of evolution. Finally, we show how the evolutionary characteristics of real binding motifs can be used to distinguish them from artifacts of computational motif finding algorithms. As has been observed for protein sequences, the rate of evolution in transcription factor binding sites varies with position, suggesting that some regions are under stronger functional constraint than others. This variation likely reflects the varying importance of different positions in the formation of the protein-DNA complex. The characterization of the pattern of evolution in known binding sites will likely contribute to the effective use of comparative

  14. A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites

    KAUST Repository

    Kulakovskiy, Ivan V.; Belostotsky, A. A.; Kasianov, Artem S.; Esipova, Natalia G.; Medvedeva, Yulia; Eliseeva, Irina A.; Makeev, Vsevolod J.

    2011-01-01

    Motivation: Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding

  15. When Factorization Meets Heterogeneous Latent Topics:An Interpretable Cross-Site Recommendation Framework

    Institute of Scientific and Technical Information of China (English)

    辛欣; 林钦佑; 魏骁驰; 黄河燕

    2015-01-01

    Data sparsity is a well-known challenge in recommender systems. Previous studies alleviate this problem by incorporating the information within the corresponding social media site. In this paper, we solve this challenge by exploring cross-site information. Specifically, we examine: 1) how to effectively and efficiently utilize cross-site ratings and content features to improve recommendation performance and 2) how to make the recommendation interpretable by utilizing content features. We propose a joint model of matrix factorization and latent topic analysis. Heterogeneous content features are modeled by multiple kinds of latent topics. In addition, the combination of matrix factorization and latent topics makes the recommendation result interpretable. Therefore, the above two issues are simultaneously solved. Through a real-world dataset, where user behaviors in three social media sites are collected, we demonstrate that the proposed model is effective in improving recommendation performance and interpreting the rationale of ratings.

  16. Factors affecting Malaysian university students’ purchase intention in social networking sites

    OpenAIRE

    Saeideh Sharifi fard; Ezhar Tamam; Md Salleh Hj Hassan; Moniza Waheed; Zeinab Zaremohzzabieh

    2016-01-01

    This study applied the unified theory of acceptance and use of technology 2 to examine acceptance and use of social networking sites in a marketing setting. This study uses 370 regular higher education students in Malaysia as respondents. Quantitative method is used. The findings revealed that performance expectancy (PE) and hedonic motivation were the main factors that influence users’ online purchase intention (PI) through social networking sites (SNSs) in Malaysia. As for moderating influe...

  17. Workers’ Age and the Impact of Psychological Factors on the Perception of Safety at Construction Sites

    Directory of Open Access Journals (Sweden)

    Muhammad Dawood Idrees

    2017-05-01

    Full Text Available The safety of construction workers is always a major concern at construction sites as the construction industry is inherently dangerous with many factors influencing worker safety. Several studies concluded that psychological factors such as workload, organizational relationships, mental stress, job security, and job satisfaction have significant effects on workers’ safety. However, research on psychological factors that are characteristic of different age groups have been limited. The aim of this study was to examine the impact of psychological factors on the perception of worker safety for two different age groups. After an extensive literature review, different psychological factors were identified, and a hypothetical research model was developed based on psychological factors that could affect workers’ perception of safety. A survey instrument was developed, and data were collected from seven different construction sites in Pakistan. Structural equation modeling (SEM was employed to test the hypothetical model for both age groups. The results revealed that workload and job satisfaction are significantly dominant factors on workers’ perception of safety in older workers, whereas organizational relationships, mental stress, and job security are dominant factors for younger workers at construction sites.

  18. Asap: a framework for over-representation statistics for transcription factor binding sites

    DEFF Research Database (Denmark)

    Marstrand, Troels T; Frellsen, Jes; Moltke, Ida

    2008-01-01

    -founded choice. METHODOLOGY: We introduce a software package, Asap, for fast searching with position weight matrices that include several standard methods for assessing over-representation. We have compared the ability of these methods to detect over-represented transcription factor binding sites in artificial......BACKGROUND: In studies of gene regulation the efficient computational detection of over-represented transcription factor binding sites is an increasingly important aspect. Several published methods can be used for testing whether a set of hypothesised co-regulated genes share a common regulatory...... regime based on the occurrence of the modelled transcription factor binding sites. However there is little or no information available for guiding the end users choice of method. Furthermore it would be necessary to obtain several different software programs from various sources to make a well...

  19. Determination of antenna factors using a three-antenna method at open-field test site

    Science.gov (United States)

    Masuzawa, Hiroshi; Tejima, Teruo; Harima, Katsushige; Morikawa, Takao

    1992-09-01

    Recently NIST has used the three-antenna method for calibration of the antenna factor of an antenna used for EMI measurements. This method does not require the specially designed standard antennas which are necessary in the standard field method or the standard antenna method, and can be used at an open-field test site. This paper theoretically and experimentally examines the measurement errors of this method and evaluates the precision of the antenna-factor calibration. It is found that the main source of the error is the non-ideal propagation characteristics of the test site, which should therefore be measured before the calibration. The precision of the antenna-factor calibration at the test site used in these experiments, is estimated to be 0.5 dB.

  20. Analysis of usability factors affecting purchase intention in online e-commerce sites

    Science.gov (United States)

    Perdana, R. A.; Suzianti, A.

    2017-03-01

    The growing number of internet users plays a significant role in the emergence of a variety of online e-commerce sites to meet the needs of Indonesians. However, there are still some problems faced by the users in using e-commerce sites. Therefore, a research related to user experience on their purchase intention to foster e-commerce sites is required. This study is conducted to find out the relationship between usability factors on e-commerce users’ purchase intention using a case study by using SEM to analyse the usability of the website. The result of this study shows that credibility, readability and telepresence are usability factors that directly affect purchase intention, while simplicity, consistency and interactivity are usability factors that indirectly affect purchase intention. Therefore, we can conclude that Indonesian consumers are on the Early Majority phase in adopting Company A.

  1. Evaluation factors for verification and validation of low-level waste disposal site models

    International Nuclear Information System (INIS)

    Moran, M.S.; Mezga, L.J.

    1982-01-01

    The purpose of this paper is to identify general evaluation factors to be used to verify and validate LLW disposal site performance models in order to assess their site-specific applicability and to determine their accuracy and sensitivity. It is intended that the information contained in this paper be employed by model users involved with LLW site performance model verification and validation. It should not be construed as providing protocols, but rather as providing a framework for the preparation of specific protocols or procedures. A brief description of each evaluation factor is provided. The factors have been categorized according to recommended use during either the model verification or the model validation process. The general responsibilities of the developer and user are provided. In many cases it is difficult to separate the responsibilities of the developer and user, but the user is ultimately accountable for both verification and validation processes. 4 refs

  2. Site-SpecificCu Labeling of the Serine Protease, Active Site Inhibited Factor Seven Azide (FVIIai-N), Using Copper Free Click Chemistry

    DEFF Research Database (Denmark)

    Jeppesen, Troels E; Kristensen, Lotte K; Nielsen, Carsten H

    2018-01-01

    A method for site-specific radiolabeling of the serine protease active site inhibited factor seven (FVIIai) with64Cu has been applied using a biorthogonal click reaction. FVIIai binds to tissue factor (TF), a trans-membrane protein involved in hemostasis, angiogenesis, proliferation, cell migrati...

  3. Does work-site physical activity improve self-reported psychosocial workplace factors and job satisfaction?

    DEFF Research Database (Denmark)

    Roessler, K K; Rugulies, R; Bilberg, R

    2013-01-01

    PURPOSE: To investigate whether a work-site strength-training program has a positive effect on self-reported psychosocial workplace factors and job satisfaction. METHODS: We conducted a randomized controlled trial among laboratory technicians implementing neck and shoulder exercises for pain relief......, with 199 participants in the training group and 228 in the control group. Influence at work, sense of community, time pressure, and job satisfaction were measured with the Copenhagen Psychosocial Questionnaire at baseline and post-intervention after 20 weeks. RESULTS: There was no statistically significant...... of a work-site strength-training program on self-reported psychosocial workplace factors and job satisfaction....

  4. Site Amplification in the Central U.S.: Towards and understanding of factors influencing the site effect

    Science.gov (United States)

    Yassminh, R.; Sandvol, E. A.

    2017-12-01

    We have mapped site amplification using a Reverse Two Station (RTS) approach across much of the Central United States. We have found several unexpected results including a lack of amplification in Paleozoic basins such as the Illinois and Michigan basins. In general, we found that the amplification of high frequency regional waves is related to the topography. We also suggest that the HVSR spectra are primarily a function of the shallow velocity structure. The Central United States Seismic Observatory (CUSSO) is a vertical seismic array located adjacent to the central segment of the NMSZ. CUSSO data gives us the opportunity to understand the amplification of the ground motion at different depths within the uppermost crust. Simulating ground motions throughout the CUSSO borehole and examining the factors affecting the ground amplification, such as the velocity and thicknesses of the model layers and the source sizes, is an effective way to understand the role different factors playing in modifying the ground motion for both the local and regional seismic phases. We have used the spectral-element method (SEMs) with a 1D crustal velocity structure derived from logging data taken from CUSSO borehole. This model is comprised of near surface sediment layers and a Paleozoic basement. Utilizing the software package SPECFEM2D with virtual seismometers located on the surface and in the bottom of the different sediment layers, we have computed the true synthetic site amplification for frequencies between 0.01-3 Hz. For the local model, we have tested the sensitivity of the ground motion amplification to the source magnitude. For frequencies>0.6, the ground motions have been amplified with decreasing the magnitudes while for HZ2Hz.

  5. Real-time correction of tsunami site effect by frequency-dependent tsunami-amplification factor

    Science.gov (United States)

    Tsushima, H.

    2017-12-01

    For tsunami early warning, I developed frequency-dependent tsunami-amplification factor and used it to design a recursive digital filter that can be applicable for real-time correction of tsunami site response. In this study, I assumed that a tsunami waveform at an observing point could be modeled by convolution of source, path and site effects in time domain. Under this assumption, spectral ratio between offshore and the nearby coast can be regarded as site response (i.e. frequency-dependent amplification factor). If the amplification factor can be prepared before tsunamigenic earthquakes, its temporal convolution to offshore tsunami waveform provides tsunami prediction at coast in real time. In this study, tsunami waveforms calculated by tsunami numerical simulations were used to develop frequency-dependent tsunami-amplification factor. Firstly, I performed numerical tsunami simulations based on nonlinear shallow-water theory from many tsuanmigenic earthquake scenarios by varying the seismic magnitudes and locations. The resultant tsunami waveforms at offshore and the nearby coastal observing points were then used in spectral-ratio analysis. An average of the resulted spectral ratios from the tsunamigenic-earthquake scenarios is regarded as frequency-dependent amplification factor. Finally, the estimated amplification factor is used in design of a recursive digital filter that can be applicable in time domain. The above procedure is applied to Miyako bay at the Pacific coast of northeastern Japan. The averaged tsunami-height spectral ratio (i.e. amplification factor) between the location at the center of the bay and the outside show a peak at wave-period of 20 min. A recursive digital filter based on the estimated amplification factor shows good performance in real-time correction of tsunami-height amplification due to the site effect. This study is supported by Japan Society for the Promotion of Science (JSPS) KAKENHI grant 15K16309.

  6. AN ASSESSMENT OF FACTORS AFFECTING MATERIAL STOCK CONTROL PRACTICE ON SELECTED CONSTRUCTION SITES IN NIGERIA

    OpenAIRE

    Adafin, Johnson Kayode; Ayodele, Elijah Olusegun; Daramola, Olufemi

    2011-01-01

    This research examines the stock control methods utilized by construction firms on construction sites with a view to assessing the factors affecting material stock control practice by construction firms as well as determining the impact of factors affecting material stock control on building project performance. Data were collected with the aid of well-structured questionnaire administered on a number of construction professionals and technicians in some randomly selected building constructio...

  7. Health behaviors of victims and related factors in Wenchuan earthquake resettlement sites.

    Science.gov (United States)

    Liu, Qiaolan; Zhou, Hongyu; Zhou, Huan; Yang, Yang; Yang, Xiaoyan; Yu, Lingyun; Qiu, Peiyuan; Ma, Xiao

    2011-03-01

    The purpose of this study was to describe the health behaviors of earthquake victims related to gastrointestinal and respiratory infectious diseases in the centralized transitional earthquake resettlement sites in Wenchuan, China; and to identify key factors related to health behaviors that may inform local infectious diseases prevention and control strategies. Data were collected using a questionnaire that included questions about socio-demographic characteristics and health beliefs and behaviors. In total, 1411 participants were included through a two-stage random sampling strategy. A bivariate multilevel model was used to explore the related factors. Approximately 67% of the participants wash their hands after going to lavatories every time, and 87% felt uncomfortable spitting on the ground. The more the participants perceived their susceptibility to and the severity of infectious diseases, the better their health-related behaviors (P resettlement sites (P resettlement sites. Copyright © 2011 Elsevier Inc. All rights reserved.

  8. Friend me: which factors influence top global brands participation in social network sites

    NARCIS (Netherlands)

    Araujo, T.; Neijens, P.

    2012-01-01

    Purpose - This study focuses on how brands participate in social network sites (SNSs) and investigates both the different strategies they adopt and the factors that influence these strategies. Design/methodology/approach - The activities of top brands in SNSs were investigated through a content

  9. Incidence of and risk factors for surgical site infections in women undergoing hysterectomy for endometrial carcinoma.

    Science.gov (United States)

    Tuomi, Taru; Pasanen, Annukka; Leminen, Arto; Bützow, Ralf; Loukovaara, Mikko

    2016-04-01

    The purpose of this study was to determine the incidence of, and risk factors for, surgical site infections in a contemporary cohort of women with endometrial carcinoma. We retrospectively studied 1164 women treated for endometrial carcinoma by hysterectomy at a single institution in 2007-2013. In all, 912 women (78.4%) had minimally invasive hysterectomy. Data on surgical site infections were collected from medical records. Univariate and multivariate analyses were used to identify risk factors for incisional and organ/space infections. Ninety-four women (8.1%) were diagnosed with a surgical site infection. Twenty women (1.7%) had an incisional infection and 74 (6.4%) had an organ/space infection. The associations of 17 clinico-pathologic and surgical variables were tested by univariate analyses. Those variables that were identified as potential risk factors in univariate analyses (p infections as dependent variables. Obesity (body mass index ≥ 30 kg/m(2)), diabetes, and long operative time (>80th centile) were independently associated with a higher risk of incisional infection, whereas minimally invasive surgery was associated with a smaller risk. Smoking, conversion to laparotomy, and lymphadenectomy were associated with a higher risk of organ/space infection. Organ/space infections comprised the majority of surgical site infections. Risk factors for incisional and organ/space infections differed. Minimally invasive hysterectomy was associated with a smaller risk of incisional infections but not of organ/space infections. © 2015 Nordic Federation of Societies of Obstetrics and Gynecology.

  10. Conversion of MyoD to a Neurogenic Factor: Binding Site Specificity Determines Lineage

    Directory of Open Access Journals (Sweden)

    Abraham P. Fong

    2015-03-01

    Full Text Available MyoD and NeuroD2, master regulators of myogenesis and neurogenesis, bind to a “shared” E-box sequence (CAGCTG and a “private” sequence (CAGGTG or CAGATG, respectively. To determine whether private-site recognition is sufficient to confer lineage specification, we generated a MyoD mutant with the DNA-binding specificity of NeuroD2. This chimeric mutant gained binding to NeuroD2 private sites but maintained binding to a subset of MyoD-specific sites, activating part of both the muscle and neuronal programs. Sequence analysis revealed an enrichment for PBX/MEIS motifs at the subset of MyoD-specific sites bound by the chimera, and point mutations that prevent MyoD interaction with PBX/MEIS converted the chimera to a pure neurogenic factor. Therefore, redirecting MyoD binding from MyoD private sites to NeuroD2 private sites, despite preserved binding to the MyoD/NeuroD2 shared sites, is sufficient to change MyoD from a master regulator of myogenesis to a master regulator of neurogenesis.

  11. Neighborhood geographical factors and the presence of advanced community pharmacy practice sites in Greater Chicago.

    Science.gov (United States)

    Johnson, Charisse L; Crawford, Stephanie Y; Lin, Swu-Jane; Salmon, J Warren; Smith, Miriam Mobley

    2009-02-19

    To determine the availability of experiential learning opportunities in culturally diverse areas and to identify opportunities and barriers to attract and sustain sites for the University of Illinois at Chicago College of Pharmacy. Utilizing variables of census tract income, racial/ethnicity composition and crime index, data analyses included descriptive statistics and multivariate logistic regression. Faculty members involved in experiential education were interviewed to identify other factors influencing site placement and selection for community-based advanced pharmacy practice experiences (APPEs). Median family income and Asian population were significantly higher and black population was significantly lower in census tracts with community APPE sites than in census tracts without APPE sites (p managers, and strategic initiatives were critical considerations in site establishment and overall sustainability. Advanced community pharmacy practice sites were fairly well distributed across metropolitan Chicago, indicating that exposure to diverse populations during the advanced community practice experiences parallels with strategic College objectives of expanding and diversifying experiential sites to enhance pharmacy students' abilities to meet emerging patient care challenges and opportunities.

  12. Infirmity and injury complexity are risk factors for surgical-site infection after operative fracture care.

    Science.gov (United States)

    Bachoura, Abdo; Guitton, Thierry G; Smith, R Malcolm; Vrahas, Mark S; Zurakowski, David; Ring, David

    2011-09-01

    Orthopaedic surgical-site infections prolong hospital stays, double rehospitalization rates, and increase healthcare costs. Additionally, patients with orthopaedic surgical-site infections (SSI) have substantially greater physical limitations and reductions in their health-related quality of life. However, the risk factors for SSI after operative fracture care are unclear. We determined the incidence and quantified modifiable and nonmodifiable risk factors for SSIs in patients with orthopaedic trauma undergoing surgery. We retrospectively indentified, from our prospective trauma database and billing records, 1611 patients who underwent 1783 trauma-related procedures between 2006 and 2008. Medical records were reviewed and demographics, surgery-specific data, and whether the patients had an SSI were recorded. We determined which if any variables predicted SSI. Six factors independently predicted SSI: (1) the use of a drain, OR 2.3, 95% CI (1.3-3.8); (2) number of operations OR 3.4, 95% CI (2.0-6.0); (3) diabetes, OR 2.1, 95% CI (1.2-3.8); (4) congestive heart failure (CHF), OR 2.8, 95% CI (1.3-6.5); (5) site of injury tibial shaft/plateau, OR 2.3, 95% CI (1.3-4.2); and (6) site of injury, elbow, OR 2.2, 95% CI (1.1-4.7). The risk factors for SSIs after skeletal trauma are most strongly determined by nonmodifiable factors: patient infirmity (diabetes and heart failure) and injury complexity (site of injury, number of operations, use of a drain). Level II, prognostic study. See the Guideline for Authors for a complete description of levels of evidence.

  13. Hydrologic factors and 90Sr transport at a low-level waste disposal site

    International Nuclear Information System (INIS)

    Huff, D.D.

    1982-01-01

    There are several hydrologic factors that can affect contaminant migration at a waste disposal site. Many studies recognize surface water and groundwater controls as major factors. But what are the specific hydrologic processes most often associated with contaminant transport. Studies of solid waste storage areas (SWSAs) for low-level radioactive wastes at Oak Ridge National Laboratory, which is located in the humid environment of east Tennessee, have identified several mechanisms. Most of the processes are associated with groundwater movement, but in at least one case, surface runoff has played a dominant role. In all cases, consideration of localized hydrologic conditions has been the key to understanding the factors responsible for radionuclide migration

  14. Factors Affecting Intention to Use in Social Networking Sites: An Empirical Study on Thai Society

    Science.gov (United States)

    Jairak, Rath; Sahakhunchai, Napath; Jairak, Kallaya; Praneetpolgrang, Prasong

    This research aims to explore the factors that affect the intention to use in Social Networking Sites (SNS). We apply the theory of Technology Acceptance Model (TAM), intrinsic motivation, and trust properties to develop the theoretical framework for SNS users' intention. The results show that the important factors influencing SNS users' intention for general purpose and collaborative learning are task-oriented, pleasure-oriented, and familiarity-based trust. In marketing usage, dispositional trust and pleasure-oriented are two main factors that reflect intention to use in SNS.

  15. Synthesis and characterization of 18F-labeled active site inhibited factor VII (ASIS)

    DEFF Research Database (Denmark)

    Erlandsson, Maria; Nielsen, Carsten Haagen; Jeppesen, Troels Elmer

    2015-01-01

    Activated factor VII blocked in the active site with Phe-Phe-Arg-chloromethyl ketone (active site inhibited factor VII (ASIS)) is a 50-kDa protein that binds with high affinity to its receptor, tissue factor (TF). TF is a transmembrane glycoprotein that plays an important role in, for example......, thrombosis, metastasis, tumor growth, and tumor angiogenesis. The aim of this study was to develop an 18F-labeled ASIS derivative to assess TF expression in tumors. Active site inhibited factor VII was labeled using N-succinimidyl-4-[18F]fluorobenzoate, and the [18F]ASIS was purified on a PD-10 desalting...... column. The radiochemical yield was 25 ± 6%, the radiochemical purity was >97%, and the pseudospecific radioactivity was 35 ± 9 GBq/µmol. The binding efficacy was evaluated in pull-down experiments, which monitored the binding of unlabeled ASIS and [18F]ASIS to TF and to a specific anti-factor VII...

  16. Occupancy classification of position weight matrix-inferred transcription factor binding sites.

    Directory of Open Access Journals (Sweden)

    Hollis Wright

    Full Text Available BACKGROUND: Computational prediction of Transcription Factor Binding Sites (TFBS from sequence data alone is difficult and error-prone. Machine learning techniques utilizing additional environmental information about a predicted binding site (such as distances from the site to particular chromatin features to determine its occupancy/functionality class show promise as methods to achieve more accurate prediction of true TFBS in silico. We evaluate the Bayesian Network (BN and Support Vector Machine (SVM machine learning techniques on four distinct TFBS data sets and analyze their performance. We describe the features that are most useful for classification and contrast and compare these feature sets between the factors. RESULTS: Our results demonstrate good performance of classifiers both on TFBS for transcription factors used for initial training and for TFBS for other factors in cross-classification experiments. We find that distances to chromatin modifications (specifically, histone modification islands as well as distances between such modifications to be effective predictors of TFBS occupancy, though the impact of individual predictors is largely TF specific. In our experiments, Bayesian network classifiers outperform SVM classifiers. CONCLUSIONS: Our results demonstrate good performance of machine learning techniques on the problem of occupancy classification, and demonstrate that effective classification can be achieved using distances to chromatin features. We additionally demonstrate that cross-classification of TFBS is possible, suggesting the possibility of constructing a generalizable occupancy classifier capable of handling TFBS for many different transcription factors.

  17. Risk factors for surgical site infection following operative ankle fracture fixation.

    Science.gov (United States)

    Kelly, E G; Cashman, J P; Groarke, P J; Morris, S F

    2013-09-01

    Ankle fracture is a common injury and there is an increasingly greater emphasis on operative fixation. The purpose of the study was to determine the complication rate in this cohort of patients and, in doing so, determine risk factors which predispose to surgical site infection. A prospective cohort study was performed at a tertiary referral trauma center examining risk factors for surgical site infection in operatively treated ankle fractures. Univariate and multivariate analysis was performed. Female gender and advancing age were determined to be the risk factors in univariate analysis. Drain usage and peri-operative pyrexia were found to be significant for infection in multivariate analysis. This study allows surgeons to identify those at increased risk of infection and counsel them appropriately. It also allows for a high level of vigilance with regard to soft tissue handling intra-operatively in this higher risk group.

  18. What Factors are Associated With a Surgical Site Infection After Operative Treatment of an Elbow Fracture?

    Science.gov (United States)

    Claessen, Femke M A P; Braun, Yvonne; van Leeuwen, Wouter F; Dyer, George S; van den Bekerom, Michel P J; Ring, David

    2016-02-01

    Surgical site infections are one of the more common major complications of elbow fracture surgery and can contribute to other adverse outcomes, prolonged hospital stays, and increased healthcare costs. We asked: (1) What are the factors associated with a surgical site infection after elbow fracture surgery? (2) When taking the subset of closed elbow fractures only, what are the factors associated with a surgical site infection? (3) What are the common organisms isolated from an elbow infection after open treatment? One thousand three hundred twenty adult patients underwent surgery for an elbow fracture between January 2002 and July 2014 and were included in our study. Forty-eight of 1320 patients (4%) had a surgical site infection develop. Thirty-four of 1113 patients with a closed fracture (3%) had a surgical site infection develop. For all elbow fractures, use of plate and screw fixation (adjusted odds ratio [OR]= 2.2; 95% CI, 1.0-4.5; p = 0.041) and use of external fixation before surgery (adjusted OR = 4.7; 95% CI, 1.1-21; p = 0.035) were associated with higher infection rates. When subset analysis was performed for closed fractures, only smoking (adjusted OR = 2.2; 95% CI, 1.1-4.5; p = 0.023) was associated with higher infection rates. Staphylococcus aureus was the most common bacteria cultured (59%). The only modifiable risk factor for a surgical site infection after open reduction and internal fixation was cigarette smoking. Plate fixation and temporary external fixation are likely surrogates for more complex injuries, therefore no recommendations should be inferred from this association. Surgeons should counsel patients who smoke. Level IV, prognostic study.

  19. Quantitative PET Imaging of Tissue Factor Expression Using 18F-labled Active Site Inhibited Factor VII

    DEFF Research Database (Denmark)

    Nielsen, Carsten H; Erlandsson, Maria; Jeppesen, Troels E

    2016-01-01

    Tissue factor (TF) is up regulated in many solid tumors and its expression is linked to tumor angiogenesis, invasion, metastasis and prognosis. A non-invasive assessment of tumor TF expression status is therefore of obvious clinical relevance. Factor VII (FVII) is the natural ligand to TF. Here we...... report the development of a new PET tracer for specific imaging of TF using an (18)F-labeled derivative of FVII. METHODS: Active site inhibited factor VIIa (FVIIai) was obtained by inactivation with phenylalanine-phenylalanine-arginine-chloromethyl ketone. FVIIai was radiolabeled with N-succinimidyl 4......-[(18)F]-fluorobenzoate ([(18)F]SFB) and purified. The corresponding product, [(18)F]FVIIai, was injected into nude mice with subcutaneous human pancreatic xenograft tumors (BxPC-3) and investigated using small animal PET/CT imaging 1, 2 and 4 hours after injection. Ex vivo biodistribution was performed...

  20. Radiological bioconcentration factors for aquatic, terrestrial, and wetland ecosystems at the Savannah River site

    International Nuclear Information System (INIS)

    Friday, G.P.; Cummins, C.L.; Schwartzman, A.L.

    1996-01-01

    Since the early 1950s, the Savannah River Site (SRS) released over 50 radionuclides into the environment while producing nuclear defense materials. These releases directly exposed aquatic and terrestrial biota to ionizing radiation from surface water, soil, and sediment, and also indirectly by the ingestion of items in the food chain. As part of new missions to develop waste management strategies and identify cost-effective environmental restoration options, knowledge concerning the uptake and distribution of these radionuclides is essential. This report compiles and summarizes site-specific bioconcentration factors for selected radionuclides released at SRS

  1. Radiological bioconcentration factors for aquatic, terrestrial, and wetland ecosystems at the Savannah River site

    Energy Technology Data Exchange (ETDEWEB)

    Friday, G.P.; Cummins, C.L.; Schwartzman, A.L.

    1996-12-31

    Since the early 1950s, the Savannah River Site (SRS) released over 50 radionuclides into the environment while producing nuclear defense materials. These releases directly exposed aquatic and terrestrial biota to ionizing radiation from surface water, soil, and sediment, and also indirectly by the ingestion of items in the food chain. As part of new missions to develop waste management strategies and identify cost-effective environmental restoration options, knowledge concerning the uptake and distribution of these radionuclides is essential. This report compiles and summarizes site-specific bioconcentration factors for selected radionuclides released at SRS.

  2. Factors influencing unsafe behaviors and accidents on construction sites: a review.

    Science.gov (United States)

    Khosravi, Yahya; Asilian-Mahabadi, Hassan; Hajizadeh, Ebrahim; Hassanzadeh-Rangi, Narmin; Bastani, Hamid; Behzadan, Amir H

    2014-01-01

    Construction is a hazardous occupation due to the unique nature of activities involved and the repetitiveness of several field behaviors. The aim of this methodological and theoretical review is to explore the empirical factors influencing unsafe behaviors and accidents on construction sites. In this work, results and findings from 56 related previous studies were investigated. These studies were categorized based on their design, type, methods of data collection, analytical methods, variables, and key findings. A qualitative content analysis procedure was used to extract variables, themes, and factors. In addition, all studies were reviewed to determine the quality rating and to evaluate the strength of provided evidence. The content analysis identified 8 main categories: (a) society, (b) organization, (c) project management, (d) supervision, (e) contractor, (f) site condition, (g) work group, and (h) individual characteristics. The review highlighted the importance of more distal factors, e.g., society and organization, and project management, that may contribute to reducing the likelihood of unsafe behaviors and accidents through the promotion of site condition and individual features (as proximal factors). Further research is necessary to provide a better understanding of the links between unsafe behavior theories and empirical findings, challenge theoretical assumptions, develop new applied theories, and make stronger recommendations.

  3. Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors.

    Directory of Open Access Journals (Sweden)

    Georgi K Marinov

    Full Text Available Mitochondria contain their own circular genome, with mitochondria-specific transcription and replication systems and corresponding regulatory proteins. All of these proteins are encoded in the nuclear genome and are post-translationally imported into mitochondria. In addition, several nuclear transcription factors have been reported to act in mitochondria, but there has been no comprehensive mapping of their occupancy patterns and it is not clear how many other factors may also be found in mitochondria. Here we address these questions by using ChIP-seq data from the ENCODE, mouseENCODE and modENCODE consortia for 151 human, 31 mouse and 35 C. elegans factors. We identified 8 human and 3 mouse transcription factors with strong localized enrichment over the mitochondrial genome that was usually associated with the corresponding recognition sequence motif. Notably, these sites of occupancy are often the sites with highest ChIP-seq signal intensity within both the nuclear and mitochondrial genomes and are thus best explained as true binding events to mitochondrial DNA, which exist in high copy number in each cell. We corroborated these findings by immunocytochemical staining evidence for mitochondrial localization. However, we were unable to find clear evidence for mitochondrial binding in ENCODE and other publicly available ChIP-seq data for most factors previously reported to localize there. As the first global analysis of nuclear transcription factors binding in mitochondria, this work opens the door to future studies that probe the functional significance of the phenomenon.

  4. De-novo discovery of differentially abundant transcription factor binding sites including their positional preference.

    Science.gov (United States)

    Keilwagen, Jens; Grau, Jan; Paponov, Ivan A; Posch, Stefan; Strickert, Marc; Grosse, Ivo

    2011-02-10

    Transcription factors are a main component of gene regulation as they activate or repress gene expression by binding to specific binding sites in promoters. The de-novo discovery of transcription factor binding sites in target regions obtained by wet-lab experiments is a challenging problem in computational biology, which has not been fully solved yet. Here, we present a de-novo motif discovery tool called Dispom for finding differentially abundant transcription factor binding sites that models existing positional preferences of binding sites and adjusts the length of the motif in the learning process. Evaluating Dispom, we find that its prediction performance is superior to existing tools for de-novo motif discovery for 18 benchmark data sets with planted binding sites, and for a metazoan compendium based on experimental data from micro-array, ChIP-chip, ChIP-DSL, and DamID as well as Gene Ontology data. Finally, we apply Dispom to find binding sites differentially abundant in promoters of auxin-responsive genes extracted from Arabidopsis thaliana microarray data, and we find a motif that can be interpreted as a refined auxin responsive element predominately positioned in the 250-bp region upstream of the transcription start site. Using an independent data set of auxin-responsive genes, we find in genome-wide predictions that the refined motif is more specific for auxin-responsive genes than the canonical auxin-responsive element. In general, Dispom can be used to find differentially abundant motifs in sequences of any origin. However, the positional distribution learned by Dispom is especially beneficial if all sequences are aligned to some anchor point like the transcription start site in case of promoter sequences. We demonstrate that the combination of searching for differentially abundant motifs and inferring a position distribution from the data is beneficial for de-novo motif discovery. Hence, we make the tool freely available as a component of the open

  5. Low nucleosome occupancy is encoded around functional human transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Daenen Floris

    2008-07-01

    Full Text Available Abstract Background Transcriptional regulation of genes in eukaryotes is achieved by the interactions of multiple transcription factors with arrays of transcription factor binding sites (TFBSs on DNA and with each other. Identification of these TFBSs is an essential step in our understanding of gene regulatory networks, but computational prediction of TFBSs with either consensus or commonly used stochastic models such as Position-Specific Scoring Matrices (PSSMs results in an unacceptably high number of hits consisting of a few true functional binding sites and numerous false non-functional binding sites. This is due to the inability of the models to incorporate higher order properties of sequences including sequences surrounding TFBSs and influencing the positioning of nucleosomes and/or the interactions that might occur between transcription factors. Results Significant improvement can be expected through the development of a new framework for the modeling and prediction of TFBSs that considers explicitly these higher order sequence properties. It would be particularly interesting to include in the new modeling framework the information present in the nucleosome positioning sequences (NPSs surrounding TFBSs, as it can be hypothesized that genomes use this information to encode the formation of stable nucleosomes over non-functional sites, while functional sites have a more open chromatin configuration. In this report we evaluate the usefulness of the latter feature by comparing the nucleosome occupancy probabilities around experimentally verified human TFBSs with the nucleosome occupancy probabilities around false positive TFBSs and in random sequences. Conclusion We present evidence that nucleosome occupancy is remarkably lower around true functional human TFBSs as compared to non-functional human TFBSs, which supports the use of this feature to improve current TFBS prediction approaches in higher eukaryotes.

  6. Influencing Factors of University Students’ Use of Social Network Sites: An Empirical Analysis in China

    Directory of Open Access Journals (Sweden)

    Liqiong Liu

    2018-03-01

    Full Text Available This paper explores the influencing factors of Chinese university students in accepting and using social networking sites (SNS to propose measures and recommendations that can guide and help these students correctly use SNS. In addition, this paper aims to provide theoretical support in increasing user loyalty for the SNS service providers and attract new users. The correlation and multiple regression analyses showed that perceived value, enjoyment, and influence positively influence the intention of individuals to use SNS.

  7. Risk factors for surgical site infection and urinary tract infection after spine surgery.

    Science.gov (United States)

    Tominaga, Hiroyuki; Setoguchi, Takao; Ishidou, Yasuhiro; Nagano, Satoshi; Yamamoto, Takuya; Komiya, Setsuro

    2016-12-01

    This study aimed to identify and compare risk factors for surgical site infection (SSI) and non-surgical site infections (non-SSIs), particularly urinary tract infection (UTI), after spine surgery. We retrospectively reviewed 825 patients (median age 59.0 years (range 33-70 years); 442 males) who underwent spine surgery at Kagoshima University Hospital from January 2009 to December 2014. Patient parameters were compared using the Mann-Whitney U and Fisher's exact tests. Risk factors associated with SSI and UTI were analyzed via the multiple logistic regression analysis. P operation time (P = 0.0019 and 0.0162, respectively) and ASA classification 3 (P = 0.0132 and 0.0356, respectively). The 1 week post-operative C-reactive protein (CRP) level was a risk factor for UTI (P = 0.0299), but not for SSI (P = 0.4996). There was no relationship between SSI and symptomatic UTI after spine surgery. Risk factors for post-operative SSI and UTI were operative time and ASA classification 3; 1 week post-operative CRP was a risk factor for UTI only.

  8. Mutation in the factor VII hepatocyte nuclear factor 4α-binding site contributes to factor VII deficiency.

    Science.gov (United States)

    Zheng, Xing-Wu; Kudaravalli, Rama; Russell, Theresa T; DiMichele, Donna M; Gibb, Constance; Russell, J Eric; Margaritis, Paris; Pollak, Eleanor S

    2011-10-01

    Severe coagulant factor VII (FVII) deficiency in postpubertal dizygotic twin males results from two point mutations in the FVII gene, a promoter region T→C transition at -60 and a His-to-Arg substitution at amino acid 348; both mutations prevent persistence of plasma functional FVII. This report documents longitudinal laboratory measurements from infancy to adulthood of FVII coagulant activity (FVII:C) in the twin FVII-deficient patients; it also details specific biochemical analyses of the -60 T→C mutation. The results revealed FVII:C levels of less than 1% in infancy that remain severely decreased through puberty and into adulthood. In-vitro analyses utilizing hepatocyte nuclear factor 4α (HNF4α) co-transfection and a chromatin immunoprecipitation assay indicate that the -60 T→C mutation severely diminishes functional interaction between the FVII promoter and transcription factor HNF4α. The importance of interaction between the FVII gene and HNF4α in normal FVII expression provides an in-vivo illustration of the regulated expression of an autosomal gene encoding a coagulation protein. The constancy of FVII:C and peripubertal patient symptomatology reported here illustrates androgen-independent expression in contrast to expression with an analogous mutation in the promoter region of the gene encoding coagulation FIX.

  9. Discovery and validation of information theory-based transcription factor and cofactor binding site motifs.

    Science.gov (United States)

    Lu, Ruipeng; Mucaki, Eliseos J; Rogan, Peter K

    2017-03-17

    Data from ChIP-seq experiments can derive the genome-wide binding specificities of transcription factors (TFs) and other regulatory proteins. We analyzed 765 ENCODE ChIP-seq peak datasets of 207 human TFs with a novel motif discovery pipeline based on recursive, thresholded entropy minimization. This approach, while obviating the need to compensate for skewed nucleotide composition, distinguishes true binding motifs from noise, quantifies the strengths of individual binding sites based on computed affinity and detects adjacent cofactor binding sites that coordinate with the targets of primary, immunoprecipitated TFs. We obtained contiguous and bipartite information theory-based position weight matrices (iPWMs) for 93 sequence-specific TFs, discovered 23 cofactor motifs for 127 TFs and revealed six high-confidence novel motifs. The reliability and accuracy of these iPWMs were determined via four independent validation methods, including the detection of experimentally proven binding sites, explanation of effects of characterized SNPs, comparison with previously published motifs and statistical analyses. We also predict previously unreported TF coregulatory interactions (e.g. TF complexes). These iPWMs constitute a powerful tool for predicting the effects of sequence variants in known binding sites, performing mutation analysis on regulatory SNPs and predicting previously unrecognized binding sites and target genes. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. A Parzen window-based approach for the detection of locally enriched transcription factor binding sites.

    Science.gov (United States)

    Vandenbon, Alexis; Kumagai, Yutaro; Teraguchi, Shunsuke; Amada, Karlou Mar; Akira, Shizuo; Standley, Daron M

    2013-01-21

    Identification of cis- and trans-acting factors regulating gene expression remains an important problem in biology. Bioinformatics analyses of regulatory regions are hampered by several difficulties. One is that binding sites for regulatory proteins are often not significantly over-represented in the set of DNA sequences of interest, because of high levels of false positive predictions, and because of positional restrictions on functional binding sites with regard to the transcription start site. We have developed a novel method for the detection of regulatory motifs based on their local over-representation in sets of regulatory regions. The method makes use of a Parzen window-based approach for scoring local enrichment, and during evaluation of significance it takes into account GC content of sequences. We show that the accuracy of our method compares favourably to that of other methods, and that our method is capable of detecting not only generally over-represented regulatory motifs, but also locally over-represented motifs that are often missed by standard motif detection approaches. Using a number of examples we illustrate the validity of our approach and suggest applications, such as the analysis of weaker binding sites. Our approach can be used to suggest testable hypotheses for wet-lab experiments. It has potential for future analyses, such as the prediction of weaker binding sites. An online application of our approach, called LocaMo Finder (Local Motif Finder), is available at http://sysimm.ifrec.osaka-u.ac.jp/tfbs/locamo/.

  11. Nucleotide Interdependency in Transcription Factor Binding Sites in the Drosophila Genome.

    Science.gov (United States)

    Dresch, Jacqueline M; Zellers, Rowan G; Bork, Daniel K; Drewell, Robert A

    2016-01-01

    A long-standing objective in modern biology is to characterize the molecular components that drive the development of an organism. At the heart of eukaryotic development lies gene regulation. On the molecular level, much of the research in this field has focused on the binding of transcription factors (TFs) to regulatory regions in the genome known as cis-regulatory modules (CRMs). However, relatively little is known about the sequence-specific binding preferences of many TFs, especially with respect to the possible interdependencies between the nucleotides that make up binding sites. A particular limitation of many existing algorithms that aim to predict binding site sequences is that they do not allow for dependencies between nonadjacent nucleotides. In this study, we use a recently developed computational algorithm, MARZ, to compare binding site sequences using 32 distinct models in a systematic and unbiased approach to explore nucleotide dependencies within binding sites for 15 distinct TFs known to be critical to Drosophila development. Our results indicate that many of these proteins have varying levels of nucleotide interdependencies within their DNA recognition sequences, and that, in some cases, models that account for these dependencies greatly outperform traditional models that are used to predict binding sites. We also directly compare the ability of different models to identify the known KRUPPEL TF binding sites in CRMs and demonstrate that a more complex model that accounts for nucleotide interdependencies performs better when compared with simple models. This ability to identify TFs with critical nucleotide interdependencies in their binding sites will lead to a deeper understanding of how these molecular characteristics contribute to the architecture of CRMs and the precise regulation of transcription during organismal development.

  12. Barriers and enabling factors for work-site physical activity programs: a qualitative examination.

    Science.gov (United States)

    Fletcher, Gena M; Behrens, Timothyh K; Domina, Lorie

    2008-05-01

    Work sites offer a productive setting for physical activity (PA) promoting interventions. Still, PA participation remains low. Thus, the purpose of this study was to examine the reasoning behind commonly reported barriers and enabling factors to participation in PA programs in a work-site setting. Employees from a large city government were recruited to participate in focus groups, stratified by white- and blue-collar occupations. Responses from open-ended questions about factors influencing participation in PA programs were audio recorded and transcribed verbatim. Resulting data were analyzed with open and axial coding. The sample consisted of 60 employees composing 9 focus groups. Although time was the most common barrier between both groups, white-collars workers responded that scheduling and work conflicts were the most common barrier concerning time. Blue-collar workers indicated shift work as their most common barrier. In addition, health was a significant enabling factor for both occupational categories. White-collar workers were much more concerned with appearances and were more highly motivated by weight loss and the hopefulness of quick results than were blue-collar workers. These findings are important in the understanding of PA as it relates to the reasoning behind participation in work-site programs in regard to occupational status.

  13. Synthesis and characterization of (18)F-labeled active site inhibited factor VII (ASIS).

    Science.gov (United States)

    Erlandsson, Maria; Nielsen, Carsten H; Jeppesen, Troels E; Kristensen, Jesper B; Petersen, Lars C; Madsen, Jacob; Kjaer, Andreas

    2015-05-15

    Activated factor VII blocked in the active site with Phe-Phe-Arg-chloromethyl ketone (active site inhibited factor VII (ASIS)) is a 50-kDa protein that binds with high affinity to its receptor, tissue factor (TF). TF is a transmembrane glycoprotein that plays an important role in, for example, thrombosis, metastasis, tumor growth, and tumor angiogenesis. The aim of this study was to develop an (18)F-labeled ASIS derivative to assess TF expression in tumors. Active site inhibited factor VII was labeled using N-succinimidyl-4-[(18)F]fluorobenzoate, and the [(18)F]ASIS was purified on a PD-10 desalting column. The radiochemical yield was 25 ± 6%, the radiochemical purity was >97%, and the pseudospecific radioactivity was 35 ± 9 GBq/µmol. The binding efficacy was evaluated in pull-down experiments, which monitored the binding of unlabeled ASIS and [(18)F]ASIS to TF and to a specific anti-factor VII antibody (F1A2-mAb). No significant difference in binding efficacy between [(18)F]ASIS and ASIS could be detected. Furthermore, [(18)F]ASIS was relatively stable in vitro and in vivo in mice. In conclusion, [(18)F]ASIS has for the first time been successfully synthesized as a possible positron emission tomography tracer to image TF expression levels. In vivo positron emission tomography studies to evaluate the full potential of [(18)F]ASIS are in progress. Copyright © 2015 John Wiley & Sons, Ltd.

  14. Technical factors in the site selection for a radioactive wastes storage of low and intermediate level

    International Nuclear Information System (INIS)

    Badillo A, V. E.; Ramirez S, J. R.; Palacios H, J. C.

    2009-10-01

    The storage on surface or near surface it is viable for wastes of low and intermediate level which contain radio nuclides of short half life that would decay at insignificant levels of radioactivity in some decades and also radio nuclides of long half life but in very low concentrations. The sites selection, for the construction of radioactive waste storages, that present an appropriate stability at long term, a foreseeable behavior to future and a capacity to fulfill other operational requirements, is one of the great tasks that confront the waste disposal agencies. In the selection of potential sites for the construction of a radioactive wastes storage of low and intermediate level, several basic judgments should be satisfied that concern to physiography, climatology, geologic, geo-hydrology, tectonic and seismic aspects; as well as factors like the population density, socioeconomic develops and existent infrastructure. the necessary technician-scientific investigations for the selection of a site for the construction of radioactive waste storages are presented in this work and they are compared with the pre-selection factors realized in specify areas in previous studies in different regions of the Mexican Republic. (Author)

  15. Risk factors for deep surgical site infection following operative treatment of ankle fractures.

    Science.gov (United States)

    Ovaska, Mikko T; Mäkinen, Tatu J; Madanat, Rami; Huotari, Kaisa; Vahlberg, Tero; Hirvensalo, Eero; Lindahl, Jan

    2013-02-20

    Surgical site infection is one of the most common complications following ankle fracture surgery. These infections are associated with substantial morbidity and lead to increased resource utilization. Identification of risk factors is crucial for developing strategies to prevent these complications. We performed an age and sex-matched case-control study to identify patient and surgery-related risk factors for deep surgical site infection following operative ankle fracture treatment. We identified 1923 ankle fracture operations performed in 1915 patients from 2006 through 2009. A total of 131 patients with deep infection were identified and compared with an equal number of uninfected control patients. Risk factors for infection were determined with use of conditional logistic regression analysis. The incidence of deep infection was 6.8%. Univariate analysis showed diabetes (odds ratio [OR] = 2.2, 95% confidence interval [CI] = 1.0, 4.9), alcohol abuse (OR = 3.8, 95% CI = 1.6, 9.4), fracture-dislocation (OR = 2.0, 95% CI = 1.2, 3.5), and soft-tissue injury (a Tscherne grade of ≥1) (OR = 2.6, 95% CI = 1.3, 5.3) to be significant patient-related risk factors for infection. Surgery-related risk factors were suboptimal timing of prophylactic antibiotics (OR = 1.9, 95% CI = 1.0, 3.4), difficulties encountered during surgery, (OR = 2.1, 95% CI = 1.1, 4.0), wound complications (OR = 4.8, 95% CI = 1.6, 14.0), and fracture malreduction (OR = 3.4, 95% CI = 1.3, 9.2). Independent risk factors for infection identified by multivariable analyses were tobacco use (OR = 3.7, 95% CI = 1.6, 8.5) and a duration of surgery of more than ninety minutes (OR = 2.5, 95% CI = 1.1, 5.7). Cast application in the operating room was independently associated with a decreased infection rate (OR = 0.4, 95% CI = 0.2, 0.8). We identified several modifiable risk factors for deep surgical site infection following operative treatment of ankle fractures.

  16. Factors affecting Malaysian university students’ purchase intention in social networking sites

    Directory of Open Access Journals (Sweden)

    Saeideh Sharifi fard

    2016-12-01

    Full Text Available This study applied the unified theory of acceptance and use of technology 2 to examine acceptance and use of social networking sites in a marketing setting. This study uses 370 regular higher education students in Malaysia as respondents. Quantitative method is used. The findings revealed that performance expectancy (PE and hedonic motivation were the main factors that influence users’ online purchase intention (PI through social networking sites (SNSs in Malaysia. As for moderating influences of gender and age, the results showed that gender significantly moderated purposed association between these four elements and the online PI, while the moderating effect of age was only recognized in PE. Findings of this research offer practitioners with better insights that would aid them in developing effective online marketing strategies to attract online purchasing users through SNSs.

  17. Biosphere analysis - a complementary assessment of dose conversion factors for the Olkiluoto site

    International Nuclear Information System (INIS)

    Kylloenen, J.; Keto, V.

    2010-04-01

    The Olkiluoto site is currently the primary candidate for the final disposal site for spent nuclear fuel from the Olkiluoto and Loviisa NPPs. Safety analysis calculations must be performed to verify the compliance with the long-term safety requirements. The behaviour and distribution of radionuclides in the biosphere is of high importance in these calculations. The aim of this study was to perform a complementary assessment of dose conversion factors for the Olkiluoto site. Posiva has performed extensive analysis on the different ecosystems. In this work the biosphere analysis model of Fortum Nuclear Services (FNS) is used to give an independent estimate of biosphere dose conversion factors for the Olkiluoto site. The following nuclides are analysed: Cl-36, Ni-59, Se-79, Mo-93, Nb-94, Sn-126, I-129 and Cs-135. The FNS model is an equilibrium compartment model in which a steady annual release of 1 Bq of each radionuclide is distributed in different scenarios. The scenarios are the well scenario, which models a small agricultural ecosystem, the lake scenario which models a larger ecosystem with both agriculture and lake use, and sea and transition scenario, which models the behaviour of the radionuclides in marine environments. The scenarios are described and the transfer equations written for the lake scenario. The parameter values are taken from the FNS biosphere database, which has been used in the Finnish L/ILW waste repository safety analyses since mid 1990's. The results of the FNS analysis are compared to those presented in Posiva working report 2000-20 (POSIVA-WR-00-20). The results are of the same order of magnitude for all nuclides except I-129. Since the Posiva and FNS models were independently constructed, the results can be considered as convincing, and the compliance of the results give confidence to the modelling results. (orig.)

  18. Stratification of surgical site infection by operative factors and comparison of infection rates after hernia repair.

    Science.gov (United States)

    Olsen, Margaret A; Nickel, Katelin B; Wallace, Anna E; Mines, Daniel; Fraser, Victoria J; Warren, David K

    2015-03-01

    To investigate whether operative factors are associated with risk of surgical site infection (SSI) after hernia repair. Retrospective cohort study. Patients Commercially insured enrollees aged 6 months-64 years with International Classification of Diseases, Ninth Revision, Clinical Modification procedure or Current Procedural Terminology, fourth edition, codes for inguinal/femoral, umbilical, and incisional/ventral hernia repair procedures from January 1, 2004, through December 31, 2010. SSIs within 90 days after hernia repair were identified by diagnosis codes. The χ2 and Fisher exact tests were used to compare SSI incidence by operative factors. A total of 119,973 hernia repair procedures were analyzed. The incidence of SSI differed significantly by anatomic site, with rates of 0.45% (352/77,666) for inguinal/femoral, 1.16% (288/24,917) for umbilical, and 4.11% (715/17,390) for incisional/ventral hernia repair. Within anatomic sites, the incidence of SSI was significantly higher for open versus laparoscopic inguinal/femoral (0.48% [295/61,142] vs 0.34% [57/16,524], P=.020) and incisional/ventral (4.20% [701/16,699] vs 2.03% [14/691], P=.005) hernia repairs. The rate of SSI was higher following procedures with bowel obstruction/necrosis than procedures without obstruction/necrosis for open inguinal/femoral (0.89% [48/5,422] vs 0.44% [247/55,720], Poperative factors may facilitate accurate comparison of SSI rates between facilities.

  19. Number of active transcription factor binding sites is essential for the Hes7 oscillator

    Directory of Open Access Journals (Sweden)

    de Angelis Martin

    2006-02-01

    Full Text Available Abstract Background It is commonly accepted that embryonic segmentation of vertebrates is regulated by a segmentation clock, which is induced by the cycling genes Hes1 and Hes7. Their products form dimers that bind to the regulatory regions and thereby repress the transcription of their own encoding genes. An increase of the half-life of Hes7 protein causes irregular somite formation. This was shown in recent experiments by Hirata et al. In the same work, numerical simulations from a delay differential equations model, originally invented by Lewis, gave additional support. For a longer half-life of the Hes7 protein, these simulations exhibited strongly damped oscillations with, after few periods, severely attenuated the amplitudes. In these simulations, the Hill coefficient, a crucial model parameter, was set to 2 indicating that Hes7 has only one binding site in its promoter. On the other hand, Bessho et al. established three regulatory elements in the promoter region. Results We show that – with the same half life – the delay system is highly sensitive to changes in the Hill coefficient. A small increase changes the qualitative behaviour of the solutions drastically. There is sustained oscillation and hence the model can no longer explain the disruption of the segmentation clock. On the other hand, the Hill coefficient is correlated with the number of active binding sites, and with the way in which dimers bind to them. In this paper, we adopt response functions in order to estimate Hill coefficients for a variable number of active binding sites. It turns out that three active transcription factor binding sites increase the Hill coefficient by at least 20% as compared to one single active site. Conclusion Our findings lead to the following crucial dichotomy: either Hirata's model is correct for the Hes7 oscillator, in which case at most two binding sites are active in its promoter region; or at least three binding sites are active, in which

  20. HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

    KAUST Repository

    Kulakovskiy, Ivan V.

    2015-11-19

    Models of transcription factor (TF) binding sites provide a basis for a wide spectrum of studies in regulatory genomics, from reconstruction of regulatory networks to functional annotation of transcripts and sequence variants. While TFs may recognize different sequence patterns in different conditions, it is pragmatic to have a single generic model for each particular TF as a baseline for practical applications. Here we present the expanded and enhanced version of HOCOMOCO (http://hocomoco.autosome.ru and http://www.cbrc.kaust.edu.sa/hocomoco10), the collection of models of DNA patterns, recognized by transcription factors. HOCOMOCO now provides position weight matrix (PWM) models for binding sites of 601 human TFs and, in addition, PWMs for 396 mouse TFs. Furthermore, we introduce the largest up to date collection of dinucleotide PWM models for 86 (52) human (mouse) TFs. The update is based on the analysis of massive ChIP-Seq and HT-SELEX datasets, with the validation of the resulting models on in vivo data. To facilitate a practical application, all HOCOMOCO models are linked to gene and protein databases (Entrez Gene, HGNC, UniProt) and accompanied by precomputed score thresholds. Finally, we provide command-line tools for PWM and diPWM threshold estimation and motif finding in nucleotide sequences.

  1. Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome.

    Directory of Open Access Journals (Sweden)

    Guillermo I Perez Perez

    Full Text Available We studied skin microbiota present in three skin sites (forearm, axilla, scalp in men from six ethnic groups living in New York City.Samples were obtained at baseline and after four days following use of neutral soap and stopping regular hygiene products, including shampoos and deodorants. DNA was extracted using the MoBio Power Lyzer kit and 16S rRNA gene sequences determined on the IIlumina MiSeq platform, using QIIME for analysis.Our analysis confirmed skin swabbing as a useful method for sampling different areas of the skin because DNA concentrations and number of sequences obtained across subject libraries were similar. We confirmed that skin location was the main factor determining the composition of bacterial communities. Alpha diversity, expressed as number of species observed, was greater in arm than on scalp or axilla in all studied groups. We observed an unexpected increase in α-diversity on arm, with similar tendency on scalp, in the South Asian group after subjects stopped using their regular shampoos and deodorants. Significant differences at phylum and genus levels were observed between subjects of the different ethnic origins at all skin sites.We conclude that ethnicity and particular soap and shampoo practices are secondary factors compared to the ecological zone of the human body in determining cutaneous microbiota composition.

  2. Model calculating annual mean atmospheric dispersion factor for coastal site of nuclear power plant

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper describes an atmospheric dispersion field experiment performed on the coastal site of nuclear power plant in the east part of China during 1995 to 1996. The three-dimension joint frequency are obtained by hourly observation of wind and temperature on a 100m high tower; the frequency of the “event day of land and sea breezes” are given by observation of surface wind and land and sea breezes; the diffusion parameters are got from measurements of turbulent and wind tunnel simulation test.A new model calculating the annual mean atmospheric dispersion factor for coastal site of nuclear power plant is developed and established.This model considers not only the effect from mixing release and mixed layer but also the effect from the internal boundary layer and variation of diffusion parameters due to the distance from coast.The comparison between results obtained by the new model and current model shows that the ratio of annual mean atmospheric dispersion factor gained by the new model and the current one is about 2.0.

  3. Psychological risk factors of addiction to social networking sites among Chinese smartphone users.

    Science.gov (United States)

    Wu, Anise M S; Cheung, Vivi I; Ku, Lisbeth; Hung, Eva P W

    2013-09-01

    Smartphones allow users to access social networking sites (SNSs) whenever and wherever they want. Such easy availability and accessibility may increase their vulnerability to addiction. Based on the social cognitive theory (SCT), we examined the impacts of outcome expectancies, self-efficacy, and impulsivity on young Chinese smartphone users' addictive tendencies toward SNSs. Two hundred seventy-seven Macau young smartphone users (116 males and 161 females; mean age = 26.62) filled out an online Chinese questionnaire concerning their usage of social networking sites via smartphones, addiction tendencies toward SNSs, impulsivity trait, outcome expectancies toward the use, and Internet self-efficacy. The findings revealed that those who spent more time on SNSs also reported higher addictive tendencies. Addictive tendencies were positively correlated with both outcome expectancies and impulsivity, but negatively associated with Internet self-efficacy. These three psychological variables explained 23% of the variance in addictive tendencies. The findings of this study suggest that, compared to demographics, psychological factors provide a better account for addictive tendencies towards SNSs among Chinese smartphone users in Macau. The three psychological risk factors were low Internet self-efficacy, favorable outcome expectancies, and high impulsivity trait. Educational campaigns with screening procedures for high-risk groups are recommended for effective prevention and treatment.

  4. The brain-derived neurotrophic factor pathway, life stress, and chronic multi-site musculoskeletal pain.

    Science.gov (United States)

    Generaal, Ellen; Milaneschi, Yuri; Jansen, Rick; Elzinga, Bernet M; Dekker, Joost; Penninx, Brenda W J H

    2016-01-01

    Brain-derived neurotrophic factor (BDNF) disturbances and life stress, both independently and in interaction, have been hypothesized to induce chronic pain. We examined whether (a) the BDNF pathway (val(66)met genotype, gene expression, and serum levels), (b) early and recent life stress, and (c) their interaction are associated with the presence and severity of chronic multi-site musculoskeletal pain. Cross-sectional data are from 1646 subjects of the Netherlands Study of Depression and Anxiety. The presence and severity of chronic multi-site musculoskeletal pain were determined using the Chronic Pain Grade (CPG) questionnaire. The BDNF val(66)met polymorphism, BDNF gene expression, and BDNF serum levels were measured. Early life stress before the age of 16 was assessed by calculating a childhood trauma index using the Childhood Trauma Interview. Recent life stress was assessed as the number of recent adverse life events using the List of Threatening Events Questionnaire. Compared to val(66)val, BDNF met carriers more often had chronic pain, whereas no differences were found for BDNF gene expression and serum levels. Higher levels of early and recent stress were both associated with the presence and severity of chronic pain (p stress in the associations with chronic pain presence and severity. This study suggests that the BDNF gene marks vulnerability for chronic pain. Although life stress did not alter the impact of BDNF on chronic pain, it seems an independent factor in the onset and persistence of chronic pain. © The Author(s) 2016.

  5. Landscape dose conversion factors used in the safety assessment SR-Site

    International Nuclear Information System (INIS)

    Avila, Rodolfo; Ekstroem, Per-Anders; Aastrand, Per-Gustav

    2010-12-01

    In this report two types of Dose Conversion Factors have been derived: i) a Landscape Dose Conversion Factor (LDF) that is applicable to continuous long-term releases to the biosphere at a constant rate, and ii) a Landscape Dose Conversion Factor for pulse releases (LDF pulse) that is applicable to a radionuclide release that reaches the biosphere in a pulse within years to hundreds of years. In SR-Site these Dose Factors are multiplied with modelled release rates or pulse releases from the geosphere to obtain dose estimates used in assessment of compliance with the regulatory risk criterion. The LDFs were calculated for three different periods of the reference glacial cycle; a period of submerged conditions following the deglaciation, the temperate period, and a prolonged period of periglacial conditions. Additionally, LDFs were calculated for the global warming climate case. The LDF pulse was calculated only for temperate climate conditions. The LDF and LDF pulse can be considered as Best Estimate values, which can be used in calculations of Best Estimate values of doses to a representative individual of the most exposed group from potential releases from a future repository. A systematic analysis of the effects of system, model and parameter uncertainties on the LDFs has been carried out. This analysis has shown that the use of the derived LDF would lead to cautious or realistic dose estimates. The models and methods that were used for derivation of the LDFs and LDF pulse are also described in this report

  6. Landscape dose conversion factors used in the safety assessment SR-Site

    Energy Technology Data Exchange (ETDEWEB)

    Avila, Rodolfo; Ekstroem, Per-Anders; Aastrand, Per-Gustav (Facilia AB (Sweden))

    2010-12-15

    In this report two types of Dose Conversion Factors have been derived: i) a Landscape Dose Conversion Factor (LDF) that is applicable to continuous long-term releases to the biosphere at a constant rate, and ii) a Landscape Dose Conversion Factor for pulse releases (LDF pulse) that is applicable to a radionuclide release that reaches the biosphere in a pulse within years to hundreds of years. In SR-Site these Dose Factors are multiplied with modelled release rates or pulse releases from the geosphere to obtain dose estimates used in assessment of compliance with the regulatory risk criterion. The LDFs were calculated for three different periods of the reference glacial cycle; a period of submerged conditions following the deglaciation, the temperate period, and a prolonged period of periglacial conditions. Additionally, LDFs were calculated for the global warming climate case. The LDF pulse was calculated only for temperate climate conditions. The LDF and LDF pulse can be considered as Best Estimate values, which can be used in calculations of Best Estimate values of doses to a representative individual of the most exposed group from potential releases from a future repository. A systematic analysis of the effects of system, model and parameter uncertainties on the LDFs has been carried out. This analysis has shown that the use of the derived LDF would lead to cautious or realistic dose estimates. The models and methods that were used for derivation of the LDFs and LDF pulse are also described in this report

  7. Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility.

    Science.gov (United States)

    Liu, Sheng; Zibetti, Cristina; Wan, Jun; Wang, Guohua; Blackshaw, Seth; Qian, Jiang

    2017-07-27

    Computational prediction of transcription factor (TF) binding sites in different cell types is challenging. Recent technology development allows us to determine the genome-wide chromatin accessibility in various cellular and developmental contexts. The chromatin accessibility profiles provide useful information in prediction of TF binding events in various physiological conditions. Furthermore, ChIP-Seq analysis was used to determine genome-wide binding sites for a range of different TFs in multiple cell types. Integration of these two types of genomic information can improve the prediction of TF binding events. We assessed to what extent a model built upon on other TFs and/or other cell types could be used to predict the binding sites of TFs of interest. A random forest model was built using a set of cell type-independent features such as specific sequences recognized by the TFs and evolutionary conservation, as well as cell type-specific features derived from chromatin accessibility data. Our analysis suggested that the models learned from other TFs and/or cell lines performed almost as well as the model learned from the target TF in the cell type of interest. Interestingly, models based on multiple TFs performed better than single-TF models. Finally, we proposed a universal model, BPAC, which was generated using ChIP-Seq data from multiple TFs in various cell types. Integrating chromatin accessibility information with sequence information improves prediction of TF binding.The prediction of TF binding is transferable across TFs and/or cell lines suggesting there are a set of universal "rules". A computational tool was developed to predict TF binding sites based on the universal "rules".

  8. Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.

    Directory of Open Access Journals (Sweden)

    Arnoldo J Müller-Molina

    Full Text Available To know the map between transcription factors (TFs and their binding sites is essential to reverse engineer the regulation process. Only about 10%-20% of the transcription factor binding motifs (TFBMs have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory "DNA words." From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%-far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of "DNA words," newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters.

  9. Quantitative PET Imaging of Tissue Factor Expression Using 18F-Labeled Active Site-Inhibited Factor VII.

    Science.gov (United States)

    Nielsen, Carsten H; Erlandsson, Maria; Jeppesen, Troels E; Jensen, Mette M; Kristensen, Lotte K; Madsen, Jacob; Petersen, Lars C; Kjaer, Andreas

    2016-01-01

    Tissue factor (TF) is upregulated in many solid tumors, and its expression is linked to tumor angiogenesis, invasion, metastasis, and prognosis. A noninvasive assessment of tumor TF expression status is therefore of obvious clinical relevance. Factor VII is the natural ligand to TF. Here we report the development of a new PET tracer for specific imaging of TF using an (18)F-labeled derivative of factor VII. Active site-inhibited factor VIIa (FVIIai) was obtained by inactivation with phenylalanine-phenylalanine-arginine-chloromethyl ketone. FVIIai was radiolabeled with N-succinimidyl 4-(18)F-fluorobenzoate and purified. The corresponding product, (18)F-FVIIai, was injected into nude mice with subcutaneous human pancreatic xenograft tumors (BxPC-3) and investigated using small-animal PET/CT imaging 1, 2, and 4 h after injection. Ex vivo biodistribution was performed after the last imaging session, and tumor tissue was preserved for molecular analysis. A blocking experiment was performed in a second set of mice. The expression pattern of TF in the tumors was visualized by immunohistochemistry and the amount of TF in tumor homogenates was measured by enzyme-linked immunosorbent assay and correlated with the uptake of (18)F-FVIIai in the tumors measured in vivo by PET imaging. The PET images showed high uptake of (18)F-FVIIai in the tumor regions, with a mean uptake of 2.5 ± 0.3 percentage injected dose per gram (%ID/g) (mean ± SEM) 4 h after injection of 7.3-9.3 MBq of (18)F-FVIIai and with an average maximum uptake in the tumors of 7.1 ± 0.7 %ID/g at 4 h. In comparison, the muscle uptake was 0.2 ± 0.01 %ID/g at 4 h. At 4 h, the tumors had the highest uptake of any organ. Blocking with FVIIai significantly reduced the uptake of (18)F-FVIIai from 2.9 ± 0.1 to 1.4 ± 0.1 %ID/g (P < 0.001). The uptake of (18)F-FVIIai measured in vivo by PET imaging correlated (r = 0.72, P < 0.02) with TF protein level measured ex vivo. (18)F-FVIIai is a promising PET tracer for

  10. Trust and Product/Sellers Reviews as Factors Influencing Online Product Comparison Sites Usage by Young Consumers

    OpenAIRE

    Radoslaw Macik; Dorota Macik

    2016-01-01

    Paper describes young consumers’ behaviour connected with online product comparison sites usage as an example of online decision shopping aids. Authors’ main goal is to check whether or not such factors as: previous experience in such sites usage, personal innovativeness in domain of information technology – PIIT, and particularly cognitive trust (in several subdimensions), as well as affective trust toward online product comparison site, influence purchase intention via men...

  11. Ovarian metastases resection from extragenital primary sites: outcome and prognostic factor analysis of 147 patients

    International Nuclear Information System (INIS)

    Li, Wenhua; Wang, Huaying; Wang, Jian; LV, Fangfang; Zhu, Xiaodong; Wang, Zhonghua

    2012-01-01

    To explore the outcomes and prognostic factors of ovarian metastasectomy intervention on overall survival from extragenital primary cancer. Patients with ovarian metastases from extragenital primary cancer confirmed by laparotomy surgery and ovarian metastases resection were retrospectively collected in a single institution during an 8-year period. A total of 147 cases were identified and primary tumor sites were colorectal region (49.0%), gastric (40.8%), breast (8.2%), biliary duct (1.4%) and liver (0.7%). The pathological and clinical features were evaluated. Patients’ outcome with different primary tumor sites and predictive factors for overall survival were also investigated by univariate and multivariate analysis. Metachronous ovarian metastasis occurred in 92 (62.6%) and synchronous in 55 (37.4%) patients. Combined metastases occurred in 40 (27.2%). Bilateral metastasis was found in 97 (66%) patients. The median ovarian metastasis tumor size was 9 cm. There were 39 (26.5%) patients with massive ascites ≥ 1000 mL on intraoperative evaluation. With a median follow-up of 48 months, the median OS after ovarian metastasectomy for all patients was 8.2 months (95% CI 7.2-9.3 months). In univariate analyses, there is significant (8.0 months vs. 41.0 months, P = 0.000) difference in OS between patients with gastrointestinal cancer origin from breast origin, and between patients with gastric origin from colorectal origin (7.4 months vs. 8.8 months, P = 0.036). In univariate analyses, synchronous metastases, locally invasion, massive intraoperative ascites (≥ 1000 mL), and combined metastasis, were identified as significant poor prognostic factors. In multivariate analyses combined metastasis (RR, 1.72; 95% CI, 1.09-2.69, P = 0.018), locally invasion (RR, 1.62; 95% CI, 1.03-2.54, P = 0.038) and massive intraoperative ascites (RR, 1.58; 95% CI, 1.02-2.49, P = 0.04) were independent factors for predicting unfavorable overall survival. Ovarian metastases are more

  12. Development of variable LRFD \\0x03C6 factors for deep foundation design due to site variability.

    Science.gov (United States)

    2012-04-01

    The current design guidelines of Load and Resistance Factor Design (LRFD) specifies constant values : for deep foundation design, based on analytical method selected and degree of redundancy of the pier. : However, investigation of multiple sites in ...

  13. Self-absorption alpha particle factor in water: interest in the monitoring of specific military sites

    International Nuclear Information System (INIS)

    Cazoulat, A.; Lecompte, Y.; Bohand, S.; Gerasimo, P.

    2007-01-01

    Self-absorption alpha particle factor validation in water: Interest in the monitoring of specific military sites. The population internal intake prevention by radionuclides present in water needs to monitor the radioactive Level of this water. The French public health legislation introduces four radiological parameters for monitoring water, such as the gross alpha radioactivity. Regarding the alpha particle characteristics, a self-absorption factor has to be established beforehand, not to underestimate the real alpha radioactivity in water samples. The aim of this paper is to describe the procedure used by the laboratory of the French army radioprotection service to determine this f factor, which depends on the water residue mass m after evaporation. The relation is f = 0.0253 m + 1.2813. This formula can be employed for such waters used in this experiment and for masses between 0 and 100 mg. The uncertainty associated is about 11% (k = 2). Some water monitoring examples are given. It is specially the case of depleted uranium shells experiment centres, localized in Gramat and Bourges. (authors)

  14. Hydrogeologic factors in the selection of shallow land burial sites for the disposal of low-level radioactive waste

    Science.gov (United States)

    Fischer, John N.

    1986-01-01

    In the United States, low-level radioactive waste is disposed of by shallow land burial. Commercial low-level radioactive waste has been buried at six sites, and low-level radioactive waste generated by the Federal Government has been buried at nine major and several minor sites. Several existing low-level radioactive waste sites have not provided expected protection of the environment. These shortcomings are related, at least in part, to an inadequate understanding of site hydrogeology at the time the sites were selected. To better understand the natural systems and the effect of hydrogeologic factors on long-term site performance, the U.S. Geological Survey has conducted investigations at five of the six commercial low-level radioactive waste sites and at three Federal sites. These studies, combined with those of other Federal and State agencies, have identified and confirmed important hydrogeologic factors in the effective disposal of low-level radioactive waste by shallow land burial. These factors include precipitation, surface drainage, topography, site stability, geology, thickness of the host soil-rock horizon, soil and sediment permeability, soil and water chemistry, and depth to the water table.

  15. Standardized UXO Technology Demonstration Site Open Field Scoring Recording Number 231 (Human Factors Applications, Inc.)

    National Research Council Canada - National Science Library

    Overbay, Larry; Robitaille, George

    2005-01-01

    ...) utilizing the APG Standardized UXO Technology Demonstration Site Open Field. The scoring record was coordinated by Larry Overbuy and by the Standardized UXO Technology Demonstration Site Scoring Committee...

  16. Risk factors for cardiovascular diseases among male workers of building construction site in Delhi

    Directory of Open Access Journals (Sweden)

    Mamta Parashar

    2017-01-01

    Full Text Available Background: Cardiovascular disease (CVD is mainly attributable to a combination of risk factors (RFs: tobacco use, alcohol use, high blood pressure, diabetes, unhealthy diet, and obesity which are amenable to interventions. Building construction workers are poor and vulnerable. They are also the victims of adverse working environmental conditions and subjected to health hazards of occupational origin. Objective: The aim was to study the RFs and associated sociodemographics for CVD among construction site workers. Materials and Methods: This cross-sectional study was conducted among construction site workers. A total of 172 male workers over the age of 18 years were included in the study. Modified World Health Organization Step-wise approach to chronic disease RF surveillance was used to collect data. The data were analyzed in SPSS version 17 and the Chi-square test was applied to analyze the qualitative data. Results: At least one RF for CVD was present in all the subjects, with majority (93.6% of them having at least two RFs. The presence of the RFs (moderate to high, 3–11 was found to be significantly associated with lower income group, unskilled workers, migration year <1, alcoholics, personal tobacco use, family history of tobacco use, and the low knowledge score regarding tobacco use (0–2. Conclusions: Community-based comprehensive behavioral and life style communication package should be established for workers to reduce the modifiable RFs of CVD.

  17. Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus.

    Science.gov (United States)

    Schaefke, Bernhard; Wang, Tzi-Yuan; Wang, Chuen-Yi; Li, Wen-Hsiung

    2015-07-27

    Gene expression evolution occurs through changes in cis- or trans-regulatory elements or both. Interactions between transcription factors (TFs) and their binding sites (TFBSs) constitute one of the most important points where these two regulatory components intersect. In this study, we investigated the evolution of TFBSs in the promoter regions of different Saccharomyces strains and species. We divided the promoter of a gene into the proximal region and the distal region, which are defined, respectively, as the 200-bp region upstream of the transcription starting site and as the 200-bp region upstream of the proximal region. We found that the predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions. Additionally, Saccharomyces cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments (wild strains, laboratory strains, and clinical strains). We also showed that differences in TFBSs correlate with the cis component of gene expression evolution between species (comparing S. cerevisiae and its sister species Saccharomyces paradoxus) and within species (comparing two closely related S. cerevisiae strains). © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus

    Science.gov (United States)

    Schaefke, Bernhard; Wang, Tzi-Yuan; Wang, Chuen-Yi; Li, Wen-Hsiung

    2015-01-01

    Gene expression evolution occurs through changes in cis- or trans-regulatory elements or both. Interactions between transcription factors (TFs) and their binding sites (TFBSs) constitute one of the most important points where these two regulatory components intersect. In this study, we investigated the evolution of TFBSs in the promoter regions of different Saccharomyces strains and species. We divided the promoter of a gene into the proximal region and the distal region, which are defined, respectively, as the 200-bp region upstream of the transcription starting site and as the 200-bp region upstream of the proximal region. We found that the predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions. Additionally, Saccharomyces cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments (wild strains, laboratory strains, and clinical strains). We also showed that differences in TFBSs correlate with the cis component of gene expression evolution between species (comparing S. cerevisiae and its sister species Saccharomyces paradoxus) and within species (comparing two closely related S. cerevisiae strains). PMID:26220934

  19. Ontogeny of basic fibroblast growth factor binding sites in mouse ocular tissues

    International Nuclear Information System (INIS)

    Fayein, N.A.; Courtois, Y.; Jeanny, J.C.

    1990-01-01

    Basic fibroblast growth factor (bFGF) binding to ocular tissues has been studied by autoradiographical and biochemical approaches directly performed on sections during mouse embryonic and postnatal development. Frozen sections of embryos (9 to 18 days), newborns, and adults (1 day to 6 months) were incubated with iodinated bFGF. One specific FGF binding site (KD = 2.5 nM) is colocalized with heparan sulfate proteoglycans of the basement membranes and is heparitinase sensitive. It first appears at Day 9 around the neural tube, the optic vesicles, and below the head ectoderm and by Day 14 of embryonic development is found in all basement membranes of the eye. At Day 16, very intensely labeled patches appear, corresponding to mast cells which have been characterized by metachromatic staining of their heparin-rich granulations with toluidine blue. In addition to the latter binding, we have also observed a general diffuse distribution of silver grains on all tissues and preferentially in the ecto- and neuroectodermic tissues. From Days 17-18, there is heterogeneous labeling inside the retina, localized in the pigmented epithelium and in three different layers colocalized with the inner and outer plexiform layers and with the inner segments of the photoreceptors. This binding is heparitinase resistant but N-glycanase sensitive and may represent a second specific binding site corresponding to cellular FGF receptors (KD = 280 pM). Both types of binding patterns observed suggest a significant role for bFGF in eye development and physiology

  20. Cell-type specificity of ChIP-predicted transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Håndstad Tony

    2012-08-01

    Full Text Available Abstract Background Context-dependent transcription factor (TF binding is one reason for differences in gene expression patterns between different cellular states. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq identifies genome-wide TF binding sites for one particular context—the cells used in the experiment. But can such ChIP-seq data predict TF binding in other cellular contexts and is it possible to distinguish context-dependent from ubiquitous TF binding? Results We compared ChIP-seq data on TF binding for multiple TFs in two different cell types and found that on average only a third of ChIP-seq peak regions are common to both cell types. Expectedly, common peaks occur more frequently in certain genomic contexts, such as CpG-rich promoters, whereas chromatin differences characterize cell-type specific TF binding. We also find, however, that genotype differences between the cell types can explain differences in binding. Moreover, ChIP-seq signal intensity and peak clustering are the strongest predictors of common peaks. Compared with strong peaks located in regions containing peaks for multiple transcription factors, weak and isolated peaks are less common between the cell types and are less associated with data that indicate regulatory activity. Conclusions Together, the results suggest that experimental noise is prevalent among weak peaks, whereas strong and clustered peaks represent high-confidence binding events that often occur in other cellular contexts. Nevertheless, 30-40% of the strongest and most clustered peaks show context-dependent regulation. We show that by combining signal intensity with additional data—ranging from context independent information such as binding site conservation and position weight matrix scores to context dependent chromatin structure—we can predict whether a ChIP-seq peak is likely to be present in other cellular contexts.

  1. Measured and predicted aerosol light scattering enhancement factors at the high alpine site Jungfraujoch

    Directory of Open Access Journals (Sweden)

    R. Fierz-Schmidhauser

    2010-03-01

    Full Text Available Ambient relative humidity (RH determines the water content of atmospheric aerosol particles and thus has an important influence on the amount of visible light scattered by particles. The RH dependence of the particle light scattering coefficient (σsp is therefore an important variable for climate forcing calculations. We used a humidification system for a nephelometer which allows for the measurement of σsp at a defined RH in the range of 20–95%. In this paper we present measurements of light scattering enhancement factors f(RH=σsp(RH/σsp(dry from a 1-month campaign (May 2008 at the high alpine site Jungfraujoch (3580 m a.s.l., Switzerland. Measurements at the Jungfraujoch are representative for the lower free troposphere above Central Europe. For this aerosol type hardly any information about the f(RH is available so far. At this site, f(RH=85% varied between 1.2 and 3.3. Measured f(RH agreed well with f(RH calculated with Mie theory using measurements of the size distribution, chemical composition and hygroscopic diameter growth factors as input. Good f(RH predictions at RH<85% were also obtained with a simplified model, which uses the Ångström exponent of σsp(dry as input. RH influences further intensive optical aerosol properties. The backscatter fraction decreased by about 30% from 0.128 to 0.089, and the single scattering albedo increased on average by 0.05 at 85% RH compared to dry conditions. These changes in σsp, backscatter fraction and single scattering albedo have a distinct impact on the radiative forcing of the Jungfraujoch aerosol.

  2. The Human Splicing Factor ASF/SF2 can Specifically Recognize Pre-mRNA 5' Splice Sites

    Science.gov (United States)

    Zuo, Ping; Manley, James L.

    1994-04-01

    ASF/SF2 is a human protein previously shown to function in in vitro pre-mRNA splicing as an essential factor necessary for all splices and also as an alternative splicing factor, capable of switching selection of 5' splice sites. To begin to study the protein's mechanism of action, we have investigated the RNA binding properties of purified recombinant ASF/SF2. Using UV crosslinking and gel shift assays, we demonstrate that the RNA binding region of ASF/SF2 can interact with RNA in a sequence-specific manner, recognizing the 5' splice site in each of two different pre-mRNAs. Point mutations in the 5' splice site consensus can reduce binding by as much as a factor of 100, with the largest effects observed in competition assays. These findings support a model in which ASF/SF2 aids in the recognition of pre-mRNA 5' splice sites.

  3. Harvest surgical site infection following coronary artery bypass grafting: risk factors, microbiology, and outcomes.

    Science.gov (United States)

    Sharma, Mamta; Fakih, Mohamad G; Berriel-Cass, Dorine; Meisner, Susan; Saravolatz, Louis; Khatib, Riad

    2009-10-01

    Our goals were to evaluate the risk factors predisposing to saphenous vein harvest surgical site infection (HSSI), the microbiology implicated, associated outcomes including 30-day mortality, and identify opportunities for prevention of infection. All patients undergoing coronary artery bypass grafting (CABG) procedures from January 2000 through September 2004 were included. Data were collected on preoperative, intraoperative, and postoperative factors, in addition to microbiology and outcomes. Eighty-six of 3578 (2.4%) patients developed HSSI; 28 (32.6%) of them were classified as deep. The median time to detection was 17 (range, 4-51) days. An organism was identified in 64 (74.4%) cases; of them, a single pathogen was implicated in 50 (78%) cases. Staphylococcus aureus was the most frequently isolated pathogen: 19 (38% [methicillin-susceptible S aureus (MSSA) = 12, methicillin-resistant S aureus (MRSA) = 7]). Gram-negative organisms were recovered in 50% of cases, with Pseudomonas aeruginosa predominating in 11 (22%) because of a single pathogen. Multiple pathogens were identified in 14 (22%) cases. The 30-day mortality was not significantly different in patients with or without HSSI. Multivariate analysis showed age, diabetes mellitus, obesity, congestive heart failure, renal insufficiency, and duration of surgery to be associated with increased risk. Diabetes mellitus, obesity, congestive heart failure, renal insufficiency, and duration of surgery were associated with increased risk for HSSI. S aureus was the most frequently isolated pathogen.

  4. Risk Factors for Social Networking Site Scam Victimization Among Malaysian Students.

    Science.gov (United States)

    Kirwan, Gráinne H; Fullwood, Chris; Rooney, Brendan

    2018-02-01

    Social networking sites (SNSs) can provide cybercriminals with various opportunities, including gathering of user data and login credentials to enable fraud, and directing of users toward online locations that may install malware onto their devices. The techniques employed by such cybercriminals can include clickbait (text or video), advertisement of nonexistent but potentially desirable products, and hoax competitions/giveaways. This study aimed to identify risk factors associated with falling victim to these malicious techniques. An online survey was completed by 295 Malaysian undergraduate students, finding that more than one-third had fallen victim to SNS scams. Logistic regression analysis identified several victimization risk factors including having higher scores in impulsivity (specifically cognitive complexity), using fewer devices for SNSs, and having been on an SNS for a longer duration. No reliable model was found for vulnerability to hoax valuable gift giveaways and "friend view application" advertising specifically, but vulnerability to video clickbait was predicted by lower extraversion scores, higher levels of openness to experience, using fewer devices, and being on an SNS for a longer duration. Other personality traits were not associated with either overall victimization susceptibility or increased risk of falling victim to the specific techniques. However, age approached significance within both the video clickbait and overall victimization models. These findings suggest that routine activity theory may be particularly beneficial in understanding and preventing SNSs scam victimization.

  5. Transcriptional activation of transforming growth factor alpha by estradiol: requirement for both a GC-rich site and an estrogen response element half-site.

    Science.gov (United States)

    Vyhlidal, C; Samudio, I; Kladde, M P; Safe, S

    2000-06-01

    17beta-Estradiol (E2) induces transforming growth factor alpha (TGFalpha) gene expression in MCF-7 cells and previous studies have identified a 53 bp (-252 to -200) sequence containing two imperfect estrogen responsive elements (EREs) that contribute to E2 responsiveness. Deletion analysis of the TGFalpha gene promoter in this study identified a second upstream region of the promoter (-623 to -549) that is also E2 responsive. This sequence contains three GC-rich sites and an imperfect ERE half-site, and the specific cis-elements and trans-acting factors were determined by promoter analysis in transient transfection experiments, gel mobility shift assays and in vitro DNA footprinting. The results are consistent with an estrogen receptor alpha (ERalpha)/Sp1 complex interacting with an Sp1(N)(30) ERE half-site ((1/2)) motif in which both ERalpha and Sp1 bind promoter DNA. The ER/Sp1-DNA complex is formed using nuclear extracts from MCF-7 cells but not with recombinant human ERalpha or Sp1 proteins, suggesting that other nuclear factor(s) are required for complex stabilization. The E2-responsive Sp1(N)(x)ERE(1/2) motif identified in the TGFalpha gene promoter has also been characterized in the cathepsin D and heat shock protein 27 gene promoters; however, in the latter two promoters the numbers of intervening nucleotides are 23 and 10 respectively.

  6. PET Imaging of Tissue Factor in Pancreatic Cancer Using 64Cu-Labeled Active Site-Inhibited Factor VII.

    Science.gov (United States)

    Nielsen, Carsten H; Jeppesen, Troels E; Kristensen, Lotte K; Jensen, Mette M; El Ali, Henrik H; Madsen, Jacob; Wiinberg, Bo; Petersen, Lars C; Kjaer, Andreas

    2016-07-01

    Tissue factor (TF) is the main initiator of the extrinsic coagulation cascade. However, TF also plays an important role in cancer. TF expression has been reported in 53%-89% of all pancreatic adenocarcinomas, and the expression level of TF has in clinical studies correlated with advanced stage, increased microvessel density, metastasis, and poor overall survival. Imaging of TF expression is of clinical relevance as a prognostic biomarker and as a companion diagnostic for TF-directed therapies currently under clinical development. Factor VII (FVII) is the natural ligand to TF. The purpose of this study was to investigate the possibility of using active site-inhibited FVII (FVIIai) labeled with (64)Cu for PET imaging of TF expression. FVIIai was conjugated to 2-S-(4-isothiocyanatobenzyl)-1,4,7-triazacyclononane-1,4,7-triacetic acid (p-SCN-Bn-NOTA) and labeled with (64)Cu ((64)Cu-NOTA-FVIIai). Longitudinal in vivo PET imaging was performed at 1, 4, 15, and 36 h after injection of (64)Cu-NOTA-FVIIai in mice with pancreatic adenocarcinomas (BxPC-3). The specificity of TF imaging with (64)Cu-NOTA-FVIIai was investigated in subcutaneous pancreatic tumor models with different levels of TF expression and in a competition experiment. In addition, imaging of orthotopic pancreatic tumors was performed using (64)Cu-NOTA-FVIIai and PET/MRI. In vivo imaging data were supported by ex vivo biodistribution, flow cytometry, and immunohistochemistry. Longitudinal PET imaging with (64)Cu-NOTA-FVIIai showed a tumor uptake of 2.3 ± 0.2, 3.7 ± 0.3, 3.4 ± 0.3, and 2.4 ± 0.3 percentage injected dose per gram at 1, 4, 15, and 36 h after injection, respectively. An increase in tumor-to-normal-tissue contrast was observed over the imaging time course. Competition with unlabeled FVIIai significantly (P < 0.001) reduced the tumor uptake. The tumor uptake observed in models with different TF expression levels was significantly different from each other (P < 0.001) and was in agreement with

  7. Risk factors for surgical site infection after transvaginal mesh placement in a nationwide Japanese cohort.

    Science.gov (United States)

    Kamei, Jun; Yazawa, Satoshi; Yamamoto, Shingo; Kaburaki, Naoto; Takahashi, Satoru; Takeyama, Masami; Koyama, Masayasu; Homma, Yukio; Arakawa, Soichi; Kiyota, Hiroshi

    2018-03-01

    We conducted a nationwide survey on perioperative management and antimicrobial prophylaxis of transvaginal mesh surgeries for pelvic organ prolapse in Japan to understand the practice and risk factors for surgical site infection (SSI). Health records of women undergoing tension-free vaginal mesh (TVM) surgeries from 2010 to 2012 were obtained from 135 medical centers belonging to the Japanese Society of Pelvic Organ Prolapse Surgery. The questionnaire addressed hospital volume, perioperative management, and SSI. Risk factors for SSI were investigated by comparing cases with and without SSI. The hospital volume among institutions varied from 0 to 248 per year (median 16.7). Preoperative hair removal, bowel preparation, and urine culture were routinely performed at 74 (55%), 66 (49%), and 24 (18%) hospitals, respectively. Prophylactic antimicrobials used were mostly first-generation (43%) or second-generation (42%) cephalosporin. SSI was reported in 86 of 9323 patients (0.92%). A multivariate analysis indicated lower hospital volume (odds ratio [OR], 0.995 [by 1-point increase]; P < 0.001), preoperative bowel preparation (OR, 2.08; P = 0.013), non-routine urine culture (OR, 3.00; P = 0.0006), and the use of antibiotics other than first-generation cephalosporin (OR, 5.29; P = 0.0011) as significant risk factors for SSI. In contrast, the cut-off points of hospital volume for preventing SSI was 116.7 cases (area under curve: 0.61). The prevalence of SSI in TVM surgeries was 0.92% in Japan. Lower hospital volume, bowel preparation, non-routine preoperative urine culture, and prophylactic antibiotics other than first-generation cephalosporin significantly elevated the incidence of SSI. © 2018 Wiley Periodicals, Inc.

  8. Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters.

    Directory of Open Access Journals (Sweden)

    Fu-Jou Lai

    Full Text Available Transcription factor binding site (TFBS identification plays an important role in deciphering gene regulatory codes. With comprehensive knowledge of TFBSs, one can understand molecular mechanisms of gene regulation. In the recent decades, various computational approaches have been proposed to predict TFBSs in the genome. The TFBS dataset of a TF generated by each algorithm is a ranked list of predicted TFBSs of that TF, where top ranked TFBSs are statistically significant ones. However, whether these statistically significant TFBSs are functional (i.e. biologically relevant is still unknown. Here we develop a post-processor, called the functional propensity calculator (FPC, to assign a functional propensity to each TFBS in the existing computationally predicted TFBS datasets. It is known that functional TFBSs reveal strong positional preference towards the transcriptional start site (TSS. This motivates us to take TFBS position relative to the TSS as the key idea in building our FPC. Based on our calculated functional propensities, the TFBSs of a TF in the original TFBS dataset could be reordered, where top ranked TFBSs are now the ones with high functional propensities. To validate the biological significance of our results, we perform three published statistical tests to assess the enrichment of Gene Ontology (GO terms, the enrichment of physical protein-protein interactions, and the tendency of being co-expressed. The top ranked TFBSs in our reordered TFBS dataset outperform the top ranked TFBSs in the original TFBS dataset, justifying the effectiveness of our post-processor in extracting functional TFBSs from the original TFBS dataset. More importantly, assigning functional propensities to putative TFBSs enables biologists to easily identify which TFBSs in the promoter of interest are likely to be biologically relevant and are good candidates to do further detailed experimental investigation. The FPC is implemented as a web tool at http://santiago.ee.ncku.edu.tw/FPC/.

  9. Theory of site-specific interactions of the combinatorial transcription factors with DNA

    International Nuclear Information System (INIS)

    Murugan, R

    2010-01-01

    We derive a functional relationship between the mean first passage time associated with the concurrent binding of multiple transcription factors (TFs) at their respective combinatorial cis-regulatory module sites (CRMs) and the number n of TFs involved in the regulation of the initiation of transcription of a gene of interest. Our results suggest that the overall search time τ s that is required by the n TFs to locate their CRMs which are all located on the same DNA chain scales with n as τ s ∼n α where α ∼ (2/5). When the jump size k that is associated with the dynamics of all the n TFs along DNA is higher than that of the critical jump size k c that scales with the size of DNA N as k c ∼ N 2/3 , we observe a similar power law scaling relationship and also the exponent α. When k c , α shows a strong dependence on both n and k. Apparently there is a critical number of combinatorial TFs n c ∼ 20 that is required to efficiently regulate the initiation of transcription of a given gene below which (2/5) 1. These results seem to be independent of the initial distances between the TFs and their corresponding CRMs and also suggest that the maximum number of TFs involved in a given combinatorial regulation of the initiation of transcription of a gene of interest seems to be restricted by the degree of condensation of the genomic DNA. The optimum number m opt of roadblock protein molecules per genome at which the search time associated with these n TFs to locate their binding sites is a minimum seems to scale as m opt ∼Ln α/2 where L is the sliding length of TFs whose maximum value seems to be such that L ≤ 10 4 bps for the E. coli bacterial genome.

  10. Abdominal surgical site infections: incidence and risk factors at an Iranian teaching hospital

    Directory of Open Access Journals (Sweden)

    Sabouri Kashani Ahmad

    2005-02-01

    Full Text Available Abstract Background Abdominal surgical site infections are among the most common complications of inpatient admissions and have serious consequences for outcomes and costs. Different risk factors may be involved, including age, sex, nutrition and immunity, prophylactic antibiotics, operation type and duration, type of shaving, and secondary infections. This study aimed to determine the risk factors affecting abdominal surgical site infections and their incidence at Imam Khomeini, a major referral teaching hospital in Iran. Methods Patients (n = 802 who had undergone abdominal surgery were studied and the relationships among variables were analyzed by Student's t and Chi-square tests. The subjects were followed for 30 days and by a 20-item questionnaire. Data were collected through pre- and post-operative examinations and telephone follow-ups. Results Of the 802 patients, 139 suffered from SSI (17.4%. In 40.8% of the cases, the wound was dirty infected. The average age for the patients was 46.7 years. The operations were elective in 75.7% of the cases and 24.7% were urgent. The average duration of the operation was 2.24 hours, the average duration of pre-operative hospital stay 4.31 days and the average length of (pre- and post-operation hospital stay 11.2 days. Three quarters of the cases were shaved 12 hours before the operation. The increased operation time, increased bed stay, electivity of the operation, septicity of the wound, type of incision, the administration of prophylactic antibiotic, type of operation, background disease, and the increased time lapse between shaving and operation all significantly associated with SSI with a p-value less than 0.001. Conclusion In view of the high rate of SSI reported here (17.4% compared with the 14% quoted in literature, this study suggests that by reducing the average operation time to less than 2 hours, the average preoperative stay to 4 days and the overall stay to less than 11 days, and

  11. Manipulation of the membrane binding site of vitamin K-dependent proteins: Enhanced biological function of human factor VII

    OpenAIRE

    Shah, Amit M.; Kisiel, Walter; Foster, Donald C.; Nelsestuen, Gary L.

    1998-01-01

    Recent studies suggested that modification of the membrane contact site of vitamin K-dependent proteins may enhance the membrane affinity and function of members of this protein family. The properties of a factor VII mutant, factor VII-Q10E32, relative to wild-type factor VII (VII, containing P10K32), have been compared. Membrane affinity of VII-Q10E32 was about 20-fold higher than that of wild-type factor VII. The rate of autoactivation VII-Q10E32 with soluble tissue factor was 100-fold fast...

  12. Factors Associated with the Risk of Persistent Gastrostomy Site Infection Following Laparoscopic or Open Nissen Fundoplication

    Directory of Open Access Journals (Sweden)

    Hisayuki Miyagi

    2017-01-01

    Full Text Available Background: Gastrostomy for feeding disorders or swallowing dysfunctions can be complicated by persistent gastrostomy site infection (PGSI. PGSI causes nutrient leakage, with dilated PGSI requiring gastrostomy reconstruction. The purpose of this study was to evaluate the causes, patient characteristics, and perioperative management of PGSI after Nissen fundoplication and gastrostomy for patients with gastro-oesophageal reflux. Patients and Methods: The records of all patients who underwent Nissen fundoplication and gastrostomy for gastro-oesophageal reflux over the past 12 years were retrieved. Risk factors were analysed, including age at surgery, gender, operative procedure, use of postoperative ventilator management, gastrostomy tube migration towards the pylorus, bacterial culture results, and length of hospital stay. PGSI as a cause of inflammation was analysed statistically. Results: Forty patients were identified, ranging in age from 1 to 49 years (median, 11 years surgically. Twenty each underwent laparoscopic and open surgery, with all undergoing gastrostomy using the Stamm technique. Four patients developed PGSI. Gastrostomy tubes had migrated postoperatively to the pyloric side in three of these four patients (P < 0.005, increasing intragastric pressure. Three of these four patients also required positive pressure ventilation during the perioperative period (P < 0.001. Conclusion: PGSI correlates with the perioperative management of positive pressure and with increased intragastric pressure resulting from pyloric obstruction, which is caused by aberrant distribution of the gastrostomy tube to the pyloric side. Statistical Analysis Used: Factors in the two groups were compared statistically by Mann–Whitney U-test to determine whether PGSI caused inflammation. Statistical significance was defined as P < 0.05.

  13. Coarse-grained molecular simulation of epidermal growth factor receptor protein tyrosine kinase multi-site self-phosphorylation.

    Directory of Open Access Journals (Sweden)

    John G Koland

    2014-01-01

    Full Text Available Upon the ligand-dependent dimerization of the epidermal growth factor receptor (EGFR, the intrinsic protein tyrosine kinase (PTK activity of one receptor monomer is activated, and the dimeric receptor undergoes self-phosphorylation at any of eight candidate phosphorylation sites (P-sites in either of the two C-terminal (CT domains. While the structures of the extracellular ligand binding and intracellular PTK domains are known, that of the ∼225-amino acid CT domain is not, presumably because it is disordered. Receptor phosphorylation on CT domain P-sites is critical in signaling because of the binding of specific signaling effector molecules to individual phosphorylated P-sites. To investigate how the combination of conventional substrate recognition and the unique topological factors involved in the CT domain self-phosphorylation reaction lead to selectivity in P-site phosphorylation, we performed coarse-grained molecular simulations of the P-site/catalytic site binding reactions that precede EGFR self-phosphorylation events. Our results indicate that self-phosphorylation of the dimeric EGFR, although generally believed to occur in trans, may well occur with a similar efficiency in cis, with the P-sites of both receptor monomers being phosphorylated to a similar extent. An exception was the case of the most kinase-proximal P-site-992, the catalytic site binding of which occurred exclusively in cis via an intramolecular reaction. We discovered that the in cis interaction of P-site-992 with the catalytic site was facilitated by a cleft between the N-terminal and C-terminal lobes of the PTK domain that allows the short CT domain sequence tethering P-site-992 to the PTK core to reach the catalytic site. Our work provides several new mechanistic insights into the EGFR self-phosphorylation reaction, and demonstrates the potential of coarse-grained molecular simulation approaches for investigating the complexities of self-phosphorylation in

  14. Rotation of nucleotide sites is not required for the enzymatic activity of chloroplast coupling factor

    Energy Technology Data Exchange (ETDEWEB)

    Musier, K.M.; Hammes, G.G.

    1987-09-22

    New heterobifunctional photoaffinity cross-linking reagents, 6-maleimido-N-(4-benzoylphenyl)hexanamide, 12-maleimido-N-(4-benzoylphenyl)dodecanamide, and 12-(/sup 14/C)maleimido-N-(4-benzoylphenyo)dodecanamide, were synthesized to investigate the mechanism of ATP hydrolysis by chloroplast coupling factor 1. These reagents react with sulfhydryl groups on the ..gamma..-polypeptide. Subsequent photolysis cross-links the ..gamma..-polypeptide covalently to ..cap alpha..- and ..beta..-polypeptides. The cross-linkers prevent major movements of the ..gamma..-polypeptide with respect to the ..cap alpha..- and ..beta..-polypeptides but are sufficiently long to permit some flexibility in the enzyme structure. When approx. 50% of the ..gamma..-polypeptide was cross-linked to a ..cap alpha..- and ..beta..-polypeptides, a 7% loss in ATPase activity was observed for the longer cross-linker and a 12% loss for the shorter. These results indicate that large movements of ..cap alpha..- and ..beta..-polypeptides with respect to the ..gamma..-polypeptide are not essential for catalysis. In particular, rotation of the polypeptide chains to crease structurally equivalent sites during catalysis is not a required feature of the enzyme mechanism.

  15. Predicting transcription factor binding sites using local over-representation and comparative genomics

    Directory of Open Access Journals (Sweden)

    Touzet Hélène

    2006-08-01

    Full Text Available Abstract Background Identifying cis-regulatory elements is crucial to understanding gene expression, which highlights the importance of the computational detection of overrepresented transcription factor binding sites (TFBSs in coexpressed or coregulated genes. However, this is a challenging problem, especially when considering higher eukaryotic organisms. Results We have developed a method, named TFM-Explorer, that searches for locally overrepresented TFBSs in a set of coregulated genes, which are modeled by profiles provided by a database of position weight matrices. The novelty of the method is that it takes advantage of spatial conservation in the sequence and supports multiple species. The efficiency of the underlying algorithm and its robustness to noise allow weak regulatory signals to be detected in large heterogeneous data sets. Conclusion TFM-Explorer provides an efficient way to predict TFBS overrepresentation in related sequences. Promising results were obtained in a variety of examples in human, mouse, and rat genomes. The software is publicly available at http://bioinfo.lifl.fr/TFM-Explorer.

  16. HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

    Science.gov (United States)

    Kulakovskiy, Ivan V.; Medvedeva, Yulia A.; Schaefer, Ulf; Kasianov, Artem S.; Vorontsov, Ilya E.; Bajic, Vladimir B.; Makeev, Vsevolod J.

    2013-01-01

    Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. PMID:23175603

  17. A novel method for improved accuracy of transcription factor binding site prediction

    KAUST Repository

    Khamis, Abdullah M.; Motwalli, Olaa Amin; Oliva, Romina; Jankovic, Boris R.; Medvedeva, Yulia; Ashoor, Haitham; Essack, Magbubah; Gao, Xin; Bajic, Vladimir B.

    2018-01-01

    Identifying transcription factor (TF) binding sites (TFBSs) is important in the computational inference of gene regulation. Widely used computational methods of TFBS prediction based on position weight matrices (PWMs) usually have high false positive rates. Moreover, computational studies of transcription regulation in eukaryotes frequently require numerous PWM models of TFBSs due to a large number of TFs involved. To overcome these problems we developed DRAF, a novel method for TFBS prediction that requires only 14 prediction models for 232 human TFs, while at the same time significantly improves prediction accuracy. DRAF models use more features than PWM models, as they combine information from TFBS sequences and physicochemical properties of TF DNA-binding domains into machine learning models. Evaluation of DRAF on 98 human ChIP-seq datasets shows on average 1.54-, 1.96- and 5.19-fold reduction of false positives at the same sensitivities compared to models from HOCOMOCO, TRANSFAC and DeepBind, respectively. This observation suggests that one can efficiently replace the PWM models for TFBS prediction by a small number of DRAF models that significantly improve prediction accuracy. The DRAF method is implemented in a web tool and in a stand-alone software freely available at http://cbrc.kaust.edu.sa/DRAF.

  18. HOCOMOCO: A comprehensive collection of human transcription factor binding sites models

    KAUST Repository

    Kulakovskiy, Ivan V.; Medvedeva, Yulia A.; Schaefer, Ulf; Kasianov, Artem S.; Vorontsov, Ilya E.; Bajic, Vladimir B.; Makeev, Vsevolod J.

    2012-01-01

    Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/ hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. The Author(s) 2012.

  19. A novel method for improved accuracy of transcription factor binding site prediction

    KAUST Repository

    Khamis, Abdullah M.

    2018-03-20

    Identifying transcription factor (TF) binding sites (TFBSs) is important in the computational inference of gene regulation. Widely used computational methods of TFBS prediction based on position weight matrices (PWMs) usually have high false positive rates. Moreover, computational studies of transcription regulation in eukaryotes frequently require numerous PWM models of TFBSs due to a large number of TFs involved. To overcome these problems we developed DRAF, a novel method for TFBS prediction that requires only 14 prediction models for 232 human TFs, while at the same time significantly improves prediction accuracy. DRAF models use more features than PWM models, as they combine information from TFBS sequences and physicochemical properties of TF DNA-binding domains into machine learning models. Evaluation of DRAF on 98 human ChIP-seq datasets shows on average 1.54-, 1.96- and 5.19-fold reduction of false positives at the same sensitivities compared to models from HOCOMOCO, TRANSFAC and DeepBind, respectively. This observation suggests that one can efficiently replace the PWM models for TFBS prediction by a small number of DRAF models that significantly improve prediction accuracy. The DRAF method is implemented in a web tool and in a stand-alone software freely available at http://cbrc.kaust.edu.sa/DRAF.

  20. HOCOMOCO: A comprehensive collection of human transcription factor binding sites models

    KAUST Repository

    Kulakovskiy, Ivan V.

    2012-11-21

    Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/ hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. The Author(s) 2012.

  1. Demonstration of epidermal growth factor binding sites in the adult rat pancreas by light microscopic autoradiography

    International Nuclear Information System (INIS)

    Chabot, J.G.; Walker, P.; Pelletier, G.

    1987-01-01

    The distribution of epidermal growth factor (EGF) receptors was studied in the pancreas using light microscopic autoradiography, which was performed at different time intervals (2-60 min) after injecting 125 I-labeled EGF intravenously into the adult rat. In the exocrine pancreas, a labeling was found to occur over the pyramidal cells of the acini and cells lining the intercalated ducts. Moreover, substantial binding of EGF to cells of the islets of Langerhans was also revealed. At the 2-min time interval, most silver grains were found at the periphery of the target cells. The localization, as well as the diminution of silver grains over the cytoplasm of these cells, between 7 and 60 min, suggested the internalization and degradation of 125 I-labeled EGF. Control experiments indicated that the autoradiography reaction was due to specific interaction of 125 I-labeled EGF with its receptor. These results clearly indicate that EGF receptors are present in the acinar cells and the cells of intercalated ducts of the exocrine pancreas, as well as the cells of the endocrine pancreas. Finding that there are EGF binding sites in pancreatic acinar cells supports the physiological role of EGF in the regulation of pancreatic exocrine function. The presence of EGF receptors in cells of the islets of Langerhans suggests that EGF may play a role in the regulation of the endocrine pancreas

  2. Two signaling molecules share a phosphotyrosine-containing binding site in the platelet-derived growth factor receptor.

    OpenAIRE

    Nishimura, R; Li, W; Kashishian, A; Mondino, A; Zhou, M; Cooper, J; Schlessinger, J

    1993-01-01

    Autophosphorylation sites of growth factor receptors with tyrosine kinase activity function as specific binding sites for Src homology 2 (SH2) domains of signaling molecules. This interaction appears to be a crucial step in a mechanism by which receptor tyrosine kinases relay signals to downstream signaling pathways. Nck is a widely expressed protein consisting exclusively of SH2 and SH3 domains, the overexpression of which causes cell transformation. It has been shown that various growth fac...

  3. Identification and Analysis of Significant Factors Influencing Visitor Satisfaction at Heritage Sites – The Case of Serbian Medieval Fortresses

    Directory of Open Access Journals (Sweden)

    Ivana Blešić

    2013-01-01

    Full Text Available With increased appreciation of general public, heritage sites gained more attention regarding contemporary tourism and management studies. Accordingly, the assessment of visitors’ satisfaction on these sites is important tool for both financial and organization management. The aim of this research is to identify the main (statistically significant factors that influence visitors’ satisfaction. Data was obtained by survey conducted during the visit of three medieval fortresses in Serbia, with aim to capture tourist’s expectations and perceptions on ten given attributes. The results of factor and descriptive statistical analysis indicate three factors: “regional settings”, “marketing”, “aesthetic appeal” significant for visitors’ satisfaction of the investigated heritage sites.

  4. Deep subsurface structure modeling and site amplification factor estimation in Niigata plain for broadband strong motion prediction

    International Nuclear Information System (INIS)

    Sato, Hiroaki

    2009-01-01

    This report addresses a methodology of deep subsurface structure modeling in Niigata plain, Japan to estimate site amplification factor in the broadband frequency range for broadband strong motion prediction. In order to investigate deep S-wave velocity structures, we conduct microtremor array measurements at nine sites in Niigata plain, which are important to estimate both long- and short-period ground motion. The estimated depths of the top of the basement layer agree well with those of the Green tuff formation as well as the Bouguer anomaly distribution. Dispersion characteristics derived from the observed long-period ground motion records are well explained by the theoretical dispersion curves of Love wave group velocities calculated from the estimated subsurface structures. These results demonstrate the deep subsurface structures from microtremor array measurements make it possible to estimate long-period ground motions in Niigata plain. Moreover an applicability of microtremor array exploration for inclined basement structure like a folding structure is shown from the two dimensional finite difference numerical simulations. The short-period site amplification factors in Niigata plain are empirically estimated by the spectral inversion analysis from S-wave parts of strong motion data. The resultant characteristics of site amplification are relative large in the frequency range of about 1.5-5 Hz, and decay significantly with the frequency increasing over about 5 Hz. However, these features can't be explained by the calculations from the deep subsurface structures. The estimation of site amplification factors in the frequency range of about 1.5-5 Hz are improved by introducing a shallow detailed structure down to GL-20m depth at a site. We also propose to consider random fluctuation in a modeling of deep S-wave velocity structure for broadband site amplification factor estimation. The Site amplification in the frequency range higher than about 5 Hz are filtered

  5. Two signaling molecules share a phosphotyrosine-containing binding site in the platelet-derived growth factor receptor.

    Science.gov (United States)

    Nishimura, R; Li, W; Kashishian, A; Mondino, A; Zhou, M; Cooper, J; Schlessinger, J

    1993-11-01

    Autophosphorylation sites of growth factor receptors with tyrosine kinase activity function as specific binding sites for Src homology 2 (SH2) domains of signaling molecules. This interaction appears to be a crucial step in a mechanism by which receptor tyrosine kinases relay signals to downstream signaling pathways. Nck is a widely expressed protein consisting exclusively of SH2 and SH3 domains, the overexpression of which causes cell transformation. It has been shown that various growth factors stimulate the phosphorylation of Nck and its association with autophosphorylated growth factor receptors. A panel of platelet-derived growth factor (PDGF) receptor mutations at tyrosine residues has been used to identify the Nck binding site. Here we show that mutation at Tyr-751 of the PDGF beta-receptor eliminates Nck binding both in vitro and in living cells. Moreover, the Y751F PDGF receptor mutant failed to mediate PDGF-stimulated phosphorylation of Nck in intact cells. A phosphorylated Tyr-751 is also required for binding of phosphatidylinositol-3 kinase to the PDGF receptor. Hence, the SH2 domains of p85 and Nck share a binding site in the PDGF receptor. Competition experiments with different phosphopeptides derived from the PDGF receptor suggest that binding of Nck and p85 is influenced by different residues around Tyr-751. Thus, a single tyrosine autophosphorylation site is able to link the PDGF receptor to two distinct SH2 domain-containing signaling molecules.

  6. Pipeline for Efficient Mapping of Transcription Factor Binding Sites and Comparison of Their Models

    KAUST Repository

    Ba alawi, Wail

    2011-06-01

    The control of genes in every living organism is based on activities of transcription factor (TF) proteins. These TFs interact with DNA by binding to the TF binding sites (TFBSs) and in that way create conditions for the genes to activate. Of the approximately 1500 TFs in human, TFBSs are experimentally derived only for less than 300 TFs and only in generally limited portions of the genome. To be able to associate TF to genes they control we need to know if TFs will have a potential to interact with the control region of the gene. For this we need to have models of TFBS families. The existing models are not sufficiently accurate or they are too complex for use by ordinary biologists. To remove some of the deficiencies of these models, in this study we developed a pipeline through which we achieved the following: 1. Through a comparison analysis of the performance we identified the best models with optimized thresholds among the four different types of models of TFBS families. 2. Using the best models we mapped TFBSs to the human genome in an efficient way. The study shows that a new scoring function used with TFBS models based on the position weight matrix of dinucleotides with remote dependency results in better accuracy than the other three types of the TFBS models. The speed of mapping has been improved by developing a parallelized code and shows a significant speed up of 4x when going from 1 CPU to 8 CPUs. To verify if the predicted TFBSs are more accurate than what can be expected with the conventional models, we identified the most frequent pairs of TFBSs (for TFs E4F1 and ATF6) that appeared close to each other (within the distance of 200 nucleotides) over the human genome. We show unexpectedly that the genes that are most close to the multiple pairs of E4F1/ATF6 binding sites have a co-expression of over 90%. This indirectly supports our hypothesis that the TFBS models we use are more accurate and also suggests that the E4F1/ATF6 pair is exerting the

  7. Factors for Successful Use of Social Networking Sites in Higher Education

    OpenAIRE

    L Schlenkrich; Dave Sewry

    2012-01-01

    Social networking sites are extremely popular online destinations that offer users easy ways to build and maintain relationships with each other, and to disseminate information in an activity referred to as social networking. Students, lecturers, teachers, parents and businesses, in increasing numbers, use tools available on social networking sites to communicate with each other in a fast and cost-effective manner. The use of social networking sites to support educational initiatives has rece...

  8. A 5' splice site enhances the recruitment of basal transcription initiation factors in vivo

    DEFF Research Database (Denmark)

    Damgaard, Christian Kroun; Kahns, Søren; Lykke-Andersen, Søren

    2008-01-01

    RNAs, harboring wild-type or various 5′ splice site mutations, we demonstrate a strong positive correlation between splicing efficiency and transcription activity. Interestingly, a 5′ splice site can stimulate transcription even in the absence of splicing. Chromatin immunoprecipitation experiments show enhanced...... a promoter-proximal 5′ splice site via its U1 snRNA interaction can feed back to stimulate transcription initiation by enhancing preinitiation complex assembly....

  9. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

    Directory of Open Access Journals (Sweden)

    Anil Raj

    Full Text Available Understanding global gene regulation depends critically on accurate annotation of regulatory elements that are functional in a given cell type. CENTIPEDE, a powerful, probabilistic framework for identifying transcription factor binding sites from tissue-specific DNase I cleavage patterns and genomic sequence content, leverages the hypersensitivity of factor-bound chromatin and the information in the DNase I spatial cleavage profile characteristic of each DNA binding protein to accurately infer functional factor binding sites. However, the model for the spatial profile in this framework fails to account for the substantial variation in the DNase I cleavage profiles across different binding sites. Neither does it account for variation in the profiles at the same binding site across multiple replicate DNase I experiments, which are increasingly available. In this work, we introduce new methods, based on multi-scale models for inhomogeneous Poisson processes, to account for such variation in DNase I cleavage patterns both within and across binding sites. These models account for the spatial structure in the heterogeneity in DNase I cleavage patterns for each factor. Using DNase-seq measurements assayed in a lymphoblastoid cell line, we demonstrate the improved performance of this model for several transcription factors by comparing against the Chip-seq peaks for those factors. Finally, we explore the effects of DNase I sequence bias on inference of factor binding using a simple extension to our framework that allows for a more flexible background model. The proposed model can also be easily applied to paired-end ATAC-seq and DNase-seq data. msCentipede, a Python implementation of our algorithm, is available at http://rajanil.github.io/msCentipede.

  10. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

    Science.gov (United States)

    Raj, Anil; Shim, Heejung; Gilad, Yoav; Pritchard, Jonathan K; Stephens, Matthew

    2015-01-01

    Understanding global gene regulation depends critically on accurate annotation of regulatory elements that are functional in a given cell type. CENTIPEDE, a powerful, probabilistic framework for identifying transcription factor binding sites from tissue-specific DNase I cleavage patterns and genomic sequence content, leverages the hypersensitivity of factor-bound chromatin and the information in the DNase I spatial cleavage profile characteristic of each DNA binding protein to accurately infer functional factor binding sites. However, the model for the spatial profile in this framework fails to account for the substantial variation in the DNase I cleavage profiles across different binding sites. Neither does it account for variation in the profiles at the same binding site across multiple replicate DNase I experiments, which are increasingly available. In this work, we introduce new methods, based on multi-scale models for inhomogeneous Poisson processes, to account for such variation in DNase I cleavage patterns both within and across binding sites. These models account for the spatial structure in the heterogeneity in DNase I cleavage patterns for each factor. Using DNase-seq measurements assayed in a lymphoblastoid cell line, we demonstrate the improved performance of this model for several transcription factors by comparing against the Chip-seq peaks for those factors. Finally, we explore the effects of DNase I sequence bias on inference of factor binding using a simple extension to our framework that allows for a more flexible background model. The proposed model can also be easily applied to paired-end ATAC-seq and DNase-seq data. msCentipede, a Python implementation of our algorithm, is available at http://rajanil.github.io/msCentipede.

  11. SP Transcription Factor Paralogs and DNA-Binding Sites Coevolve and Adaptively Converge in Mammals and Birds

    Science.gov (United States)

    Yokoyama, Ken Daigoro; Pollock, David D.

    2012-01-01

    Functional modification of regulatory proteins can affect hundreds of genes throughout the genome, and is therefore thought to be almost universally deleterious. This belief, however, has recently been challenged. A potential example comes from transcription factor SP1, for which statistical evidence indicates that motif preferences were altered in eutherian mammals. Here, we set out to discover possible structural and theoretical explanations, evaluate the role of selection in SP1 evolution, and discover effects on coregulatory proteins. We show that SP1 motif preferences were convergently altered in birds as well as mammals, inducing coevolutionary changes in over 800 regulatory regions. Structural and phylogenic evidence implicates a single causative amino acid replacement at the same SP1 position along both lineages. Furthermore, paralogs SP3 and SP4, which coregulate SP1 target genes through competitive binding to the same sites, have accumulated convergent replacements at the homologous position multiple times during eutherian and bird evolution, presumably to preserve competitive binding. To determine plausibility, we developed and implemented a simple model of transcription factor and binding site coevolution. This model predicts that, in contrast to prevailing beliefs, even small selective benefits per locus can drive concurrent fixation of transcription factor and binding site mutants under a broad range of conditions. Novel binding sites tend to arise de novo, rather than by mutation from ancestral sites, a prediction substantiated by SP1-binding site alignments. Thus, multiple lines of evidence indicate that selection has driven convergent evolution of transcription factors along with their binding sites and coregulatory proteins. PMID:23019068

  12. Quantification of source impact to PM using three-dimensional weighted factor model analysis on multi-site data

    Science.gov (United States)

    Shi, Guoliang; Peng, Xing; Huangfu, Yanqi; Wang, Wei; Xu, Jiao; Tian, Yingze; Feng, Yinchang; Ivey, Cesunica E.; Russell, Armistead G.

    2017-07-01

    Source apportionment technologies are used to understand the impacts of important sources of particulate matter (PM) air quality, and are widely used for both scientific studies and air quality management. Generally, receptor models apportion speciated PM data from a single sampling site. With the development of large scale monitoring networks, PM speciation are observed at multiple sites in an urban area. For these situations, the models should account for three factors, or dimensions, of the PM, including the chemical species concentrations, sampling periods and sampling site information, suggesting the potential power of a three-dimensional source apportionment approach. However, the principle of three-dimensional Parallel Factor Analysis (Ordinary PARAFAC) model does not always work well in real environmental situations for multi-site receptor datasets. In this work, a new three-way receptor model, called "multi-site three way factor analysis" model is proposed to deal with the multi-site receptor datasets. Synthetic datasets were developed and introduced into the new model to test its performance. Average absolute error (AAE, between estimated and true contributions) for extracted sources were all less than 50%. Additionally, three-dimensional ambient datasets from a Chinese mega-city, Chengdu, were analyzed using this new model to assess the application. Four factors are extracted by the multi-site WFA3 model: secondary source have the highest contributions (64.73 and 56.24 μg/m3), followed by vehicular exhaust (30.13 and 33.60 μg/m3), crustal dust (26.12 and 29.99 μg/m3) and coal combustion (10.73 and 14.83 μg/m3). The model was also compared to PMF, with general agreement, though PMF suggested a lower crustal contribution.

  13. Interaction between nucleotide binding sites on chloroplast coupling factor 1 during ATP hydrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Leckband, D.; Hammes, G.G.

    1987-04-21

    The initial hydrolysis of radioactively-labelled CaATP by chloroplast coupling factor 1 was studied with the quenched-flow method. The time course of hydrolysis can be described as a first-order conversion of the enzyme to an active form followed by steady-state formation of product. The rate constant for the first-order process is independent of substrate concentration but increased hyperbolically to a limiting value of 0.43 s/sup -1/ with increasing concentrations of free Ca/sup 2 +/. A mechanism involving a Ca/sup 2 +/-triggered conversion to an active form of the enzyme is consistent with the data. The steady-state rate varied sigmoidally with the CaATP concentration. Initial exchange of tightly bound ADP is complex: approx. 50% of the bound nucleotide is lost within 30 s, with complete exchange requiring several minutes. The first-order rate constant characterizing the rapid phase of the reaction increases hyperbolically to a limiting value of 0.26 s/sup -1/ as the concentration of CaATP is increased, indicating that the binding of CaATP to the enzyme promotes the exchange process. Modification of the quenched-flow apparatus permitted measurement of the rate of nucleotide exchange during steady-state catalysis. The value of the first-order rate constant characterizing this process is similar to the catalytic rate constant determined under identical conditions. When MgATP is tightly bound to the enzyme, none of the kinetic properties of the enzyme described above were significantly changes. The results obtained suggest a mechanism in which two sites on the enzyme participate in catalysis. Several possible mechanisms consistent with the data are discussed.

  14. Factors for assessment of human health risk associated with remedial action at hazardous waste sites

    International Nuclear Information System (INIS)

    Stephenson, D.E.; King, C.M.; Looney, B.B.; Holmes, W.G.; Gordon, D.E.

    1985-01-01

    A risk assessment strategy that is cost effective and minimized human health risks was developed for closure of hazardous waste sites at the Savannah River Plant. The strategy consists of (1) site characterization, (2) contaminant transport modeling, and (3) determination of relative merits of alternative remedial actions according to the degree of health protection they provide

  15. Study on the binding sites of radiosensitivity associated transcription factor in the promoter region of Ier5 gene

    International Nuclear Information System (INIS)

    Cui Wei; Yin Lingling; Dong Lingyue

    2012-01-01

    Objective: To clarify the mechanism of immediate early response gene 5 (Ier5) transcription induced by radiation. Methods: Deletant construction, site-specific mutagenesis,electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) were used to forecast the promoter region, binding sites and transcription factors of Ier5 gene in HeLa cells. Results: The promoter region of Ier5 gene might be in the region of Ier5 -8 deletant (-408 - -238 bp). The Ier5 gene had two transcription factors of GCF and NFI, and GCF had two binding sites located in the region of -388 - -382 bp and -274 - -270 bp of Ier5 promoter. The binding site of NFI was located in -362 - -357 bp of Ier5 promoter. GCF could inhibit the expression of Ier5 gene and this inhibition was diminished when the radiation dose increased. In contrast, NFI increased the expression of Ier5. Conclusions: The most possible region of Ier5 promoter is from -408 to -238 bp which has two binding sites for the radiosensitivity transcription factors of GCF and NFI that could negatively and positively regulate the expression of Ier5 respectively. (authors)

  16. Site-response Estimation by 1D Heterogeneous Velocity Model using Borehole Log and its Relationship to Damping Factor

    International Nuclear Information System (INIS)

    Sato, Hiroaki

    2014-01-01

    In the Niigata area, which suffered from several large earthquakes such as the 2007 Chuetsu-oki earthquake, geographical observation that elucidates the S-wave structure of the underground is advancing. Modeling of S-wave velocity structure in the subsurface is underway to enable simulation of long-period ground motion. The one-dimensional velocity model by inverse analysis of micro-tremors is sufficiently appropriate for long-period site response but not for short-period, which is important for ground motion evaluation at NPP sites. The high-frequency site responses may be controlled by the strength of heterogeneity of underground structure because the heterogeneity of the 1D model plays an important role in estimating high-frequency site responses and is strongly related to the damping factor of the 1D layered velocity model. (author)

  17. Occult Radiographically Evident Port-Site Hernia After Robot-Assisted Urologic Surgery: Incidence and Risk Factors.

    Science.gov (United States)

    Christie, Matthew C; Manger, Jules P; Khiyami, Abdulaziz M; Ornan, Afshan A; Wheeler, Karen M; Schenkman, Noah S

    2016-01-01

    Laparoscopic trocar-site hernias (TSH) are rare, with a reported incidence of 1% or less. The incidence of occult radiographically evident hernias has not been described after robot-assisted urologic surgery. We evaluated the incidence and risk factors of this problem. A single-institution retrospective review of robot-assisted urologic surgery was performed from April 2009 to December 2012. Patients with preoperative and postoperative CT were included for analysis. Imaging was reviewed by two radiologists and one urologist. One hundred four cases were identified, including 60 partial nephrectomy, 38 prostatectomy, and 6 cystectomy. Mean age was 58 years and mean body mass index (BMI) was 29 kg/m(2). The cohort was 77% male. Ten total hernias were identified by CT in 8 patients, 2 of which were clinically evident hernias. Excluding these two hernias, occult port-site hernias were identified radiographically in seven patients. Per-patient incidence of occult TSH was 6.7% (7/104), and per-port incidence was 1.4% (8/564). All hernias were midline and 30% contained bowel. Eight of the 10 occurred at 12 mm sites (p = 0.0065) and 3 of the 10 occurred at extended incisions. Age, gender, BMI, smoking status, diabetes mellitus, immunosuppressive drug therapy, ASA score, procedure, blood loss, prior abdominal surgery, and history of hernia were not significant risk factors. Specimen size >40 g (p = 0.024) and wound infection (p = 0.0052) were significant risk factors. While the incidence of clinically evident port-site hernia remains low in robot-assisted urologic surgery, the incidence of CT-detected occult hernia was 6.7% in this series. These occurred most often in sites extended for specimen extraction and at larger port sites. This suggests more attention should be paid to fascial closure at these sites.

  18. NAGRA - Sites for geological repositories - Technical safety factors: Suggestions for stage 3

    International Nuclear Information System (INIS)

    2015-01-01

    This comprehensive brochure published by the Swiss National Cooperative for the Disposal of Radioactive Waste (NAGRA) examines the six sites for repositories for nuclear wastes in Switzerland which have been proposed in Stage 1 of the program concerning nuclear waste repositories. Three of these sites are proposed for both highly radioactive wastes as well as for low and medium-active wastes, the other three for low and medium-active wastes only. The evaluation of the sites is discussed. The sites are to be further evaluated in Stage 2 of the program. The work to be done in the further stages involved in the selection of the final site (or sites) is described. Along with definition of the regions where deep repositories could possibly be built, suggestions for the placing of the facilities required on the surface are discussed. Geological requirements on the repositories and safety-relevant characteristics of the various site options are discussed. The results of the assessments made are presented in tabular form. Maps and geological cross-sections of all the suggested areas are included

  19. Some interactive factors affecting trench-cover integrity on low-level waste sites

    International Nuclear Information System (INIS)

    Hakonson, T.E.; Lane, L.J.; Steger, J.G.; DePoorter, G.L.

    1982-01-01

    This paper describes important mechanisms by which radionuclide can be transported from low-level waste disposal sites into biological pathways, discuss interactions of abiotic and biotic processes, and recommends environmental characteristics that should be measured to design sites that minimize this transport. Past experience at shallow land burial sites for low-level radioactive wastes suggest that occurrences of waste exposure and radionuclide transport are often related to inadequate trench cover designs. Meeting performance standards at low-level waste sites can only be achieved by recognizing that physical, chemical, and biological processes operating on and in a trench cover profile are highly interactive. Failure to do so can lead to improper design criteria and subsequent remedial action procedures that can adversely affect site stability. Based upon field experiments and computer modeling, recommendations are made on site characteristics that require measurement in order to design systems that reduce surface runoff and erosion, manage soil moisture and biota in the cover profile to maximize evapotranspiration and minimize percolation, and place bounds on the intrusion potential of plants and animals into the waste material. Major unresolved problems include developing probabilistic approaches that include climatic variability, improved knowledge of soil-water-plant-erosion relationships, development of practical vegetation establishment and maintenance procedures, prediction and quantification of site potential and plant succession, and understanding the interaction of processes occurring on and in the cover profile with deeper subsurface processes

  20. Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein.

    Science.gov (United States)

    Velmurugu, Yogambigai; Vivas, Paula; Connolly, Mitchell; Kuznetsov, Serguei V; Rice, Phoebe A; Ansari, Anjum

    2018-02-28

    The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate potential binding sites prior to recognition have remained elusive for most systems. Here we present these dynamics for Integration Host factor (IHF), a nucleoid-associated architectural protein, using a μs-resolved T-jump approach. Our studies show two distinct DNA-bending steps during site recognition by IHF. While the faster (∼100 μs) step is unaffected by changes in DNA or protein sequence that alter affinity by >100-fold, the slower (1-10 ms) step is accelerated ∼5-fold when mismatches are introduced at DNA sites that are sharply kinked in the specific complex. The amplitudes of the fast phase increase when the specific complex is destabilized and decrease with increasing [salt], which increases specificity. Taken together, these results indicate that the fast phase is non-specific DNA bending while the slow phase, which responds only to changes in DNA flexibility at the kink sites, is specific DNA kinking during site recognition. Notably, the timescales for the fast phase overlap with one-dimensional diffusion times measured for several proteins on DNA, suggesting that these dynamics reflect partial DNA bending during interrogation of potential binding sites by IHF as it scans DNA.

  1. A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites.

    Directory of Open Access Journals (Sweden)

    Tony Håndstad

    Full Text Available BACKGROUND: Transcription factors are important controllers of gene expression and mapping transcription factor binding sites (TFBS is key to inferring transcription factor regulatory networks. Several methods for predicting TFBS exist, but there are no standard genome-wide datasets on which to assess the performance of these prediction methods. Also, it is believed that information about sequence conservation across different genomes can generally improve accuracy of motif-based predictors, but it is not clear under what circumstances use of conservation is most beneficial. RESULTS: Here we use published ChIP-seq data and an improved peak detection method to create comprehensive benchmark datasets for prediction methods which use known descriptors or binding motifs to detect TFBS in genomic sequences. We use this benchmark to assess the performance of five different prediction methods and find that the methods that use information about sequence conservation generally perform better than simpler motif-scanning methods. The difference is greater on high-affinity peaks and when using short and information-poor motifs. However, if the motifs are specific and information-rich, we find that simple motif-scanning methods can perform better than conservation-based methods. CONCLUSIONS: Our benchmark provides a comprehensive test that can be used to rank the relative performance of transcription factor binding site prediction methods. Moreover, our results show that, contrary to previous reports, sequence conservation is better suited for predicting strong than weak transcription factor binding sites.

  2. Regional Variations of Public Perception on Contaminated Industrial Sites in China and Its Influencing Factors.

    Science.gov (United States)

    Li, Xiaonuo; Jiao, Wentao; Xiao, Rongbo; Chen, Weiping; Bai, Yanying

    2016-04-08

    Public involvement is critical in sustainable contaminated site management. It is important for China to improve public knowledge and participation, foster dialogue between urban managers and laypeople, and accelerate the remediation and redevelopment processes in contaminated site management. In this study, we collected 1812 questionnaires from nine cities around China through face-to-face interviews and statistically analyzed the perception of residents concerning contaminated sites. The results show that respondents' concern about soil pollution was lower than for other environmental issues and their knowledge of soil contamination was limited. The risks posed by contaminated industrial sites were well recognized by respondents, but they were unsatisfied with the performance of local agencies regarding information disclosure, publicity and education and public participation. Respondents believed that local governments and polluters should take the primary responsibility for contaminated site remediation. Most of them were unwilling to pay for contaminated site remediation and preferred recreational or public service redevelopment. Moreover, our research indicated that public perception varied among different cities. This variation was mainly determined by implementations of policy instruments and additionally affected by remediation technology, pollutant type, regional policy response and living distance.

  3. The seasonal factor at the prehistoric site of Shag River Mouth, New Zealand

    International Nuclear Information System (INIS)

    Higham, T.F.G.

    1997-01-01

    This paper addresses moa hunters' seasonality at the Shag River Mouth site. A two meters section in layer 4 of the SM/C: Dune site was left as a baulk in 1988 to enable the stratigraphic profile (∼2m) to be more carefully investigated. Within the baulk, detailed lensing and microstrata could be identified. Claassen (1991) has suggested that one of the most important variables in determining seasonal and prehistoric shell-bearing site formation more accurately is emphasizing finer stratigraphic resolution and more rigorous attention to retrieving midden components. At Shag River Mouth, seven sub-layers, or spits, were excavated within the 2m baulk to refine the precision of subsequent seasonal analyses and enable a detailed assessment of the components of each and their season of deposition. A variety of seasonal methods were utilised including 18 O analysis of blue mussel shell carbonate and growth ring analysis of estuarine bivalves. In addition, sagital otoliths of red cod excavated from the site were sectioned and the annual and seasonal growth rings formed during the fishes' life were analysed for seasonal information. This has enabled a detailed analysis of the seasonality of this discrete area of the Shag River Mouth site. The significance of the results for understanding the prehistoric seasonal round of activities within the site and its wider orbit is presented

  4. Transcription factor binding site enrichment analysis predicts drivers of altered gene expression in nonalcoholic steatohepatitis

    Czech Academy of Sciences Publication Activity Database

    Lake, A.D.; Chaput, A.L.; Novák, Petr; Cherrington, N.J.; Smith, C.L.

    2016-01-01

    Roč. 122, December 15 (2016), s. 62-71 ISSN 0006-2952 Institutional support: RVO:60077344 Keywords : Transcription factor * Liver * Gene expression * Bioinformatics Subject RIV: CE - Biochemistry Impact factor: 4.581, year: 2016

  5. A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites

    KAUST Repository

    Kulakovskiy, Ivan V.

    2011-08-18

    Motivation: Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding of the transcription regulatory code. Results: We constructed binding motifs for TFs forming a complex with HIF-1α at the erythropoietin 3\\'-enhancer. Corresponding TFBSs were predicted in the segments around transcription start sites (TSSs) of all human genes. Using the genome-wide set of regulatory regions, we observed several strongly preferred distances between hypoxia-responsive element (HRE) and binding sites of a particular cofactor protein. The set of preferred distances was called as a preferred pair distance template (PPDT). PPDT dramatically depended on the TF and orientation of its binding sites relative to HRE. PPDT evaluated from the genome-wide set of regulatory sequences was used to detect significant PPDT-consistent binding site pairs in regulatory regions of hypoxia-responsive genes. We believe PPDT can help to reveal the layout of eukaryotic regulatory segments. © The Author 2011. Published by Oxford University Press. All rights reserved.

  6. PET Imaging of Tissue Factor in Pancreatic Cancer Using 64Cu-Labeled Active Site-Inhibited Factor VII

    DEFF Research Database (Denmark)

    Nielsen, Carsten H; Jeppesen, Troels E; Kristensen, Lotte K

    2016-01-01

    with advanced stage, increased microvessel density, metastasis, and poor overall survival. Imaging of TF expression is of clinical relevance as a prognostic biomarker and as a companion diagnostic for TF-directed therapies currently under clinical development. Factor VII (FVII) is the natural ligand to TF......UNLABELLED: Tissue factor (TF) is the main initiator of the extrinsic coagulation cascade. However, TF also plays an important role in cancer. TF expression has been reported in 53%-89% of all pancreatic adenocarcinomas, and the expression level of TF has in clinical studies correlated...

  7. Sources identification of the atmospheric aerosol at urban and suburban sites in Indonesia by positive matrix factorization

    International Nuclear Information System (INIS)

    Santoso, Muhayatun; Hopke, Philip K.; Hidayat, Achmad; Diah Dwiana L

    2008-01-01

    Samples of fine and coarse fractions of airborne particulate matter were collected in Indonesia (west central Java) at an urban site in Bandung and in suburban Lembang from January 2002 to December 2004. The samples were collected using a Gent stacked filter sampler in two size fractions of 2.5-10 mass at both sites comes from soil dust and road dust. The biomass burning factor contributes about 40% of the PM 2.5 mass in case of suburban Lembang and about 20% in urban Bandung

  8. Factors of site selection for nuclear power plants in selected industrial states

    International Nuclear Information System (INIS)

    Hoffmann, L.; Obermair, G.; Ringler, W.; Romahn, B.; Sanders, H.

    1978-01-01

    The range of the tasks within the project consists of working out an optimal catalogue of criteria for the site selection for nuclear power plants; establishing a structured documentation system for the criteria and licensing procedures used by selected industrial countries when selecting sites for nuclear power plants; analyzing and evaluating the documented material with the aim of supplying the basis for decisions concerning land use. The tasks are being realized within a technological ring of data (for the period until 1990, reactor types, cooling, power-heat coupling, special sites, block sizes, local concentration) and a set politico-economical ring of data for the following countries: F.R. Germany, Belgium, Switzerland, Great Britain, Sweden, Denmark, Austria, France, Netherlands, USA, Japan, Yougoslavia. (HP) [de

  9. Genome-wide profiling of H3K56 acetylation and transcription factor binding sites in human adipocytes.

    Directory of Open Access Journals (Sweden)

    Kinyui Alice Lo

    Full Text Available The growing epidemic of obesity and metabolic diseases calls for a better understanding of adipocyte biology. The regulation of transcription in adipocytes is particularly important, as it is a target for several therapeutic approaches. Transcriptional outcomes are influenced by both histone modifications and transcription factor binding. Although the epigenetic states and binding sites of several important transcription factors have been profiled in the mouse 3T3-L1 cell line, such data are lacking in human adipocytes. In this study, we identified H3K56 acetylation sites in human adipocytes derived from mesenchymal stem cells. H3K56 is acetylated by CBP and p300, and deacetylated by SIRT1, all are proteins with important roles in diabetes and insulin signaling. We found that while almost half of the genome shows signs of H3K56 acetylation, the highest level of H3K56 acetylation is associated with transcription factors and proteins in the adipokine signaling and Type II Diabetes pathways. In order to discover the transcription factors that recruit acetyltransferases and deacetylases to sites of H3K56 acetylation, we analyzed DNA sequences near H3K56 acetylated regions and found that the E2F recognition sequence was enriched. Using chromatin immunoprecipitation followed by high-throughput sequencing, we confirmed that genes bound by E2F4, as well as those by HSF-1 and C/EBPα, have higher than expected levels of H3K56 acetylation, and that the transcription factor binding sites and acetylation sites are often adjacent but rarely overlap. We also discovered a significant difference between bound targets of C/EBPα in 3T3-L1 and human adipocytes, highlighting the need to construct species-specific epigenetic and transcription factor binding site maps. This is the first genome-wide profile of H3K56 acetylation, E2F4, C/EBPα and HSF-1 binding in human adipocytes, and will serve as an important resource for better understanding adipocyte

  10. Site of ADP-ribosylation and the RNA-binding site are situated in different domains of the elongation factor EF-2

    International Nuclear Information System (INIS)

    Davydova, E.K.

    1987-01-01

    One of the proteins participating in the process of elongation of polypeptide chains - elongation factor 2 (EF-2) - can be ADP-ribosylated at a unique amino acid residue - diphthamide. Since the ADP-ribosylation of EF-2 at dipthamide leads to a loss of affinity of the factor for RNA while the presence of RNA inhibits the ADP-ribosylation reaction, it seemed probable to the authors that diphthamide participated directly in the binding of EF-2 to DNA. The experiments presented in this article showed that this was not the case: diphthamide and the RNA-binding site are situated on different domains of EF-2. Thus, ADP-ribosylation of factor EF-2 in one domain leads to a loss of the ability to bind to RNA in the other. The authors investigated the mutual arrangement of diphthamide and the RNA-binding site on the EF-2 molecule by preparing a factor from rabbit reticulocytes and subjecting it to proteolytic digestion with elastase. The factor was incubated with elastase for 15 min at 37 0 C at an enzyme:substrate ratio of 1:100 in buffer solution containing 20 mM Tris-HCl, pH 7.6, 10 mM KCl, 1 mM MgCl 2 , and 2 mM dithiothreitol. The reaction was stopped by adding para-methylsulfonyl fluoride to 50 micro-M. The authors obtained a preparation as a result of proteolysis and applied it on a column with RNA-Sepharose and separated into two fractions: RNA-binding and without affinity for RNA. The initial preparation and its fractions were subjected to exhaustive ADP-ribosylation in the presence of diphtheria toxin and [U- 14 C] nicotinaide adenine dinucleotide ([ 14 C]NAD) (296 mCi/mmole). The samples were analyzed electrophoretically in a polyacrylamide gel gradient in the presence of sodium dodecyl sulfate. For the detection of [ 14 C] ADP-ribosylated components, the gels were dried and exposed with RM-V x-ray film

  11. Factors relating to the selection of sites for nuclear power stations in certain industrial countries

    International Nuclear Information System (INIS)

    1979-08-01

    The subject is discussed under the following headings: framework conditions of energy supply (energy supply in general (economics, planning); supply of nuclear energy (objectives, national nuclear industry, technology, development, public conflict)); environmental planning (legal foundations, planning levels, public site-provision investigations, electrical utilities); general and statutory atomic licensing procedure, criteria. (U.K.)

  12. Hydrologic factors and 90Sr transport at a low-level waste disposal site

    International Nuclear Information System (INIS)

    Huff, D.D.

    1982-01-01

    A case study of a solid waste storage area at Oak Ridge National Laboratory is presented. The purpose of the study is to devise effective remedial actions based upon understanding of the underlying processes governing radionuclide migration. Discussion is presented under the following headings: site history; radionuclide transport studies; analysis of field results; and recommended remedial action

  13. Activation of the Arabidopsis membrane-bound transcription factor bZIP28 is mediated by site-2 protease, but not site-1 protease.

    Science.gov (United States)

    Iwata, Yuji; Ashida, Makoto; Hasegawa, Chisa; Tabara, Kazuki; Mishiba, Kei-Ichiro; Koizumi, Nozomu

    2017-08-01

    The unfolded protein response (UPR) is a homeostatic cellular response conserved in eukaryotic cells to alleviate the accumulation of unfolded proteins in the endoplasmic reticulum (ER). Arabidopsis bZIP28 is a membrane-bound transcription factor activated by proteolytic cleavage in response to ER stress, thereby releasing its cytosolic portion containing the bZIP domain from the membrane to translocate into the nucleus where it induces the transcription of genes encoding ER-resident molecular chaperones and folding enzymes. It has been widely recognized that the proteolytic activation of bZIP28 is mediated by the sequential cleavage of site-1 protease (S1P) and site-2 protease (S2P). In the present study we provide evidence that bZIP28 protein is cleaved by S2P, but not by S1P. We demonstrated that wild-type and s1p mutant plants produce the active, nuclear form of bZIP28 in response to the ER stress inducer tunicamycin. In contrast, tunicamycin-treated s2p mutants do not accumulate the active, nuclear form of bZIP28. Consistent with these observations, s2p mutants, but not s1p mutants, exhibited a defective transcriptional response of ER stress-responsive genes and significantly higher sensitivity to tunicamycin. Interestingly, s2p mutants accumulate two membrane-bound bZIP28 fragments with a shorter ER lumen-facing C-terminal domain. Importantly, the predicted cleavage sites are located far from the canonical S1P recognition motif previously described. We propose that ER stress-induced proteolytic activation of bZIP28 is mediated by the sequential actions of as-yet-unidentified protease(s) and S2P, and does not require S1P. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  14. Identification of a mammalian nuclear factor and human cDNA-encoded proteins that recognize DNA containing apurinic sites

    International Nuclear Information System (INIS)

    Lenz, J.; Okenquist, S.A.; LoSardo, J.E.; Hamilton, K.K.; Doetsch, P.W.

    1990-01-01

    Damage to DNA can have lethal or mutagenic consequences for cells unless it is detected and repaired by cellular proteins. Repair depends on the ability of cellular factors to distinguish the damaged sites. Electrophoretic binding assays were used to identify a factor from the nuclei of mammalian cells that bound to DNA containing apurinic sites. A binding assay based on the use of β-galactosidase fusion proteins was subsequently used to isolate recombinant clones of human cDNAs that encoded apurinic DNA-binding proteins. Two distinct human cDNAs were identified that encoded proteins that bound apurinic DNA preferentially over undamaged, methylated, or UV-irradiated DNA. These approaches may offer a general method for the detection of proteins that recognize various types of DNA damage and for the cloning of genes encoding such proteins

  15. STIMULATION OF DEFENSE FACTORS FOR OYSTERS DEPLOYED TO CONTAMINATED SITES IN PENSACOLA BAY, FLORIDA

    Science.gov (United States)

    A positive association between chemical contaminants and defense factors has been established for eastern oysters (Crassostrea virginica) from Florida, but it is unknown whether such factors can be stimulated through short-term exposure to contaminants in the field. Hatchery oyst...

  16. Obstacle factors and overcoming plans of public communication: With an emphasis on radioactive waste disposal facility siting

    International Nuclear Information System (INIS)

    Yoo, Hae-Woon; Oh, Chang-Taeg

    1996-01-01

    Korea is confronting a serious social conflict, which is phenomenon of local residents reaction to radioactive waste disposal facility. This phenomenon is traced back to the reason that the project sponsors and local residents do not communicate sufficiently each other. Accordingly, in order to overcome local residents' reaction to radioactive waste disposal facility siting effectively, it is absolutely necessary to consider the way of solutions and strategies with regard to obstacle factors for public communication. In this content, this study will review three cases (An-myon Island, Gul-up Island, Yang-yang) on local residents reaction to facility siting. As a result of analysis, authoritarian behavior of project sponsors, local stigma, risk, antinuclear activities of environmental group, failures in siting the radioactive waste disposal facility, etc. has negative impact on public communication of the radioactive waste disposal facility siting. In this study, 5 strategies (reform of project sponsor's authoritarianism, incentive offer, strengthening PA activities, more active talks with environmental groups, promoting credibility of project sponsors) arc suggested to cope with obstacle factors of public communication

  17. Monitoring human factor risk characteristics at nuclear legacy sites in northwest Russia in support of radiation safety regulation.

    Science.gov (United States)

    Scheblanov, V Y; Sneve, M K; Bobrov, A F

    2012-12-01

    This paper describes research aimed at improving regulatory supervision of radiation safety during work associated with the management of spent nuclear fuel and radioactive waste at legacy sites in northwest Russia through timely identification of employees presenting unfavourable human factor risk characteristics. The legacy sites of interest include sites of temporary storage now operated by SevRAO on behalf of Rosatom. The sites were previously operational bases for servicing nuclear powered submarines and are now subject to major remediation activities. These activities include hazardous operations for recovery of spent nuclear fuel and radioactive waste from sub-optimal storage conditions. The paper describes the results of analysis of methods, procedures, techniques and informational issues leading to the development of an expert-diagnostic information system for monitoring of workers involved in carrying out the most hazardous operations. The system serves as a tool for human factor and professional reliability risk monitoring and has been tested in practical working environments and implemented as part of regulatory supervision. The work has been carried out by the Burnasyan Federal Medical Biophysical Center, within the framework of the regulatory cooperation programme between the Federal Medical-Biological Agency of Russia and the Norwegian Radiation Protection Authority.

  18. Factors Related to Initiating Interpersonal Contacts on Internet Dating Sites: A View From the Social Exchange Theory

    Directory of Open Access Journals (Sweden)

    Rivka Shtatfeld

    2009-12-01

    Full Text Available The purpose of this study was to identify factors that influence dating-site users to initiate contact with potential romantic partners. The study was carried out by observing online behaviors and analyzing the profiles and authentic messages of these users (N = 106 over seven months. Contacts made by and with the research participants were analyzed in terms of the relationships between initiators‘ and receivers‘ demographic variables (marital status, age, level of education, income, writing skills, and stated physical appearance. In addition, the relationship between contacting partners and site accessibility was examined. The findings revealed that dating-site users initiated contact primarily with those having a similar marital status or slightly better characteristics (income, education, writing skills. In regard to writing skills, it was found that skilled writers attracted more contacts than did less skilled writers. However, the factor that was found to be most significantly related to initiating contact was the length of time that elapsed from last connection to the site, which implies the perceived accessibility of potential romantic partners. The findings were explained in terms of the Social Exchange Theory: people are attracted to those who grant them rewards.

  19. Monitoring human factor risk characteristics at nuclear legacy sites in northwest Russia in support of radiation safety regulation

    International Nuclear Information System (INIS)

    Scheblanov, V Y; Bobrov, A F; Sneve, M K

    2012-01-01

    This paper describes research aimed at improving regulatory supervision of radiation safety during work associated with the management of spent nuclear fuel and radioactive waste at legacy sites in northwest Russia through timely identification of employees presenting unfavourable human factor risk characteristics. The legacy sites of interest include sites of temporary storage now operated by SevRAO on behalf of Rosatom. The sites were previously operational bases for servicing nuclear powered submarines and are now subject to major remediation activities. These activities include hazardous operations for recovery of spent nuclear fuel and radioactive waste from sub-optimal storage conditions. The paper describes the results of analysis of methods, procedures, techniques and informational issues leading to the development of an expert-diagnostic information system for monitoring of workers involved in carrying out the most hazardous operations. The system serves as a tool for human factor and professional reliability risk monitoring and has been tested in practical working environments and implemented as part of regulatory supervision. The work has been carried out by the Burnasyan Federal Medical Biophysical Center, within the framework of the regulatory cooperation programme between the Federal Medical–Biological Agency of Russia and the Norwegian Radiation Protection Authority. (paper)

  20. Distribution of basic fibroblast growth factor binding sites in various tissue membrane preparations from adult guinea pig

    International Nuclear Information System (INIS)

    Ledoux, D.; Mereau, A.; Dauchel, M.C.; Barritault, D.; Courty, J.

    1989-01-01

    In order to localize a rich source of basic FGF receptor, we examined the distribution of basic FGF binding sites in brain, stomach, lung, spleen, kidney, liver and intestine membrane preparations from adult guinea pig. Comparative binding studies using iodinated basic FGF showed that a specific binding was detected in all the membrane preparations tested. Scatchard plots from iodinated basic FGF competition experiment with native basic FGF in various membrane preparations, suggested the presence of one class of binding sites in some tissues such as liver, kidney, spleen, lung, stomach, and intestine with an apparent dissociation constant (appKD) value ranging from 4 to 7.5 nM and the existence of a second class of higher affinity sites in brain membranes with appKD value of 15 pM. Characterization of these basic FGF high affinity interaction sites was performed using a cross-linking reagent. These results show for the first time that specific interaction sites for basic FGF are widely distributed, suggesting that this growth factor might play a role in the physiological functions of a number of adult organs

  1. PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information

    Science.gov (United States)

    Wu, Hao; Ji, Hongkai

    2014-01-01

    ChIP-seq is a powerful technology for detecting genomic regions where a protein of interest interacts with DNA. ChIP-seq data for mapping transcription factor binding sites (TFBSs) have a characteristic pattern: around each binding site, sequence reads aligned to the forward and reverse strands of the reference genome form two separate peaks shifted away from each other, and the true binding site is located in between these two peaks. While it has been shown previously that the accuracy and resolution of binding site detection can be improved by modeling the pattern, efficient methods are unavailable to fully utilize that information in TFBS detection procedure. We present PolyaPeak, a new method to improve TFBS detection by incorporating the peak shape information. PolyaPeak describes peak shapes using a flexible Pólya model. The shapes are automatically learnt from the data using Minorization-Maximization (MM) algorithm, then integrated with the read count information via a hierarchical model to distinguish true binding sites from background noises. Extensive real data analyses show that PolyaPeak is capable of robustly improving TFBS detection compared with existing methods. An R package is freely available. PMID:24608116

  2. Site selection factors for repositories of solid high-level and alpha-bearing wastes in geological formations

    International Nuclear Information System (INIS)

    1977-01-01

    The purpose of this report is to provide guidelines for the selection and evaluation of suitable areas and sites for the disposal of solid high-level and alpha-bearing wastes into geological formations. This report is also intended to provide summary information on many types of geological formations underlying the land masses that might be considered as well as guidance on the geological and hydrological factors that should be investigated to demonstrate the suitability of the formations. In addition, other factors that should be considered in selecting a site for a radioactive waste repository are discussed briefly. The information, as presented, was developed to the extent of current technology for application to the evaluation of deep (greater than about 300 metres below ground level) geological formations in the selection of suitable areas for the disposal of solid or solidified high-level and alpha-bearing wastes. The extreme complexity of many geological environments and of the rock features that govern the presence and circulation of groundwater does not make it feasible to derive strict criteria for the selection of a site for a radioactive waste repository in a geological formation. Each potential repository location must be evaluated according to its own unique geological and hydrological setting. Therefore, only general guidance is offered, and this is done through discussion of the many factors that need to be considered in order to obtain the necessary assurances that the radionuclides will be confined in the geological repository over the required period of time

  3. Site selection factors for repositories of solid high-level and alpha-bearing wastes in geological formations

    Energy Technology Data Exchange (ETDEWEB)

    1977-01-01

    The purpose of this report is to provide guidelines for the selection and evaluation of suitable areas and sites for the disposal of solid high-level and alpha-bearing wastes into geological formations. This report is also intended to provide summary information on many types of geological formations underlying the land masses that might be considered as well as guidance on the geological and hydrological factors that should be investigated to demonstrate the suitability of the formations. In addition, other factors that should be considered in selecting a site for a radioactive waste repository are discussed briefly. The information, as presented, was developed to the extent of current technology for application to the evaluation of deep (greater than about 300 meters below ground level) geological formations in the selection of suitable areas for the disposal of solid or solidified high-level and alpha-bearing wastes. The extreme complexity of many geological environments and of the rock features that govern the presence and circulation of groundwater does not make it feasible to derive strict criteria for the selection of a site for a radioactive waste repository in a geological formation. Each potential repository location must be evaluated according to its own unique geological and hydrological setting. Therefore, only general guidance is offered, and this is done through discussion of the many factors that need to be considered in order to obtain the necessary assurances that the radionuclides will be confined in the geological repository over the required period of time.

  4. Psychological risk factors of addiction to social networking site among Chinese smart phone users

    OpenAIRE

    Wu, Anise M. S.; Cheung, Vivi I.; Ku, L.; Hung, Eva P. W.

    2013-01-01

    Background and aims: Smartphones allow users to access social networking sites (SNSs) whenever and wherever they want. Such easy availability and accessibility may increase their vulnerability to addiction. Based on the social cognitive theory (SCT), we examined the impacts of outcome expectancies, self-efficacy, and impulsivity on young Chinese smartphone users' addictive tendencies toward SNSs. Methods: Two hundred seventy-seven Macau young smartphone users (116 males and 161 females; mean ...

  5. Seasonal and Topographical Factors Affecting Breeding Sites of Culex Larvae in Nakhon Si Thammarat, Thailand

    OpenAIRE

    Warabhorn PREECHAPORN; Mullica JAROENSUTASINEE; Krisanadej JAROENSUTASINEE; Jirawat SAETON

    2007-01-01

    This study investigated how the seasons affect the key breeding sites of Culex larvae in three topographical areas: mangrove, rice paddy and mountainous areas. We examined how the number of Culex larvae varied in different types of water containers. Water containers were categorised into the following groups: indoor/outdoor containers, artificial/natural containers, earthen/plastic containers, containers with/without lids and dark/light coloured containers. Samples were collected from 300 hou...

  6. Distribution of epidermal growth factor binding sites in the adult rat anterior pituitary gland

    International Nuclear Information System (INIS)

    Chabot, J.G.; Walker, P.; Pelletier, G.

    1986-01-01

    The distribution of epidermal growth (EGF) binding sites was studied in the pituitary gland using light and electron microscope autoradiography which was performed at different time intervals (2 to 60 min) after intravenous (IV) injection of [ 125 I]EGF into adult rats. At the light microscopic level, the labeling was found over cells of the anterior pituitary gland. The time-course study performed by light microscope autoradiography showed that the maximal values were reached at the 2 min time interval. At this time interval, most silver grains were found at the periphery of the target cells. After, the number of silver grains decreased progressively and the localization of silver grains in the cytoplasm indicated the internalization of [ 125 I]EGF. Electron microscope autoradiography showed that labeling was mostly restricted to mammotrophs and somatotrophs. Control experiments indicated that the autoradiographic labeling was due specific interaction of [ 125 I]EGF with its binding site. These results indicate that EGF binding sites are present in at least two anterior pituitary cell types and suggest that EGF can exert a physiological role in the pituitary gland

  7. DNA Binding Drugs Targeting the Regulatory DNA Binding Site of the ETS Domain Family Transcription Factor Associated With Human Breast Cancer

    National Research Council Canada - National Science Library

    Wang, Yong-Dong

    1999-01-01

    .... The key approach is to prevent the binding of two transcription factors, ESX and AP-2, to the consensus DNA binding sites contained within the Her2/neu promoter resulting in inhibition of transcription factor function...

  8. Evaluation of site-specific factors influencing heavy metal contents in the topsoil of vegetated infiltration swales

    International Nuclear Information System (INIS)

    Horstmeyer, Nils; Huber, Maximilian; Drewes, Jörg E.; Helmreich, Brigitte

    2016-01-01

    Stormwater runoff of traffic areas is usually polluted by organic and inorganic substances and must be treated prior to discharge into groundwater. One widely used treatment method is infiltrating the runoff over the topsoil of vegetated swales. The aim of this study was to evaluate the factors influencing the heavy metal contents in such topsoil layers of vegetated infiltration swales near highways, roads, and parking lots. In total, 262 topsoil samples were taken from 35 sampling sites, which varied in age, traffic volume, road design, driving style, and site-specific conditions. In the evaluation of all soil samples, the median heavy metal values of cadmium, chromium, copper, lead, and zinc were yielding 0.36 (mean: 1.21) mg/kg DM, 37.0 (mean: 44.5) mg/kg DM, 28.0 (mean: 61.5) mg/kg DM, 27.0 (mean: 71.9) mg/kg DM, and 120 (mean: 257) mg/kg DM, respectively. The main purpose was to evaluate the site-specific data (i.e., surrounding land use characteristics, traffic area site data, and operational characteristics). In general, heavy metal contents increased with increasing traffic volumes. However, other factors also had a notable impact. Factors such as road design (e.g., curves, crossings, and roundabouts) and grade of congestion significantly influenced the heavy metal contents. High heavy metal contents were detected for stop-and-go areas, roundabouts, crossings, and sites with traffic lights, signs, and guardrails. Findings of this study can be used to identify highly polluted traffic areas and to verify or improve standards regarding the treatment of runoff from traffic areas. - Highlights: • Correlation of contents with traffic volume, road design, and stop-and-go traffic • Increased heavy metal contents at stop-and-go sites, roundabouts, and crossings • Different soil contents and behavior of cadmium, chromium, copper, lead, and zinc • Identification of factors influencing the variability of zinc in topsoil samples

  9. Evaluation of site-specific factors influencing heavy metal contents in the topsoil of vegetated infiltration swales

    Energy Technology Data Exchange (ETDEWEB)

    Horstmeyer, Nils; Huber, Maximilian; Drewes, Jörg E.; Helmreich, Brigitte, E-mail: b.helmreich@tum.de

    2016-08-01

    Stormwater runoff of traffic areas is usually polluted by organic and inorganic substances and must be treated prior to discharge into groundwater. One widely used treatment method is infiltrating the runoff over the topsoil of vegetated swales. The aim of this study was to evaluate the factors influencing the heavy metal contents in such topsoil layers of vegetated infiltration swales near highways, roads, and parking lots. In total, 262 topsoil samples were taken from 35 sampling sites, which varied in age, traffic volume, road design, driving style, and site-specific conditions. In the evaluation of all soil samples, the median heavy metal values of cadmium, chromium, copper, lead, and zinc were yielding 0.36 (mean: 1.21) mg/kg DM, 37.0 (mean: 44.5) mg/kg DM, 28.0 (mean: 61.5) mg/kg DM, 27.0 (mean: 71.9) mg/kg DM, and 120 (mean: 257) mg/kg DM, respectively. The main purpose was to evaluate the site-specific data (i.e., surrounding land use characteristics, traffic area site data, and operational characteristics). In general, heavy metal contents increased with increasing traffic volumes. However, other factors also had a notable impact. Factors such as road design (e.g., curves, crossings, and roundabouts) and grade of congestion significantly influenced the heavy metal contents. High heavy metal contents were detected for stop-and-go areas, roundabouts, crossings, and sites with traffic lights, signs, and guardrails. Findings of this study can be used to identify highly polluted traffic areas and to verify or improve standards regarding the treatment of runoff from traffic areas. - Highlights: • Correlation of contents with traffic volume, road design, and stop-and-go traffic • Increased heavy metal contents at stop-and-go sites, roundabouts, and crossings • Different soil contents and behavior of cadmium, chromium, copper, lead, and zinc • Identification of factors influencing the variability of zinc in topsoil samples.

  10. Blood donor show behaviour after an invitation to donate : The influence of collection site factors

    NARCIS (Netherlands)

    Merz, E.-M.; Zijlstra, B.J.H.; de Kort, W.L.A.M.

    2017-01-01

    Background and Objectives Show behaviour after invitation to donate varies considerably across donors. More insight into this variation is important for blood banks in achieving stable stocks. This study examined individual factors determining intended show behaviour. Most importantly, however, this

  11. Blood donor show behavior after an invitation to donate: The influence of collection site factors

    NARCIS (Netherlands)

    Merz, E.M.; Zijlstra, Bonne; De Kort, Wim L.A.M.

    2017-01-01

    Background and Objectives Show behaviour after invitation to donate varies considerably across donors. More insight into this variation is important for blood banks in achieving stable stocks. This study examined individual factors determining intended show behaviour. Most importantly, however, this

  12. Sites of recurrent disease and prognostic factors in SCLC patients treated with radiochemotherapy

    Directory of Open Access Journals (Sweden)

    Rebecca Bütof

    2017-12-01

    Full Text Available Objectives: Concurrent radiochemotherapy (RCHT is standard treatment in locally advanced small cell lung cancer (SCLC patients. Due to conflicting results on elective nodal irradiation (ENI or selective node irradiation (SNI there is no clear evidence on optimal target volumes. Therefore, the purposes of this study were to assess the sites of recurrent disease in SCLC and to evaluate the feasibility of SNI versus ENI. Methods: A retrospective single-institution study of 43 consecutive patients treated with RCHT was performed. After state-of-the-art staging including FDG-PET/CT, all patients underwent three-dimensional conformal radiotherapy to a total dose of 45 Gy in twice-daily fractions of 1.5 Gy starting concurrently with the first or second chemotherapy cycle. All sites of loco-regional recurrences were correlated to the initial tumor and dose delivered. The impact of potential prognostic variables on outcome was evaluated using the Cox-regression model. Results: 13 patients (30% relapsed locally or regionally: six within the initial primary tumor volume, five within the initially affected lymph nodes, one metachronously within primary tumor and initially affected lymph nodes, and one both inside and outside of the initial nodal disease. All sites of loco-regional recurrence had received 92–106% of the prescribed dose. Conclusion: In our study most recurrences occurred within the primary tumor or initially affected lymph nodes, or distantly. We did not register any case of isolated nodal failure, supporting the use of selective nodal irradiation, possibly with the addition of supraclavicular irradiation in patients with nodal disease in the upper mediastinum. Keywords: Small cell lung cancer, Recurrence, Radiotherapy, Selective node irradiation

  13. Snow precipitation at four ice core sites in East Antarctica: provenance, seasonality and blocking factors

    Energy Technology Data Exchange (ETDEWEB)

    Scarchilli, Claudio [ENEA, Rome (Italy); Universita degli studi di Trieste, Trieste (Italy); Frezzotti, Massimo; Ruti, Paolo Michele [ENEA, Rome (Italy)

    2011-11-15

    Snow precipitation is the primary mass input to the Antarctic ice sheet and is one of the most direct climatic indicators, with important implications for paleoclimatic reconstruction from ice cores. Provenance of precipitation and the dynamic conditions that force these precipitation events at four deep ice core sites (Dome C, Law Dome, Talos Dome, and Taylor Dome) in East Antarctica were analysed with air mass back trajectories calculated using the Lagrangian model and the mean composite data for precipitation, geopotential height and wind speed field data from the European Centre for Medium Range Weather Forecast from 1980 to 2001. On an annual basis, back trajectories showed that the Atlantic-Indian and Ross-Pacific Oceans were the main provenances of precipitation in Wilkes Land (80%) and Victoria Land (40%), respectively, whereas the greatest influence of the ice sheet was on the interior near the Vostok site (80%) and in the Southwest Ross Sea (50%), an effect that decreased towards the coast and along the Antarctic slope. Victoria Land received snowfall atypically with respect to other Antarctica areas in terms of pathway (eastern instead of western), seasonality (summer instead of winter) and velocity (old air age). Geopotential height patterns at 500 hPa at low (>10 days) and high (2-6 days) frequencies during snowfall cycles at two core sites showed large positive anomalies at low frequencies developing in the Tasman Sea-Eastern Indian Ocean at higher latitudes (60-70 S) than normal. This could be considered part of an atmospheric blocking event, with transient eddies acting to decelerate westerlies in a split region area and accelerate the flow on the flanks of the low-frequency positive anomalies. (orig.)

  14. Haemophilia B caused by mutation of a potential thrombin cleavage site in factor IX

    Energy Technology Data Exchange (ETDEWEB)

    Winship, P.R. (Univ. of Oxford (England))

    1990-03-11

    Haemophilia B is a blood coagulation disorder caused by mutations in the factor IX gene giving functionally defective or reduced levels of factor IX protein circulating in the plasma. The mutation in the Caucasian patient under investigation, Haemophilia B Oxford h5 (Oxh5), was characterized at the DNA level by constructing a genomic library using leucocyte-derived DNA from the patient. Overlapping recombinant clones spanning the entire factor IX locus were isolated which then allowed the generation of a series of sub-clones across all eight exons (a-h) plus the 5{prime} and 3{prime} flanking sequences known to be important in regulation of the gene and polyadenylation of the mRNA species.

  15. The land use as a factor in the nuclear power plant site selection; Upotreba zemljista kao faktor u izboru lokacije za nuklearna postrojenja

    Energy Technology Data Exchange (ETDEWEB)

    Marsicanin, B [Institut za Nuklearne Nauke Boris Kidric, Belgrade (Yugoslavia)

    1981-07-01

    In this paper the methodology for the site comparison, taking into account the land use in the vicinity of a potential nuclear site is presented. Due to the established risk values and cost/benefit factors a quantitative comparison could be made. This, also makes possible a approach, common for the most of relevant factors, in order to make the optimization process practical. (author)

  16. Unbiased proteomics analysis demonstrates significant variability in mucosal immune factor expression depending on the site and method of collection.

    Directory of Open Access Journals (Sweden)

    Kenzie M Birse

    Full Text Available Female genital tract secretions are commonly sampled by lavage of the ectocervix and vaginal vault or via a sponge inserted into the endocervix for evaluating inflammation status and immune factors critical for HIV microbicide and vaccine studies. This study uses a proteomics approach to comprehensively compare the efficacy of these methods, which sample from different compartments of the female genital tract, for the collection of immune factors. Matching sponge and lavage samples were collected from 10 healthy women and were analyzed by tandem mass spectrometry. Data was analyzed by a combination of differential protein expression analysis, hierarchical clustering and pathway analysis. Of the 385 proteins identified, endocervical sponge samples collected nearly twice as many unique proteins as cervicovaginal lavage (111 vs. 61 with 55% of proteins common to both (213. Each method/site identified 73 unique proteins that have roles in host immunity according to their gene ontology. Sponge samples enriched for specific inflammation pathways including acute phase response proteins (p = 3.37×10(-24 and LXR/RXR immune activation pathways (p = 8.82×10(-22 while the role IL-17A in psoriasis pathway (p = 5.98×10(-4 and the complement system pathway (p = 3.91×10(-3 were enriched in lavage samples. Many host defense factors were differentially enriched (p<0.05 between sites including known/potential antimicrobial factors (n = 21, S100 proteins (n = 9, and immune regulatory factors such as serpins (n = 7. Immunoglobulins (n = 6 were collected at comparable levels in abundance in each site although 25% of those identified were unique to sponge samples. This study demonstrates significant differences in types and quantities of immune factors and inflammation pathways collected by each sampling technique. Therefore, clinical studies that measure mucosal immune activation or factors assessing HIV transmission should utilize

  17. Intraoperative technique as a factor in the prevention of surgical site infection.

    LENUS (Irish Health Repository)

    McHugh, S M

    2012-02-01

    Approximately five percent of patients who undergo surgery develop surgical site infections (SSIs) which are associated with an extra seven days as an inpatient and with increased postoperative mortality. The competence and technique of the surgeon is considered important in preventing SSI. We have reviewed the evidence on different aspects of surgical technique and its role in preventing SSI. The most recent guidelines from the National Institute for Health and Clinical Excellence in the UK recommend avoiding diathermy for skin incision even though this reduces incision time and blood loss, both associated with lower infection rates. Studies comparing different closure techniques, i.e. continuous versus interrupted sutures, have not found a statistically significant difference in the SSI rate, but using continuous sutures is quicker. For contaminated wounds, the surgical site should be left open for four days to allow for treatment of local infection before subsequent healing by primary intention. Surgical drains should be placed through separate incisions, closed suction drains are preferable to open drains, and all drains should be removed as soon as possible. There are relatively few large studies on the impact of surgical techniques on SSI rates. Larger multicentre prospective studies are required to define what aspects of surgical technique impact on SSI, to better inform surgical practice and support education programmes for surgical trainees.

  18. Intraoperative technique as a factor in the prevention of surgical site infection.

    LENUS (Irish Health Repository)

    McHugh, S M

    2011-02-28

    Approximately five percent of patients who undergo surgery develop surgical site infections (SSIs) which are associated with an extra seven days as an inpatient and with increased postoperative mortality. The competence and technique of the surgeon is considered important in preventing SSI. We have reviewed the evidence on different aspects of surgical technique and its role in preventing SSI. The most recent guidelines from the National Institute for Health and Clinical Excellence in the UK recommend avoiding diathermy for skin incision even though this reduces incision time and blood loss, both associated with lower infection rates. Studies comparing different closure techniques, i.e. continuous versus interrupted sutures, have not found a statistically significant difference in the SSI rate, but using continuous sutures is quicker. For contaminated wounds, the surgical site should be left open for four days to allow for treatment of local infection before subsequent healing by primary intention. Surgical drains should be placed through separate incisions, closed suction drains are preferable to open drains, and all drains should be removed as soon as possible. There are relatively few large studies on the impact of surgical techniques on SSI rates. Larger multicentre prospective studies are required to define what aspects of surgical technique impact on SSI, to better inform surgical practice and support education programmes for surgical trainees.

  19. Identification of nucleic acid binding sites on translin-associated factor X (TRAX protein.

    Directory of Open Access Journals (Sweden)

    Gagan Deep Gupta

    Full Text Available Translin and TRAX proteins play roles in very important cellular processes such as DNA recombination, spatial and temporal expression of mRNA, and in siRNA processing. Translin forms a homomeric nucleic acid binding complex and binds to ssDNA and RNA. However, a mutant translin construct that forms homomeric complex lacking nucleic acid binding activity is able to form fully active heteromeric translin-TRAX complex when co-expressed with TRAX. A substantial progress has been made in identifying translin sites that mediate its binding activity, while TRAX was thought not to bind DNA or RNA on its own. We here for the first time demonstrate nucleic acid binding to TRAX by crosslinking radiolabeled ssDNA to heteromeric translin-TRAX complex using UV-laser. The TRAX and translin, photochemically crosslinked with ssDNA, were individually detected on SDS-PAGE. We mutated two motifs in TRAX and translin, designated B2 and B3, to help define the nucleic acid binding sites in the TRAX sequence. The most pronounced effect was observed in the mutants of B3 motif that impaired nucleic acid binding activity of the heteromeric complexes. We suggest that both translin and TRAX are binding competent and contribute to the nucleic acid binding activity.

  20. Identification of Nucleic Acid Binding Sites on Translin-Associated Factor X (TRAX) Protein

    Science.gov (United States)

    Gupta, Gagan Deep; Kumar, Vinay

    2012-01-01

    Translin and TRAX proteins play roles in very important cellular processes such as DNA recombination, spatial and temporal expression of mRNA, and in siRNA processing. Translin forms a homomeric nucleic acid binding complex and binds to ssDNA and RNA. However, a mutant translin construct that forms homomeric complex lacking nucleic acid binding activity is able to form fully active heteromeric translin-TRAX complex when co-expressed with TRAX. A substantial progress has been made in identifying translin sites that mediate its binding activity, while TRAX was thought not to bind DNA or RNA on its own. We here for the first time demonstrate nucleic acid binding to TRAX by crosslinking radiolabeled ssDNA to heteromeric translin-TRAX complex using UV-laser. The TRAX and translin, photochemically crosslinked with ssDNA, were individually detected on SDS-PAGE. We mutated two motifs in TRAX and translin, designated B2 and B3, to help define the nucleic acid binding sites in the TRAX sequence. The most pronounced effect was observed in the mutants of B3 motif that impaired nucleic acid binding activity of the heteromeric complexes. We suggest that both translin and TRAX are binding competent and contribute to the nucleic acid binding activity. PMID:22427937

  1. Environmental factors determining spontaneous recovery of industrially mined peat bogs: A multi-site analysis

    Czech Academy of Sciences Publication Activity Database

    Konvalinková, Petra; Prach, Karel

    2014-01-01

    Roč. 69, Aug 2014 (2014), s. 38-45 ISSN 0925-8574 R&D Projects: GA ČR(CZ) GAP505/11/0256 Institutional support: RVO:67985939 Keywords : peatland * restoration * succession Subject RIV: EH - Ecology, Behaviour Impact factor: 2.580, year: 2014

  2. Composite organization of the cobalamin binding and cubilin recognition sites of intrinsic factor

    DEFF Research Database (Denmark)

    Fedosov, Sergey N; Fedosova, Natalya U; Berglund, Lars

    2005-01-01

    Intrinsic factor (IF(50)) is a cobalamin (Cbl)-transporting protein of 50 kDa, which can be cleaved into two fragments: the 30 kDa N-terminal peptide IF(30) and the 20 kDa C-terminal glycopeptide IF(20). Experiments on binding of Cbl to IF(30), IF(20), and IF(50) revealed comparable association r...

  3. Functional studies of elongation factor Tu from Escherichia coli : Site-directed mutagenesis and antibiotic action

    NARCIS (Netherlands)

    Krab, Ivo Maarten

    2001-01-01

    This PhD thesis describes several studies into the structure and function of Escherichia coli Elongation Factor Tu (EF-Tu). EF-Tu plays a central role in the bacterial protein synthesis machinery as the carrier of "coded building blocks" for protein synthesis, aminoacylated tRNA (aa-tRNA). Without

  4. Trust and Product/Sellers Reviews as Factors Influencing Online Product Comparison Sites Usage by Young Consumers

    Directory of Open Access Journals (Sweden)

    Radoslaw Macik

    2016-06-01

    Full Text Available Paper describes young consumers’ behaviour connected with online product comparison sites usage as an example of online decision shopping aids. Authors’ main goal is to check whether or not such factors as: previous experience in such sites usage, personal innovativeness in domain of information technology – PIIT, and particularly cognitive trust (in several subdimensions, as well as affective trust toward online product comparison site, influence purchase intention via mentioned sites (acting as intermediaries in online sales channel, and anticipated satisfaction from choice made by consumer. Also indirect influence of users’ opinions about product and sellers on mentioned constructs has been researched. Study on effective sample of 456 young consumers with data collected through CAWI questionnaire confirmed reliability and validity of measurement scales. Path model estimated via PLS-SEM confirmed most hypotheses settled, particularly confirming strong positive relationships between cognitive trust (mostly in competence on affective trust, and later on purchase intention and choice satisfaction. Product and sellers reviews were partially mediating some of those relationships.

  5. Composite organization of the cobalamin binding and cubilin recognition sites of intrinsic factor

    DEFF Research Database (Denmark)

    Fedosov, Sergey N; Fedosova, Natalya U; Berglund, Lars

    2005-01-01

    of the ligand. Each isolated fragment of IF was tested for the binding to the specific receptor cubilin in the presence or absence of Cbl. Neither apo nor holo forms of IF(20) and IF(30) were recognized by the receptor. When two fragments were mixed and incubated with Cbl, they associated into a stable complex......; however, efficient retention of the ligand required the presence of both fragments. Detailed schemes of the interaction of Cbl with IF(50) and with IF(30) and IF(20) are presented, where the sequential attachment of Cbl to the IF(20) and IF(30) domains plays the key role in recognition and retention......, IF(30+20).Cbl, which bound to cubilin as well as the noncleaved IF(50).Cbl complex. We suggest that formation of the cubilin recognition site on IF is caused by assembly of two distant domains, which allows the saturated protein to be recognized by the receptor. The obtained parameters for ligand...

  6. Eco-hydrology: Groundwater flow and site factors in plant ecology

    Science.gov (United States)

    Klijn, Frans; Witte, Jan-Philip M.

    Résumé En écologie végétale, le site est un concept central. Un site, c'est l'endroit où une espèce végétale ou une communauté de plantes se développe le site assure un ensemble de conditions dans lesquelles elles vivent. Dans un matériau homogène à l'origine, l'écoulement gravitaire d'une nappe influence les conditions du site par l'intermédiaire de la distribution spatiale des nutriments et d'autres composés chimiques associés. Les remontées d'eau peuvent tout spécialement produire et maintenir les conditions du site essentielles pour différentes espèces et communautés de plantes relativement rares. Les écologues ont porté une attention accrue à ces remontées d'eau, en sorte qu'une coopération avec les hydrologues en a résulté, avec l'émergence d'une discipline propre, l'éco-hydrologie, à la limite des deux domaines scientifiques et liée au concept de site. Aux Pays-Bas, une classification des types d'eau, basée sur l'histoire de l'eau souterraine à proximité de la surface, a été mise en oeuvre pour constituer une base nationale de données géographiques sur les remontées d'eau d'intérêt écologique. Des analyses des correspondances des données de cette base, portant sur l'existence de certaines espèces de plantes, montrent que dans les sols sableux pauvres du Pléistocène la remontée d'eau explique très bien la présence de certaines espèces et communautés, alors que, dans les plaines fluviales et les régions de polders à sols argileux riches, l'influence de la remontée d'eau est masquée par l'importance des caractéristiques des sols. En conclusion donc, certaines espèces de plantes peuvent être utilisées comme des indicateurs de la remontée d'eau dans des diagnostiques et des levés de terrain rapides, mais à condition de prendre en permanence des précautions sur les limites de l'approche. Resumen En ecología botánica un concepto de gran importancia es el de emplazamiento, definido como el lugar que

  7. Soil- to-Whole Body Transfer Factors of Radionuclides for Terrestrial Wild Animals Living around the Gyeongju Nuclear Site

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Kwang-Muk; Choi, Yong-Ho; Jun, In; Kim, Byung-Ho; Keum, Dong-Kwon [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2015-05-15

    In the Gyeongju nuclear site, a low and medium level radioactive waste repository and five nuclear reactors are currently operating. The IAEA and ICRP consider it necessary to demonstrate that not only men but also wild organisms are protected from ionizing radiations. Therefore, it may not be long before the dose assessment for wildlife should be carried out in Korea. The transfer factor (TF) defined as the concentration ratio between an organism and an environmental medium is a key parameter in assessing the radiation dose to wildlife. For eight animal species inhabiting mountainous areas around the Gyeongju nuclear site, the TF values of 22 stable elements were measured. The acquired values varied considerably with the elements and animal species. Further TF data need to be produced for various Korean wild animal and plant species in preparation for future governmental regulations of wildlife exposure to ionizing radiations.

  8. The association between measurement sites of visceral adipose tissue and cardiovascular risk factors after caloric restriction in obese Korean women.

    Science.gov (United States)

    Lee, Hye-Ok; Yim, Jung-Eun; Lee, Jeong-Sook; Kim, Young-Seol; Choue, Ryowon

    2013-02-01

    Quantities as well as distributions of adipose tissue (AT) are significantly related to cardiovascular disease (CVD) risk factors and can be altered with caloric restriction. This study investigated which cross-sectional slice location of AT is most strongly correlated with changes in CVD risk factors after caloric restriction in obese Korean women. Thirty-three obese pre-menopausal Korean women (32.4 ± 8.5 yrs, BMI 27.1 ± 2.3 kg/m(2)) participated in a 12 weeks caloric restriction program. Subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) were measured using computed tomography (CT) scans at the sites of L2-L3, L3-L4, and L4-L5. Fasting serum levels of glucose, insulin, triglyceride, total cholesterol (TC), low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C), leptin and homeostasis model assessment-insulin resistance (HOMA-IR) were observed. Pearson's partial correlation coefficients were used to assess the relationship between AT measurement sites and changes in CVD risk factors after calorie restriction. When calories were reduced by 350 kcal/day for 12 weeks, body weight (-2.7%), body fat mass (-8.2%), and waist circumference (-5.8%) all decreased (P restriction, serum levels of glucose (-4.6%), TC (-6.2%), LDL-C (-5.3%), leptin (-17.6%) and HOMA-IR (-18.2%) decreased significantly (P restriction.

  9. A RANDOMIZED CONTROLLED STUDY OF RISK FACTORS AND ROLE OF PROPHYLACTIC ANTIBIOTICS IN PREVENTION OF SURGICAL SITE INFECTIONS

    Directory of Open Access Journals (Sweden)

    Avijeet Mukherjee, Naveen N

    2015-01-01

    Full Text Available Background and Objectives: Surgical site infection (SSI is the most common nosocomial infection encountered in post operative surgical wards. The use of prophylactic antibiotic in clean elective surgical cases is still a subject of controversy to surgeons. The objective of the study is to identify the need for using prophylactic antibiotics in clean surgeries, prevalence of organisms in patients who are not given prophylactic antibiotics and to study whether the presence of risk factors increase the incidence of surgical site infection. Methodology: The comparative study consists of 100 cases admitted under two groups of 50 each: Group A was given prophylactic antibiotic and Group B didn’t receive any. All surgeries other than clean surgical cases were excluded from the study. Results: Out of 50 patients in group B who were not given prophylactic antibiotic, 2 patients had more than one risk factor for development of SSI and both of them developed SSI. Of the 50 patients who received prophylactic antibiotic, none developed SSI. The rate of infection in group A was nil and in Group B was 4%. Conclusion: Prophylactic antibiotics are not recommended for clean elective surgical cases as there is no statistically significant change in the infection rate seen in patients not receiving prophylactic antibiotic(P=0.4952. Meticulous surgical technique and correcting risk factors prior to surgery is a must for reducing incidence of SSI.

  10. Overweight/obesity and underweight are both risk factors for osteoporotic fractures at different sites in Japanese postmenopausal women.

    Science.gov (United States)

    Tanaka, S; Kuroda, T; Saito, M; Shiraki, M

    2013-01-01

    This cohort study of 1,614 postmenopausal Japanese women followed for 6.7 years showed that overweight/obesity and underweight are both risk factors for fractures at different sites. Fracture risk assessment may be improved if fracture sites are taken into account and BMI is categorized. The effect of body mass index (BMI) on fracture at a given level of bone mineral density (BMD) is controversial, since varying associations between BMI and fracture sites have been reported. A total of 1,614 postmenopausal Japanese women were followed for 6.7 years in a hospital-based cohort study. Endpoints included incident vertebral, femoral neck, and long-bone fractures. Rate ratios were estimated by Poisson regression models adjusted for age, diabetes mellitus, BMD, prior fracture, back pain, and treatment by estrogen. Over a mean follow-up period of 6.7 years, a total of 254 clinical and 335 morphometric vertebral fractures, 48 femoral neck fractures, and 159 long-bone fractures were observed. Incidence rates of vertebral fracture in underweight and normal weight women were significantly lower than overweight or obese women by 0.45 (95 % confidence interval: 0.32 to 0.63) and 0.61 (0.50 to 0.74), respectively, if BMD and other risk factors were adjusted, and by 0.66 (0.48 to 0.90) and 0.70 (0.58 to 0.84) if only BMD was not adjusted. Incidence rates of femoral neck and long-bone fractures in the underweight group were higher than the overweight/obese group by 2.15 (0.73 to 6.34) and 1.51 (0.82 to 2.77) and were similar between normal weight and overweight/obesity. Overweight/obesity and underweight are both risk factors for fractures at different sites. Fracture risk assessment may be improved if fracture sites are taken into account and BMI is categorized.

  11. Environmental Factors Affecting the Whale Shark Aggregation site in the South Central Red Sea

    KAUST Repository

    Hozumi, Aya

    2015-12-01

    Motivation behind the spring whale shark (Rhincodon typus) aggregation in Al-Lith, on the Saudi Arabian coast of the South Central Red Sea, is uncertain. A plausible hypothesis is that whale sharks gather to feed on high prey density, leading to questions about the cause of the prey density. A bottom-up process fueled by nutrient input or accumulation from physical advection could create a peak in prey biomass. Wastewater discharged from an aquaculture facility could affect productivity or provide a chemosensory cue for whale sharks. Yet, basic physico-biological oceanography of this region is unresolved. Monthly profiles, long-term moorings, and spatial surveys were used to describe the temporal variability of potential prey biomass and water masses in this region for the first time. Plankton abundance of individuals larger than ~0.7 cm did not peak during whale shark season. Rather, a decrease coinciding the trailing end of whale shark detections was observed. Sites 180 m apart had differences in acoustic backscatter, suggesting small-scale biomass patchiness, supporting the small-scale variability in whale shark habitat selectivity. Red Sea Deep Water, a nutrient-rich water mass formed in the northern Red Sea, appeared in July at the same time the Tokar wind jet from the Sudanese mountain gap is the highest. Gulf of Aden Water, a nutrient-rich water mass from the Indian Ocean, arrived as episodes from May to September, contrary to previous expectations that the water arrives continuously. It is unlikely that these natural nutrient sources are directly responsible for the high prey density attracting the whale sharks. The aquaculture plume, observed at the aggregation site, had a distinct seasonality from the ambient waters. The plume’s highest salinity (>48) approached the extreme limits of coral tolerances. Nutrient concentrations (nitrate, nitrite, phosphate, silica), suspended particulate matter, phytoplankton biomass, bacteria and cyanobacteria cell counts

  12. Peptides derived from specific interaction sites of the fibroblast growth factor 2 - FGF receptor complexes induce receptor activation and signaling

    DEFF Research Database (Denmark)

    Manfè, Valentina; Kochoyan, Artur; Bock, Elisabeth

    2010-01-01

    J. Neurochem. (2010) 10.1111/j.1471-4159.2010.06718.x Abstract Basic fibroblast growth factor (FGF2, bFGF) is the most extensively studied member of the FGF family and is involved in neurogenesis, differentiation, neuroprotection, and synaptic plasticity in the CNS. FGF2 executes its pleiotropic...... biologic actions by binding, dimerizing, and activating FGF receptors (FGFRs). The present study reports the physiologic impact of various FGF2-FGFR1 contact sites employing three different synthetic peptides, termed canofins, designed based on structural analysis of the interactions between FGF2 and FGFR1...

  13. Physiochemical, site, and bidirectional reflectance factor characteristics of uniformly moist soils. [Brazil, Spain and the United States of America

    Science.gov (United States)

    Stoner, E. R.; Baumgardner, M. F. (Principal Investigator)

    1980-01-01

    The author has identified the following significant results. The bidirectional reflectance factor (0.5 micron to 2.3 micron wavelength interval) and physiochemical properties of over 500 soils from 39 states, Brazil and Spain were measured. Site characteristics of soil temperature regime and moisture zone were used as selection criteria. Parent material and internal drainage were noted for each soil. At least five general types of soil reflectance curves were identified based primarily on the presence or absence of ferric iron absorption bands, organic matter content, and soil drainage characteristics. Reflectance in 10 bands across the spectrum was found to be negatively correlated with the natural log of organic matter content.

  14. Ligand-induced expansion of the S1' site in the anthrax toxin lethal factor

    Energy Technology Data Exchange (ETDEWEB)

    Maize, Kimberly M.; Kurbanov, Elbek K.; Johnson, Rodney L.; Amin, Elizabeth Ambrose; Finzel, Barry C. (UMM)

    2016-07-05

    The Bacillus anthracis lethal factor (LF) is one component of a tripartite exotoxin partly responsible for persistent anthrax cytotoxicity after initial bacterial infection. Inhibitors of the zinc metalloproteinase have been investigated as potential therapeutic agents, but LF is a challenging target because inhibitors lack sufficient selectivity or possess poor pharmaceutical properties. These structural studies reveal an alternate conformation of the enzyme, induced upon binding of specific inhibitors, that opens a previously unobserved deep pocket termed S1'* which might afford new opportunities to design selective inhibitors that target this subsite.

  15. The use of social networking sites: A risk factor for using alcohol, marijuana, and synthetic cannabinoids?

    Science.gov (United States)

    Gutierrez, Kevin M; Cooper, Theodore V

    2016-06-01

    The use of social networking sites (SNS) has become a central aspect of youth culture allowing individuals to explore and assert their identities. A commonly portrayed online identity is an "alcohol identity," and past research suggests such identities may contribute to one's risk of using alcohol. The present study builds on past research by examining the relationship between alcohol, marijuana, and synthetic cannabinoid use (e.g., Spice, K2) and time spent on SNS in a sample of college students. Six hundred ninety nine undergraduates (62.4% female; Mage=21.0, SD=8.56) were recruited from a university on the U.S./Mexico border for an online study. Participants completed measures assessing demographics, substance use history, and amount of time spent on SNS. Participants reported spending 46h per month on SNS. Seventy-one percent, 14%, and 3% of the sample reported past month use of alcohol, marijuana, and synthetic cannabinoids, respectively. Regression analyses revealed that hours spent on SNS in the past month were significantly associated with frequency of alcohol (psynthetic cannabinoid use (pmarijuana use in the past month (p<0.001 and p<0.001, respectively). These findings suggest that assessment of time spent on SNS is warranted in studies investigating drug use among college students. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  16. Site dependent factors affecting the economic feasibility of solar powered absorption cooling

    Science.gov (United States)

    Bartlett, J. C.

    1978-01-01

    A procedure was developed to evaluate the cost effectiveness of combining an absorption cycle chiller with a solar energy system. A basic assumption of the procedure is that a solar energy system exists for meeting the heating load of the building, and that the building must be cooled. The decision to be made is to either cool the building with a conventional vapor compression cycle chiller or to use the existing solar energy system to provide a heat input to the absorption chiller. Two methods of meeting the cooling load not supplied by solar energy were considered. In the first method, heat is supplied to the absorption chiller by a boiler using fossil fuel. In the second method, the load not met by solar energy is net by a conventional vapor compression chiller. In addition, the procedure can consider waste heat as another form of auxiliary energy. Commercial applications of solar cooling with an absorption chiller were found to be more cost effective than the residential applications. In general, it was found that the larger the chiller, the more economically feasible it would be. Also, it was found that a conventional vapor compression chiller is a viable alternative for the auxiliary cooling source, especially for the larger chillers. The results of the analysis gives a relative rating of the sites considered as to their economic feasibility of solar cooling.

  17. Factors contributing to intervention fidelity in a multi-site chronic disease self-management program.

    Science.gov (United States)

    Perrin, Karen M; Burke, Somer Goad; O'Connor, Danielle; Walby, Gary; Shippey, Claire; Pitt, Seraphine; McDermott, Robert J; Forthofer, Melinda S

    2006-10-26

    Disease self-management programs have been a popular approach to reducing morbidity and mortality from chronic disease. Replicating an evidence-based disease management program successfully requires practitioners to ensure fidelity to the original program design. The Florida Health Literacy Study (FHLS) was conducted to investigate the implementation impact of the Pfizer, Inc. Diabetes Mellitus and Hypertension Disease Self-Management Program based on health literacy principles in 14 community health centers in Florida. The intervention components discussed include health educator recruitment and training, patient recruitment, class sessions, utilization of program materials, translation of program manuals, patient retention and follow-up, and technical assistance. This report describes challenges associated with achieving a balance between adaptation for cultural relevance and fidelity when implementing the health education program across clinic sites. This balance was necessary to achieve effectiveness of the disease self-management program. The FHLS program was implemented with a high degree of fidelity to the original design and used original program materials. Adaptations identified as advantageous to program participation are discussed, such as implementing alternate methods for recruiting patients and developing staff incentives for participation. Effective program implementation depends on the talent, skill and willing participation of clinic staff. Program adaptations that conserve staff time and resources and recognize their contribution can increase program effectiveness without jeopardizing its fidelity.

  18. Factors contributing to intervention fidelity in a multi-site chronic disease self-management program

    Directory of Open Access Journals (Sweden)

    Pitt Seraphine

    2006-10-01

    Full Text Available Abstract Background and objectives Disease self-management programs have been a popular approach to reducing morbidity and mortality from chronic disease. Replicating an evidence-based disease management program successfully requires practitioners to ensure fidelity to the original program design. Methods The Florida Health Literacy Study (FHLS was conducted to investigate the implementation impact of the Pfizer, Inc. Diabetes Mellitus and Hypertension Disease Self-Management Program based on health literacy principles in 14 community health centers in Florida. The intervention components discussed include health educator recruitment and training, patient recruitment, class sessions, utilization of program materials, translation of program manuals, patient retention and follow-up, and technical assistance. Results This report describes challenges associated with achieving a balance between adaptation for cultural relevance and fidelity when implementing the health education program across clinic sites. This balance was necessary to achieve effectiveness of the disease self-management program. The FHLS program was implemented with a high degree of fidelity to the original design and used original program materials. Adaptations identified as advantageous to program participation are discussed, such as implementing alternate methods for recruiting patients and developing staff incentives for participation. Conclusion Effective program implementation depends on the talent, skill and willing participation of clinic staff. Program adaptations that conserve staff time and resources and recognize their contribution can increase program effectiveness without jeopardizing its fidelity.

  19. Factors structuring the phytoplankton community in the upwelling site off El Loa River in northern Chile

    Science.gov (United States)

    Herrera, Liliana; Escribano, Ruben

    2006-06-01

    Understanding processes affecting the structure of the autotrophic community in marine ecosystems is relevant because species-dependent characters may affect productivity and carbon fluxes of the ocean. In this work, we studied the influence of oceanographic variability on phytoplankton species composition at a coastal upwelling site off northern Chile. Four seasonal cruises carried out during 2003 off El Loa River (21°S) showed that upwelling occurs year-round supporting a large number of diatoms, dinoflagellates, naked nanoflagellates, and silicoflagellates. The analysis of species composition showed that changes in the structure of the autotrophic community are expressed both in abundance and in differences in species assemblages. These changes occurred not only over the seasonal scale but also over the spatial pattern of distribution, and they correlated well to temporal variability of upwelling and spatial variation of upwelling conditions over the cross-shelf axis. A K-means clustering and principal component analyses showed that species assemblages can be represented by few dominant species strongly coupled to alternate upwelling vs. non-upwelling conditions. Both conditions are well defined, and mostly explained by changes in depth of the upper boundary of the oxygen minimum zone (OMZ) (a prominent feature in northern Chile), surface temperature and water column stratification. Abundance of dominant phytoplankton species were strongly correlated to both OMZ depth and water column stratification. Processes through which OMZ depth might influence species abundance and composition are unknown, although they may relate to changes in redox conditions which affect the nutrient field. Another explanation may relate to changes in grazing pressure derived from the effect of low oxygen water on zooplankton vertical distribution.

  20. [3H]52770 RP, a platelet-activating factor receptor antagonist, and tritiated platelet-activating factor label a common specific binding site in human polymorphonuclear leukocytes

    International Nuclear Information System (INIS)

    Marquis, O.; Robaut, C.; Cavero, I.

    1988-01-01

    In human polymorphonuclear leukocytes (PMNs), the tritiated platelet activating factor ([ 3 H]PAF) labels in a saturable manner a single class of binding sites with a Kd of 3.5 +/- 0.5 nM (n = 7) and a maximum binding capacity (Bmax) of 206 +/- 13 fmol/2.5 X 10(6) PMNs (n = 7). 52770 RP, a nonphospholipid antagonist of PAF receptors, fully and competitively displaced the [ 3 H]PAF from its binding sites with a Ki of 7.0 +/- 0.7 nM (n = 4). The high potency and the low solubility in cellular membranes of this compound led us to prepare [ 3 H]52770 RP. This ligand was characterized by a binding which was rapid, reversible, confined to a single site, saturable, specific and stereoselective. Its Kd and Bmax were 4.2 +/- 0.3 nM and 181 +/- 11 fmol/2.5 X 10(6) PMNs, respectively. The stereoselectivity of the binding was suggested by the 600- and 1050-fold higher potency of the d-enantiomer with respect to l-52770 RP in displacing [ 3 H]52770 RP or [ 3 H]PAF, respectively. Several PAF analogs (e.g., lyso-PAF, 2-O-methyl-lyso-PAF), which are poorly active as PAF receptor agonists in functional tests, were weak displacers of [ 3 H]PAF and [ 3 H]52770 RP. Furthermore, for a series of 14 known PAF receptor agonists or antagonists belonging to different chemical families, there was an excellent correlation (r = 0.98) between their ability to displace [ 3 H]PAF and [ 3 H]52770 RP. Thus, [ 3 H]52770 RP and [ 3 H]PAF appear to interact with the same binding site on human PMNs which is proposed to be the PAF receptor mediating functional responses

  1. Improving regulatory effectiveness in Federal/State siting actions. Success factor evaluation panel. Final report

    International Nuclear Information System (INIS)

    Haggard, J.

    1977-06-01

    An independent appraisal of the factors that determine efficiency in reaching environmental decisions with respect to nuclear facilities was addressed. The Panel recommended to substitute 'effectiveness' for 'efficiency.' Thus, an effective decision is: 'A timely final decision, that provides for necessary change, consistent with societal objectives and law, and which is equitable and practical, and is based upon fully and candidly expressed premises utilizing a commonly available data base.' The measurement criteria for evaluating the effectiveness of the environmental decision making process are: timely decision, final decision, provision for change, consistency with societal goals and law, equitable, practical, fully and candidly expressed premises, commonly available data base, and public confidence. The Panel evaluated the 8 policies proposed by NRC staff as essential to licensing reform: national fuels policy, regional review, early disclosure, State role, technical assistance to State, role of utilities, radiation health and safety, and modification of the Atomic Energy Act. The five NRC scenarios were evaluated in terms of regulatory effectiveness

  2. Risk factors and outcomes of organ-space surgical site infections after elective colon and rectal surgery

    Directory of Open Access Journals (Sweden)

    Aina Gomila

    2017-04-01

    Full Text Available Abstract Background Organ-space surgical site infections (SSI are the most serious and costly infections after colorectal surgery. Most previous studies of risk factors for SSI have analysed colon and rectal procedures together. The aim of the study was to determine whether colon and rectal procedures have different risk factors and outcomes for organ-space SSI. Methods A multicentre observational prospective cohort study of adults undergoing elective colon and rectal procedures at 10 Spanish hospitals from 2011 to 2014. Patients were followed up until 30 days post-surgery. Surgical site infection was defined according to the Centers for Disease Control and Prevention criteria. Oral antibiotic prophylaxis (OAP was considered as the administration of oral antibiotics the day before surgery combined with systemic intravenous antibiotic prophylaxis. Results Of 3,701 patients, 2,518 (68% underwent colon surgery and 1,183 (32% rectal surgery. In colon surgery, the overall SSI rate was 16.4% and the organ-space SSI rate was 7.9%, while in rectal surgery the rates were 21.6% and 11.5% respectively (p < 0.001. Independent risk factors for organ-space SSI in colon surgery were male sex (Odds ratio -OR-: 1.57, 95% CI: 1.14–2.15 and ostomy creation (OR: 2.65, 95% CI: 1.8–3.92 while laparoscopy (OR: 0.5, 95% CI: 0.38–0.69 and OAP combined with intravenous antibiotic prophylaxis (OR: 0.7, 95% CI: 0.51–0.97 were protective factors. In rectal surgery, independent risk factors for organ-space SSI were male sex (OR: 2.11, 95% CI: 1.34–3.31 and longer surgery (OR: 1.49, 95% CI: 1.03–2.15, whereas OAP with intravenous antibiotic prophylaxis (OR: 0.49, 95% CI: 0.32–0.73 was a protective factor. Among patients with organ-space SSI, we found a significant difference in the overall 30-day mortality, being higher in colon surgery than in rectal surgery (11.5% vs 5.1%, p = 0.04. Conclusions Organ-space SSI in colon and rectal surgery has some

  3. Identification and positional distribution analysis of transcription factor binding sites for genes from the wheat fl-cDNA sequences.

    Science.gov (United States)

    Chen, Zhen-Yong; Guo, Xiao-Jiang; Chen, Zhong-Xu; Chen, Wei-Ying; Wang, Ji-Rui

    2017-06-01

    The binding sites of transcription factors (TFs) in upstream DNA regions are called transcription factor binding sites (TFBSs). TFBSs are important elements for regulating gene expression. To date, there have been few studies on the profiles of TFBSs in plants. In total, 4,873 sequences with 5' upstream regions from 8530 wheat fl-cDNA sequences were used to predict TFBSs. We found 4572 TFBSs for the MADS TF family, which was twice as many as for bHLH (1951), B3 (1951), HB superfamily (1914), ERF (1820), and AP2/ERF (1725) TFs, and was approximately four times higher than the remaining TFBS types. The percentage of TFBSs and TF members showed a distinct distribution in different tissues. Overall, the distribution of TFBSs in the upstream regions of wheat fl-cDNA sequences had significant difference. Meanwhile, high frequencies of some types of TFBSs were found in specific regions in the upstream sequences. Both TFs and fl-cDNA with TFBSs predicted in the same tissues exhibited specific distribution preferences for regulating gene expression. The tissue-specific analysis of TFs and fl-cDNA with TFBSs provides useful information for functional research, and can be used to identify relationships between tissue-specific TFs and fl-cDNA with TFBSs. Moreover, the positional distribution of TFBSs indicates that some types of wheat TFBS have different positional distribution preferences in the upstream regions of genes.

  4. Factors and Drivers Effecting the Decision of Using Off-Site Manufacturing (OSM Systems in House Building Industry

    Directory of Open Access Journals (Sweden)

    Hussein Elnaas

    2014-01-01

    Full Text Available Much has been written on Off-site Manufacturing (OSM in construction, particularly regarding the perceived benefits and barriers to implementation. However, there seems to be a wide misunderstanding of the state of OSM associated with the concept of decision by many of those involved in decision making process within the house building industry. This has led to a demand for guidance’s on decision making process for construction project leaders particularly at early project stages. Choosing a construction method for a project will require an optimum decision strategy which involves careful understanding, measurement and evaluation of a number of decision factors that can have the most influence on successful decision action. This paper, therefore, aims to identify the key decision factors to be considered at evaluation stage when choosing to use Off-Site Manufacturing (OSM as a construction strategy in house building projects. This will reveal the key drivers for change in the industry towards the use of OSM in house building.

  5. Genome-wide mapping of boundary element-associated factor (BEAF) binding sites in Drosophila melanogaster links BEAF to transcription.

    Science.gov (United States)

    Jiang, Nan; Emberly, Eldon; Cuvier, Olivier; Hart, Craig M

    2009-07-01

    Insulator elements play a role in gene regulation that is potentially linked to nuclear organization. Boundary element-associated factors (BEAFs) 32A and 32B associate with hundreds of sites on Drosophila polytene chromosomes. We hybridized DNA isolated by chromatin immunoprecipitation to genome tiling microarrays to construct a genome-wide map of BEAF binding locations. A distinct difference in the association of 32A and 32B with chromatin was noted. We identified 1,820 BEAF peaks and found that more than 85% were less than 300 bp from transcription start sites. Half are between head-to-head gene pairs. BEAF-associated genes are transcriptionally active as judged by the presence of RNA polymerase II, dimethylated histone H3 K4, and the alternative histone H3.3. Forty percent of these genes are also associated with the polymerase negative elongation factor NELF. Like NELF-associated genes, most BEAF-associated genes are highly expressed. Using quantitative reverse transcription-PCR, we found that the expression levels of most BEAF-associated genes decrease in embryos and cultured cells lacking BEAF. These results provide an unexpected link between BEAF and transcription, suggesting that BEAF plays a role in maintaining most associated promoter regions in an environment that facilitates high transcription levels.

  6. Large enhancement of functional activity of active site-inhibited factor VIIa due to protein dimerization: insights into mechanism of assembly/disassembly from tissue factor.

    Science.gov (United States)

    Stone, Matthew D; Harvey, Stephen B; Martinez, Michael B; Bach, Ronald R; Nelsestuen, Gary L

    2005-04-26

    Active site-inhibited blood clotting factor VIIa (fVIIai) binds to tissue factor (TF), a cell surface receptor that is exposed upon injury and initiates the blood clotting cascade. FVIIai blocks binding of the corresponding enzyme (fVIIa) or zymogen (fVII) forms of factor VII and inhibits coagulation. Although several studies have suggested that fVIIai may have superior anticoagulation effects in vivo, a challenge for use of fVIIai is cost of production. This study reports the properties of dimeric forms of fVIIai that are cross-linked through their active sites. Dimeric wild-type fVIIai was at least 75-fold more effective than monomeric fVIIai in blocking fVIIa association with TF. The dimer of a mutant fVIIai with higher membrane affinity was 1600-fold more effective. Anticoagulation by any form of fVIIai differed substantially from agents such as heparin and showed a delayed mode of action. Coagulation proceeded normally for the first minutes, and inhibition increased as equilibrium binding was established. It is suggested that association of fVIIa(i) with TF in a collision-dependent reaction gives equal access of inhibitor and enzyme to TF. Assembly was not influenced by the higher affinity and slower dissociation of the dimer. As a result, anticoagulation was delayed until the reaction reached equilibrium. Properties of different dissociation experiments suggested that dissociation of fVIIai from TF occurred by a two-step mechanism. The first step was separation of TF-fVIIa(i) while both proteins remained bound to the membrane, and the second step was dissociation of the fVIIa(i) from the membrane. These results suggest novel actions of fVIIai that distinguish it from most of the anticoagulants that block later steps of the coagulation cascade.

  7. Factor VIII S373L: mutation at P1' site confers thrombin cleavage resistance, causing mild haemophilia A.

    Science.gov (United States)

    Johnson, D J; Pemberton, S; Acquila, M; Mori, P G; Tuddenham, E G; O'Brien, D P

    1994-04-01

    A novel CRM+ mutation, factor VIII position 373 serine to leucine substitution (FVIII 373-Leu) was identified during a survey of Factor VIII (FVIII) mutations. We have purified the variant protein from the patient's plasma in order to allow further characterisation of the molecule. The CRM+ plasma contained 120% Factor VIII antigen (FVIII:Ag) and 6% Factor VIII coagulant activity (FVIII:C). After purification the mutant FVIII was subjected to thrombin proteolysis, and was thereby activated 5.6-fold compared with 7-fold for wild type molecule. Subsequently, spontaneous inactivation of the mutant was much slower than noted for wild type FVIII. Western blot analysis using monoclonal antibodies demonstrated that thrombin cleavage of FVIII 373-Leu at positions 740 and 1689 were normal but that cleavage at position 372 was completely absent. Crystallographic coordinates of the active site of thrombin complexed to fibrinopeptide A were used to explore possible mechanistic reasons for the failure of thrombin to cleave the mutant FVIII at position 372. Steric hindrance between the mutant side chain and the side chain of the P1 residue was apparent. We conclude that the functional defect of FVIII 373-Leu results from the inability of thrombin to cleave the mutant at position 372-373, and propose that this is due to steric hindrance by the side chain of leucine 373, preventing correct formation of the enzyme substrate complex.

  8. Description of Some Ecological Factors in Three Forest Sites in Lorestan Province and Their Impact on Myrtle (Myrtus communis L. Essential Oil Yield and Chemical Components

    Directory of Open Access Journals (Sweden)

    Z. Mir-Azadi

    2013-03-01

    Full Text Available Due to the side effects of chemical drugs, special attention is given recently to pharmaceutical plants. Myrtle (Myrtus communis L. is one of the valuable pharmaceutical plants, which is distributed over the vast areas of Iran. Yield and components of essential oil of this plant is dependent on ecological and genetic factors. In order to describe some ecological factors that affect myrtle in Lorestan province, three forest sites (Sepiddasht, Chame-moord, and Hamzeh Camp were selected. Some effective ecological factors on type of essential oil were measured and compared among the sites. To compare the yield and components of essential oil, myrtle leaves were collected during flowering stage in each site. Leaves were dried in open air conditions and the oil was extracted by distillation. Yield of essential oil was calculated and its components were identified by GC and GC/MS. Results showed that maximum yield belongs to Sepiddasht site. The altitude and soil Na, P, and organic carbon content of this site is quite different from other two sites. The main components of essential oils of these three sites had considerable differences. The amount of 9,10 anthracenedione was 29.1% in Sepiddasht site, while it was not found in the oil of Chame-moord site. It seems that differences in ecological and soil properties of the tree sites could have major effect on essential oil yield and its composition.

  9. A cross-site comparison of factors influencing soil nitrification rates in northeastern USA forested watersheds

    Science.gov (United States)

    Ross, D.S.; Wemple, B.C.; Jamison, A.E.; Fredriksen, G.; Shanley, J.B.; Lawrence, G.B.; Bailey, S.W.; Campbell, J.L.

    2009-01-01

    Elevated N deposition is continuing on many forested landscapes around the world and our understanding of ecosystem response is incomplete. Soil processes, especially nitrification, are critical. Many studies of soil N transformations have focused on identifying relationships within a single watershed but these results are often not transferable. We studied 10 small forested research watersheds in the northeastern USA to determine if there were common factors related to soil ammonification and nitrification. Vegetation varied between mixed northern hardwoods and mixed conifers. Watershed surface soils (Oa or A horizons) were sampled at grid or transect points and analyzed for a suite of chemical characteristics. At each sampling point, vegetation and topographic metrics (field and GIS-based) were also obtained. Results were examined by watershed averages (n = 10), seasonal/watershed averages (n = 28), and individual sampling points (n = 608). Using both linear and tree regression techniques, the proportion of conifer species was the single best predictor of nitrification rates, with lower rates at higher conifer dominance. Similar to other studies, the soil C/N ratio was also a good predictor and was well correlated with conifer dominance. Unlike other studies, the presence of Acer saccharum was not by itself a strong predictor, but was when combined with the presence of Betula alleghaniensis. Topographic metrics (slope, aspect, relative elevation, and the topographic index) were not related to N transformation rates across the watersheds. Although found to be significant in other studies, neither soil pH, Ca nor Al was related to nitrification. Results showed a strong relationship between dominant vegetation, soil C, and soil C/N. ?? 2008 Springer Science+Business Media, LLC.

  10. Prospective multicenter surveillance and risk factor analysis of deep surgical site infection after posterior thoracic and/or lumbar spinal surgery in adults.

    Science.gov (United States)

    Ogihara, Satoshi; Yamazaki, Takashi; Maruyama, Toru; Oka, Hiroyuki; Miyoshi, Kota; Azuma, Seiichi; Yamada, Takashi; Murakami, Motoaki; Kawamura, Naohiro; Hara, Nobuhiro; Terayama, Sei; Morii, Jiro; Kato, So; Tanaka, Sakae

    2015-01-01

    Surgical site infection is a serious and significant complication after spinal surgery and is associated with high morbidity rates, high healthcare costs and poor patient outcomes. Accurate identification of risk factors is essential for developing strategies to prevent devastating infections. The purpose of this study was to identify independent risk factors for surgical site infection among posterior thoracic and/or lumbar spinal surgery in adult patients using a prospective multicenter surveillance research method. From July 2010 to June 2012, we performed a prospective surveillance study in adult patients who had developed surgical site infection after undergoing thoracic and/or lumbar posterior spinal surgery at 11 participating hospitals. Detailed preoperative and operative patient characteristics were prospectively recorded using a standardized data collection format. Surgical site infection was based on the definition established by the Centers for Disease Control and Prevention. A total of 2,736 consecutive adult patients were enrolled, of which 24 (0.9%) developed postoperative deep surgical site infection. Multivariate regression analysis indicated four independent risk factors. Preoperative steroid therapy (P = 0.001), spinal trauma (P = 0.048) and gender (male) (P = 0.02) were statistically significant independent patient-related risk factors, whereas an operating time ≥3 h (P operating time ≥3 h were independent risk factors for deep surgical site infection after thoracic and/or lumbar spinal surgery in adult patients. Identification of these risk factors can be used to develop protocols aimed at decreasing the risk of surgical site infection.

  11. Social media in tourism: Establishing factors influencing attitudes towards the usage of social networking sites for trip organisation

    Directory of Open Access Journals (Sweden)

    Rosemary Matikiti

    2017-01-01

    Full Text Available Purpose: The main aim of this study was to determine the attitude towards the use of SNSs for trip organisation and its precursors. Problem investigated: Tourism organisations and destination policy makers need to understand factors that influence tourist use of SNSs for trip organisation in order for them to be able to effectively utilise SNSs. Methodology: The methodological approach followed was exploratory and quantitative in nature. Data were collected from a total of 340 respondents using a structured questionnaire. Structural equation modelling through the use of Partial Least Squares was for data analysis. Findings and implications: The results show that attitude towards the use of SNSs for trip organisation is affected by perceived benefits, subjective norm and perceived behavioural control, with perceived usefulness having the greatest influence. The implication is that managers of tourism organisations need to ensure that their sites are informative, easy to use and able to safeguard users’ online privacy if they are to attract more and loyal users to their sites. Value of the research: Very little research in the South African context exists with specific reference to how SNSs are being utilised for trip organisation. This article contributes by unravelling factors that influence the use of SNSs for trip organisation. Conclusion: Perceived usefulness measured by functional benefits and social benefits is the key factor that influences attitude towards the use of SNSs for trip organisation. It is the responsibility of destination marketers to provide all the necessary or valuable information on their SNS accounts, in order to encourage travellers to use SNSs

  12. Pre-operative and early post-operative factors associated with surgical site infection after laparoscopic sleeve gastrectomy.

    Science.gov (United States)

    Ruiz-Tovar, Jaime; Oller, Inmaculada; Llavero, Carolina; Arroyo, Antonio; Muñoz, Jose Luis; Calero, Alicia; Diez, María; Zubiaga, Lorea; Calpena, Rafael

    2013-08-01

    Surgical procedures on obese patients are expected to have a high incidence of surgical site infection (SSI). The identification of pre-operative or early post-operative risk factors for SSI may help the surgeon to identify subjects in risk and adequately optimize their status. We conducted a study of the association of comorbidities and pre- and post-operative analytical variables with SSI following laparoscopic sleeve gastrectomy for the treatment of morbid obesity. We performed a prospective study of all morbidly obese patients undergoing laparoscopic sleeve gastrectomy as a bariatric procedure between 2007 and 2011. An association of clinical and analytical variables with SSI was investigated. The study included 40 patients with a mean pre-operative body mass index (BMI) of 51.2±7.9 kg/m(2). Surgical site infections appeared in three patients (7.5%), of whom two had an intra-abdominal abscess located in the left hypochondrium and the third had a superficial incisional SSI. Pre-operatively, a BMI >45 kg/m(2) (OR 8.7; p=0.008), restrictive disorders identified by pulmonary function tests (OR 10.0; p=0.012), a serum total protein concentration 30 mcg/dL (OR 13.0; p=0.003), and a mean corpuscular volume (MCV) operative SSI. Post-operatively, a serum glucose >128 mg/dL (OR 4.7; p=0.012) and hemoglobin operative anemia and hyperglycemia as risk factors for SSI. In these situations, the surgeon must be aware of and seek to control these risk factors.

  13. Modelling site-specific N2O emission factors from Austrian agricultural soils for targeted mitigation measures (NitroAustria)

    Science.gov (United States)

    Amon, Barbara; Zechmeister-Boltenstern, Sophie; Kasper, Martina; Foldal, Cecilie; Schiefer, Jasmin; Kitzler, Barbara; Schwarzl, Bettina; Zethner, Gerhard; Anderl, Michael; Sedy, Katrin; Gaugitsch, Helmut; Dersch, Georg; Baumgarten, Andreas; Haas, Edwin; Kiese, Ralf

    2016-04-01

    Results from a previous project "FarmClim" highlight that the IPCC default emission factor is not able to reflect region specific N2O emissions from Austrian arable soils. The methodology is limited in identifying hot spots and hot moments of N2O emissions. When estimations are based on default emission factors no recommendations can be given on optimisation measures that would lead to a reduction of soil N2O emissions. The better the knowledge is about Nitrogen and Carbon budgets in Austrian agricultural managed soils the better the situation can be reflected in the Austrian GHG emission inventory calculations. Therefore national and regionally modelled emission factors should improve the evidence for national deviation from the IPCC default emission factors and reduce the uncertainties. The overall aim of NitroAustria is to identify the drivers for N2O emissions on a regional basis taking different soil types, climate, and agricultural management into account. We use the LandscapeDNDC model to update the N2O emission factors for N fertilizer and animal manure applied to soils. Key regions in Austria were selected and region specific N2O emissions calculated. The model runs at sub-daily time steps and uses data such as maximum and minimum air temperature, precipitation, radiation, and wind speed as meteorological drivers. Further input data are used to reflect agricultural management practices, e.g., planting/harvesting, tillage, fertilizer application, irrigation and information on soil and vegetation properties for site characterization and model initialization. While at site scale, arable management data (crop cultivation, rotations, timings etc.) is obtained by experimental data from field trials or observations, at regional scale such data need to be generated using region specific proxy data such as land use and management statistics, crop cultivations and yields, crop rotations, fertilizer sales, manure resulting from livestock units etc. The farming

  14. Novel factor VIII variants with a modified furin cleavage site improve the efficacy of gene therapy for hemophilia A.

    Science.gov (United States)

    Nguyen, G N; George, L A; Siner, J I; Davidson, R J; Zander, C B; Zheng, X L; Arruda, V R; Camire, R M; Sabatino, D E

    2017-01-01

    Essentials Factor (F) VIII is an inefficiently expressed protein. Furin deletion FVIII variants were purified and characterized using in vitro and in vivo assays. These minimally modified novel FVIII variants have enhanced function. These variants provide a strategy for increasing FVIII expression in hemophilia A gene therapy. Background The major challenge for developing gene-based therapies for hemophilia A is that human factor VIII (hFVIII) has intrinsic properties that result in inefficient biosynthesis. During intracellular processing, hFVIII is predominantly cleaved at a paired basic amino acid cleaving enzyme (PACE) or furin cleavage site to yield a heterodimer that is the major form of secreted protein. Previous studies with B-domain-deleted (BDD) canine FVIII and hFVIII-R1645H, both differing from hFVIII by a single amino acid at this site, suggested that these proteins are secreted mainly in a single polypeptide chain (SC) form and exhibit enhanced function. Objective We hypothesized that deletion(s) of the furin site modulates FVIII biology and may enhance its function. Methods A series of recombinant hFVIII-furin deletion variants were introduced into hFVIII-BDD [Δ1645, 1645-46(Δ2), 1645-47(Δ3), 1645-48(Δ4), or Δ1648] and characterized. Results In vitro, recombinant purified Δ3 and Δ4 were primarily SC and, interestingly, had 2-fold higher procoagulant activity compared with FVIII-BDD. In vivo, the variants also have improved hemostatic function. After adeno-associated viral (AAV) vector delivery, the expression of these variants is 2-4-fold higher than hFVIII-BDD. Protein challenges of each variant in mice tolerant to hFVIII-BDD showed no anti-FVIII immune response. Conclusions These data suggest that the furin deletion hFVIII variants are superior to hFVIII-BDD without increased immunogenicity. In the setting of gene-based therapeutics, these novel variants provide a unique strategy to increase FVIII expression, thus lowering the vector dose, a

  15. The Role of Individual-Media Relationship and Consumer Personal Factors on Spanish Teenagers' Mobile Social Networking Sites Usage

    OpenAIRE

    Carla Ruiz-Mafé; Silvia Sanz-Blas; José Martí-Parreño

    2014-01-01

    Social Networking Sites (SNS) are gaining momentum as powerful tools of marketing communications. Mobile phones are becoming one of the most popular devices for accessing Social Networking Sites. In Spain, 44% of Social Networking Sites users access these sites on a daily basis while 79% of them access these sites on a weekly basis. Furthermore, it is notable that over 70% of Social Networking Sites users talk about and recommend commercial brands. This justifies the interest of the study of ...

  16. Relating Magnetic Parameters to Heavy Metal Concentrations and Environmental Factors at Formosa Mine Superfund Site, Douglas County, OR

    Science.gov (United States)

    Upton, T. L.

    2016-12-01

    Advances in the field of environmental magnetism have led to exciting new applications for this field. Magnetic minerals are ubiquitous in the environment and tend to have an affinity for heavy metals. Hence, it has been demonstrated that magnetic properties are often significantly related to concentrations of heavy metals and other pollutants. As a result, magnetic techniques have been used as proxy for determining hot spots of several types of pollution produced from a diversity of anthropogenic sources. Magnetic measurements are non-destructive and relatively inexpensive compared to geochemical analyses. The utility of environmental magnetic methods varies widely depending on biological, chemical and physical processes that create and transform soils and sediments. Applications in the direction of mapping heavy metals have been studied and shown to be quite useful in countries such as China and India but to date, little research has been done in the US. As such, there is need to expand the scope of research to a wider range of soil types and land uses, especially within the US. This study investigates the application of environmental magnetic techniques to mapping of heavy metal concentrations at the Formosa Mine Superfund Site, an abandoned mine about 25 miles southwest of Roseburg, OR. The soils and sediment at this site are derived from pyrite-rich bedrock which is weak in terms of magnetic susceptibility. Using hotspot analysis, correlation and cluster analyses, interactions between metals and magnetic parameters are investigated in relation to environmental factors such as proximity to seeps and adits. Preliminary results suggest significant correlation of magnetic susceptibility with certain heavy metals, signifying that magnetic methods may be useful in mapping heavy metal hotspots at this site. Further analysis examines the relation of various land use differences in magnetic signatures obtained throughout the Cow Creek watershed.

  17. Weibo or WeChat? Assessing Preference for Social Networking Sites and Role of Personality Traits and Psychological Factors.

    Science.gov (United States)

    Hou, Juan; Ndasauka, Yamikani; Pan, Xuefei; Chen, Shuangyi; Xu, Fei; Zhang, Xiaochu

    2018-01-01

    Research trying to understand individual difference in the use of different social networking sites (SNSs) is minimal. In the present study, we collected data from 714 college students in China (273 males) to assess how personality traits and psychological factors relate to excessive use of WeChat and Weibo. We found that excessive use of Weibo and WeChat correlated positively with neuroticism, loneliness, and external locus of control and negatively with agreeableness, social support, and social interaction. Furthermore, people that scored high on loneliness, lack of social support, and poor social interaction skills excessively used Weibo more than WeChat. These results entail that by fulfilling different needs, WeChat and Weibo attract different kinds of people; significant lesson for future development of SNSs.

  18. Weibo or WeChat? Assessing Preference for Social Networking Sites and Role of Personality Traits and Psychological Factors

    Science.gov (United States)

    Hou, Juan; Ndasauka, Yamikani; Pan, Xuefei; Chen, Shuangyi; Xu, Fei; Zhang, Xiaochu

    2018-01-01

    Research trying to understand individual difference in the use of different social networking sites (SNSs) is minimal. In the present study, we collected data from 714 college students in China (273 males) to assess how personality traits and psychological factors relate to excessive use of WeChat and Weibo. We found that excessive use of Weibo and WeChat correlated positively with neuroticism, loneliness, and external locus of control and negatively with agreeableness, social support, and social interaction. Furthermore, people that scored high on loneliness, lack of social support, and poor social interaction skills excessively used Weibo more than WeChat. These results entail that by fulfilling different needs, WeChat and Weibo attract different kinds of people; significant lesson for future development of SNSs. PMID:29755384

  19. Cox17 Protein Is an Auxiliary Factor Involved in the Control of the Mitochondrial Contact Site and Cristae Organizing System.

    Science.gov (United States)

    Chojnacka, Magdalena; Gornicka, Agnieszka; Oeljeklaus, Silke; Warscheid, Bettina; Chacinska, Agnieszka

    2015-06-12

    The mitochondrial contact site and cristae organizing system (MICOS) is a recently discovered protein complex that is crucial for establishing and maintaining the proper inner membrane architecture and contacts with the outer membrane of mitochondria. The ways in which the MICOS complex is assembled and its integrity is regulated remain elusive. Here, we report a direct link between Cox17, a protein involved in the assembly of cytochrome c oxidase, and the MICOS complex. Cox17 interacts with Mic60, thereby modulating MICOS complex integrity. This interaction does not involve Sco1, a partner of Cox17 in transferring copper ions to cytochrome c oxidase. However, the Cox17-MICOS interaction is regulated by copper ions. We propose that Cox17 is a newly identified factor involved in maintaining the architecture of the MICOS complex. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Weibo or WeChat? Assessing Preference for Social Networking Sites and Role of Personality Traits and Psychological Factors

    Directory of Open Access Journals (Sweden)

    Juan Hou

    2018-04-01

    Full Text Available Research trying to understand individual difference in the use of different social networking sites (SNSs is minimal. In the present study, we collected data from 714 college students in China (273 males to assess how personality traits and psychological factors relate to excessive use of WeChat and Weibo. We found that excessive use of Weibo and WeChat correlated positively with neuroticism, loneliness, and external locus of control and negatively with agreeableness, social support, and social interaction. Furthermore, people that scored high on loneliness, lack of social support, and poor social interaction skills excessively used Weibo more than WeChat. These results entail that by fulfilling different needs, WeChat and Weibo attract different kinds of people; significant lesson for future development of SNSs.

  1. Estimation of site specific deposition velocities and mass interception factor using 7Be as a tracer in Kudankulam environment

    International Nuclear Information System (INIS)

    Selvi, B.S.; Vijayakumar, B.; Ravi, P.M.

    2018-01-01

    Beryllium-7 ( 7 Be) is a cosmogenic radionuclide formed in the atmosphere when cosmic ray produced neutrons and protons disintegrate the atomic nucleus of nitrogen and oxygen in to lighter fragments. ' 7 Be is found naturally in air, rainwater, vegetation, soils and sediments as well as lake and ocean waters. Due to its continuous production in the atmosphere, its relatively short half-life (53.3 days), and its ease of measurement by gamma spectrometry, 7 Be has proven to be a useful tool for tracing and quantifying environmental processes such as atmospheric deposition, atmospheric transport and soil erosion etc. A systematic study is carried out to estimate the site specific deposition velocities and the mass interception factor around the Kudankulam environment

  2. Factors influencing U(VI adsorption onto soil from a candidate very low level radioactive waste disposal site in China

    Directory of Open Access Journals (Sweden)

    Zuo Rui

    2016-01-01

    Full Text Available The properties of soil at disposal sites are very important for geological disposal of very low level radioactive waste in terms of U(VI. In this study, soil from a candidate very low level radioactive waste disposal site in China was evaluated for its capacity on uranium sorption. Specifically, the equilibrium time, initial concentration, soil particle, pH, temperature, and carbonate were evaluated. The results indicated that after 15-20 days of sorption, the Kd value fluctuated and stabilized at 355-360 mL/g. The adsorptive capacity of uranium was increased as the initial uranium concentration increased, while it decreased as the soil particle size increased. The pH value played an important role in the U(VI sorption onto soil, especially under alkaline conditions, and had a great effect on the sorption capacity of soil for uranium. Moreover, the presence of carbonate decreased the sorption of U(VI onto soil because of the role of the strong complexation of carbonate with U(VI in the groundwater. Overall, this study assessed the behavior of U(VI sorption onto natural soil, which would be an important factor in the geological barrier of the repository, has contribution on mastering the characteristic of the adsorption of uranium in the particular soil media for the process of very low level radioactive waste disposal.

  3. Molecular cloning of the human gene for von Willebrand factor and identification of the transcription initiation site

    International Nuclear Information System (INIS)

    Collins, C.J.; Underdahl, J.P.; Levene, R.B.; Ravera, C.P.; Morin, M.J.; Dombalagian, M.J.; Ricca, G.; Livingston, D.M.; Lynch, D.C.

    1987-01-01

    A series of overlapping cosmid genomic clones have been isolated that contain the entire coding unit of the human gene for van Willebrand factor (vWf), a major component of the hemostatic system. The cloned segments span ≅ 175 kilobases of human DNA sequence, and hybridization analysis suggest that the vWf coding unit is ≅150 kilobases in length. Within one of these clones, the vWF transcription initiation site has been mapped and a portion of the vWf promoter region has been sequenced, revealing a typical TATA box, a downstream CCAAT box, and a perfect downstream repeat of the 8 base pairs containing the transcription start site. Sequencing of a segment of another genomic clone has revealed the vWF translation termination codon. Where tested, comparative restriction analysis of cloned and chromosomal DNA segments strongly suggests that no major alterations occurred during cloning and that there is only one complete copy of the vWf gene in the human haploid genome. Similar analyses of DNA from vWf-producing endothelial cells and nonexpressing leukocytes suggest that vWf gene expression is not accompanied by gross genomic rearrangements. In addition, there is significant homology of C-terminal coding sequences among the vWf genes of several vertebrate species

  4. Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules.

    Directory of Open Access Journals (Sweden)

    Bin Z He

    2011-04-01

    Full Text Available Transcription factor binding site(s (TFBS gain and loss (i.e., turnover is a well-documented feature of cis-regulatory module (CRM evolution, yet little attention has been paid to the evolutionary force(s driving this turnover process. The predominant view, motivated by its widespread occurrence, emphasizes the importance of compensatory mutation and genetic drift. Positive selection, in contrast, although it has been invoked in specific instances of adaptive gene expression evolution, has not been considered as a general alternative to neutral compensatory evolution. In this study we evaluate the two hypotheses by analyzing patterns of single nucleotide polymorphism in the TFBS of well-characterized CRM in two closely related Drosophila species, Drosophila melanogaster and Drosophila simulans. An important feature of the analysis is classification of TFBS mutations according to the direction of their predicted effect on binding affinity, which allows gains and losses to be evaluated independently along the two phylogenetic lineages. The observed patterns of polymorphism and divergence are not compatible with neutral evolution for either class of mutations. Instead, multiple lines of evidence are consistent with contributions of positive selection to TFBS gain and loss as well as purifying selection in its maintenance. In discussion, we propose a model to reconcile the finding of selection driving TFBS turnover with constrained CRM function over long evolutionary time.

  5. An efficient method to transcription factor binding sites imputation via simultaneous completion of multiple matrices with positional consistency.

    Science.gov (United States)

    Guo, Wei-Li; Huang, De-Shuang

    2017-08-22

    Transcription factors (TFs) are DNA-binding proteins that have a central role in regulating gene expression. Identification of DNA-binding sites of TFs is a key task in understanding transcriptional regulation, cellular processes and disease. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) enables genome-wide identification of in vivo TF binding sites. However, it is still difficult to map every TF in every cell line owing to cost and biological material availability, which poses an enormous obstacle for integrated analysis of gene regulation. To address this problem, we propose a novel computational approach, TFBSImpute, for predicting additional TF binding profiles by leveraging information from available ChIP-seq TF binding data. TFBSImpute fuses the dataset to a 3-mode tensor and imputes missing TF binding signals via simultaneous completion of multiple TF binding matrices with positional consistency. We show that signals predicted by our method achieve overall similarity with experimental data and that TFBSImpute significantly outperforms baseline approaches, by assessing the performance of imputation methods against observed ChIP-seq TF binding profiles. Besides, motif analysis shows that TFBSImpute preforms better in capturing binding motifs enriched in observed data compared with baselines, indicating that the higher performance of TFBSImpute is not simply due to averaging related samples. We anticipate that our approach will constitute a useful complement to experimental mapping of TF binding, which is beneficial for further study of regulation mechanisms and disease.

  6. MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters

    Directory of Open Access Journals (Sweden)

    Huynen Martijn A

    2011-06-01

    Full Text Available Abstract Background MicroRNAs (miRNAs play a fundamental role in the regulation of gene expression by translational repression or target mRNA degradation. Regulatory elements in miRNA promoters are less well studied, but may reveal a link between their expression and a specific cell type. Results To explore this link in myeloid cells, miRNA expression profiles were generated from monocytes and dendritic cells (DCs. Differences in miRNA expression among monocytes, DCs and their stimulated progeny were observed. Furthermore, putative promoter regions of miRNAs that are significantly up-regulated in DCs were screened for Transcription Factor Binding Sites (TFBSs based on TFBS motif matching score, the degree to which those TFBSs are over-represented in the promoters of the up-regulated miRNAs, and the extent of conservation of the TFBSs in mammals. Conclusions Analysis of evolutionarily conserved TFBSs in DC promoters revealed preferential clustering of sites within 500 bp upstream of the precursor miRNAs and that many mRNAs of cognate TFs of the conserved TFBSs were indeed expressed in the DCs. Taken together, our data provide evidence that selected miRNAs expressed in DCs have evolutionarily conserved TFBSs relevant to DC biology in their promoters.

  7. Differences in risk factors associated with surgical site infections following two types of cardiac surgery in Japanese patients.

    Science.gov (United States)

    Morikane, K; Honda, H; Yamagishi, T; Suzuki, S

    2015-05-01

    Differences in the risk factors for surgical site infection (SSI) following open heart surgery and coronary artery bypass graft surgery are not well described. To identify and compare risk factors for SSI following open heart surgery and coronary artery bypass graft surgery. SSI surveillance data on open heart surgery (CARD) and coronary artery bypass graft surgery (CBGB) submitted to the Japan Nosocomial Infection Surveillance (JANIS) system between 2008 and 2010 were analysed. Factors associated with SSI were analysed using univariate modelling analysis followed by multi-variate logistic regression analysis. Non-binary variables were analysed initially to determine the most appropriate category. The cumulative incidence rates of SSI for CARD and CBGB were 2.6% (151/5895) and 4.1% (160/3884), respectively. In both groups, the duration of the operation and a high American Society of Anesthesiologists' (ASA) score were significant in predicting SSI risk in the model. Wound class was independently associated with SSI in CARD but not in CBGB. Implants, multiple procedures and emergency operations predicted SSI in CARD, but none of these factors predicted SSI in CBGB. There was a remarkable difference in the prediction of risk for SSI between the two types of cardiac surgery. Risk stratification in CARD could be improved by incorporating variables currently available in the existing surveillance systems. Risk index stratification in CBGB could be enhanced by collecting additional variables, because only two of the current variables were found to be significant for the prediction of SSI. Copyright © 2015 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

  8. Persistent seroma after intraoperative placement of MammoSite for accelerated partial breast irradiation: Incidence, pathologic anatomy, and contributing factors

    International Nuclear Information System (INIS)

    Evans, Suzanne B.; Kaufman, Seth A.; Price, Lori Lyn; Cardarelli, Gene; Dipetrillo, Thomas A.; Wazer, David E.

    2006-01-01

    Purpose: To investigate the incidence of, and possible factors associated with, seroma formation after intraoperative placement of the MammoSite catheter for accelerated partial breast irradiation. Methods and Materials: This study evaluated 38 patients who had undergone intraoperative MammoSite catheter placement at lumpectomy or reexcision followed by accelerated partial breast irradiation with 34 Gy in 10 fractions. Data were collected regarding dosimetric parameters, including the volume of tissue enclosed by the 100%, 150%, and 200% isodose shells, dose homogeneity index, and maximal dose at the surface of the applicator. Clinical and treatment-related factors were analyzed, including patient age, patient weight, history of diabetes and smoking, use of reexcision, interval between surgery and radiotherapy, total duration of catheter placement, total excised specimen volume, and presence or absence of postprocedural infection. Seroma was verified by clinical examination, mammography, and/or ultrasonography. Persistent seroma was defined as seroma that was clinically detectable >6 months after radiotherapy completion. Results: After a median follow-up of 17 months, the overall rate of any detectable seroma was 76.3%. Persistent seroma (>6 months) occurred in 26 (68.4%) of 38 patients, of whom 46% experienced at least modest discomfort at some point during follow-up. Of these symptomatic patients, 3 required biopsy or complete cavity excision, revealing squamous metaplasia, foreign body giant cell reaction, fibroblasts, and active collagen deposition. Of the analyzed dosimetric, clinical, and treatment-related variables, only body weight correlated positively with the risk of seroma formation (p = 0.04). Postprocedural infection correlated significantly (p = 0.05) with a reduced risk of seroma formation. Seroma was associated with a suboptimal cosmetic outcome, because excellent scores were achieved in 61.5% of women with seroma compared with 83% without seroma

  9. Analysis of influencing factors on public perception in contaminated site management: Simulation by structural equation modeling at four sites in China.

    Science.gov (United States)

    Li, Xiaonuo; Chen, Weiping; Cundy, Andrew B; Chang, Andrew C; Jiao, Wentao

    2018-03-15

    Public perception towards contaminated site management, a not readily quantifiable latent parameter, was linked through structural equation modeling in this paper to 22 measurable/observable manifest variables associated with the extent of information dissemination and public knowledge of soil pollution, attitude towards remediation policies, and participation in risk mitigation processes. Data obtained through a survey of 412 community residents at four remediation sites in China were employed in the model validation. The outcomes showed that public perception towards contaminated site management might be explained through selected measurable parameters in five categories, namely information disclosure, knowledge of soil pollution, expectations of remediation and redevelopment outcomes, public participation, and site policy, along with their interactions. Among these, information dissemination and attitude towards management policies exhibited significant influence in promoting positive public perception. Based on these examples, responsible agencies therefore should focus on public accessibility to reliable information, and encourage public inputs into policies for contaminated site management, in order to gain public confidence during remediation and regeneration projects. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Incidence and risk factors for surgical site infections in obstetric and gynecological surgeries from a teaching hospital in rural India

    Directory of Open Access Journals (Sweden)

    Ashish Pathak

    2017-06-01

    Full Text Available Abstract Background Surgical site infections (SSI are one of the most common healthcare associated infections in the low-middle income countries. Data on incidence and risk factors for SSI following surgeries in general and Obstetric and Gynecological surgeries in particular are scare. This study set out to identify risk factors for SSI in patients undergoing Obstetric and Gynecological surgeries in an Indian rural hospital. Methods Patients who underwent a surgical procedure between September 2010 to February 2013 in the 60-bedded ward of Obstetric and Gynecology department were included. Surveillance for SSI was based on the Centre for Disease Control (CDC definition and methodology. Incidence and risk factors for SSI, including those for specific procedure, were calculated from data collected on daily ward rounds. Results A total of 1173 patients underwent a surgical procedure during the study period. The incidence of SSI in the cohort was 7.84% (95% CI 6.30–9.38. Majority of SSI were superficial. Obstetric surgeries had a lower SSI incidence compared to gynecological surgeries (1.2% versus 10.3% respectively. The risk factors for SSI identified in the multivariate logistic regression model were age (OR 1.03, vaginal examination (OR 1.31; presence of vaginal discharge (OR 4.04; medical disease (OR 5.76; American Society of Anesthesia score greater than 3 (OR 12.8; concurrent surgical procedure (OR 3.26; each increase in hour of surgery, after the first hour, doubled the risk of SSI; inappropriate antibiotic prophylaxis increased the risk of SSI by nearly 5 times. Each day increase in stay in the hospital after the surgery increased the risk of contacting an SSI by 5%. Conclusions Incidence and risk factors from prospective SSI surveillance can be reported simultaneously for the Obstetric and Gynecological surgeries and can be part of routine practice in resource-constrained settings. The incidence of SSI was lower for Obstetric surgeries

  11. Assessment of algorithms for inferring positional weight matrix motifs of transcription factor binding sites using protein binding microarray data.

    Directory of Open Access Journals (Sweden)

    Yaron Orenstein

    Full Text Available The new technology of protein binding microarrays (PBMs allows simultaneous measurement of the binding intensities of a transcription factor to tens of thousands of synthetic double-stranded DNA probes, covering all possible 10-mers. A key computational challenge is inferring the binding motif from these data. We present a systematic comparison of four methods developed specifically for reconstructing a binding site motif represented as a positional weight matrix from PBM data. The reconstructed motifs were evaluated in terms of three criteria: concordance with reference motifs from the literature and ability to predict in vivo and in vitro bindings. The evaluation encompassed over 200 transcription factors and some 300 assays. The results show a tradeoff between how the methods perform according to the different criteria, and a dichotomy of method types. Algorithms that construct motifs with low information content predict PBM probe ranking more faithfully, while methods that produce highly informative motifs match reference motifs better. Interestingly, in predicting high-affinity binding, all methods give far poorer results for in vivo assays compared to in vitro assays.

  12. Surveillance of surgical site infections at a tertiary care hospital in Greece: incidence, risk factors, microbiology, and impact.

    Science.gov (United States)

    Roumbelaki, Maria; Kritsotakis, Evangelos I; Tsioutis, Constantinos; Tzilepi, Penelope; Gikas, Achilleas

    2008-12-01

    In this first attempt to implement a standardized surveillance system of surgical site infections (SSI) in a Greek hospital, our objective was to identify areas for improvement by comparing main epidemiologic and microbiologic features of SSI with international data. The National Nosocomial Infections Surveillance (NNIS) system protocols were employed to prospectively collect data for patients in 8 surgical wards who underwent surgery during a 9-month period. SSI rates were benchmarked with international data using standardized infection ratios. Risk factors were evaluated by multivariate logistic regression. A total of 129 SSI was identified in 2420 operations (5.3%), of which 47.3% developed after discharge. SSI rates were higher for 2 of 20 operation categories compared with Spanish and Italian data and for 12 of 20 categories compared with NNIS data. Gram-positive microorganisms accounted for 52.1% of SSI isolates, and Enterococci were predominant. Alarming resistance patterns for Enterococcus faecium and Acinetobacter baumannii were recorded. Potentially modifiable risk factors for SSI included multiple procedures, extended duration of operation, and antibiotic prophylaxis. SSI was associated with prolongation of postoperative stay but not with mortality. Comparisons of surveillance data in our hospital with international benchmarks provided useful information for infection control interventions to reduce the incidence of SSI.

  13. Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region

    Directory of Open Access Journals (Sweden)

    Alonso Ángel

    2006-03-01

    Full Text Available Abstract Background Papillomaviruses (PVs infect stratified squamous epithelia in warm-blooded vertebrates and have undergone a complex evolutionary process. The control of the expression of the early ORFs in PVs depends on the binding of cellular and viral transcription factors to the upstream regulatory region (URR of the virus. It is believed that there is a core of transcription factor binding sites (TFBS common to all PVs, with additional individual differences, although most of the available information focuses only on a handful of viruses. Results We have studied the URR of sixty-one PVs, covering twenty different hosts. We have predicted the TFBS present in the URR and analysed these results by principal component analysis and genetic algorithms. The number and nature of TFBS in the URR might be much broader than thus far described, and different PVs have different repertoires of TFBS. Conclusion There are common fingerprints in the URR in PVs that infect primates, although the ancestors of these viruses diverged a long time ago. Additionally, there are obvious differences between the URR of alpha and beta PVs, despite these PVs infect similar histological cell types in the same host, i.e. human. A thorough analysis of the TFBS in the URR might provide crucial information about the differential biology of cancer-associated PVs.

  14. Incidence and risk factors for surgical site infection after open reduction and internal fixation of tibial plateau fracture: A systematic review and meta-analysis.

    Science.gov (United States)

    Shao, Jiashen; Chang, Hengrui; Zhu, Yanbin; Chen, Wei; Zheng, Zhanle; Zhang, Huixin; Zhang, Yingze

    2017-05-01

    This study aimed to quantitatively summarize the risk factors associated with surgical site infection after open reduction and internal fixation of tibial plateau fracture. Medline, Embase, CNKI, Wanfang database and Cochrane central database were searched for relevant original studies from database inception to October 2016. Eligible studies had to meet quality assessment criteria according to the Newcastle-Ottawa Scale, and had to evaluate the risk factors for surgical site infection after open reduction and internal fixation of tibial plateau fracture. Stata 11.0 software was used for this meta-analysis. Eight studies involving 2214 cases of tibial plateau fracture treated by open reduction and internal fixation and 219 cases of surgical site infection were included in this meta-analysis. The following parameters were identified as significant risk factors for surgical site infection after open reduction and internal fixation of tibial plateau fracture (p operative time (OR 2.15; 95% CI 1.53-3.02), tobacco use (OR 2.13; 95% CI 1.13-3.99), and external fixation (OR 2.07; 95% CI 1.05-4.09). Other factors, including male sex, were not identified as risk factors for surgical site infection. Patients with the abovementioned medical conditions are at risk of surgical site infection after open reduction and internal fixation of tibial plateau fracture. Surgeons should be cognizant of these risks and give relevant preoperative advice. Copyright © 2017. Published by Elsevier Ltd.

  15. Defining the plasticity of transcription factor binding sites by Deconstructing DNA consensus sequences: the PhoP-binding sites among gamma/enterobacteria.

    Directory of Open Access Journals (Sweden)

    Oscar Harari

    2010-07-01

    Full Text Available Transcriptional regulators recognize specific DNA sequences. Because these sequences are embedded in the background of genomic DNA, it is hard to identify the key cis-regulatory elements that determine disparate patterns of gene expression. The detection of the intra- and inter-species differences among these sequences is crucial for understanding the molecular basis of both differential gene expression and evolution. Here, we address this problem by investigating the target promoters controlled by the DNA-binding PhoP protein, which governs virulence and Mg(2+ homeostasis in several bacterial species. PhoP is particularly interesting; it is highly conserved in different gamma/enterobacteria, regulating not only ancestral genes but also governing the expression of dozens of horizontally acquired genes that differ from species to species. Our approach consists of decomposing the DNA binding site sequences for a given regulator into families of motifs (i.e., termed submotifs using a machine learning method inspired by the "Divide & Conquer" strategy. By partitioning a motif into sub-patterns, computational advantages for classification were produced, resulting in the discovery of new members of a regulon, and alleviating the problem of distinguishing functional sites in chromatin immunoprecipitation and DNA microarray genome-wide analysis. Moreover, we found that certain partitions were useful in revealing biological properties of binding site sequences, including modular gains and losses of PhoP binding sites through evolutionary turnover events, as well as conservation in distant species. The high conservation of PhoP submotifs within gamma/enterobacteria, as well as the regulatory protein that recognizes them, suggests that the major cause of divergence between related species is not due to the binding sites, as was previously suggested for other regulators. Instead, the divergence may be attributed to the fast evolution of orthologous target

  16. The origins of enhanced activity in factor VIIa analogs and the interplay between key allosteric sites revealed by hydrogen exchange mass spectrometry

    DEFF Research Database (Denmark)

    Rand, Kasper D; Andersen, Mette D; Olsen, Ole H

    2008-01-01

    Factor VIIa (FVIIa) circulates in the blood in a zymogen-like state. Only upon association with membrane-bound tissue factor (TF) at the site of vascular injury does FVIIa become active and able to initiate blood coagulation. Here we used hydrogen exchange monitored by mass spectrometry to invest......Factor VIIa (FVIIa) circulates in the blood in a zymogen-like state. Only upon association with membrane-bound tissue factor (TF) at the site of vascular injury does FVIIa become active and able to initiate blood coagulation. Here we used hydrogen exchange monitored by mass spectrometry...... to investigate the conformational effects of site-directed mutagenesis at key positions in FVIIa and the origins of enhanced intrinsic activity of FVIIa analogs. The differences in hydrogen exchange of two highly active variants, FVIIa(DVQ) and FVIIa(VEAY), imply that enhanced catalytic efficiency was attained...

  17. Interaction of hookworm 14-3-3 with the forkhead transcription factor DAF-16 requires intact Akt phosphorylation sites

    Directory of Open Access Journals (Sweden)

    Hawdon John M

    2009-04-01

    Full Text Available Abstract Background Third-stage infective larvae (L3 of hookworms are in an obligatory state of developmental arrest that ends upon entering the definitive host, where they receive a signal that re-activates development. Recovery from the developmentally arrested dauer stage of Caenorhabditis elegans is analogous to the resumption of development during hookworm infection. Insulin-like signaling (ILS mediates recovery from arrest in C. elegans and activation of hookworm dauer L3. In C. elegans, phosphorylation of the forkhead transcription factor DAF-16 in response to ILS creates binding cites for the 14-3-3 protein Ce-FTT-2, which translocates DAF-16 out of the nucleus, resulting in resumption of reproductive development. Results To determine if hookworm 14-3-3 proteins play a similar role in L3 activation, hookworm FTT-2 was identified and tested for its ability to interact with A. caninum DAF-16 in vitro. The Ac-FTT-2 amino acid sequence was 91% identical to the Ce-FTT-2, and was most closely related to FTT-2 from other nematodes. Ac-FTT-2 was expressed in HEK 293T cells, and was recognized by an antibody against human 14-3-3β isoform. Reciprocal co-immunoprecipitations using anti-epitope tag antibodies indicated that Ac-FTT-2 interacts with Ac-DAF-16 when co-expressed in serum-stimulated HEK 293T cells. This interaction requires intact Akt consensus phosphorylation sites at serine107 and threonine312, but not serine381. Ac-FTT-2 was undetectable by Western blot in excretory/secretory products from serum-stimulated (activated L3 or adult A. caninum. Conclusion The results indicate that Ac-FTT-2 interacts with DAF-16 in a phosphorylation-site dependent manner, and suggests that Ac-FTT-2 mediates activation of L3 by binding Ac-DAF-16 during hookworm infection.

  18. Influence of region and site-specific factors on the degree of general validity of ecological and primary-energy-related assessments of biogas

    International Nuclear Information System (INIS)

    Dressler, Daniela

    2015-01-01

    As described in this publication, since the early 1990s numerous studies based on the life cycle assessment methodology have been dedicated to assessments of different kinds of bioenergy in comparison with fossil energy resources in terms of their energy balance and environmental impact. On reviewing the results of these studies one finds a strikingly wide range of variation. One major factor of influence on the results of life cycle assessments, besides methodological factors such as the choice of allocation method, is the representativeness of the data used. Thus, widely varying results are also obtained when balance calculations and assessments are performed on energy crops with due consideration to regional and site-specific factors. To address this problem the present study endeavoured to identify region and site-specific factors and assess them in terms of their influence on the life cycle assessment of the cultivation and conversion to biogas of different kinds of energy crops. For this purpose the following questions were explored: What influence do region, site and equipment-specific factors have on the results of ecological and primary-energy-related assessments; and how large are the differences in results between region and site-specific assessments on the one hand and assessments based on general assumptions on the other? It transpires that the results of region and site-specific assessments differ from one another in terms of both the assessment of energy cropping and the assessment of the entire process chain of biogas production and conversion to electricity.

  19. Synthesis, purification, and characterization of an Arg152 → Glu site-directed mutant of recombinant human blood clotting factor VII

    International Nuclear Information System (INIS)

    Wildgoose, P.; Kisiel, W.; Berkner, K.L.

    1990-01-01

    Coagulation factor VII circulates in blood as a single-chain zymogen of a serine protease and is converted to its activated two-chain form, factor VIIa, by cleavage of an internal peptide bond located at Arg 152 -Ile 153 . Previous studies using serine protease active-site inhibitors suggest that zymogen factor VII may possess sufficient proteolytic activity to initiate the extrinsic pathway of blood coagulation. In order to assess the putative intrinsic proteolytic activity of single-chain factor VII, the authors have constructed a site-specific mutant of recombinant human factor VII in which arginine-152 has been replaced with a glutamic acid residue. Mutant factor VII was purified in a single step from culture supernatants of baby hamster kidney cells transfected with a plasmid containing the sequence for Arg 152 → Glu factor VII using a calcium-dependent, murine anti-factor VII monoclonal antibody column. The clotting activity of mutant factor VII was completely inhibited following incubation with dansyl-Glu-Gly-Arg chloromethyl ketone, suggesting that the apparent clotting activity of mutant factor VII was due to a contaminating serine protease. Immunoblots of mutant factor VII with human factor IXa revealed no cleavage, whereas incubation of mutant factor VII with human factor Xa resulted in cleavage of mutant factor VII and the formation of a lower molecular weight degradation product migrating at M r ∼40 000. The results are consistent with the proposal that zymogen factor VII possesses no intrinsic proteolytic activity toward factor X or factor IX

  20. Synthesis, purification, and characterization of an Arg sub 152 yields Glu site-directed mutant of recombinant human blood clotting factor VII

    Energy Technology Data Exchange (ETDEWEB)

    Wildgoose, P.; Kisiel, W. (Univ. of New Mexico, Albuquerque (USA)); Berkner, K.L. (ZymoGenetics, Inc., Seattle, WA (USA))

    1990-04-03

    Coagulation factor VII circulates in blood as a single-chain zymogen of a serine protease and is converted to its activated two-chain form, factor VIIa, by cleavage of an internal peptide bond located at Arg{sub 152}-Ile{sub 153}. Previous studies using serine protease active-site inhibitors suggest that zymogen factor VII may possess sufficient proteolytic activity to initiate the extrinsic pathway of blood coagulation. In order to assess the putative intrinsic proteolytic activity of single-chain factor VII, the authors have constructed a site-specific mutant of recombinant human factor VII in which arginine-152 has been replaced with a glutamic acid residue. Mutant factor VII was purified in a single step from culture supernatants of baby hamster kidney cells transfected with a plasmid containing the sequence for Arg{sub 152} {yields} Glu factor VII using a calcium-dependent, murine anti-factor VII monoclonal antibody column. The clotting activity of mutant factor VII was completely inhibited following incubation with dansyl-Glu-Gly-Arg chloromethyl ketone, suggesting that the apparent clotting activity of mutant factor VII was due to a contaminating serine protease. Immunoblots of mutant factor VII with human factor IXa revealed no cleavage, whereas incubation of mutant factor VII with human factor Xa resulted in cleavage of mutant factor VII and the formation of a lower molecular weight degradation product migrating at M{sup r}{approx}40 000. The results are consistent with the proposal that zymogen factor VII possesses no intrinsic proteolytic activity toward factor X or factor IX.

  1. The incidence of surgical site dehiscence following full-thickness gastrointestinal biopsy in dogs and cats and associated risk factors.

    Science.gov (United States)

    Swinbourne, F; Jeffery, N; Tivers, M S; Artingstall, R; Bird, F; Charlesworth, T; Doran, I; Freeman, A; Hall, J; Hattersley, R; Henken, J; Hughes, J; de la Puerta, B; Rutherford, L; Ryan, T; Williams, H; Woods, S; Nicholson, I

    2017-09-01

    The objectives of this study were to: (1) document the incidence of surgical site dehiscence after full-thickness gastrointestinal biopsy in dogs and cats and (2) identify potential risk factors. Data relating to dogs and cats undergoing full-thickness gastrointestinal biopsy were reviewed retrospectively following submission of a completed questionnaire by 12 referral institutions. Outcome measures were definite dehiscence, possible dehiscence (clinical records suggestive of dehiscence but not confirmed), suspected dehiscence (definite and possible combined) and death within 14 days. Logistic regression was planned for analysis of association of dehiscence with low preoperative serum albumin, biopsy through neoplastic tissue, biopsy alongside another major abdominal surgical procedure and biopsy of the colon. Of 172 cats, two (1·2%) had definite dehiscence, and four (2·3%) had possible dehiscence. Low preoperative serum albumin was significantly associated with definite dehiscence in univariable analysis and with suspected dehiscence and death within 14 days in univariable analysis, but all odds ratios had wide 95% confidence intervals. A histopathological diagnosis of neoplasia was significantly associated with death within 14 days in univariable analysis. Of 195 dogs, two (1·0%) had definite dehiscence, and three (1·5%) had possible dehiscence. In dogs, there was no association between any outcome measure and the putative risk factors. Incidence of dehiscence following full-thickness gastrointestinal biopsy was low in this study. When determining the appropriateness of biopsy in individual cases, this information should be balanced against the potentially life-threatening consequences of dehiscence. © 2017 British Small Animal Veterinary Association.

  2. Bioinformatics Identification of Modules of Transcription Factor Binding Sites in Alzheimer's Disease-Related Genes by In Silico Promoter Analysis and Microarrays

    Directory of Open Access Journals (Sweden)

    Regina Augustin

    2011-01-01

    Full Text Available The molecular mechanisms and genetic risk factors underlying Alzheimer's disease (AD pathogenesis are only partly understood. To identify new factors, which may contribute to AD, different approaches are taken including proteomics, genetics, and functional genomics. Here, we used a bioinformatics approach and found that distinct AD-related genes share modules of transcription factor binding sites, suggesting a transcriptional coregulation. To detect additional coregulated genes, which may potentially contribute to AD, we established a new bioinformatics workflow with known multivariate methods like support vector machines, biclustering, and predicted transcription factor binding site modules by using in silico analysis and over 400 expression arrays from human and mouse. Two significant modules are composed of three transcription factor families: CTCF, SP1F, and EGRF/ZBPF, which are conserved between human and mouse APP promoter sequences. The specific combination of in silico promoter and multivariate analysis can identify regulation mechanisms of genes involved in multifactorial diseases.

  3. Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression

    Directory of Open Access Journals (Sweden)

    Sakaki Yoshiyuki

    2004-02-01

    Full Text Available Abstract Background Gene expression is regulated mainly by transcription factors (TFs that interact with regulatory cis-elements on DNA sequences. To identify functional regulatory elements, computer searching can predict TF binding sites (TFBS using position weight matrices (PWMs that represent positional base frequencies of collected experimentally determined TFBS. A disadvantage of this approach is the large output of results for genomic DNA. One strategy to identify genuine TFBS is to utilize local concentrations of predicted TFBS. It is unclear whether there is a general tendency for TFBS to cluster at promoter regions, although this is the case for certain TFBS. Also unclear is the identification of TFs that have TFBS concentrated in promoters and to what level this occurs. This study hopes to answer some of these questions. Results We developed the cluster score measure to evaluate the correlation between predicted TFBS clusters and promoter sequences for each PWM. Non-promoter sequences were used as a control. Using the cluster score, we identified a PWM group called PWM-PCP, in which TFBS clusters positively correlate with promoters, and another PWM group called PWM-NCP, in which TFBS clusters negatively correlate with promoters. The PWM-PCP group comprises 47% of the 199 vertebrate PWMs, while the PWM-NCP group occupied 11 percent. After reducing the effect of CpG islands (CGI against the clusters using partial correlation coefficients among three properties (promoter, CGI and predicted TFBS cluster, we identified two PWM groups including those strongly correlated with CGI and those not correlated with CGI. Conclusion Not all PWMs predict TFBS correlated with human promoter sequences. Two main PWM groups were identified: (1 those that show TFBS clustered in promoters associated with CGI, and (2 those that show TFBS clustered in promoters independent of CGI. Assessment of PWM matches will allow more positive interpretation of TFBS in

  4. Size-resolved source apportionment of ambient particles by positive matrix factorization at Gosan background site in East Asia

    Directory of Open Access Journals (Sweden)

    J. S. Han

    2006-01-01

    Full Text Available Size- and time-resolved aerosol samples were collected using an eight-stage Davis rotating unit for monitoring (DRUM sampler from 29 March to 29 May in 2002 at Gosan, Jeju Island, Korea, which is one of the representative background sites in East Asia. These samples were analyzed using synchrotron X-ray fluorescence for 3-h average concentrations of 19 elements consisting of S, Si, Al, Fe, Ca, Cl, Cu, Zn, Ti, K, Mn, Pb, Ni, V, Se, As, Rb, Cr, Br. The size-resolved data sets were then analyzed using the positive matrix factorization (PMF technique in order to identify possible sources and estimate their contribution to particulate matter mass. PMF analysis uses the uncertainty of the measured data to provide an optimal weighting. Fifteen sources were resolved in eight size ranges (0.07~12 μm and included continental soil, local soil, sea salt, biomass/biofuel burning, coal combustion, oil heating furnace, residual oil fired boiler, municipal incineration, nonferrous metal source, ferrous metal source, gasoline vehicle, diesel vehicle, copper smelter and volcanic emission. PMF analysis of size-resolved source contributions showed that natural sources represented by local soil, sea salt and continental soil contributed about 79% to the predicted primary particulate matter (PM mass in the coarse size range (1.15~12 μm. On the other hand, anthropogenic sources such as coal combustion and biomass/biofuel burning contributed about 60% in the fine size range (0.56~2.5 μm. The diesel vehicle source contributed the most in the ultra-fine size range (0.07~0.56 μm and was responsible for about 52% of the primary PM mass.

  5. Age Factor in Business Education Students' Use of Social Networking Sites in Tertiary Institutions in Anambra State, Nigeria

    Science.gov (United States)

    Ementa, Christiana Ngozi; Ile, Chika Madu

    2015-01-01

    There are diverse social networking sites which range from those that provide social sharing and interaction to those that provide networks for professionals within same and other fields. Social networking sites require a user to sign up, create a profile and begin sending short messages about what the user is doing or thinking. The study sought…

  6. Breeding site selection by coho salmon (Oncorhynchus kisutch) in relation to large wood additions and factors that influence reproductive success

    Science.gov (United States)

    Clark, Steven M.; Dunham, Jason B.; McEnroe, Jeffery R.; Lightcap, Scott W.

    2014-01-01

    The fitness of female Pacific salmon (Oncorhynchus spp.) with respect to breeding behavior can be partitioned into at least four fitness components: survival to reproduction, competition for breeding sites, success of egg incubation, and suitability of the local environment near breeding sites for early rearing of juveniles. We evaluated the relative influences of habitat features linked to these fitness components with respect to selection of breeding sites by coho salmon (Oncorhynchus kisutch). We also evaluated associations between breeding site selection and additions of large wood, as the latter were introduced into the study system as a means of restoring habitat conditions to benefit coho salmon. We used a model selection approach to organize specific habitat features into groupings reflecting fitness components and influences of large wood. Results of this work suggest that female coho salmon likely select breeding sites based on a wide range of habitat features linked to all four hypothesized fitness components. More specifically, model parameter estimates indicated that breeding site selection was most strongly influenced by proximity to pool-tail crests and deeper water (mean and maximum depths). Linkages between large wood and breeding site selection were less clear. Overall, our findings suggest that breeding site selection by coho salmon is influenced by a suite of fitness components in addition to the egg incubation environment, which has been the emphasis of much work in the past.

  7. Factors affecting food chain transfer of mercury in the vicinity of the Nyanza site, Sudbury River, Massachusetts

    Science.gov (United States)

    Haines, T.A.; May, T.W.; Finlayson, R.T.; Mierzykowski, S.E.

    2003-01-01

    The influence of the Nyanza Chemical Waste Dump Superfund Site on the Sudbury River, Massachusetts, was assessed by analysis of sediment, fish prey organisms, and predator fish from four locations in the river system. Whitehall Reservoir is an impoundment upstream of the site, and Reservoir #2 is an impoundment downstream of the site. Cedar Street is a flowing reach upstream of the site, and Sherman Bridge is a flowing reach downstream of the site. Collections of material for analysis were made three times, in May, July, and October. Sediment was analyzed for acid-volatile sulfide (AVS), simultaneously-extracted (SEM) metals (As, Cd, Cr, Hg, Pb, Sb, Zn), and total recoverable Hg. The dominant predatory fish species collected at all sites, largemouth bass (Micropterus salmoides), was analyzed for the same suite of metals as sediment. Analysis of stomach contents of bass identified small fish (yellow perch Perca flavescens, bluegill Lepomis macrochirus, and pumpkinseed Lepomis gibbosus), crayfish, and dragonfly larvae as the dominant prey organisms. Samples of the prey were collected from the same locations and at the same times as predator fish, and were analyzed for total and methyl mercury. Results of AVS and SEM analyses indicated that sediments were not toxic to aquatic invertebrates at any site. The SEM concentrations of As, Cd, and Cr were significantly higher at Reservoir #2 than at the reference sites, and SEM As and Cd were significantly higher at Sherman Bridge than at Cedar St. Sediment total Hg was elevated only at Reservoir #2. Hg was higher at site-influenced locations in all fish species except brown bullhead (Ameiurus nebulosus). Cd was higher in bluegill, black crappie (Pomoxis nigromaculatus), and brown bullhead, and Cr was higher in largemouth bass fillet samples but not in whole-body samples. There were no seasonal differences in sediment or prey organism metals, but some metals in some fish species did vary over time in an inconsistent manner

  8. Geological factors of disposal site selection for low-and intermediate-level solid radwastes in China

    International Nuclear Information System (INIS)

    Chen Zhangru

    1993-01-01

    For disposal of low- and intermediate-level solid radioactive wastes, shallow-ground disposal can provide adequate isolation of waste from human for a fairly long period of time. The objective of disposal site selection is to ensure that the natural properties of the site together with the engineered barrier site shall provide adequate isolation of radionuclides from the human beings and environment, so the whole disposal system can keep the radiological impact within an acceptable level. Since the early 1980's, complying with the national standards and the expert's conception as well as the related IAEA Criteria, geological selection of disposal sites for low-and intermediate-level solid radwastes has been carried out in East China, South China, Northwest China and Southwest China separately. Finally, 5 candidate sites were recommended to the CNNC

  9. Sites involved in intra- and interdomain allostery associated with the activation of factor VIIa pinpointed by hydrogen-deuterium exchange and electron transfer dissociation mass spectrometry.

    Science.gov (United States)

    Song, Hongjian; Olsen, Ole H; Persson, Egon; Rand, Kasper D

    2014-12-19

    Factor VIIa (FVIIa) is a trypsin-like protease that plays an important role in initiating blood coagulation. Very limited structural information is available for the free, inactive form of FVIIa that circulates in the blood prior to vascular injury and the molecular details of its activity enhancement remain elusive. Here we have applied hydrogen/deuterium exchange mass spectrometry coupled to electron transfer dissociation to pinpoint individual residues in the heavy chain of FVIIa whose conformation and/or local interaction pattern changes when the enzyme transitions to the active form, as induced either by its cofactor tissue factor or a covalent active site inhibitor. Identified regulatory residues are situated at key sites across one continuous surface of the protease domain spanning the TF-binding helix across the activation pocket to the calcium binding site and are embedded in elements of secondary structure and at the base of flexible loops. Thus these residues are optimally positioned to mediate crosstalk between functional sites in FVIIa, particularly the cofactor binding site and the active site. Our results unambiguously show that the conformational allosteric activation signal extends to the EGF1 domain in the light chain of FVIIa, underscoring a remarkable intra- and interdomain allosteric regulation of this trypsin-like protease. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Meta-analysis of the effects of soil properties, site factors and experimental conditions on solute transport

    Directory of Open Access Journals (Sweden)

    J. K. Koestel

    2012-06-01

    Full Text Available Preferential flow is a widespread phenomenon that is known to strongly affect solute transport in soil, but our understanding and knowledge is still poor of the site factors and soil properties that promote it. To investigate these relationships, we assembled a database from the peer-reviewed literature containing information on 733 breakthrough curve experiments under steady-state flow conditions. Most of the collected experiments (585 of the 733 datasets had been conducted on undisturbed soil columns, although some experiments on repacked soil, clean sands, and glass beads were also included. In addition to the apparent dispersivity, we focused our attention on three indicators of preferential solute transport: namely the 5%-arrival time, the holdback factor, and the ratio of piston-flow and average transport velocities. Our results suggest that, in contrast to the 5%-arrival time and the holdback factor, the piston-flow to transport velocity ratio is not related to preferential macropore transport but rather to the exclusion or retardation of the applied tracer. Confirming that the apparent longitudinal dispersivity is positively correlated with the travel distance of the tracer, our results also illustrate that this relationship is refined if the normalized 5%-tracer arrival time is also taken into account. In particular, we found that the degree of preferential solute transport increases with apparent dispersivity and decreases with travel distance. A similar but weaker relationship was observed between apparent dispersivity, 5%-tracer arrival time, and lateral observation scale, such that the degree of preferential transport increases with lateral observation scale. However, we also found that the travel distance and the lateral observation scale in the investigated dataset are correlated, which makes it difficult to distinguish their influence on these transport characteristics. We also found that the strength of preferential transport

  11. Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [ChIP-Seq

    NARCIS (Netherlands)

    Muiño, J.M.; Bruijn, de S.A.; Vingron, Martin; Angenent, G.C.; Kaufmann, K.

    2015-01-01

    Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the

  12. Multiple autophosphorylation sites of the epidermal growth factor receptor are essential for receptor kinase activity and internalization. Contrasting significance of tyrosine 992 in the native and truncated receptors

    DEFF Research Database (Denmark)

    Sorkin, A; Helin, K; Waters, C M

    1992-01-01

    The role of epidermal growth factor (EGF) receptor autophosphorylation sites in the regulation of receptor functions has been studied using cells transfected with mutant EGF receptors. Simultaneous point mutation of 4 tyrosines (Y1068, Y1086, Y1148, Y1173) to phenylalanine, as well as removal of ...

  13. Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq

    NARCIS (Netherlands)

    Muiño, J.M.; Bruijn, de S.A.; Vingron, Martin; Angenent, G.C.; Kaufmann, Kerstin

    2015-01-01

    Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the

  14. Climate and site management as driving factors for the atmospheric greenhouse gas exchange of a restored wetland

    Directory of Open Access Journals (Sweden)

    M. Herbst

    2013-01-01

    Full Text Available The atmospheric greenhouse gas (GHG budget of a restored wetland in western Denmark was established for the years 2009–2011 from eddy covariance measurements of carbon dioxide (CO2 and methane (CH4 fluxes. The water table in the wetland, which was restored in 2002, was unregulated, and the vegetation height was limited through occasional grazing by cattle and grass cutting. The annual net CO2 uptake varied between 195 and 983 g m−2 and the annual net CH4 release varied between 11 and 17 g m−2. In all three years the wetland was a carbon sink and removed between 42 and 259 g C m−2 from the atmosphere. However, in terms of the full annual GHG budget (assuming that 1 g CH4 is equivalent to 25 g CO2 with respect to the greenhouse effect over a time horizon of 100 years the wetland was a sink in 2009, a source in 2010 and neutral in 2011. Complementary observations of meteorological factors and management activities were used to explain the large inter-annual variations in the full atmospheric GHG budget of the wetland. The largest impact on the annual GHG fluxes, eventually defining their sign, came from site management through changes in grazing duration and animal stocking density. These changes accounted for half of the observed variability in the CO2 fluxes and about two thirds of the variability in CH4 fluxes. An unusually long period of snow cover in 2010 had the second largest effect on the annual CO2 flux, whose interannual variability was larger than that of the CH4 flux. Since integrated CO2 and CH4 flux data from restored wetlands are still very rare, it is concluded that more long-term flux measurements are needed to quantify the effects of ecosystem disturbance, in terms of management activities and exceptional weather patterns, on the atmospheric GHG budget more

  15. Assessment of economic factors affecting the satellite power system. Volume 2: The systems implications of rectenna siting issues

    Science.gov (United States)

    Chapman, P. K.; Bugos, B. J.; Csigi, K. I.; Glaser, P. E.; Schimke, G. R.; Thomas, R. G.

    1979-01-01

    The feasibility was evaluated of finding potential sites for Solar Power Satellite (SPS) receiving antennas (rectennas) in the continental United States, in sufficient numbers to permit the SPS to make a major contribution to U.S. generating facilities, and to give statistical validity to an assessment of the characteristics of such sites and their implications for the design of the SPS system. It is found that the cost-optimum power output of the SPS does not depend on the particular value assigned to the cost per unit area of a rectenna and its site, as long as it is independent of rectenna area. Many characteristics of the sites chosen affect the optimum design of the rectenna itself.

  16. Development of variable LRFD \\0x03C6 factors for deep foundation design due to site variability [summary].

    Science.gov (United States)

    2012-01-01

    Both the Florida Department of Transportation : (FDOT) and the Federal Highway Administration : (FHWA) specify use of fixed resistance factors () : for Load and Resistance Factored Design (LRFD) of : deep foundations, depending on design approach :...

  17. Monitoring Ras Interactions with the Nucleotide Exchange Factor Son of Sevenless (Sos) Using Site-specific NMR Reporter Signals and Intrinsic Fluorescence*

    Science.gov (United States)

    Vo, Uybach; Vajpai, Navratna; Flavell, Liz; Bobby, Romel; Breeze, Alexander L.; Embrey, Kevin J.; Golovanov, Alexander P.

    2016-01-01

    The activity of Ras is controlled by the interconversion between GTP- and GDP-bound forms partly regulated by the binding of the guanine nucleotide exchange factor Son of Sevenless (Sos). The details of Sos binding, leading to nucleotide exchange and subsequent dissociation of the complex, are not completely understood. Here, we used uniformly 15N-labeled Ras as well as [13C]methyl-Met,Ile-labeled Sos for observing site-specific details of Ras-Sos interactions in solution. Binding of various forms of Ras (loaded with GDP and mimics of GTP or nucleotide-free) at the allosteric and catalytic sites of Sos was comprehensively characterized by monitoring signal perturbations in the NMR spectra. The overall affinity of binding between these protein variants as well as their selected functional mutants was also investigated using intrinsic fluorescence. The data support a positive feedback activation of Sos by Ras·GTP with Ras·GTP binding as a substrate for the catalytic site of activated Sos more weakly than Ras·GDP, suggesting that Sos should actively promote unidirectional GDP → GTP exchange on Ras in preference of passive homonucleotide exchange. Ras·GDP weakly binds to the catalytic but not to the allosteric site of Sos. This confirms that Ras·GDP cannot properly activate Sos at the allosteric site. The novel site-specific assay described may be useful for design of drugs aimed at perturbing Ras-Sos interactions. PMID:26565026

  18. Experimental study of a model and parameters calculating annual mean atmospheric dispersion factor for a nuclear power plant to be build in coastal site

    International Nuclear Information System (INIS)

    Hu Erbang; Chen Jiayi; Zhang Maoshuan; Gao Zhanrong; Yao Rentai; Jia Peirong; Qiao Qingdang

    1999-01-01

    The author tries to develop a new model calculating annual mean atmospheric dispersion factor for a nuclear power plant to be build in coastal site based on field experiments. This model considers not only the difference between shore ward and off-shore but also the comprehensive effect of following factors: mixed layer and thermal internal boundary layer, mixing release and variation of diffusion parameters due to the distance from coast and so on. The various parameters needed in the model are obtained from the field atmospheric experiments done on the NPP site during 1995∼1996. There dimension joint frequency is got from wind and temperature measurements at 4 heights of a tower of 100 m; diffusion parameters shore ward and off-shore from turbulent measurement and wind tunnel simulation test; the parameters relative to sea and land breeze and thermal internal boundary layer are obtained from tests with low altitude radiosonde and lost balloon at 3 sites during two periods of Summer and Winter. Finally a comparison of the results given by this model and commonly used model provided by relative guides is done. The comparison shows that about 1 times under estimation is found for the maximum of annual mean atmospheric dispersion factor in common model because the effect from thermal internal boundary layer and other factors are neglected

  19. Attenuation characteristics of seismic motion based on earthquake observation records. Identification of damping factor at hard rock sites and its influences on ground stability evaluation

    International Nuclear Information System (INIS)

    Sato, Hiroaki; Kanatani, Mamoru; Ohtori, Yasuki

    2005-01-01

    In this report, we examined validity of currently available ground stability evaluation method by applying commonly used damping factor which was invariant for frequency. First, we conducted a survey of the actual conditions of damping factors, which were used in ground stability evaluation, on 10 existing nuclear power plants. As a result, we found that damping factor of 0.03(3%) was used in of 80 percent investigated plants. Next, a spectral inversion method using very fast simulated annealing was proposed for identifying damping factor and its lower limit. Here, the lower limit of damping factor means intrinsic damping factor. The developed inversion method was applied to borehole array data recorded at hard rock ground. From the inversion, it was found that intrinsic damping factor of hard rock ground distributed between about 0.03(3%) and 0.06(3%) at a depth of less than 100m, and between about 0.003(0.3%) and 0.01(1%) at a depth of more than 100m. Furthermore, we indicated that scattering damping factor with in a depth of less than 100m was in proportion to the almost -1.0 power of the frequency, and the factor in a depth of more than 100m had a peak in a frequency range from about 1.0 to 5.0 Hz. Therefore, it was recognized that commonly used damping of 0.03(3%) expressed intrinsic damping factor of shallower hard rock ground. Finally, we estimated the influences of damping factor on ground stability evaluation by 2D dynamic FEM analyses of hard rock foundation ground considering 8 slipping lines using 6 combinations of damping factor. It was demonstrated that the variation of damping factor was not so decisive on the results of ground stability evaluation. This suggests present ground stability evaluation method by applying commonly used damping factor is reasonable for hard rock sites. (author)

  20. Source identification of water-soluble organic aerosols at a roadway site using a positive matrix factorization analysis.

    Science.gov (United States)

    Park, Seungshik; Cho, Sung Yong; Bae, Min-Suk

    2015-11-15

    Daily PM2.5 measurements were carried out at a local roadway every sixth day from May 2011 to August 2013 to obtain seasonal quantitative information on the primary and secondary sources of two water-soluble organic carbon (WSOC) fractions. Filter samples were analyzed for OC, elemental carbon (EC), WSOC, hydrophilic and hydrophobic WSOC fractions (WSOC(HPI) and WSOC(HPO)), and ionic species. An XAD solid phase extraction method and a total organic carbon analyzer were used to isolate the two WSOC fractions and determine their amounts, respectively. The WSOC/OC and WSOC(HPI)/WSOC ratios were 0.62±0.13 and 0.47±0.14, respectively. Similar seasonal profiles in EC, OC, and WSOC concentrations were observed, with higher concentrations occurring in the cold season and lower concentrations in the warm season. However, opposite results were obtained in WSOC/OC and WSOC(HPI)/WSOC ratios, with the higher in the warm season and the lower in the cold season. Correlation analyses indicated that two WSOC fractions in winter were likely attributed to secondary formation processes, biomass burning (BB), and traffic emissions, while WSOC(HPI) observed in other seasons were associated with secondary formation processes similar to those of oxalate and secondary inorganic species. A positive matrix factorization (PMF) model was employed to investigate the sources of two WSOC fractions. PMF indicated that concentrations of WSOC fractions were affected by five sources: secondary NO3(-) related, secondary SO4(2-) and oxalate related, traffic emissions, BB emissions, and sea-salt. Throughout the study period, secondary organic aerosols were estimated to be the most dominant contributor of WSOC fractions, with higher contributions occurring in the warm seasons. The contribution of secondary aerosol formation processes (NO3(-) related+SO4(2-) and oxalate related) to WSOC(HPI) and WSOC(HPO) was on an average 56.2% (45.0-73.8%) and 47.7% (39.6-52.1%), respectively. The seasonal average

  1. Mental stress and psychosocial factors at work in relation to multiple-site musculoskeletal pain: a longitudinal study of kitchen workers.

    Science.gov (United States)

    Haukka, Eija; Leino-Arjas, Päivi; Ojajärvi, Anneli; Takala, Esa-Pekka; Viikari-Juntura, Eira; Riihimäki, Hilkka

    2011-04-01

    Among 385 female kitchen workers, we examined (1) whether mental stress and psychosocial factors at work (job control, skill discretion, supervisor support, co-worker relationships, and hurry) predict multiple-site musculoskeletal pain (MSP; defined as pain at ≥ 3 of seven sites) and (2) reversedly, whether MSP predicts these psychosocial factors. Data were collected by questionnaire at 3-month intervals during 2 years. Trajectory analysis was applied. Four trajectories of MSP prevalence emerged: Low, Descending, Ascending, and High. For the psychosocial factors, a two-trajectory model (Ascending or High vs. Low) yielded the best fit. In logistic regression analysis, with the Low MSP trajectory as reference, poor co-worker relationships (odds ratio [OR] 3.9), mental stress (3.1) and hurry (2.1) at baseline predicted belonging to the High MSP trajectory. Also MSP at baseline predicted the trajectories (Ascending vs. Low) of low job control (2.2) and mental stress (3.2). Adverse changes in most psychosocial factors were associated with belonging to the High (ORs between 2.3 and 8.6) and Ascending (2.7-5.5) MSP trajectories. In generalized estimating equations, time-lagged by 3 months, all psychosocial factors but two predicted MSP (1.4-2.1), allowing, e.g. for MSP at baseline, and vice versa, MSP predicted low job control, low supervisor support, and mental stress (1.4-2.0), after adjustment for e.g. the relevant psychosocial factor at baseline. In conclusion, we found that several psychosocial factors predicted MSP and that MSP predicted several psychosocial factors. The results suggest a cumulative process in which adverse psychosocial factors and MSP influence each other. Copyright © 2010 European Federation of International Association for the Study of Pain Chapters. Published by Elsevier Ltd. All rights reserved.

  2. Computational identification of developmental enhancers:conservation and function of transcription factor binding-site clustersin drosophila melanogaster and drosophila psedoobscura

    Energy Technology Data Exchange (ETDEWEB)

    Berman, Benjamin P.; Pfeiffer, Barret D.; Laverty, Todd R.; Salzberg, Steven L.; Rubin, Gerald M.; Eisen, Michael B.; Celniker, SusanE.

    2004-08-06

    The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene, and assayed embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. Measuring conservation of sequence features closely linked to function--such as binding-site clustering--makes better use of comparative sequence data than commonly used methods that examine only sequence identity.

  3. Polymorphisms in Non-coding RNA Genes and Their Targets Sites as Risk Factors of Sporadic Colorectal Cancer

    Czech Academy of Sciences Publication Activity Database

    Vodička, Pavel; Pardini, Barbara; Vymetálková, Veronika; Naccarati, Alessio

    2016-01-01

    Roč. 937, č. 2016 (2016), s. 123-149 ISSN 0065-2598 R&D Projects: GA MZd(CZ) NV15-26535A; GA ČR(CZ) GA15-08239S Institutional support: RVO:68378041 Keywords : colorectal cancer * polymorphism * risk factors Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.881, year: 2016

  4. Dansyl (5-dimethylaminonaphthalene-1-sulphonyl)-heparin binds antithrombin III and platelet factor 4 at separate sites

    Science.gov (United States)

    Piepkorn, Michael W.

    1981-01-01

    Antithrombin III binds to, and thereby augments the fluorescence of, dansyl-(5-dimethylaminonaphthalene-1-sulphonyl)-heparin; platelet factor 4 binding to the fluorescent heparin has little of this effect. Competition studies in which antithrombin III competes with platelet factor 4 for heparin binding demonstrate that heparin can simultaneously bind both proteins. PMID:7317004

  5. Lentivector Integration Sites in Ependymal Cells From a Model of Metachromatic Leukodystrophy: Non-B DNA as a New Factor Influencing Integration

    Science.gov (United States)

    McAllister, Robert G; Liu, Jiahui; Woods, Matthew W; Tom, Sean K; Rupar, C Anthony; Barr, Stephen D

    2014-01-01

    The blood–brain barrier controls the passage of molecules from the blood into the central nervous system (CNS) and is a major challenge for treatment of neurological diseases. Metachromatic leukodystrophy is a neurodegenerative lysosomal storage disease caused by loss of arylsulfatase A (ARSA) activity. Gene therapy via intraventricular injection of a lentiviral vector is a potential approach to rapidly and permanently deliver therapeutic levels of ARSA to the CNS. We present the distribution of integration sites of a lentiviral vector encoding human ARSA (LV-ARSA) in murine brain choroid plexus and ependymal cells, administered via a single intracranial injection into the CNS. LV-ARSA did not exhibit a strong preference for integration in or near actively transcribed genes, but exhibited a strong preference for integration in or near satellite DNA. We identified several genomic hotspots for LV-ARSA integration and identified a consensus target site sequence characterized by two G-quadruplex-forming motifs flanking the integration site. In addition, our analysis identified several other non-B DNA motifs as new factors that potentially influence lentivirus integration, including human immunodeficiency virus type-1 in human cells. Together, our data demonstrate a clinically favorable integration site profile in the murine brain and identify non-B DNA as a potential new host factor that influences lentiviral integration in murine and human cells. PMID:25158091

  6. The influence of home-site factors on residents' willingness to pay: An application for power generation from scrubland in Galicia, Spain

    International Nuclear Information System (INIS)

    Solino, Mario; Farizo, Begona A.; Campos, Pablo

    2009-01-01

    The main objective of this paper is to measure how much home-site factors can help to explain the individual WTP for an environmental improvement in power generation in Galicia, Spain. The results show that home-site variables such as a dispersed population, local community income, population growth and coastal/inland emplacements have significant effects on the residents' WTP. Individual and home-site models are compared using goodness-of-fit measures, and implications for forestry resources management and energy planning are discussed. The results favor to take into account the home-site variables into the WTP function. Moreover, a different structure of preferences for coastal and inland inhabitants is identified. A cross-validity analysis shows that some home-site coefficients are common to both sub-samples, but the scale parameters are not homogenous. This analysis could be useful to inform and support the public energy policy when designing incentives that promote the electric use of biomass.

  7. What Factors Impact Consumer Perception of the Effectiveness of Health Information Sites? An Investigation of the Korean National Health Information Portal.

    Science.gov (United States)

    Choung, Ji Tae; Lee, Yoon Seong; Jo, Heui Sug; Shim, Minsun; Lee, Hun Jae; Jung, Su Mi

    2017-07-01

    Lay public's concerns around health and health information are increasing. In response, governments and government agencies are establishing websites to address such concerns and improve health literacy by providing better access to validated health information. Since 2011, the Korean government has constructed the National Health Information Portal (NHIP) website run in collaboration with the Korean Academy of Medical Sciences (KAMS). This study therefore aimed to 1) examine consumer use of NHIP, with respect to the usage patterns, evaluation on health information provided, and perceived effectiveness of the site; and 2) identify factors that may impact perceived effectiveness of the site. An online survey was conducted with 164 NHIP users, recruited through a popup window on the main screen of the portal website from October to November 2015. The significant predicting factors supported by the data include the relevance of health information on the site, the usefulness of information in making health decisions, and the effective visualization of information. These factors can inform future efforts to design more effective health information websites, possibly based on metadata systems, to further advance the lay public's information seeking and health literacy. © 2017 The Korean Academy of Medical Sciences.

  8. Site selection

    International Nuclear Information System (INIS)

    Olsen, C.W.

    1983-07-01

    The conditions and criteria for selecting a site for a nuclear weapons test at the Nevada Test Site are summarized. Factors considered are: (1) scheduling of drill rigs, (2) scheduling of site preparation (dirt work, auger hole, surface casing, cementing), (3) schedule of event (when are drill hole data needed), (4) depth range of proposed W.P., (5) geologic structure (faults, Pz contact, etc.), (6) stratigraphy (alluvium, location of Grouse Canyon Tuff, etc.), (7) material properties (particularly montmorillonite and CO 2 content), (8) water table depth, (9) potential drilling problems (caving), (10) adjacent collapse craters and chimneys, (11) adjacent expended but uncollapsed sites, (12) adjacent post-shot or other small diameter holes, (13) adjacent stockpile emplacement holes, (14) adjacent planned events (including LANL), (15) projected needs of Test Program for various DOB's and operational separations, and (16) optimal use of NTS real estate

  9. The positive transcription factor of the 5S RNA gene proteolyses during direct exchange between 5S DNA sites

    OpenAIRE

    1986-01-01

    We have examined the association, dissociation, and exchange of the 5S specific transcription factor (TFIIIA) with somatic- and oocyte-type 5S DNA. The factor associates faster with somatic than with oocyte 5S DNA, and the rate of complex formation is accelerated by vector DNA. Once formed, the TFIIIA-5S DNA complex is stable for greater than 4 h in the absence of free 5S DNA, and its dissociation is identical for somatic and for oocyte 5S DNA. In the presence of free 5S DNA, the factor trans...

  10. Determination of the Sites with Conservation Priority in Research Forests of Yasouj University Based on Physiographic Factors

    Directory of Open Access Journals (Sweden)

    R. Zolfaghari

    2013-03-01

    Full Text Available Regarding high economic and conservative values of Zagros forests, and livelihood dependency of local people these recourses, determination of sites with higher conservation index can help us to maintain biodiversity of these forests more efficiently. Therefore, 49 plots with 450 m2 in area accompanied by 1, 10 and 45 m2 subplots were taken as systematic random design in research forests of Yasouj University. The number of species in each plot and subplot was recorded. The conservation values for different physiographic regions of forest were calculated using integrative parameters such as the number of species per plot, number of rare species per plot, number of tree species per plot, Jaccards similarity coefficient and slope of species-log(area. Comparing the conservation index in different physiographic sites revealed that the areas located in the north, hills and lower altitudes can be considered for in situ conservation due to higher number of trees, rare species and total plant species, species-log (area slope and lower amount of Jaccard similarity coefficient. But, vegetative sites located in lower slopes and south, because of lower conservation index, can be used for other multipurpose forestry activities. Using this index for different forest areas can be potentially conducted for better conservation and management of Zagros forests.

  11. Factors influencing choice of site for rural clinical placements by final year medical students in a South African university

    Directory of Open Access Journals (Sweden)

    Nontsikelelo O. Mapukata

    2017-04-01

    Conclusion: This study has demonstrated the challenges faced by coordinators in balancing personal and institutional needs with country needs and the contextual factors that must be considered when implementing medical education programmes that respond to social challenges.

  12. A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Lindemose, Søren; Jensen, Michael Krogh; de Velde, Jan Van

    2014-01-01

    regulatory networks of 12 NAC transcription factors. Our data offer specific single-base resolution fingerprints for most TFs studied and indicate that NAC DNA-binding specificities might be predicted from their DNA-binding domain's sequence. The developed methodology, including the application......Target gene identification for transcription factors is a prerequisite for the systems wide understanding of organismal behaviour. NAM-ATAF1/2-CUC2 (NAC) transcription factors are amongst the largest transcription factor families in plants, yet limited data exist from unbiased approaches to resolve...... the DNA-binding preferences of individual members. Here, we present a TF-target gene identification workflow based on the integration of novel protein binding microarray data with gene expression and multi-species promoter sequence conservation to identify the DNA-binding specificities and the gene...

  13. Risk Factors and Predictive Model Development of Thirty-Day Post-Operative Surgical Site Infection in the Veterans Administration Surgical Population.

    Science.gov (United States)

    Li, Xinli; Nylander, William; Smith, Tracy; Han, Soonhee; Gunnar, William

    2018-04-01

    Surgical site infection (SSI) complicates approximately 2% of surgeries in the Veterans Affairs (VA) hospitals. Surgical site infections are responsible for increased morbidity, length of hospital stay, cost, and mortality. Surgical site infection can be minimized by modifying risk factors. In this study, we identified risk factors and developed accurate predictive surgical specialty-specific SSI risk prediction models for the Veterans Health Administration (VHA) surgery population. In a retrospective observation study, surgical patients who underwent surgery from October 2013 to September 2016 from 136 VA hospitals were included. The Veteran Affairs Surgical Quality Improvement Program (VASQIP) database was used for the pre-operative demographic and clinical characteristics, intra-operative characteristics, and 30-day post-operative outcomes. The study population represents 11 surgical specialties: neurosurgery, urology, podiatry, otolaryngology, general, orthopedic, plastic, thoracic, vascular, cardiac coronary artery bypass graft (CABG), and cardiac valve/other surgery. Multivariable logistic regression models were developed for the 30-day post-operative SSIs. Among 354,528 surgical procedures, 6,538 (1.8%) had SSIs within 30 days. Surgical site infection rates varied among surgical specialty (0.7%-3.0%). Surgical site infection rates were higher in emergency procedures, procedures with long operative duration, greater complexity, and higher relative value units. Other factors associated with increased SSI risk were high level of American Society of Anesthesiologists (ASA) classification (level 4 and 5), dyspnea, open wound/infection, wound classification, ascites, bleeding disorder, chemotherapy, smoking, history of severe chronic obstructive pulmonary disease (COPD), radiotherapy, steroid use for chronic conditions, and weight loss. Each surgical specialty had a distinct combination of risk factors. Accurate SSI risk-predictive surgery specialty

  14. Examination of the site amplification factor of OBS and their application to magnitude estimation and ground-motion prediction for EEW

    Science.gov (United States)

    Hayashimoto, N.; Hoshiba, M.

    2013-12-01

    1. Introduction Ocean bottom seismograph (OBS) is useful for making Earthquake Early Warning (EEW) earlier. However, careful handling of these data is required because the installation environment of OBSs may be different from that of land stations. Site amplification factor is an important factor to estimate the magnitudes, and to predict ground motions (e.g. seismic intensity) in EEW. In this presentation, we discuss the site amplification factor of OBS in the Tonankai area of Japan from these two points of view. 2. Examination of magnitude correction of OBS In the EEW of JMA, the magnitude is estimated from the maximum amplitude of the displacement in real time. To provide the fast magnitude estimation, the magnitude-estimation algorithm switches from the P to S formula (Meew(P) to Meew(S)) depending on the expected S-phase arrival (Kamigaichi,2004). To estimate the magnitude correction for OBS, we determine Meew(P) and Meew(S) at OBSs and compare them with JMA magnitude (Mjma). We find Meew(S) at OBS is generally larger than Mjma by approximately 0.6. The slight differences of spatial distribution of Meew(S) amplification are also found among other OBSs. From the numerical simulations, Nakamura et al. (MGR,submitted) pointed out that the oceanic layer and the low-velocity sediment layers causes the large amplifications in low frequency range (0.1-0.2Hz) at OBSs. We conclude that the site effect of OBS characterized by such a low velocity sediment layers causes those amplification of Magnitude. 3. The frequency-dependent site factor of OBS estimated from Fourier spectrum ratio and their application for prediction of seismic intensity of land station We compare Fourier spectra of S-wave portion on OBSs with those on adjacent land stations. Station pair whose distance is smaller than 50 km is analyzed, and we obtain that spectral ratio of land station (MIEH05 of the KiK-net/NIED) to OBS (KMA01 of the DONET/JAMSTEC) is 5-20 for frequencies 10-20Hz for both

  15. Global Mapping of Transcription Factor Binding Sites by Sequencing Chromatin Surrogates: a Perspective on Experimental Design, Data Analysis, and Open Problems.

    Science.gov (United States)

    Wei, Yingying; Wu, George; Ji, Hongkai

    2013-05-01

    Mapping genome-wide binding sites of all transcription factors (TFs) in all biological contexts is a critical step toward understanding gene regulation. The state-of-the-art technologies for mapping transcription factor binding sites (TFBSs) couple chromatin immunoprecipitation (ChIP) with high-throughput sequencing (ChIP-seq) or tiling array hybridization (ChIP-chip). These technologies have limitations: they are low-throughput with respect to surveying many TFs. Recent advances in genome-wide chromatin profiling, including development of technologies such as DNase-seq, FAIRE-seq and ChIP-seq for histone modifications, make it possible to predict in vivo TFBSs by analyzing chromatin features at computationally determined DNA motif sites. This promising new approach may allow researchers to monitor the genome-wide binding sites of many TFs simultaneously. In this article, we discuss various experimental design and data analysis issues that arise when applying this approach. Through a systematic analysis of the data from the Encyclopedia Of DNA Elements (ENCODE) project, we compare the predictive power of individual and combinations of chromatin marks using supervised and unsupervised learning methods, and evaluate the value of integrating information from public ChIP and gene expression data. We also highlight the challenges and opportunities for developing novel analytical methods, such as resolving the one-motif-multiple-TF ambiguity and distinguishing functional and non-functional TF binding targets from the predicted binding sites. The online version of this article (doi:10.1007/s12561-012-9066-5) contains supplementary material, which is available to authorized users.

  16. Soil-to-Rice Seeds Transfer Factors of Radioiodine and Technetium for Paddy Fields around the Radioactive-Waste Disposal Site in Gyeongju

    International Nuclear Information System (INIS)

    Choi, Yong Ho; Lim, Kwang Muk; Jun, In; Park, Doo Won; Keum, Dong Kwon; Han, Moon Hee

    2010-01-01

    Radiotracer experiments were performed over two years using pot cultures in a greenhouse to investigate soil-torice seeds transfer factors of radioiodine and technetium for paddy fields around the radioactive-waste disposal site in Gyeongju. Before transplanting rice seedlings, the top about 20 cm soils were thoroughly mixed with 125 I (2007) and 99 Tc (2008), and the pots were irrigated to simulate flooded rice fields. Transfer factors were determined as the ratios of the radionuclide concentrations in dry rice seeds (brown rice) to those in dry soils. Transfer factors of radioiodine and technetium were in the ranges of 1.1 x 10 -3 ∼ 6.4 x 10 -3 (three soils) and 5.4 x 10 -4 ∼ 2.5 x 10 -3 (four soils), respectively, for different soils. It seems that the differences in the clay content among soils played a more important role for such variations than those in the organic matter content and pH. As the representative values of radioiodine and technetium transfer factors for rice seeds, 2.9 x 10 -3 and 1.1 x 10 -3 , respectively, were proposed. In order to obtain more highly representative values in the future, investigations for the sites of interest need to be carried out continuously

  17. Quantification and site-specification of the support practice factor when mapping soil erosion risk associated with olive plantations in the Mediterranean island of Crete.

    Science.gov (United States)

    Karydas, Christos G; Sekuloska, Tijana; Silleos, Georgios N

    2009-02-01

    Due to inappropriate agricultural management practices, soil erosion is becoming one of the most dangerous forms of soil degradation in many olive farming areas in the Mediterranean region, leading to significant decrease of soil fertility and yield. In order to prevent further soil degradation, proper measures are necessary to be locally implemented. In this perspective, an increase in the spatial accuracy of remote sensing datasets and advanced image analysis are significant tools necessary and efficient for mapping soil erosion risk on a fine scale. In this study, the Revised Universal Soil Loss Equation (RUSLE) was implemented in the spatial domain using GIS, while a very high resolution satellite image, namely a QuickBird image, was used for deriving cover management (C) and support practice (P) factors, in order to map the risk of soil erosion in Kolymvari, a typical olive farming area in the island of Crete, Greece. The results comprised a risk map of soil erosion when P factor was taken uniform (conventional approach) and a risk map when P factor was quantified site-specifically using object-oriented image analysis. The results showed that the QuickBird image was necessary in order to achieve site-specificity of the P factor and therefore to support fine scale mapping of soil erosion risk in an olive cultivation area, such as the one of Kolymvari in Crete. Increasing the accuracy of the QB image classification will further improve the resulted soil erosion mapping.

  18. Monitoring Ras Interactions with the Nucleotide Exchange Factor Son of Sevenless (Sos) Using Site-specific NMR Reporter Signals and Intrinsic Fluorescence.

    Science.gov (United States)

    Vo, Uybach; Vajpai, Navratna; Flavell, Liz; Bobby, Romel; Breeze, Alexander L; Embrey, Kevin J; Golovanov, Alexander P

    2016-01-22

    The activity of Ras is controlled by the interconversion between GTP- and GDP-bound forms partly regulated by the binding of the guanine nucleotide exchange factor Son of Sevenless (Sos). The details of Sos binding, leading to nucleotide exchange and subsequent dissociation of the complex, are not completely understood. Here, we used uniformly (15)N-labeled Ras as well as [(13)C]methyl-Met,Ile-labeled Sos for observing site-specific details of Ras-Sos interactions in solution. Binding of various forms of Ras (loaded with GDP and mimics of GTP or nucleotide-free) at the allosteric and catalytic sites of Sos was comprehensively characterized by monitoring signal perturbations in the NMR spectra. The overall affinity of binding between these protein variants as well as their selected functional mutants was also investigated using intrinsic fluorescence. The data support a positive feedback activation of Sos by Ras·GTP with Ras·GTP binding as a substrate for the catalytic site of activated Sos more weakly than Ras·GDP, suggesting that Sos should actively promote unidirectional GDP → GTP exchange on Ras in preference of passive homonucleotide exchange. Ras·GDP weakly binds to the catalytic but not to the allosteric site of Sos. This confirms that Ras·GDP cannot properly activate Sos at the allosteric site. The novel site-specific assay described may be useful for design of drugs aimed at perturbing Ras-Sos interactions. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. Problematic Internet Use among Greek university students: an ordinal logistic regression with risk factors of negative psychological beliefs, pornographic sites, and online games.

    Science.gov (United States)

    Frangos, Christos C; Frangos, Constantinos C; Sotiropoulos, Ioannis

    2011-01-01

    The aim of this paper is to investigate the relationships between Problematic Internet Use (PIU) among university students in Greece and factors such as gender, age, family condition, academic performance in the last semester of their studies, enrollment in unemployment programs, amount of Internet use per week (in general and per application), additional personal habits or dependencies (number of coffees, alcoholic drinks drunk per day, taking substances, cigarettes smoked per day), and negative psychological beliefs. Data were gathered from 2,358 university students from across Greece. The prevalence of PIU was 34.7% in our sample, and PIU was significantly associated with gender, parental family status, grade of studies during the previous semester, staying or not with parents, enrollment of the student in an unemployment program, and whether the student paid a subscription to the Internet (p pornographic sites, chat rooms, advertisement sites, Google, Yahoo!, their e-mail, ftp, games, and blogs more than non-problematic Internet users. PIU was also associated with other potential addictive personal habits of smoking, drinking alcohol or coffee, and taking drugs. Significant risk factors for PIU were being male, enrolment in unemployment programs, presence of negative beliefs, visiting pornographic sites, and playing online games. Thus PIU is prevalent among Greek university students and attention should be given to it by health officials.

  20. The environmental factors to be considered in the site selection studies of the spent fuel final disposal

    International Nuclear Information System (INIS)

    Aeikaes, Timo

    1985-10-01

    The ojective of the work has been to elucidate environmental factors, which could have an influence on the selection of areas. The factors were identified and their significance evaluated by going through the present plan for the final disposal of spent fuel. Population density and transport conditions were the most important factors. Protected areas, groundwater reservoirs and restrictions presented in regional land-use plans were also noted. The potential areas have been identified by the Geological Survey of Finland. First 327 large bedrock blocks were identified. The extent of the block areas was between 100-200 km 2 . The environmental factors of these areas were mapped and the areas were classified. The study was based on maps, published regional plans and inventory of groundwater reservoirs. The Geological Survey of Finland selected 162 block areas for preliminary characterization and geological classification. 61 block areas were chosen for further geological studies. By interpretation of aerial photographs and field reconnaissance trip the Geological Survey identified 134 potential investigation areas. A large block area typically contained two possible investigation areas. The extent of these areas varied between 5-10 km 2 . The environmental factors of 134 possible investigation areas were studied in detail. Due to the classification made earlier, the areas were typically sparsely populated forest areas. In the detailed study the main emphasis was but on evaluation of population density, transport and inventory of land ownership. The land-ownership is important for practical reasons. Land-owner's permission is needed for the operations in the field. Areas were classified separately according to population density, transport and land-ownership. In classification the most suitable areas were uninhabited regions with few landowners and locating close (less than 10 km) to the railroad. Only a minority of the areas fell in this category with the requirement

  1. Factors affecting phosphorus transport at a conventionally-farmed site in Lancaster County, Pennsylvania, 1992-95

    Science.gov (United States)

    Galeone, Daniel G.

    1996-01-01

    The U.S. Geological Survey and the Bureau of Land and Water Conservation of the Pennsylvania Department of Environmental Protection conducted a cooperative study to determine the effects of manure application and antecedent soil-phosphorus concentrations on the transport of phosphorus from the soil of a typical farm site in Lancaster County, Pa., from September 1992 to March 1995. The relation between concentrations of soil phosphorus and phosphorus transport needs to be identified because excessive phosphorus concentrations in surface-water bodies promote eutrophication.The objective of the study was to quantify and determine the significance of chemical, physical, and hydrologic factors that affected phosphorus transport. Three study plots less than 1 acre in size were tilled and planted in silage corn. Phosphorus in the form of liquid swine and dairy manure was injected to a depth of 6-8 inches on two of the three study plots in May 1993 and May 1994. Plot 1 received no inputs of phosphorus from manure while plots 2 and 3 received an average of 56 and 126 kilograms of phosphorus per acre, respectively, from the two manure applications. No other fertilizer was applied to any of the study plots. From March 30, 1993, through December 31, 1993, and March 10, 1994, through August 31, 1994 (the study period), phosphorus and selected cations were measured in precipitation, manure, soil, surface runoff, subsurface flow (at 18 inches below land surface), and corn plants before harvest. All storm events that yielded surface runoff and subsurface flow were sampled. Surface runoff was analyzed for dissolved (filtered through a 0.45-micron filter) and total concentrations. Subsurface flow was only analyzed for dissolved constituents. Laboratory soil-flask experiments and geochemical modeling were conducted to determine the maximum phosphate retention capacity of sampled soils after manure applications and primary mineralogic controls in the soils that affect phosphate

  2. Management of risk factors in the selection and use of PPE [personal protective equipment] on hazardous waste sites

    International Nuclear Information System (INIS)

    Kemplin, M.G.

    1988-01-01

    Industrial hygiene managers working in the hazardous waste area face daily decisions concerning appropriate levels of personal protective equipment (PPE) for hazards expected on various waste site projects. Typical hazards include exposures to toxic dust, chemical vapors, toxic gases, splashes of corrosive or toxic substances, radioactive materials and high noise levels. Managers who are experienced in this area recognize that each item of PPE can represent potential hazards in its own right. For example, full-face respirators typically restrict peripheral vision and can impede proper communications. In high ambient temperature conditions, coated protective suits can represent significant heat stress concerns, etc. Accordingly, this paper reviews health and safety management decision-making in this regard

  3. A cross-site comparison of factors controlling streamwater carbon flux in western North American catchments (Invited)

    Science.gov (United States)

    Brooks, P. D.; Biederman, J. A.; Condon, K.; Chorover, J.; McIntosh, J. C.; Meixner, T.; Perdrial, J. N.

    2013-12-01

    Increasing variability in climate is expected to alter the amount and form of terrestrial carbon in stream water both directly, through changes in the magnitude and timing of discharge, and indirectly through changes in land cover following disturbance (e.g. drought, fire, or insect driven mortality). Predicting how these changes will impact individual stream-catchment ecosystems however, is hampered by a lack of concurrent observations on both dissolved and particulate carbon flux across a range of spatial, temporal, and discharge scales. Because carbon is strongly coupled to most biogeochemical reactions within both aquatic and terrestrial ecosystems, this represents a critical unknown in predicting the response of catchment-ecosystems to concurrent changes in climate and land cover. This presentation will address this issue using a meta-analysis of dissolved organic, dissolved inorganic, and particulate organic carbon fluxes from multiple locations, including undisturbed sites along a climate gradient from desert rivers to seasonally snow-covered, forested mountain catchments, and sites disturbed by both fire and extensive, insect driven mortality. Initial analyses suggest that dissolved (organic and inorganic) and particulate fluxes respond differently to various types of disturbance and depend on interactions between changes in size of mobile carbon pools and changes in hydrologic routing of carbon to streamwater. Anomalously large fluxes of both dissolved and particulate organic matter are associated with episodic changes in hydrologic routing (e.g. storm floods; snowmelt) that connect normally hydrologically isolated carbon pools (e.g. surficial hillslope soils) with surface water. These events are often of short duration as the supply of mobile carbon is exhausted in short term flushing response. In contrast, disturbances that increase the size of the mobile carbon pool (e.g. widespread vegetation mortality) result smaller proportional increases in

  4. Pathways and factors for food safety and food security at PFOS contaminated sites within a problem based learning approach.

    Science.gov (United States)

    Brambilla, Gianfranco; D'Hollander, Wendy; Oliaei, Fardin; Stahl, Thorsten; Weber, Roland

    2015-06-01

    Perfluorooctanesulfonic acid (PFOS) and related substances have been listed in Annex B of the Stockholm Convention. The implementation requires inventories of use, stockpiles, and environmental contamination including contaminated sites and measures for (risk) reduction and phase out. In most countries monitoring capacity is not available and therefore other approaches for assessment of contaminated sites are needed. Available informations about PFOS contamination in hot spot areas and its bio-accumulation in the food webs have been merged to build up a worst-case scenario We model PFOS transfer from 1 to 100ngL(-1) range in water to extensive and free-range food producing animals, also via the spread of contaminated sludges on agriculture soils. The modeling indicates that forages represented 78% of the exposure in ruminants, while soil accounted for >80% in outdoor poultry/eggs and pigs. From the carry-over rates derived from literature, in pork liver, egg, and feral fish computed concentration falls at 101, 28 and 2.7ngg(-1), respectively, under the 1ngL(-1) PFOS scenario. Assuming a major consumption of food produced from a contaminated area, advisories on egg and fish, supported by good agriculture/farming practices could abate 75% of the human food intake. Such advisories would allow people to become resilient in a PFOS contaminated area through an empowerment of the food choices, bringing the alimentary exposure toward the current Tolerable Daily Intake (TDI) of 150ngkg(-1)bodyweightd(-1) proposed by the European Food Safety Authority (EFSA). Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Monitoring the efficacy of antimalarial medicines in India via sentinel sites: Outcomes and risk factors for treatment failure.

    Science.gov (United States)

    Mishra, Neelima; Srivastava, Bina; Bharti, Ram Suresh; Rana, Roma; Kaitholia, Kamlesh; Anvikar, Anupkumar R; Das, Manoj Kumar; Ghosh, Susanta K; Bhatt, Rajendra M; Tyagi, Prajesh K; Dev, Vas; Phookan, Sobhan; Wattal, Suman Lata; Sonal, Gagan Singh; Dhariwal, Akshay Chand; Valecha, Neena

    2016-01-01

    To combat the problem of antimalarial drug resistance, monitoring the changes in drug efficacy over time through periodic surveillance is essential. Since 2009, systematic and continuous monitoring is being done through nationwide sentinel site system. Potential early warning signs like partner drug resistance markers were also monitored in the clinical samples from the study areas. A total of 1864 patients with acute uncomplicated malaria were enrolled in therapeutic efficacy studies of artesunate plus sulphadoxine-pyrimethamine (AS+SP) for Plasmodium falciparum; those infected with P. vivax were given chloroquine (CQ). Polymerase chain reaction (PCR) was used to distinguish post-treatment reinfection from treatment failures. Isolates of P. falciparum were also analysed for dihydropteroate synthase (dhps) and dihydrofolate reductase (dhfr) gene mutations. Overall, 1687 (91.7%) patients completed the follow-up. In most of the falciparum patients the parasitaemia was cleared within 24 h of treatment, except 12 patients who remained parasite positive after 72 h. Presence of dhfr and dhps quintuple mutation was observed predominantly in treatment failure samples. A daily dose of artesunate of 95% cases in all the sentinel sites except in Northeastern region (NE). Chloroquine remained 100% efficacious in case of P. vivax infections. Till 2012, India's national antimalarial drug resistance monitoring system proved highly efficacious and safe towards first-line antimalarials used in the country, except in Northeastern region where a decline in efficacy of AS+SP has been observed. This led to change in first-line treatment for P. falciparum to artemether-lumefantrine in Northeastern region.

  6. Characterization of pancreatic transcription factor Pdx-1 binding sites using promoter microarray and serial analysis of chromatin occupancy

    OpenAIRE

    Keller, David M; McWeeney, Shannon; Arsenlis, Athanasios; Drouin, Jacques; Wright, Christopher V E; Wang, Haiyan; Wollheim, Claes; White, Peter; Kaestner, Klaus H; Goodman, Richard H

    2007-01-01

    The homeobox transcription factor Pdx-1 is necessary for pancreas organogenesis and beta cell function, however, most Pdx-1-regulated genes are unknown. To further the understanding of Pdx-1 in beta cell biology, we have characterized its genomic targets in NIT-1 cells, a mouse insulinoma cell line. To identify novel targets, we developed a microarray that includes traditional promoters as well as non-coding conserved elements, micro-RNAs, and elements identified through an unbiased approach ...

  7. Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation

    Directory of Open Access Journals (Sweden)

    Ronne Hans

    2008-11-01

    Full Text Available Abstract Background The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence is important for gene regulation. Results In this study we present ContextFinder, a tool that is specifically aimed at identifying cases where motif context is likely to affect gene regulation. We used ContextFinder to examine the role of motif context in S. cerevisiae both for DNA binding by transcription factors and for effects on gene expression. For DNA binding we found significant patterns of motif location bias, whereas motif orientations did not seem to matter. Motif context appears to affect gene expression even more than it affects DNA binding, as biases in both motif location and orientation were more frequent in promoters of co-expressed genes. We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy. Conclusion We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.

  8. Biogen water of the Irtysh river - the principal population health factor suffered from the nuclear test on the Semipalatinsk test site

    International Nuclear Information System (INIS)

    Inyushin, V.M.; Yurenkov, V.V.

    2001-01-01

    Authors notes, that Semipalatinsk test site activity together with other factors changes a water quality. The principal consequence of nuclear tests is build up in new cells by the 'pathogenous' water in plants, animals and human . 'Pathogenous water' is generating at steady changes of electronic strictures (spin performances) at ionizing radiation effect, radionuclides and other factors of nuclear explosions. These factors were did not known to a world-wide science. The second of very important phenomenon of nuclear explosions consequences at the Semipalatinsk test site is reduce of the hydro-plasma in the water sources the Irtysh River basin. This was proved with direct studies microcurrents density in the water as well as analysis of electronic and ionic structures with the plasma-graphic help. The water having the pathogenous memory - building up in the cells - reduces the immune status, negatively reflects on the vital functions, decreasing the resistance to unfavorable effects. It is offered for remediation of the 'pathogenous water' to use the bio-genized water as most adequate one to endogenous water of living cells. Mass usage of the bio-genized water takes out genetic consequences of nuclear explosions and increase of an immunity level. The 'Bio-genization' of the Irtysh River water is concludes a few stages

  9. Pre-operative urinary tract infection: is it a risk factor for early surgical site infection with hip fracture surgery? A retrospective analysis.

    Science.gov (United States)

    Yassa, Rafik Rd; Khalfaoui, Mahdi Y; Veravalli, Karunakar; Evans, D Alun

    2017-03-01

    The aims of the current study were to determine whether pre-operative urinary tract infections in patients presenting acutely with neck of femur fractures resulted in a delay to surgery and whether such patients were at increased risk of developing post-operative surgical site infections. A retrospective review of all patients presenting with a neck of femur fracture, at a single centre over a one-year period. The hospital hip fracture database was used as the main source of data. UK University Teaching Hospital. All patients ( n  = 460) presenting across a single year study period with a confirmed hip fracture. The presence of pre-operative urinary tract infection, the timing of surgical intervention, the occurrence of post-operative surgical site infection and the pathogens identified. A total of 367 patients were operated upon within 24 hours of admission. Urinary infections were the least common cause of delay. A total of 99 patients (21.5%) had pre-operative urinary tract infection. Post-operatively, a total of 57 (12.4%) patients developed a surgical site infection. Among the latter, 31 (54.4%) did not have a pre-operative urinary infection, 23 (40.4%) patients had a pre-operative urinary tract infection, 2 had chronic leg ulcers and one patient had a pre-operative chest infection. Statistically, there was a strong relationship between pre-operative urinary tract infection and the development of post-operative surgical site infection ( p -value: 0.0005). The results of our study indicate that pre-operative urinary tract infection has a high prevalence amongst those presenting with neck of femur fractures, and this is a risk factor for the later development of post-operative surgical site infection.

  10. Factors associated with antenatal care adequacy in rural and urban contexts-results from two health and demographic surveillance sites in Vietnam

    Science.gov (United States)

    2012-01-01

    Background Antenatal Care (ANC) is universally considered important for women and children. This study aims to identify factors, demographic, social and economic, possibly associated with three ANC indicators: number of visits, timing of visits and content of services. The aim is also to compare the patterns of association of such factors between one rural and one urban context in northern Vietnam. Methods Totally 2,132 pregnant women were followed from identification of pregnancy until birth in two Health and Demographic Surveillance Sites (HDSS). Information was obtained through quarterly face to face interviews. Results Living in the rural area was significantly associated with lower adequate use of ANC compared to living in the urban area, both regarding quantity (number and timing of visits) and content. Low education, living in poor households and exclusively using private sector ANC in both sites and self employment, becoming pregnant before 25 years of age and living in poor communities in the rural area turned out to increase the risk for overall inadequate ANC. High risk pregnancy could not be demonstrated to be associated with ANC adequacy in either site. The medical content of services offered was often inadequate, in relation to the national recommendations, especially in the private sector. Conclusion Low education, low economic status, exclusive use of private ANC and living in rural areas were main factors associated with risk for overall inadequate ANC use as related to the national recommendations. Therefore, interventions focussing on poor and less educated women, especially in rural areas should be prioritized. They should focus the importance of early attendance of ANC and sufficient use of core services. Financial support for poor and near poor women should be considered. Providers of ANC should be educated and otherwise influenced to provide sufficient core services. Adherence to ANC content guidelines must be improved through enhanced

  11. Contributing factors of elective surgical case cancellation: a retrospective cross-sectional study at a single-site hospital.

    Science.gov (United States)

    Yu, Kaiye; Xie, Xiaolei; Luo, Li; Gong, Renrong

    2017-09-11

    Case cancellation (CC) has significant impact on the efficiency of operating room (OR) management, which can be mitigated by taking preventive measures. In this study, using the data of the West China Hospital (WCH), we identified the effect of contributing factors and recommended hospital interventions to facilitate CC prevention. We conducted a retrospective review of 11,331 elective surgical cases from January 1 to December 31, 2014. CC reasons were grouped into six categories. The methods of descriptive statistics and hypothesis test were used to identify the effect of factors. CC reasons (746) were divided into six broad categories: workup related (preoperative diagnostic assessment issues or sudden medical condition changes) (25.8%), non-specified reasons (25.8%), coordination issues (15.1%), patient related (13.0%), support system issues (11.8%), and doctor related (8.5%). The types of the most frequently performed operations are identified, as well as their CRs. The cancellation rate (CR) of males was lower than that of females (16.7% to 18.3%). A large difference in the CRs existed among doctors. The CR on Monday was significantly higher than the other four weekdays. Workup related issues, the types of procedures, the menstrual cycle of females, highly imbalanced CRs among doctors, and tendency of cancellation on Monday are the major identified factors, which account for a significant amount of preventable cancellations. It is suggested that corresponding hospital interventions can reduce CR and improve OR efficiency, including maintaining effective coordination, good communication and well-designed preoperative assessment processes, focusing on the type of procedures which are more time-consuming and complex, paying special attention to the physiology of females during surgery planning, taking measures to reduce CR of top eight doctors, and improving surgery scheduling on Monday.

  12. Sequence-specific 1H NMR assignments, secondary structure, and location of the calcium binding site in the first epidermal growth factor like domain of blood coagulation factor IX

    International Nuclear Information System (INIS)

    Huang, L.H.; Cheng, H.; Sweeney, W.V.; Pardi, A.; Tam, J.P.

    1991-01-01

    Factor IX is a blood clotting protein that contains three regions, including a γ-carboxyglutamic acid (Gla) domain, two tandemly connected epidermal growth factor like (EGF-like) domains, and a serine protease region. The protein exhibits a high-affinity calcium binding site in the first EGF0like domain, in addition to calcium binding in the Gla domain. The first EGF-like domain, factor IX (45-87), has been synthesized. Sequence-specific resonance assignment of the peptide has been made by using 2D NMR techniques, and its secondary structure has been determined. The protein is found to have two antiparallel β-sheets, and preliminary distance geometry calculations indicate that the protein has two domains, separated by Trp 28 , with the overall structure being similar to that of EGF. An NMR investigation of the calcium-bound first EGF-like domain indicates the presence and location of a calcium binding site involving residues on both strands of one of the β-sheets as well as the N-terminal region of the peptide. These results suggest that calcium binding in the first EGF-like domain could induce long-range (possibly interdomain) conformational changes in factor IX, rather than causing structural alterations in the EGF-like domain itself

  13. Mineral licks: motivational factors for visitation and accompanying disease risk at communal use sites of elk and deer.

    Science.gov (United States)

    Lavelle, Michael J; Phillips, Gregory E; Fischer, Justin W; Burke, Patrick W; Seward, Nathan W; Stahl, Randal S; Nichols, Tracy A; Wunder, Bruce A; VerCauteren, Kurt C

    2014-12-01

    Free-ranging cervids acquire most of their essential minerals through forage consumption, though occasionally seek other sources to account for seasonal mineral deficiencies. Mineral sources occur as natural geological deposits (i.e., licks) or as anthropogenic mineral supplements. In both scenarios, these sources commonly serve as focal sites for visitation. We monitored 11 licks in Rocky Mountain National Park, north-central Colorado, using trail cameras to quantify daily visitation indices (DVI) and soil consumption indices (SCI) for Rocky Mountain elk (Cervus elaphus) and mule deer (Odocoileus hemionus) during summer 2006 and documented elk, mule deer, and moose (Alces alces) visiting licks. Additionally, soil samples were collected, and mineral concentrations were compared to discern levels that explain rates of visitation. Relationships between response variables; DVI and SCI, and explanatory variables; elevation class, moisture class, period of study, and concentrations of minerals were examined. We found that DVI and SCI were greatest at two wet, low-elevation licks exhibiting relatively high concentrations of manganese and sodium. Because cervids are known to seek Na from soils, we suggest our observed association of Mn with DVI and SCI was a likely consequence of deer and elk seeking supplemental dietary Na. Additionally, highly utilized licks such as these provide an area of concentrated cervid occupation and interaction, thus increasing risk for environmental transmission of infectious pathogens such as chronic wasting disease, which has been shown to be shed in the saliva, urine, and feces of infected cervids.

  14. Improved efficacy of soluble human receptor activator of nuclear factor kappa B (RANK) fusion protein by site-directed mutagenesis.

    Science.gov (United States)

    Son, Young Jun; Han, Jihye; Lee, Jae Yeon; Kim, HaHyung; Chun, Taehoon

    2015-06-01

    Soluble human receptor activator of nuclear factor kappa B fusion immunoglobulin (hRANK-Ig) has been considered as one of the therapeutic agents to treat osteoporosis or diseases associated with bone destruction by blocking the interaction between RANK and the receptor activator of nuclear factor kappa B ligand (RANKL). However, no scientific record showing critical amino acid residues within the structural interface between the human RANKL and RANK complex is yet available. In this study, we produced several mutants of hRANK-Ig by replacement of amino acid residue(s) and tested whether the mutants had increased binding affinity to human RANKL. Based on the results from flow cytometry and surface plasmon resonance analyses, the replacement of E(125) with D(125), or E(125) and C(127) with D(125) and F(127) within loop 3 of cysteine-rich domain 3 of hRANK-Ig increases binding affinity to human RANKL over the wild-type hRANK-Ig. This result may provide the first example of improvement in the efficacy of hRANK-Ig by protein engineering and may give additional information to understand a more defined structural interface between hRANK and RANKL.

  15. Keeping the golden mean: plant stiffness and anatomy as proximal factors driving endophytic oviposition site selection in a dragonfly.

    Science.gov (United States)

    Matushkina, Natalia; Lambret, Philippe; Gorb, Stanislav

    2016-12-01

    Oviposition site selection is a crucial component of habitat selection in dragonflies. The presence of appropriate oviposition plants at breeding waters is considered to be one of the key habitat determinants for species laying eggs endophytically. Thus, Lestes macrostigma, a species which is regarded as threatened in Europe because of its highly disjunct distribution, typically prefers to lay eggs in the sea club rush Bolboschoenus maritimus. However, little is known about how the anatomical and mechanical properties of plant tissues determine the choice of L. macrostigma females. We examined green shoots of six plant species used by L. macrostigma for oviposition, either in the field (actual oviposition plants) or under experimental conditions (potential oviposition plants), to analyse anatomical and mechanical properties of shoots in a framework of known preferences regarding plant substrates for oviposition. As expected, the anatomy of shoots differed between representatives of two plant families, Cyperaceae and Juncaceae, most essentially in the distribution of supporting bundles and the presence of large aeriferous cavities that may affect egg placing within a shoot. The force necessary to puncture the tested plant samples ranged from 360 to 3298 mN, and their local stiffness ranged from 777 to 3363N/m. We show that the shoots of B. maritimus, the plant most preferred by L. macrostigma, have intermediate characteristics regarding both the stiffness and specific anatomical characteristics. The bending stiffness of the ovipositor in L. macrostigma was estimated as 1414N/m, one of the highest values recorded for zygopteran dragonflies so far. The ecological and behavioural implications of plant choice mechanisms in L. macrostigma are discussed in the context of the disjunct distribution of this species. Copyright © 2016 Elsevier GmbH. All rights reserved.

  16. Factors associated with online victimisation among Malaysian adolescents who use social networking sites: a cross-sectional study

    Science.gov (United States)

    Marret, Mary J; Choo, Wan Yuen

    2017-01-01

    Objective To determine the prevalence of online interpersonal victimisation and its association with patterns of social networking site (SNS) use, offline victimisation, offline perpetration and parental conflict among Malaysian adolescents using SNS. Methods A cross-sectional study of students from randomly selected public secondary schools in the state of Negeri Sembilan was conducted using an anonymous self-administered questionnaire. The questionnaire examined patterns of SNS use and included measures of online victimisation, online perpetration, offline victimisation and parental conflict. A response rate of 91% from a total of 1634 yielded a sample of 1487 students between 15 years and 16 years of age. Results Ninety-two per cent of respondents had used at least one SNS. More than half of SNS users (52.2%) reported experiences of online victimisation over the past 12 months. Boys were significantly more likely to experience online harassment compared with girls (52.2% vs 43.3%, p<0.001). There were no significant gender differences in experiences of unwanted sexual solicitation. Adolescents who engaged in perpetration behaviours online had almost six times higher odds of reporting frequent online victimisation compared with online behaviours involving personal disclosure. There was a significant dose-response relationship between engagement in multiple types of online behaviour and the risk of frequent online victimisation. Both online and offline perpetrations were associated with an increased risk of victimisation. Those who were victimised offline or experienced parental conflict were twice as likely to report online victimisation. Conclusion Interventions to prevent online electronic aggression should target perpetration behaviour both online and offline. Youth should be equipped with skills in communication and decision-making in relationships that can be applied across a spectrum of contexts both online and offline. PMID:28667209

  17. Factors associated with online victimisation among Malaysian adolescents who use social networking sites: a cross-sectional study.

    Science.gov (United States)

    Marret, Mary J; Choo, Wan Yuen

    2017-06-30

    To determine the prevalence of online interpersonal victimisation and its association with patterns of social networking site (SNS) use, offline victimisation, offline perpetration and parental conflict among Malaysian adolescents using SNS. A cross-sectional study of students from randomly selected public secondary schools in the state of Negeri Sembilan was conducted using an anonymous self-administered questionnaire. The questionnaire examined patterns of SNS use and included measures of online victimisation, online perpetration, offline victimisation and parental conflict. A response rate of 91% from a total of 1634 yielded a sample of 1487 students between 15 years and 16 years of age. Ninety-two per cent of respondents had used at least one SNS. More than half of SNS users (52.2%) reported experiences of online victimisation over the past 12 months. Boys were significantly more likely to experience online harassment compared with girls (52.2% vs 43.3%, ponline had almost six times higher odds of reporting frequent online victimisation compared with online behaviours involving personal disclosure. There was a significant dose-response relationship between engagement in multiple types of online behaviour and the risk of frequent online victimisation. Both online and offline perpetrations were associated with an increased risk of victimisation. Those who were victimised offline or experienced parental conflict were twice as likely to report online victimisation. Interventions to prevent online electronic aggression should target perpetration behaviour both online and offline. Youth should be equipped with skills in communication and decision-making in relationships that can be applied across a spectrum of contexts both online and offline. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  18. Beyond "Facebook Addiction": The Role of Cognitive-Related Factors and Psychiatric Distress in Social Networking Site Addiction.

    Science.gov (United States)

    Pontes, Halley M; Taylor, Megan; Stavropoulos, Vasileios

    2018-04-01

    The use of social networking sites (SNSs) is rapidly increasing as billions of individuals use SNS platforms regularly to communicate with other users, follow the news, and play browser games. Given the widespread use of SNS platforms, investigating the potential predictors of addictive SNS use beyond Facebook use has become paramount given that most studies so far focused on "Facebook addiction." In this study, a total of 511 English-speaking SNS users (58.1% young adults aged 20-35 years; 64.6% female) were recruited online and asked to complete a battery of standardized psychometric tools assessing participants' sociodemographic characteristics, SNS preferences and patterns of use, SNS addiction, preference for online social interaction, maladaptive cognitions, fear of missing out (FoMo), dysfunctional emotion regulation, and general psychiatric distress. Overall, about 4.9% (n = 25) of all participants could be classed as having a high SNS addiction risk profile. Moreover, the results further indicated that FoMo (β = 0.38), maladaptive cognitions (β = 0.25), and psychiatric distress (β = 0.12) significantly predicted SNS addiction (i.e., p < 0.0001) and accounted for about 61% of the total variance in SNS addiction, with FoMo providing the strongest predictive contribution over and above the effects of sociodemographic variables and patterns of SNS use. The implications of the present findings were discussed in light of extant literature on behavioral addictions and Facebook addiction and further considerations were provided regarding the potential clinical implications for cognitive-based psychological treatment approaches to SNS addiction.

  19. Adolescent pornographic internet site use: a multivariate regression analysis of the predictive factors of use and psychosocial implications.

    Science.gov (United States)

    Tsitsika, Artemis; Critselis, Elena; Kormas, Georgios; Konstantoulaki, Eleftheria; Constantopoulos, Andreas; Kafetzis, Dimitrios

    2009-10-01

    The study objectives were to evaluate the prevalence, predictors, and implications of pornographic Internet site (PIS) use among Greek adolescents. A cross-sectional study was conducted among 529 randomly selected Greek high school students. The prevalence of overall PIS use was 19.47% (n = 96). Among PIS users, 55 (57.29%) reported infrequent and 41 (42.71%) reported frequent PIS use. The predictors of infrequent PIS use included male gender (adjusted odds ratio [AOR] = 8.33; 95% confidence interval [CI] = 3.52-19.61), Internet use for sexual education (AOR = 5.26; 95% CI = 1.78-15.55), chat rooms (AOR = 2.95; 95% CI = 1.48-5.91), and purchases (AOR = 3.06; 95% CI = 1.22-7.67). The predictors of frequent PIS use were male gender (AOR = 19.61; 95% CI = 4.46-83.33), Internet use for sexual education (AOR = 7.39; 95% CI = 2.37-23.00), and less than 10 hours per week Internet use (AOR = 1.32; 95% CI = 1.10-1.59). Compared to non-PIS users, infrequent PIS users were twice as likely to have abnormal conduct problems (odds ratio [OR] = 2.74; 95% CI = 1.19-6.28); frequent PIS users were significantly more likely to have abnormal conduct problems (OR = 4.05; 95% CI = 1.57-10.46) and borderline prosocial score (OR = 4.22; 95% CI = 1.64-10.85). Thus, both infrequent and frequent PIS use are prevalent and significantly associated with social maladjustment among Greek adolescents.

  20. Fasxiator, a novel factor XIa inhibitor from snake venom, and its site-specific mutagenesis to improve potency and selectivity.

    Science.gov (United States)

    Chen, W; Carvalho, L P D; Chan, M Y; Kini, R M; Kang, T S

    2015-02-01

    Bleeding remains a major limitation of standard anticoagulant drugs that target the extrinsic and common coagulation pathways. Recently, intrinsic coagulation factors are increasingly being investigated as alternative targets for developing anticoagulant drugs with lower bleeding risk. Goals were to (i) identify novel anticoagulants selectively targeting intrinsic coagulation pathway and (ii) characterize and further improve the properties of the identified anticoagulants. We have isolated and sequenced a specific factor XIa (FXIa) inhibitor, henceforth named Fasxiator, from the venom of the banded krait snake, Bungarus fasciatus. It is a Kunitz-type protease inhibitor that prolonged activated partial thromboplastin time without significant effects on prothrombin time. Fasxiator was recombinantly expressed (rFasxiator), purified, and characterized to be a slow-type inhibitor of FXIa that exerts its anticoagulant activities (doubled activated partial thromboplastin time at ~ 3 μmol L(-1) ) by selectively inhibiting human FXIa in in vitro assays. A series of mutants were subsequently generated to improve the potency and selectivity of recombinant rFasxiator. rFasxiatorN17R,L19E showed the best balance between potency (IC50 ~ 1 nmol L(-1) ) and selectivity (> 100 times). rFasxiatorN17R,L19E is a competitive slow-type inhibitor of FXIa (Ki  = 0.86 nmol L(-1) ), possesses anticoagulant activity that is ~ 10 times stronger in human plasma than in murine plasma, and prolonged the occlusion time of mice carotid artery in FeCl3 -induced thrombosis models. We have isolated an exogenous FXIa specific inhibitor, engineered it to improve its potency by ~ 1000 times and demonstrated its in vitro and in vivo efficacy. These proof-of-principle data supported the further development of Fasxiator as a novel anticoagulant candidate. © 2014 International Society on Thrombosis and Haemostasis.

  1. Fibrinogen binding sites P336 and Y338 of clumping factor A are crucial for Staphylococcus aureus virulence.

    Directory of Open Access Journals (Sweden)

    Elisabet Josefsson

    Full Text Available We have earlier shown that clumping factor A (ClfA, a fibrinogen binding surface protein of Staphylococcus aureus, is an important virulence factor in septic arthritis. When two amino acids in the ClfA molecule, P(336 and Y(338, were changed to serine and alanine, respectively, the fibrinogen binding property was lost. ClfAP(336Y(338 mutants have been constructed in two virulent S. aureus strains Newman and LS-1. The aim of this study was to analyze if these two amino acids which are vital for the fibrinogen binding of ClfA are of importance for the ability of S. aureus to generate disease. Septic arthritis or sepsis were induced in mice by intravenous inoculation of bacteria. The clfAP(336Y(338 mutant induced significantly less arthritis than the wild type strain, both with respect to severity and frequency. The mutant infected mice developed also a much milder systemic inflammation, measured as lower mortality, weight loss, bacterial growth in kidneys and lower IL-6 levels. The data were verified with a second mutant where clfAP(336 and Y(338 were changed to alanine and serine respectively. When sepsis was induced by a larger bacterial inoculum, the clfAP(336Y(338 mutants induced significantly less septic death. Importantly, immunization with the recombinant A domain of ClfAP(336SY(338A mutant but not with recombinant ClfA, protected against septic death. Our data strongly suggest that the fibrinogen binding activity of ClfA is crucial for the ability of S. aureus to provoke disease manifestations, and that the vaccine potential of recombinant ClfA is improved by removing its ability to bind fibrinogen.

  2. Fibrinogen binding sites P336 and Y338 of clumping factor A are crucial for Staphylococcus aureus virulence.

    Science.gov (United States)

    Josefsson, Elisabet; Higgins, Judy; Foster, Timothy J; Tarkowski, Andrej

    2008-05-21

    We have earlier shown that clumping factor A (ClfA), a fibrinogen binding surface protein of Staphylococcus aureus, is an important virulence factor in septic arthritis. When two amino acids in the ClfA molecule, P(336) and Y(338), were changed to serine and alanine, respectively, the fibrinogen binding property was lost. ClfAP(336)Y(338) mutants have been constructed in two virulent S. aureus strains Newman and LS-1. The aim of this study was to analyze if these two amino acids which are vital for the fibrinogen binding of ClfA are of importance for the ability of S. aureus to generate disease. Septic arthritis or sepsis were induced in mice by intravenous inoculation of bacteria. The clfAP(336)Y(338) mutant induced significantly less arthritis than the wild type strain, both with respect to severity and frequency. The mutant infected mice developed also a much milder systemic inflammation, measured as lower mortality, weight loss, bacterial growth in kidneys and lower IL-6 levels. The data were verified with a second mutant where clfAP(336) and Y(338) were changed to alanine and serine respectively. When sepsis was induced by a larger bacterial inoculum, the clfAP(336)Y(338) mutants induced significantly less septic death. Importantly, immunization with the recombinant A domain of ClfAP(336)SY(338)A mutant but not with recombinant ClfA, protected against septic death. Our data strongly suggest that the fibrinogen binding activity of ClfA is crucial for the ability of S. aureus to provoke disease manifestations, and that the vaccine potential of recombinant ClfA is improved by removing its ability to bind fibrinogen.

  3. Systemic administration of kainic acid induces selective time dependent decrease in [125I]insulin-like growth factor I, [125I]insulin-like growth factor II and [125I]insulin receptor binding sites in adult rat hippocampal formation

    International Nuclear Information System (INIS)

    Quirion, R.; Chabot, J.-G.; Dore, S.; Seto, D.; Kar, S.

    1997-01-01

    Administration of kainic acid evokes acute seizure in hippocampal pathways that results in a complex sequence of functional and structural alterations resembling human temporal lobe epilepsy. The structural alterations induced by kainic acid include selective loss of neurones in CA1-CA3 subfields and the hilar region of the dentate gyrus followed by sprouting and permanent reorganization of the synaptic connections of the mossy fibre pathways. Although the neuronal degeneration and process of reactive synaptogenesis have been extensively studied, at present little is known about means to prevent pathological conditions leading to kainate-induced cell death. In the present study, to address the role of insulin-like growth factors I and II, and insulin in neuronal survival as well as synaptic reorganization following kainate-induced seizure, the time course alterations of the corresponding receptors were evaluated. Additionally, using histological preparations, the temporal profile of neuronal degeneration and hypertrophy of resident astroglial cells were also studied. [ 125 I]Insulin-like growth factor I binding was found to be decreased transiently in almost all regions of the hippocampal formation at 12 h following treatment with kainic acid. The dentate hilar region however, exhibited protracted decreases in [ 125 I]insulin-like growth factor I receptor sites throughout (i.e. 30 days) the study. [ 125 I]Insulin-like growth factor II receptor binding sites in the hippocampal formation were found to be differentially altered following systemic administration of kainic acid. A significant decrease in [ 125 I]insulin-like growth factor II receptor sites was observed in CA1 subfield and the pyramidal cell layer of the Ammon's horn at all time points studied whereas the hilar region and the stratum radiatum did not exhibit alteration at any time. A kainate-induced decrease in [ 125 I]insulin receptor binding was noted at all time points in the molecular layer of the

  4. Climate warming and the recent treeline shift in the European alps: the role of geomorphological factors in high-altitude sites.

    Science.gov (United States)

    Leonelli, Giovanni; Pelfini, Manuela; di Cella, Umberto Morra; Garavaglia, Valentina

    2011-05-01

    Global warming and the stronger regional temperature trends recently recorded over the European Alps have triggered several biological and physical dynamics in high-altitude environments. We defined the present treeline altitude in three valleys of a region in the western Italian Alps and reconstructed the past treeline position for the last three centuries in a nearly undisturbed site by means of a dendrochronological approach. We found that the treeline altitude in this region is mainly controlled by human impacts and geomorphological factors. The reconstruction of the altitudinal dynamics at the study site reveals that the treeline shifted upwards of 115 m over the period 1901-2000, reaching the altitude of 2505 m in 2000 and 2515 m in 2008. The recent treeline shift and the acceleration of tree colonization rates in the alpine belt can be mainly ascribed to the climatic input. However, we point out the increasing role of geomorphological factors in controlling the future treeline position and colonization patterns in high mountains.

  5. Transforming growth factor. beta. sub 1 is present at sites of extracellular matrix gene expression in human pulmonary fibrosis

    Energy Technology Data Exchange (ETDEWEB)

    Broekelmann, T.J.; Limper, A.H.; McDonald, J.A. (Washington Univ., St. Louis, MO (United States)); Colby, T.V. (Mayo Clinic, Rochester, MN (United States))

    1991-08-01

    Idiopathic pulmonary fibrosis is an inexorably fatal disorder characterized by connective tissue deposition within the terminal air spaces resulting in loss of lung function and eventual respiratory failure. Previously, the authors demonstrated that foci of activated fibroblasts expressing high levels of fibronectin, procollagen, and smooth muscle actin and thus resembling those found in healing wounds are responsible for the connective tissue deposition and scarring in idiopathic pulmonary fibrosis. Using in situ hybridization and immunohistochemistry, they now demonstrate the presence of transforming growth factor {beta}{sub 1} (TGF-{beta}{sub 1}), a potent profibrotic cytokine, in the foci containing these activated fibroblasts. These results suggest that matrix-associated TGF-{beta}{sub 1} may serve as a stimulus for the persistent expression of connective tissue genes. One potential source of the TGF-{beta}{sub 1} is the alveolar macrophage, and they demonstrate the expression of abundant TGF-{beta}{sub 1} mRNA in alveolar macrophages in lung tissue from patients with idiopathic pulmonary fibrosis.

  6. Functions for fission yeast splicing factors SpSlu7 and SpPrp18 in alternative splice-site choice and stress-specific regulated splicing.

    Directory of Open Access Journals (Sweden)

    Geetha Melangath

    Full Text Available Budding yeast spliceosomal factors ScSlu7 and ScPrp18 interact and mediate intron 3'ss choice during second step pre-mRNA splicing. The fission yeast genome with abundant multi-intronic transcripts, degenerate splice signals and SR proteins is an apt unicellular fungal model to deduce roles for core spliceosomal factors in alternative splice-site choice, intron retention and to study the cellular implications of regulated splicing. From our custom microarray data we deduce a stringent reproducible subset of S. pombe alternative events. We examined the role of factors SpSlu7 or SpPrp18 for these splice events and investigated the relationship to growth phase and stress. Wild-type log and stationary phase cells showed ats1+ exon 3 skipped and intron 3 retained transcripts. Interestingly the non-consensus 5'ss in ats1+ intron 3 caused SpSlu7 and SpPrp18 dependent intron retention. We validated the use of an alternative 5'ss in dtd1+ intron 1 and of an upstream alternative 3'ss in DUF3074 intron 1. The dtd1+ intron 1 non-canonical 5'ss yielded an alternative mRNA whose levels increased in stationary phase. Utilization of dtd1+ intron 1 sub-optimal 5' ss required functional SpPrp18 and SpSlu7 while compromise in SpSlu7 function alone hampered the selection of the DUF3074 intron 1 non canonical 3'ss. We analysed the relative abundance of these splice isoforms during mild thermal, oxidative and heavy metal stress and found stress-specific splice patterns for ats1+ and DUF3074 intron 1 some of which were SpSlu7 and SpPrp18 dependent. By studying ats1+ splice isoforms during compromised transcription elongation rates in wild-type, spslu7-2 and spprp18-5 mutant cells we found dynamic and intron context-specific effects in splice-site choice. Our work thus shows the combinatorial effects of splice site strength, core splicing factor functions and transcription elongation kinetics to dictate alternative splice patterns which in turn serve as an additional

  7. Interactions between the R2R3-MYB transcription factor, AtMYB61, and target DNA binding sites.

    Directory of Open Access Journals (Sweden)

    Michael B Prouse

    Full Text Available Despite the prominent roles played by R2R3-MYB transcription factors in the regulation of plant gene expression, little is known about the details of how these proteins interact with their DNA targets. For example, while Arabidopsis thaliana R2R3-MYB protein AtMYB61 is known to alter transcript abundance of a specific set of target genes, little is known about the specific DNA sequences to which AtMYB61 binds. To address this gap in knowledge, DNA sequences bound by AtMYB61 were identified using cyclic amplification and selection of targets (CASTing. The DNA targets identified using this approach corresponded to AC elements, sequences enriched in adenosine and cytosine nucleotides. The preferred target sequence that bound with the greatest affinity to AtMYB61 recombinant protein was ACCTAC, the AC-I element. Mutational analyses based on the AC-I element showed that ACC nucleotides in the AC-I element served as the core recognition motif, critical for AtMYB61 binding. Molecular modelling predicted interactions between AtMYB61 amino acid residues and corresponding nucleotides in the DNA targets. The affinity between AtMYB61 and specific target DNA sequences did not correlate with AtMYB61-driven transcriptional activation with each of the target sequences. CASTing-selected motifs were found in the regulatory regions of genes previously shown to be regulated by AtMYB61. Taken together, these findings are consistent with the hypothesis that AtMYB61 regulates transcription from specific cis-acting AC elements in vivo. The results shed light on the specifics of DNA binding by an important family of plant-specific transcriptional regulators.

  8. Micro-RNA Binding Site Polymorphisms in the WFS1 Gene Are Risk Factors of Diabetes Mellitus

    Science.gov (United States)

    Elek, Zsuzsanna; Németh, Nóra; Nagy, Géza; Németh, Helga; Somogyi, Anikó; Hosszufalusi, Nóra; Sasvári-Székely, Mária; Rónai, Zsolt

    2015-01-01

    The absolute or relative lack of insulin is the key factor in the pathogenesis of diabetes mellitus. Although the connection between loss of function mutations of the WFS1 gene and DIDMOAD-syndrome including diabetes mellitus underpins the significance of wolframin in the pathogenesis, exact role of WFS1 polymorphic variants in the development of type 1 and type 2 diabetes has not been discovered yet. In this analysis, 787 patients with diabetes and 900 healthy people participated. Genotyping of the 7 WFS1 SNPs was carried out by TaqMan assays. Association study was performed by χ 2-test in combination with correction for multiple testing. For functional analysis, the entire 3’ UTR of the WFS1 gene was subcloned in a pMIR-Report plasmid and relative luciferase activities were determined. Linkage disequilibrium analysis showed a generally high LD within the investigated region, however the rs1046322 locus was not in LD with the other SNPs. The two miR-SNPs, rs1046322 and rs9457 showed significant association with T1DM and T2DM, respectively. Haplotype analysis also confirmed the association between the 3’ UTR loci and both disease types. In vitro experiments showed that miR-185 reduces the amount of the resulting protein, and rs9457 miRSNP significantly influences the rate of reduction in a luciferase reporter assay. Genetic variants of the WFS1 gene might contribute to the genetic risk of T1DM and T2DM. Furthermore demonstrating the effect of rs9457 in binding of miR-185, we suggest that the optimal level of wolframin protein, potentially influenced by miR-regulation, is crucial in normal beta cell function. PMID:26426397

  9. Micro-RNA Binding Site Polymorphisms in the WFS1 Gene Are Risk Factors of Diabetes Mellitus.

    Directory of Open Access Journals (Sweden)

    Zsuzsanna Elek

    Full Text Available The absolute or relative lack of insulin is the key factor in the pathogenesis of diabetes mellitus. Although the connection between loss of function mutations of the WFS1 gene and DIDMOAD-syndrome including diabetes mellitus underpins the significance of wolframin in the pathogenesis, exact role of WFS1 polymorphic variants in the development of type 1 and type 2 diabetes has not been discovered yet. In this analysis, 787 patients with diabetes and 900 healthy people participated. Genotyping of the 7 WFS1 SNPs was carried out by TaqMan assays. Association study was performed by χ2-test in combination with correction for multiple testing. For functional analysis, the entire 3' UTR of the WFS1 gene was subcloned in a pMIR-Report plasmid and relative luciferase activities were determined. Linkage disequilibrium analysis showed a generally high LD within the investigated region, however the rs1046322 locus was not in LD with the other SNPs. The two miR-SNPs, rs1046322 and rs9457 showed significant association with T1DM and T2DM, respectively. Haplotype analysis also confirmed the association between the 3' UTR loci and both disease types. In vitro experiments showed that miR-185 reduces the amount of the resulting protein, and rs9457 miRSNP significantly influences the rate of reduction in a luciferase reporter assay. Genetic variants of the WFS1 gene might contribute to the genetic risk of T1DM and T2DM. Furthermore demonstrating the effect of rs9457 in binding of miR-185, we suggest that the optimal level of wolframin protein, potentially influenced by miR-regulation, is crucial in normal beta cell function.

  10. Induction of human interferon gene expression is associated with a nuclear factor that interacts with the site of the human immunodeficiency virus-enhancer

    International Nuclear Information System (INIS)

    Hiscott, J.; Alper, D.; Cohen, L.; Leblanc, J.F.; Sportza, L.; Wong, A.; Xanthoudakis, S.

    1989-01-01

    The relationship between transcription of alpha and beta interferon (IFN-α and IFN-β) genes and the interaction of IFN promoter-binding transcription factors has been examined in monoblastoid U937 cells following priming with recombinant IFN-α2 (rIFN-α2) and Sendai virus induction. Pretreatment of U937 cells with rIFN-α2 prior to Sendai virus infection increased the mRNA levels of IFN-α1, IFN-α2, and IFN-β as well as the final yield of biologically active IFN. Analysis of nuclear protein-IFN promoter DNA interactions by electrophoretic mobility-shift assays demonstrated increased factor binding to IFN-α1 and IFN-β regulatory domains, although no new induction-specific complexes were identified. On the basis of competition electrophoretic mobility-shift assay results, factors interacting with the IFN-α1 and IFN-β promoters appear to be distinct DNA-binding proteins. Hybrid promoter-chloramphenicol acetyltransferase fusion plasmids, containing either the IFN-β regulatory element or the human immunodeficiency virus enhancer element linked to the simian virus 40 promoter, were analyzed for virus and phorbol ester inducibility in epithelial and lymphoid cells, respectively. These experiments suggest that induction of IFN gene expression may be controlled in part by transcription regulatory proteins binding to an NF-κB-like site within the IFN-β promoter

  11. In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

    Directory of Open Access Journals (Sweden)

    Kristopher J. L. Irizarry

    2016-01-01

    Full Text Available Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1 that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons.

  12. Genome-wide identification of hypoxia-inducible factor-1 and -2 binding sites in hypoxic human macrophages alternatively activated by IL-10.

    Science.gov (United States)

    Tausendschön, Michaela; Rehli, Michael; Dehne, Nathalie; Schmidl, Christian; Döring, Claudia; Hansmann, Martin-Leo; Brüne, Bernhard

    2015-01-01

    Macrophages (MΦ) often accumulate in hypoxic areas, where they significantly influence disease progression. Anti-inflammatory cytokines, such as IL-10, generate alternatively activated macrophages that support tumor growth. To understand how alternative activation affects the transcriptional profile of hypoxic macrophages, we globally mapped binding sites of hypoxia-inducible factor (HIF)-1α and HIF-2α in primary human monocyte-derived macrophages prestimulated with IL-10. 713 HIF-1 and 795 HIF-2 binding sites were identified under hypoxia. Pretreatment with IL-10 altered the binding pattern, with 120 new HIF-1 and 188 new HIF-2 binding sites emerging. HIF-1 binding was most prominent in promoters, while HIF-2 binding was more abundant in enhancer regions. Comparison of ChIP-seq data obtained in other cells revealed a highly cell type specific binding of HIF. In MΦ HIF binding occurred preferentially in already active enhancers or promoters. To assess the roles of HIF on gene expression, primary human macrophages were treated with siRNA against HIF-1α or HIF-2α, followed by genome-wide gene expression analysis. Comparing mRNA expression to the HIF binding profile revealed a significant enrichment of hypoxia-inducible genes previously identified by ChIP-seq. Analysis of gene expression under hypoxia alone and hypoxia/IL-10 showed the enhanced induction of a set of genes including PLOD2 and SLC2A3, while another group including KDM3A and ADM remained unaffected or was reduced by IL-10. Taken together IL-10 influences the DNA binding pattern of HIF and the level of gene induction. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Simple procedure for evaluating earthquake response spectra of large-event motions based on site amplification factors derived from smaller-event records

    International Nuclear Information System (INIS)

    Dan, Kazuo; Miyakoshi, Jun-ichi; Yashiro, Kazuhiko.

    1996-01-01

    A primitive procedure was proposed for evaluating earthquake response spectra of large-event motions to make use of records from smaller events. The result of the regression analysis of the response spectra was utilized to obtain the site amplification factors in the proposed procedure, and the formulation of the seismic-source term in the regression analysis was examined. A linear form of the moment magnitude, Mw, is good for scaling the source term of moderate earthquakes with Mw of 5.5 to 7.0, while a quadratic form of Mw and the ω-square source-spectrum model is appropriate for scaling the source term of smaller and greater earthquakes, respectively. (author). 52 refs

  14. Multiple phosphorylation sites at the C-terminus regulate nuclear import of HCMV DNA polymerase processivity factor ppUL44

    International Nuclear Information System (INIS)

    Alvisi, Gualtiero; Marin, Oriano; Pari, Gregory; Mancini, Manuela; Avanzi, Simone; Loregian, Arianna; Jans, David A.; Ripalti, Alessandro

    2011-01-01

    The processivity factor of human cytomegalovirus DNA polymerase, phosphoprotein ppUL44, is essential for viral replication. During viral infection ppUL44 is phosphorylated by the viral kinase pUL97, but neither the target residues on ppUL44 nor the effect of phosphorylation on ppUL44's activity are known. We report here that ppUL44 is phosphorylated when transiently expressed in mammalian cells and coimmunoprecipitates with cellular kinases. Of three potential phosphorylation sites (S413, S415, S418) located upstream of ppUL44's nuclear localization signal (NLS) and one (T427) within the NLS itself, protein kinase CK2 (CK2) specifically phosphorylates S413, to trigger a cascade of phosphorylation of S418 and S415 by CK1 and CK2, respectively. Negative charge at the CK2/CK1 target serine residues facilitates optimal nuclear accumulation of ppUL44, whereas negative charge on T427, a potential cyclin-dependent 1 phosphorylation site, strongly decreases nuclear accumulation. Thus, nuclear transport of ppUL44 is finely tuned during viral infection through complex phosphorylation events.

  15. Role of Pre-Operative Blood Transfusion and Subcutaneous Fat Thickness as Risk Factors for Surgical Site Infection after Posterior Thoracic Spine Stabilization.

    Science.gov (United States)

    Osterhoff, Georg; Burla, Laurin; Werner, Clément M L; Jentzsch, Thorsten; Wanner, Guido A; Simmen, Hans-Peter; Sprengel, Kai

    2015-06-01

    Surgical site infections (SSIs) increase morbidity and mortality rates and generate additional cost for the healthcare system. Pre-operative blood transfusion and the subcutaneous fat thickness (SFT) have been described as risk factors for SSI in other surgical areas. The purpose of this study was to assess the impact of pre-operative blood transfusion and the SFT on the occurrence of SSI in posterior thoracic spine surgery. In total, 244 patients (median age 55 y; 97 female) who underwent posterior thoracic spine fusions from 2008 to 2012 were reviewed retrospectively. Patient-specific characteristics, pre-operative hemoglobin concentration/hematocrit values, the amount of blood transfused, and the occurrence of a post-operative SSI were documented. The SFT was measured on pre-operative computed tomography scans. Surgical site infection was observed in 26 patients (11%). The SFT was 13 mm in patients without SSI and 14 mm in those with infection (p=0.195). The odds ratio for patients with pre-operative blood transfusion to present with SSI was 3.1 (confidence interval [CI] 1.4-7.2) and 2.7 (CI 1.1-6.4) when adjusted for age. There was no difference between the groups with regard to pre-operative hemoglobin concentration (p=0.519) or hematocrit (p=0.908). The SFT did not differ in the two groups. Allogeneic red blood cell transfusion within 48 h prior to surgery was an independent risk factor for SSI after posterior fusion for the fixation of thoracic spine instabilities. Pre-operative blood transfusion tripled the risk, whereas SFT had no influence on the occurrence of SSI.

  16. Population-based surveillance of HIV drug resistance emerging on treatment and associated factors at sentinel antiretroviral therapy sites in Namibia.

    Science.gov (United States)

    Hong, Steven Y; Jonas, Anna; DeKlerk, Michael; Shiningavamwe, Andreas; Desta, Tiruneh; Badi, Alfons; Morris, Lynn; Hunt, Gillian M; Ledwaba, Johanna; Sheehan, Heidi B; Lau, Kiger; Trotter, Andrew; Tang, Alice M; Wanke, Christine; Jordan, Michael R

    2015-04-01

    The World Health Organization (WHO) prospective surveys of acquired HIV drug resistance (HIVDR) evaluate HIVDR emerging after the first year of antiretroviral therapy (ART) and associated factors. Consecutive ART starters in 2009 were enrolled at 3 sentinel sites in Namibia. Genotyping was performed at start and after 12 months in patients with HIV viral load (VL) >1000 copies per mL. HIVDR outcomes were: HIVDR prevention (VL ≤1000 copies/mL), possible HIVDR (VL >1000 copies/mL without detectable HIVDR or loss to follow-up or ART stop), and HIVDR (VL >1000 copies/mL with detectable HIVDR). Adherence was assessed using medication possession ratio (MPR). Of 394 starters, at 12 months, 80% were on first-line ART, 1% died, 4% transferred out, 1% stopped ART, <1% switched to second-line, and 15% were lost to follow-up. Among patients on first-line, 77% had VL testing, and 94% achieved VL ≤1000 copies per mL. At baseline, 7% had HIVDR. After 12 months, among patients with VL testing, 5% had HIVDR. A majority of patients failing therapy had high-level resistance to nonnucleoside reverse transcriptase inhibitors but none to protease inhibitors. All sites achieved the WHO target of ≥70% HIVDR prevention. Factors associated with not achieving HIVDR prevention were: baseline resistance to nonnucleoside reverse transcriptase inhibitors [odds ratio (OR) 3.0, P = 0.023], WHO stage 3 or 4 at baseline (OR 2.0, P = 0.012), and MPR <75% (OR 4.9, P = 0.021). Earlier ART initiation and removal of barriers to on-time drug pickups may help to prevent HIVDR. These data inform decisions at national and global levels on the effectiveness of first- and second-line regimens.

  17. Data in support of FSH induction of IRS-2 in human granulosa cells: Mapping the transcription factor binding sites in human IRS-2 promoter

    Directory of Open Access Journals (Sweden)

    Surleen Kaur

    2016-03-01

    Full Text Available Insulin receptor substrate-2 (IRS-2 plays critical role in the regulation of various metabolic processes by insulin and IGF-1. The defects in its expression and/or function are linked to diseases like polycystic ovary syndrome (PCOS, insulin resistance and cancer. To predict the transcription factors (TFs responsible for the regulation of human IRS-2 gene expression, the transcription factor binding sites (TFBS and the corresponding TFs were investigated by analysis of IRS-2 promoter sequence using MatInspector Genomatix software (Cartharius et al., 2005 [1]. The ibid data is part of author׳s publication (Anjali et al., 2015 [2] that explains Follicle stimulating hormone (FSH mediated IRS-2 promoter activation in human granulosa cells and its importance in the pathophysiology of PCOS. Further analysis was carried out for binary interactions of TF regulatory genes in IRS-2 network using Cytoscape software tool and R-code. In this manuscript, we describe the methodology used for the identification of TFBSs in human IRS-2 promoter region and provide details on experimental procedures, analysis method, validation of data and also the raw files. The purpose of this article is to provide the data on all TFBSs in the promoter region of human IRS-2 gene as it has the potential for prediction of the regulation of IRS-2 gene in normal or diseased cells from patients with metabolic disorders and cancer. Keywords: IRS-2, TFBS, FSH, SP1, ChIP

  18. Application of geographically-weighted regression analysis to assess risk factors for malaria hotspots in Keur Soce health and demographic surveillance site.

    Science.gov (United States)

    Ndiath, Mansour M; Cisse, Badara; Ndiaye, Jean Louis; Gomis, Jules F; Bathiery, Ousmane; Dia, Anta Tal; Gaye, Oumar; Faye, Babacar

    2015-11-18

    In Senegal, considerable efforts have been made to reduce malaria morbidity and mortality during the last decade. This resulted in a marked decrease of malaria cases. With the decline of malaria cases, transmission has become sparse in most Senegalese health districts. This study investigated malaria hotspots in Keur Soce sites by using geographically-weighted regression. Because of the occurrence of hotspots, spatial modelling of malaria cases could have a considerable effect in disease surveillance. This study explored and analysed the spatial relationships between malaria occurrence and socio-economic and environmental factors in small communities in Keur Soce, Senegal, using 6 months passive surveillance. Geographically-weighted regression was used to explore the spatial variability of relationships between malaria incidence or persistence and the selected socio-economic, and human predictors. A model comparison of between ordinary least square and geographically-weighted regression was also explored. Vector dataset (spatial) of the study area by village levels and statistical data (non-spatial) on malaria confirmed cases, socio-economic status (bed net use), population data (size of the household) and environmental factors (temperature, rain fall) were used in this exploratory analysis. ArcMap 10.2 and Stata 11 were used to perform malaria hotspots analysis. From Jun to December, a total of 408 confirmed malaria cases were notified. The explanatory variables-household size, housing materials, sleeping rooms, sheep and distance to breeding site returned significant t values of -0.25, 2.3, 4.39, 1.25 and 2.36, respectively. The OLS global model revealed that it explained about 70 % (adjusted R(2) = 0.70) of the variation in malaria occurrence with AIC = 756.23. The geographically-weighted regression of malaria hotspots resulted in coefficient intercept ranging from 1.89 to 6.22 with a median of 3.5. Large positive values are distributed mainly in the southeast

  19. Role of DNA Repair Factor Xeroderma Pigmentosum Protein Group C in Response to Replication Stress As Revealed by DNA Fragile Site Affinity Chromatography and Quantitative Proteomics.

    Science.gov (United States)

    Beresova, Lucie; Vesela, Eva; Chamrad, Ivo; Voller, Jiri; Yamada, Masayuki; Furst, Tomas; Lenobel, Rene; Chroma, Katarina; Gursky, Jan; Krizova, Katerina; Mistrik, Martin; Bartek, Jiri

    2016-12-02

    Replication stress (RS) fuels genomic instability and cancer development and may contribute to aging, raising the need to identify factors involved in cellular responses to such stress. Here, we present a strategy for identification of factors affecting the maintenance of common fragile sites (CFSs), which are genomic loci that are particularly sensitive to RS and suffer from increased breakage and rearrangements in tumors. A DNA probe designed to match the high flexibility island sequence typical for the commonly expressed CFS (FRA16D) was used as specific DNA affinity bait. Proteins significantly enriched at the FRA16D fragment under normal and replication stress conditions were identified using stable isotope labeling of amino acids in cell culture-based quantitative mass spectrometry. The identified proteins interacting with the FRA16D fragment included some known CFS stabilizers, thereby validating this screening approach. Among the hits from our screen so far not implicated in CFS maintenance, we chose Xeroderma pigmentosum protein group C (XPC) for further characterization. XPC is a key factor in the DNA repair pathway known as global genomic nucleotide excision repair (GG-NER), a mechanism whose several components were enriched at the FRA16D fragment in our screen. Functional experiments revealed defective checkpoint signaling and escape of DNA replication intermediates into mitosis and the next generation of XPC-depleted cells exposed to RS. Overall, our results provide insights into an unexpected biological role of XPC in response to replication stress and document the power of proteomics-based screening strategies to elucidate mechanisms of pathophysiological significance.

  20. Nanobody®-based chromatin immunoprecipitation/micro-array analysis for genome-wide identification of transcription factor DNA binding sites

    Science.gov (United States)

    Nguyen-Duc, Trong; Peeters, Eveline; Muyldermans, Serge; Charlier, Daniel; Hassanzadeh-Ghassabeh, Gholamreza

    2013-01-01

    Nanobodies® are single-domain antibody fragments derived from camelid heavy-chain antibodies. Because of their small size, straightforward production in Escherichia coli, easy tailoring, high affinity, specificity, stability and solubility, nanobodies® have been exploited in various biotechnological applications. A major challenge in the post-genomics and post-proteomics era is the identification of regulatory networks involving nucleic acid–protein and protein–protein interactions. Here, we apply a nanobody® in chromatin immunoprecipitation followed by DNA microarray hybridization (ChIP-chip) for genome-wide identification of DNA–protein interactions. The Lrp-like regulator Ss-LrpB, arguably one of the best-studied specific transcription factors of the hyperthermophilic archaeon Sulfolobus solfataricus, was chosen for this proof-of-principle nanobody®-assisted ChIP. Three distinct Ss-LrpB-specific nanobodies®, each interacting with a different epitope, were generated for ChIP. Genome-wide ChIP-chip with one of these nanobodies® identified the well-established Ss-LrpB binding sites and revealed several unknown target sequences. Furthermore, these ChIP-chip profiles revealed auxiliary operator sites in the open reading frame of Ss-lrpB. Our work introduces nanobodies® as a novel class of affinity reagents for ChIP. Taking into account the unique characteristics of nanobodies®, in particular, their short generation time, nanobody®-based ChIP is expected to further streamline ChIP-chip and ChIP-Seq experiments, especially in organisms with no (or limited) possibility of genetic manipulation. PMID:23275538

  1. Multi-species comparative analysis of the equine ACE gene identifies a highly conserved potential transcription factor binding site in intron 16.

    Science.gov (United States)

    Hamilton, Natasha A; Tammen, Imke; Raadsma, Herman W

    2013-01-01

    Angiotensin converting enzyme (ACE) is essential for control of blood pressure. The human ACE gene contains an intronic Alu indel (I/D) polymorphism that has been associated with variation in serum enzyme levels, although the functional mechanism has not been identified. The polymorphism has also been associated with cardiovascular disease, type II diabetes, renal disease and elite athleticism. We have characterized the ACE gene in horses of breeds selected for differing physical abilities. The equine gene has a similar structure to that of all known mammalian ACE genes. Nine common single nucleotide polymorphisms (SNPs) discovered in pooled DNA were found to be inherited in nine haplotypes. Three of these SNPs were located in intron 16, homologous to that containing the Alu polymorphism in the human. A highly conserved 18 bp sequence, also within that intron, was identified as being a potential binding site for the transcription factors Oct-1, HFH-1 and HNF-3β, and lies within a larger area of higher than normal homology. This putative regulatory element may contribute to regulation of the documented inter-individual variation in human circulating enzyme levels, for which a functional mechanism is yet to be defined. Two equine SNPs occurred within the conserved area in intron 16, although neither of them disrupted the putative binding site. We propose a possible regulatory mechanism of the ACE gene in mammalian species which was previously unknown. This advance will allow further analysis leading to a better understanding of the mechanisms underpinning the associations seen between the human Alu polymorphism and enzyme levels, cardiovascular disease states and elite athleticism.

  2. A conserved motif in the linker domain of STAT1 transcription factor is required for both recognition and release from high-affinity DNA-binding sites.

    Science.gov (United States)

    Hüntelmann, Bettina; Staab, Julia; Herrmann-Lingen, Christoph; Meyer, Thomas

    2014-01-01

    Binding to specific palindromic sequences termed gamma-activated sites (GAS) is a hallmark of gene activation by members of the STAT (signal transducer and activator of transcription) family of cytokine-inducible transcription factors. However, the precise molecular mechanisms involved in the signal-dependent finding of target genes by STAT dimers have not yet been very well studied. In this study, we have characterized a sequence motif in the STAT1 linker domain which is highly conserved among the seven human STAT proteins and includes surface-exposed residues in close proximity to the bound DNA. Using site-directed mutagenesis, we have demonstrated that a lysine residue in position 567 of the full-length molecule is required for GAS recognition. The substitution of alanine for this residue completely abolished both binding to high-affinity GAS elements and transcriptional activation of endogenous target genes in cells stimulated with interferon-γ (IFNγ), while the time course of transient nuclear accumulation and tyrosine phosphorylation were virtually unchanged. In contrast, two glutamic acid residues (E559 and E563) on each monomer are important for the dissociation of dimeric STAT1 from DNA and, when mutated to alanine, result in elevated levels of tyrosine-phosphorylated STAT1 as well as prolonged IFNγ-stimulated nuclear accumulation. In conclusion, our data indicate that the kinetics of signal-dependent GAS binding is determined by an array of glutamic acid residues located at the interior surface of the STAT1 dimer. These negatively charged residues appear to align the long axis of the STAT1 dimer in a position perpendicular to the DNA, thereby facilitating the interaction between lysine 567 and the phosphodiester backbone of a bound GAS element, which is a prerequisite for transient gene induction.

  3. Multi-species comparative analysis of the equine ACE gene identifies a highly conserved potential transcription factor binding site in intron 16.

    Directory of Open Access Journals (Sweden)

    Natasha A Hamilton

    Full Text Available Angiotensin converting enzyme (ACE is essential for control of blood pressure. The human ACE gene contains an intronic Alu indel (I/D polymorphism that has been associated with variation in serum enzyme levels, although the functional mechanism has not been identified. The polymorphism has also been associated with cardiovascular disease, type II diabetes, renal disease and elite athleticism. We have characterized the ACE gene in horses of breeds selected for differing physical abilities. The equine gene has a similar structure to that of all known mammalian ACE genes. Nine common single nucleotide polymorphisms (SNPs discovered in pooled DNA were found to be inherited in nine haplotypes. Three of these SNPs were located in intron 16, homologous to that containing the Alu polymorphism in the human. A highly conserved 18 bp sequence, also within that intron, was identified as being a potential binding site for the transcription factors Oct-1, HFH-1 and HNF-3β, and lies within a larger area of higher than normal homology. This putative regulatory element may contribute to regulation of the documented inter-individual variation in human circulating enzyme levels, for which a functional mechanism is yet to be defined. Two equine SNPs occurred within the conserved area in intron 16, although neither of them disrupted the putative binding site. We propose a possible regulatory mechanism of the ACE gene in mammalian species which was previously unknown. This advance will allow further analysis leading to a better understanding of the mechanisms underpinning the associations seen between the human Alu polymorphism and enzyme levels, cardiovascular disease states and elite athleticism.

  4. The promoter for intestinal cell kinase is head-to-head with F-Box 9 and contains functional sites for TCF7L2 and FOXA factors

    Directory of Open Access Journals (Sweden)

    Cohn Steven M

    2010-05-01

    Full Text Available Abstract Background Intestinal cell kinase (ICK; GeneID 22858 is a conserved MAPK and CDK-like kinase that is widely expressed in human tissues. Data from the Cancer Genome Anatomy Project indicated ICK mRNA is increased in cancer, and that its expression correlated with expression of mRNA for an uncharacterized F-box protein, FBX9 (GeneID: 26268. ICK and FBX9 genes are arranged head-to-head on opposite strands, with start sites for transcription separated by ~3.3 kb. We hypothesized ICK and FBX9 are potentially important genes in cancer controlled by a bidirectional promoter. Results We assessed promoter activity of the intergenic region in both orientations in cancer cell lines derived from breast (AU565, SKBR3, colon (HCT-15, KM12, and stomach (AGS cancers, as well as in embryonic human kidney (HEK293T cells. The intergenic segment was active in both orientations in all of these lines, and ICK promoter activity was greater than FBX9 promoter activity. Results from deletions and truncations defined a minimal promoter for ICK, and revealed that repressors and enhancers differentially regulate ICK versus FBX9 promoter activity. The ICK promoter contains consensus motifs for several FOX-family transcription factors that align when mouse and human are compared using EMBOSS. FOXA1 and FOXA2 increase luciferase activity of a minimal promoter 10-20 fold in HEK293T cells. Consensus sites for TCF7L2 (TCF4 (Gene Id: 6934 are also present in both mouse and human. The expression of β-catenin increased activity of the minimal promoter ~10 fold. ICK reference mRNAs (NM_014920.3, NM_016513 are expressed in low copy number and increased in some breast cancers, using a ten base tag 5'-TCAACCTTAT-3' specific for both ICK transcripts. Conclusion ICK and FBX9 are divergently transcribed from a bidirectional promoter that is GC-rich and contains a CpG island. A minimal promoter for ICK contains functional sites for β-cateinin/TCF7L2 and FOXA. These data are

  5. Novel Bioconjugation Strategy Using Elevated Hydrostatic Pressure: A Case Study for the Site-Specific Attachment of Polyethylene Glycol (PEGylation) of Recombinant Human Ciliary Neurotrophic Factor.

    Science.gov (United States)

    Wang, Qi; Zhang, Chun; Guo, Fangxia; Li, Zenglan; Liu, Yongdong; Su, Zhiguo

    2017-11-15

    In this paper, we reported a novel strategy for the site-specific attachment of polyethylene glycol (PEGylation) of proteins using elevated hydrostatic pressure. The process was similar to the conventional one except the reactor was under elevated hydrostatic pressure. The model protein was recombinant human ciliary neurotrophic factor (rhCNTF), and the reagent was monomethoxy-polyethylene glycol-maleimide (mPEG-MAL). PEGylation with mPEG (40 kDa)-MAL at pH 7.0 under normal pressure for 5 h achieved a less than 5% yield. In comparison, when the pressure was elevated, the PEGylation yield was increased dramatically, reaching nearly 90% at 250 MPa. Furthermore, the following phenomena were observed: (1) high-hydrostatic-pressure PEGylation (HHPP) could operate at a low reactant ratio of 1:1.2 (rhCNTF to mPEG-MAL), while the conventional process needs a much-higher ratio. (2) Short and long chains of PEG gave a similar yield of 90% in HHPP, while the conventional yield for the short chain of the PEG was higher than that of the long chain. (3) The reaction pH in the range of 7.0 to 8.0 had almost no influence upon the yield of HHPP, while the PEGylation yield was significantly increased by a factor of three from pH 7.0 to 8.0 at normal pressure. Surface accessibility analysis was performed using GRASP2 software, and we found that Cys17 of rhCNTF was located at the concave patches, which may have steric hindrance for the PEG to approach. The speculated benefit of HHPP was the facilitation of target-site exposure, reducing the steric hindrance and making the reaction much easier. Structure and activity analysis demonstrated that the HHPP product was comparable to the PEGylated rhCNTF prepared through a conventional method. Overall, this work demonstrated that HHPP, as we proposed, may have application potentials in various conjugations of biomacromolecules.

  6. Influence of region and site-specific factors on the degree of general validity of ecological and primary-energy-related assessments of biogas; Einfluss regionaler und standortspezifischer Faktoren auf die Allgemeingueltigkeit oekologischer und primaerenergetischer Bewertungen von Biogas

    Energy Technology Data Exchange (ETDEWEB)

    Dressler, Daniela

    2015-11-01

    As described in this publication, since the early 1990s numerous studies based on the life cycle assessment methodology have been dedicated to assessments of different kinds of bioenergy in comparison with fossil energy resources in terms of their energy balance and environmental impact. On reviewing the results of these studies one finds a strikingly wide range of variation. One major factor of influence on the results of life cycle assessments, besides methodological factors such as the choice of allocation method, is the representativeness of the data used. Thus, widely varying results are also obtained when balance calculations and assessments are performed on energy crops with due consideration to regional and site-specific factors. To address this problem the present study endeavoured to identify region and site-specific factors and assess them in terms of their influence on the life cycle assessment of the cultivation and conversion to biogas of different kinds of energy crops. For this purpose the following questions were explored: What influence do region, site and equipment-specific factors have on the results of ecological and primary-energy-related assessments; and how large are the differences in results between region and site-specific assessments on the one hand and assessments based on general assumptions on the other? It transpires that the results of region and site-specific assessments differ from one another in terms of both the assessment of energy cropping and the assessment of the entire process chain of biogas production and conversion to electricity.

  7. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

    Science.gov (United States)

    Chung, Dongjun; Kuan, Pei Fen; Li, Bo; Sanalkumar, Rajendran; Liang, Kun; Bresnick, Emery H; Dewey, Colin; Keleş, Sündüz

    2011-07-01

    Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip) as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads). This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads). Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.

  8. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

    Directory of Open Access Journals (Sweden)

    Dongjun Chung

    2011-07-01

    Full Text Available Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads. This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads. Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.

  9. Soil to plant 137Cs transfer factors in Zea mays and Phaseolus vulgaris in a semi-arid ecosystem from a radioactive waste site

    International Nuclear Information System (INIS)

    Cervantes, M.L.; Segovia, N.; Gaso, M.I.; Palacios, J.C.

    2002-01-01

    A study of 137 Cs in soil, maize plants, (Zea mays) and beans (Phaseolus vulgaris) has been performed at the confined Storage Centre for Radioactive Waste from Mexico. Under field conditions the site was divided in four zones with different soil contamination characteristics. The plants were grown 'in situ' reproducing the local agricultural practices without fertilizers, pesticides or artificial irrigation.The 137 Cs determinations were performed using a low background gamma spectrometry system with an HPGe detector. The results indicate that one of the zones had a striking 137 Cs contamination in the soil and the uptake by the grown plants showed the highest specific activities at the root. For the edible parts of the plants the amount of 137 Cs in the maize grains was one order of magnitude lower than for the beans. The transfer factors ranges for the different parts of the maize plants was from 0.001 in the grain to 0.6 in the root. (author)

  10. The etiology, risk factors, and interactions of enteric infections and malnutrition and the consequences for child health and development study (MAL-ED): description of the Tanzanian site.

    Science.gov (United States)

    Mduma, Estomih R; Gratz, Jean; Patil, Crystal; Matson, Kristine; Dakay, Mary; Liu, Sarah; Pascal, John; McQuillin, Lauren; Mighay, Emmanuel; Hinken, Elizabeth; Ernst, Alexandra; Amour, Caroline; Mvungi, Regisiana; Bayyo, Eliwaza; Zakaria, Yeconia; Kivuyo, Sokoine; Houpt, Eric R; Svensen, Erling

    2014-11-01

    The Haydom, Tanzania, site (TZH) of The Etiology, Risk Factors and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) Study is in north-central Tanzania, 300 km from the nearest urban center. TZH is in a remote rural district where most of the population are agropastoralists and grow maize as the staple food. The average household size is 7. The average woman achieves a parity of 6 and has 1 child death. Socioeconomic indicators are poor, with essentially no household having access to electricity, piped water, or improved sanitary facilities (compared with 14%, 7%, and 12%, respectively, reported nationally). The Demographic Health Survey Tanzania 2004 indicated that the region had high rates of stunting and underweight (40% and 31% of children aged child mortality rate of 5.8%. Human immunodeficiency virus prevalence among 18-month-old children is rural African population with profound poverty and malnutrition, but a strong community-based research infrastructure. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  11. DNA hypomethylation of a transcription factor binding site within the promoter of a gout risk gene NRBP1 upregulates its expression by inhibition of TFAP2A binding.

    Science.gov (United States)

    Zhu, Zaihua; Meng, Weida; Liu, Peiru; Zhu, Xiaoxia; Liu, Yun; Zou, Hejian

    2017-01-01

    Genome-wide association studies (GWASs) have identified dozens of loci associated with gout, but for most cases, the risk genes and the underlying molecular mechanisms contributing to these associations are unknown. This study sought to understand the molecular mechanism of a common genetic variant, rs780093, in the development of gout, both in vitro and in vivo. Nuclear receptor binding protein 1 ( NRBP1 ), as a gout risk gene, and its regulatory region, 72 bp upstream of the transcription start site, designated as B1, were identified through integrative analyses of genome-wide genotype and DNA methylation data. We observed elevated NRBP1 expression in human peripheral blood mononuclear cells (PBMCs) from gout patients. In vitro luciferase reporter and protein pulldown assay results showed that DNA methylation could increase the binding of the transcription factor TFAP2A to B1, leading to suppressed gene expression. There results were further confirmed by in vivo bisulfite pyrosequencing showing that hypomethylation on B1 is associated with increased NRBP1 expression in gout patients. Hypomethylation at the promoter region of NRBP1 reduces the binding of TFAP2A and thus leads to elevated NRBP1 expression, which might contribute to the development of gout.

  12. Development of a surgical site infection (SSI) surveillance system, calculation of SSI rates and specification of important factors affecting SSI in a digestive organ surgical department.

    Science.gov (United States)

    Kimura, Koji; Sawa, Akihiro; Akagi, Shinji; Kihira, Kenji

    2007-06-01

    We have developed an original system to conduct surgical site infection (SSI) surveillance. This system accumulates SSI surveillance information based on the National Nosocomial Infections Surveillance (NNIS) System and the Japanese Nosocomial Infections Surveillance (JNIS) System. The features of this system are as follows: easy input of data, high generality, data accuracy, SSI rate by operative procedure and risk index category (RIC) can be promptly calculated and compared with the current NNIS SSI rate, and the SSI rates and accumulated data can be exported electronically. Using this system, we monitored 798 patients in 24 operative procedure categories in the Digestive Organs Surgery Department of Mazda Hospital, Mazda Motor Corporation, from January 2004 through December 2005. The total number and rate of SSI were 47 and 5.89%, respectively. The SSI rates of 777 patients were calculated based on 15 operative procedure categories and Risk Index Categories (RIC). The highest SSI rate was observed in the rectum surgery of RIC 1 (30%), followed by the colon surgery of RIC3 (28.57%). About 30% of the isolated infecting bacteria were Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Escherichia coli. Using quantification theory type 2, the American Society of Anesthesiology score (4.531), volume of hemorrhage under operation (3.075), wound classification (1.76), operation time (1.352), and history of diabetes (0.989) increased to higher ranks as factors for SSI. Therefore, we evaluated this system as a useful tool in safety control for operative procedures.

  13. Risk factors for surgical site infection following nonshunt pediatric neurosurgery: a review of 9296 procedures from a national database and comparison with a single-center experience.

    Science.gov (United States)

    Sherrod, Brandon A; Arynchyna, Anastasia A; Johnston, James M; Rozzelle, Curtis J; Blount, Jeffrey P; Oakes, W Jerry; Rocque, Brandon G

    2017-04-01

    OBJECTIVE Surgical site infection (SSI) following CSF shunt operations has been well studied, yet risk factors for nonshunt pediatric neurosurgery are less well understood. The purpose of this study was to determine SSI rates and risk factors following nonshunt pediatric neurosurgery using a nationwide patient cohort and an institutional data set specifically for better understanding SSI. METHODS The authors reviewed the American College of Surgeons National Surgical Quality Improvement Program-Pediatric (ACS NSQIP-P) database for the years 2012-2014, including all neurosurgical procedures performed on pediatric patients except CSF shunts and hematoma evacuations. SSI included deep (intracranial abscesses, meningitis, osteomyelitis, and ventriculitis) and superficial wound infections. The authors performed univariate analyses of SSI association with procedure, demographic, comorbidity, operative, and hospital variables, with subsequent multivariate logistic regression analysis to determine independent risk factors for SSI within 30 days of the index procedure. A similar analysis was performed using a detailed institutional infection database from Children's of Alabama (COA). RESULTS A total of 9296 nonshunt procedures were identified in NSQIP-P with an overall 30-day SSI rate of 2.7%. The 30-day SSI rate in the COA institutional database was similar (3.3% of 1103 procedures, p = 0.325). Postoperative time to SSI in NSQIP-P and COA was 14.6 ± 6.8 days and 14.8 ± 7.3 days, respectively (mean ± SD). Myelomeningocele (4.3% in NSQIP-P, 6.3% in COA), spine (3.5%, 4.9%), and epilepsy (3.4%, 3.1%) procedure categories had the highest SSI rates by procedure category in both NSQIP-P and COA. Independent SSI risk factors in NSQIP-P included postoperative pneumonia (OR 4.761, 95% CI 1.269-17.857, p = 0.021), immune disease/immunosuppressant use (OR 3.671, 95% CI 1.371-9.827, p = 0.010), cerebral palsy (OR 2.835, 95% CI 1.463-5.494, p = 0.002), emergency operation (OR 1

  14. Risk factors for surgical site infection following nonshunt pediatric neurosurgery: a review of 9296 procedures from a national database and comparison with a single-center experience

    Science.gov (United States)

    Sherrod, Brandon A.; Arynchyna, Anastasia A.; Johnston, James M.; Rozzelle, Curtis J.; Blount, Jeffrey P.; Oakes, W. Jerry; Rocque, Brandon G.

    2017-01-01

    Objective Surgical site infection (SSI) following CSF shunt operations has been well studied, yet risk factors for nonshunt pediatric neurosurgery are less well understood. The purpose of this study was to determine SSI rates and risk factors following nonshunt pediatric neurosurgery using a nationwide patient cohort and an institutional dataset specifically for better understanding SSI. Methods The authors reviewed the American College of Surgeons National Surgical Quality Improvement Program Pediatric (ACS NSQIP-P) database for the years 2012–2014, including all neurosurgical procedures performed on pediatric patients except CSF shunts and hematoma evacuations. SSI included deep (intracranial abscesses, meningitis, osteomyelitis, and ventriculitis) and superficial wound infections. The authors performed univariate analyses of SSI association with procedure, demographic, comorbidity, operative, and hospital variables, with subsequent multivariate logistic regression analysis to determine independent risk factors for SSI within 30 days of the index procedure. A similar analysis was performed using a detailed institutional infection database from Children’s Hospital of Alabama (COA). Results A total of 9296 nonshunt procedures were identified in NSQIP-P with an overall 30-day SSI rate of 2.7%. The 30-day SSI rate in the COA institutional database was similar (3.3% of 1103 procedures, p = 0.325). Postoperative time to SSI in NSQIP-P and COA was 14.6 ± 6.8 days and 14.8 ± 7.3 days, respectively (mean ± SD). Myelomeningocele (4.3% in NSQIP-P, 6.3% in COA), spine (3.5%, 4.9%), and epilepsy (3.4%, 3.1%) procedure categoriess had the highest SSI rates by procedure category in both NSQIP-P and COA. Independent SSI risk factors in NSQIP-P included postoperative pneumonia (OR 4.761, 95% CI 1.269–17.857, p = 0.021), immune disease/immunosuppressant use (OR 3.671, 95% CI 1.371–9.827, p = 0.010), cerebral palsy (OR 2.835, 95% CI 1.463–5.494, p = 0.002), emergency

  15. Site selection for nuclear power plants

    International Nuclear Information System (INIS)

    Ehjchkholz, D.

    1980-01-01

    Problem of NPP site selection in the USA including engineering factors, radiation and environmental protection factors is stated in detail. Floating and underground sites are considered especially. The attention in paid to waste storage and risk criterium in siting [ru

  16. Risk factors for surgical site infection following laparotomy: Effect of season and perioperative variables and reporting of bacterial isolates in 287 horses.

    Science.gov (United States)

    Isgren, C M; Salem, S E; Archer, D C; Worsman, F C F; Townsend, N B

    2017-01-01

    Surgical site infection (SSI) is an important cause of post operative morbidity following laparotomy. To investigate risk factors for SSI, including effect of season and surgery performed outside normal working hours, and to report bacterial isolates and antimicrobial resistance patterns. Retrospective cohort study. Data were obtained from horses that had undergone exploratory laparotomy over a 3-year period (2010-2013) in a UK hospital population. SSI was defined as any purulent or serous discharge from the laparotomy incision of >24 h duration that developed during hospitalisation. Multivariable logistic regression was used to identify associations between pre-, intra- and post operative variables and altered likelihood of SSI. Surgical site infection developed in 73/287 (25.4%) horses during hospitalisation. Horses of greater bodyweight (odds ratio [OR] 1.002, 95% confidence interval [CI] 1.0002-1.005, P = 0.03), increased packed cell volume (≥48%) on admission (OR 3.03, 95% CI 1.32-6.94, P = 0.01), small intestinal resection (OR 2.27, 95% CI 1.15-4.46, P = 0.02) and post operative colic (OR 2.86, 95% CI 1.41-5.79, P = 0.003) were significantly associated with increased likelihood of SSI in a multivariable model. SSI was also significantly more likely to occur during winter (OR 3.84, 95% CI 1.38-10.70, P = 0.01) and summer (OR 5.63, 95% CI 2.07-15.3, P = 0.001) months in the model. Three-layer closure of the incision was protective (OR 0.31, 95% CI 0.16-0.58, P<0.001) compared to 2-layer closure. There was no effect of surgery being performed outside normal working hours (P = 0.5). The most common bacterial isolates were Escherichia coli (59.5%), Enterococcus spp. (42.4%) and Staphylococcus spp. (25.4%). Penicillin resistant isolates accounted for 92% (96/104) of isolates while 18% (21/119) of isolates were gentamicin resistant. Laparotomy during winter and summer months was associated with increased likelihood of SSI but there was no effect of surgery

  17. Small Wind Site Assessment Guidelines

    Energy Technology Data Exchange (ETDEWEB)

    Olsen, Tim [Advanced Energy Systems LLC, Eugene, OR (United States); Preus, Robert [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2015-09-01

    Site assessment for small wind energy systems is one of the key factors in the successful installation, operation, and performance of a small wind turbine. A proper site assessment is a difficult process that includes wind resource assessment and the evaluation of site characteristics. These guidelines address many of the relevant parts of a site assessment with an emphasis on wind resource assessment, using methods other than on-site data collection and creating a small wind site assessment report.

  18. Establishment and Application of a High Throughput Screening System Targeting the Interaction between HCV Internal Ribosome Entry Site and Human Eukaryotic Translation Initiation Factor 3

    Directory of Open Access Journals (Sweden)

    Yuying Zhu

    2017-05-01

    Full Text Available Viruses are intracellular obligate parasites and the host cellular machinery is usually recruited for their replication. Human eukaryotic translation initiation factor 3 (eIF3 could be directly recruited by the hepatitis C virus (HCV internal ribosome entry site (IRES to promote the translation of viral proteins. In this study, we establish a fluorescence polarization (FP based high throughput screening (HTS system targeting the interaction between HCV IRES and eIF3. By screening a total of 894 compounds with this HTS system, two compounds (Mucl39526 and NP39 are found to disturb the interaction between HCV IRES and eIF3. And these two compounds are further demonstrated to inhibit the HCV IRES-dependent translation in vitro. Thus, this HTS system is functional to screen the potential HCV replication inhibitors targeting human eIF3, which is helpful to overcome the problem of viral resistance. Surprisingly, one compound HP-3, a kind of oxytocin antagonist, is discovered to significantly enhance the interaction between HCV IRES and eIF3 by this HTS system. HP-3 is demonstrated to directly interact with HCV IRES and promote the HCV IRES-dependent translation both in vitro and in vivo, which strongly suggests that HP-3 has potentials to promote HCV replication. Therefore, this HTS system is also useful to screen the potential HCV replication enhancers, which is meaningful for understanding the viral replication and screening novel antiviral drugs. To our knowledge, this is the first HTS system targeting the interaction between eIF3 and HCV IRES, which could be applied to screen both potential HCV replication inhibitors and enhancers.

  19. Elongation Factor Tu Prevents Misediting of Gly-tRNA(Gly Caused by the Design Behind the Chiral Proofreading Site of D-Aminoacyl-tRNA Deacylase.

    Directory of Open Access Journals (Sweden)

    Satya Brata Routh

    2016-05-01

    Full Text Available D-aminoacyl-tRNA deacylase (DTD removes D-amino acids mischarged on tRNAs and is thus implicated in enforcing homochirality in proteins. Previously, we proposed that selective capture of D-aminoacyl-tRNA by DTD's invariant, cross-subunit Gly-cisPro motif forms the mechanistic basis for its enantioselectivity. We now show, using nuclear magnetic resonance (NMR spectroscopy-based binding studies followed by biochemical assays with both bacterial and eukaryotic systems, that DTD effectively misedits Gly-tRNAGly. High-resolution crystal structure reveals that the architecture of DTD's chiral proofreading site is completely porous to achiral glycine. Hence, L-chiral rejection is the only design principle on which DTD functions, unlike other chiral-specific enzymes such as D-amino acid oxidases, which are specific for D-enantiomers. Competition assays with elongation factor thermo unstable (EF-Tu and DTD demonstrate that EF-Tu precludes Gly-tRNAGly misediting at normal cellular concentrations. However, even slightly higher DTD levels overcome this protection conferred by EF-Tu, thus resulting in significant depletion of Gly-tRNAGly. Our in vitro observations are substantiated by cell-based studies in Escherichia coli that show that overexpression of DTD causes cellular toxicity, which is largely rescued upon glycine supplementation. Furthermore, we provide direct evidence that DTD is an RNA-based catalyst, since it uses only the terminal 2'-OH of tRNA for catalysis without the involvement of protein side chains. The study therefore provides a unique paradigm of enzyme action for substrate selection/specificity by DTD, and thus explains the underlying cause of DTD's activity on Gly-tRNAGly. It also gives a molecular and functional basis for the necessity and the observed tight regulation of DTD levels, thereby preventing cellular toxicity due to misediting.

  20. Transcription factor HIF1A: downstream targets, associated pathways, polymorphic hypoxia response element (HRE) sites, and initiative for standardization of reporting in scientific literature.

    Science.gov (United States)

    Slemc, Lucija; Kunej, Tanja

    2016-11-01

    Hypoxia-inducible factor-1α (HIF-1α) has crucial role in adapting cells to hypoxia through expression regulation of many genes. Identification of HIF-1α target genes (HIF-1α-TGs) is important for understanding the adapting mechanism. The aim of the present study was to collect known HIF-1α-TGs and identify their associated pathways. Targets and associated genomics data were retrieved using PubMed, WoS ( http://apps.webofknowledge.com/ ), HGNC ( http://www.genenames.org/ ), NCBI ( http://www.ncbi.nlm.nih.gov/ ), Ensemblv.84 ( http://www.ensembl.org/index.html ), DAVID Bioinformatics Resources ( https://david.ncifcrf.gov /), and Disease Ontology database ( http://disease-ontology.org/ ). From 51 papers, we collected 98 HIF-1α TGs found to be associated with 20 pathways, including metabolism of carbohydrates and pathways in cancer. Reanalysis of genomic coordinates of published HREs (hypoxia response elements) revealed six polymorphisms within HRE sites (HRE-SNPs): ABCG2, ACE, CA9, and CP. Due to large heterogeneity of results presentation in scientific literature, we also propose a first step towards reporting standardization of HIF-1α-target interactions consisting of ten relevant data types. Suggested minimal checklist for reporting will enable faster development of a complete catalog of HIF-1α-TGs, data sharing, bioinformatics analyses, and setting novel more targeted hypotheses. The proposed format for data standardization is not yet complete but presents a baseline for further optimization of the protocol with additional details, for example, regarding the experimental validation.

  1. Effect of MCM09, an active site-directed inhibitor of factor Xa, on B16-BL6 melanoma lung colonies in mice.

    Science.gov (United States)

    Rossi, C; Hess, S; Eckl, R W; di Lena, A; Bruno, A; Thomas, O; Poggi, A

    2006-03-01

    Treatment with anticoagulant drugs has shown potential inhibitory effect on tumor invasion, although the relationship with clotting inhibition was not clear. The aim of our study was to evaluate the potential antitumor activity of MCM09, a newly developed, active site-directed, small molecule inhibitor of factor Xa (FXa) [WO0216312], and to relate the findings to anticlotting potency. MCM09 (0.1-10 mg kg(-1)) or heparin (H; 10 mg kg(-1)) was injected intravenously (i.v.), with 5 x 10(4) B16-BL6 melanoma cells, in C57BL/6 mice. Mice were killed after 18 days, to count lung colonies. Ex vivo anticoagulant activity was measured by activated partial thromboplastin time (APTT) on mouse plasma. MCM09, a selective inhibitor of FXa (IC-50 = 2.4 nm against human FXa), inhibited in a dose-dependent manner B16-BL6 melanoma lung colonies in mice. Mean lung metastasis number was 20.9 +/- 4.8 in controls (n = 10), 1.2 +/- 0.4 in mice treated with H, 10 mg kg(-1) i.v. (P < 0.01), 0.9 +/- 0.3, 9.2 +/- 2.2 and 15.5 +/- 2.6 in mice treated with MCM09, at 10 (P < 0.01), 1 (P < 0.05) and 0.1 mg kg(-1) i.v. (ns), respectively. MCM09 (10 mg kg(-1) i.v.) significantly prolonged APTT (57.1 +/- 10.2 s) 30 min after i.v. injection when compared with controls (25.3 +/- 1.6 s; P < 0.05). Lung colonies were 74.2-72.6% reduced by MCM09 (10 mg kg(-1)) given 60 or 120 min before cells, but not by MCM09 given 60 min thereafter, suggesting a direct cell interaction as a mechanism underlying antitumor activity.

  2. HIV preventive behavior and associated factors among mining workers in Sali traditional gold mining site Bench Maji zone, Southwest Ethiopia: a cross sectional study.

    Science.gov (United States)

    Abdissa, Hordofa Gutema; Lemu, Yohannes Kebede; Nigussie, Dejene Tilahun

    2014-09-26

    Prevalence of HIV and other STI is high among migrant mining workers due to factors such as dangerous working conditions, only masculine identities existence, living away from families, desolate and in hospitable place. This makes them known to be HIV and STI vulnerable group in different part of the world. But, in Ethiopia they were not thought as at risk group yet. So the aim of this study is to assess magnitude of HIV preventive behaviours and associated factors among gold miners in Sali traditional gold mining site. A cross sectional study was conducted to assess HIV preventive behavior of the mining worker. The data were collected using interviewer administered structured questionnaire adapted from other related behavioural studies. The data was entered using EPI data version 3.1 and analyzed using SPSS version 17. Multiple logistic regression was used to assess relationship of HIV preventive behavior with constructs of health belief model. A total of 393 respondents with response rate of 93.12% were participated. All of the study participants were male 393(100%), the mean age of the participant was 24.0 (± 5.13SD). Less than half of the respondents 187(47.6%) were engaged in HIV preventive behavior. Less than half (45.3%) of them have high perceived susceptibility to HIV/AIDS; majority (62.8%) of them has high perceived severity to HIV/AIDS. HIV preventive behavior is negatively associated with being in middle, higher and highest income [OR = 0.54, 95% CI: 0.21, 0.74], [OR = 0.40, 95% CI: 0.30, 0.98] and [OR = 0.39, 95% CI: 0.20, 0.77] respectively and positively associated with Completing secondary, tertiary school and self efficacy [OR = 2.66, 95% CI: 1.11, 6.41], [OR = 5.40, 95% CI: 1.54, 19] and [OR = 1.88, 95% CI: 1.18, 2.94] respectively. The HIV preventive behavior of the mining worker was low. Being engaged in sexual intercourse with one sexual partner is very low, Consistent condom use among these mining workers was low. Income, educational status

  3. The impact of radiotherapy dose and other treatment-related and clinical factors on control of stage I and II non-Hodgkin's lymphoma in irradiated sites

    International Nuclear Information System (INIS)

    Kamath, Sachin S.; Marcus, Robert B.; Lynch, James W.; Mendenhall, Nancy Price

    1997-01-01

    Purpose/Objective: To study the effect of radiotherapeutic and chemotherapeutic parameters on local or in-field (IF) disease control; to identify other treatment-related and clinical factors of potential prognostic significance, and to elucidate the optimal radiotherapy dose in various clinical settings. Materials and Methods: Two hundred eighty-five patients with non-CNS presentations of Stage I and II non-Hodgkin's lymphoma (NHL) were treated with either radiotherapy (RT) alone (n=159) or combined modality therapy (CMT) using induction chemotherapy followed by consolidative RT (n=126). Ninety-three percent (67 of 72 patients) with low grade lymphomas (LGLs) were treated with RT alone. Ninety-two of 213 patients with intermediate/high grade lymphomas (I/HGLs) were treated with RT alone and 121 received CMT. Ninety-one patients (72%) of those receiving CMT were given four or more cycles of chemotherapy; CHOP was the regimen used most often (n=81). The RT treatment volumes included involved field (n=151), extended field (n=123), and comprehensive lymphatic irradiation (n=11). Minimum follow-up was 2 yr (median, 6.5 yr). Variables of potential prognostic significance for IF disease control, freedom from relapse (FFR), and absolute survival (AS) were evaluated by both univariate and multivariate analyses. Results: The 5, 10, and 20 yr actuarial AS rates were 73%, 46%, and 33% for patients with LGL; and 64%, 44%, and 18% for patients with I/HGL, respectively. The 5, 10, and 20 yr actuarial FFR rates were 62%, 59%, and 49% for LGLs and 66%, 57%, and 57% for I/HGLs, respectively. Significant prognostic factors identified by the multivariate analysis were age, tumor size, and histology for AS; tumor size and treatment modality (RT alone vs. CMT) for FFR; and only tumor size for IF disease control. Of the 95 total failures, only 12 were IF. Most of the failures (65%) were observed in contiguous unirradiated sites. All 4 IF failures in the LGLs occurred in patients treated

  4. Life cycle assessment in wastewater treatment: : Influence of site-oriented normalization factors, life cycle impact assessment methods, and weighting methods

    NARCIS (Netherlands)

    Bai, Shunwen; Wang, Xiuheng; Zhang, X.; Zhao, Xinyue; Ren, N

    2017-01-01

    This present study aims to analyze the differences in results of different site-directional life cycle assessment
    (LCA) methods applied in the field of wastewater treatment. Site-generic methods were employed and
    compared with China-specific methods on a full-scale wastewater treatment case.

  5. Dispersal and disturbance as factors limiting the distribution of rare plant species at the Savannah River Site and the Carolina Sandhills National Wildlife Refuge.

    Energy Technology Data Exchange (ETDEWEB)

    Primack, Richard; Walker, Joan.

    2003-12-10

    An experiment was conducted to identify effective methods of creating new populations of herbaceous species in managed upland longleaf pine forest at two locations in the Fall-line Sandhills of South Carolina. We included thirteen species and a variety of site treatments. All sites were burned and lightly raked prior to planting. Sowing seeds on untreated or fertilized treatments resulted in the lowest establishment of all treatments. Digging the planting area to remove belowground plant structures and using hardware cloth cages to exclude potential mammalian seed predators and herbivores led to increased establishment of target species. Establishment was higher using seedling transplants compared to seeds. Success rate was highly variable among sites so population establishment efforts should try to incorporate many sites initially to find the sites that give the greatest chance of success, or increase efforts to carefully identify species, habitat requirements and screen potential sites accordingly. Some species showed very low rates of success despite the variety of methods used; for such species additional work is required on their basic ecology, in particular germination biology and site requirements, as part of a restoration project. The overall low rate of establishment success emphasizes the need to protect and manage existing populations of uncommon Sandhills species, and to recognize that establishing large, long-term, reproducing populations of such species will be difficult.

  6. Site Features

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of various site features from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different times...

  7. Occurrence and air-soil exchange of organochlorine pesticides and polychlorinated biphenyls at a CAWNET background site in central China: Implications for influencing factors and fate.

    Science.gov (United States)

    Zhan, Lingxi; Lin, Tian; Wang, Zuwu; Cheng, Zhineng; Zhang, Gan; Lyu, Xiaopu; Cheng, Hairong

    2017-11-01

    Ambient air and soil samples were collected between March 2012 and March 2013 at Jinsha, a regional background site in central China, to measure the concentrations of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs). The average concentrations of total OCPs and total PCBs were 191 ± 107 and 39.4 ± 27.1 pg/m 3 in air (gaseous and particulate phase) and 0.585 ± 0.437 and 0.083 ± 0.039 ng/g in soil, respectively. The higher concentrations of p,p'-dichlorodiphenyltrichloroethane (p,p'-DDT) and p,p'-DDT/p,p'-DDE ratios in the soil indicated recent p,p'-DDT input to the soil. A strong positive temperature dependence and average fugacity fraction value > 0.5 were observed for p,p'-DDT, suggesting that volatilization of residual DDT in the soil was the main influencing factor on atmospheric p,p'-DDT. Highly average fugacity fractions (>0.7) of trans-chlordane (TC) and cis-chlordane (CC) and high TC/CC ratios both in the soil and atmosphere suggested fresh inputs. Higher gaseous concentrations of hexachlorobenzene (HCB) were observed in winter and negative temperature dependence was directly attributed to the surrounding ongoing source (e.g. fuel consuming activities), especially in winter. Overall, most targeted OCPs and PCBs were influenced by long-range transport, and fugacity fraction values indicated highly volatile compounds (e.g. α-hexachlorocyclohexane (α-HCH) and lower chlorinated PCBs) were volatilized and low volatility compounds (e.g. p,p'-DDE and higher chlorinated PCBs) were deposited at the air-soil interface. Knowing the source and sink of OCPs and PCBs can help to control their pollution in this area and provide a reference for other studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Site decontamination

    International Nuclear Information System (INIS)

    Bicker, A.E.

    1981-01-01

    Among the several DOE sites that have been radiologically decontaminated under the auspices of the Nevada Operations Office are three whose physical characteristics are unique. These are the Tatum Dome Test Site (TDTS) near Hattiesburg, Mississippi; a location of mountainous terrain (Pahute Mesa) on the Nevada Test Site; and the GNOME site near Carlsbad, New Mexico. In each case the contamination, the terrain, and the climate conditions were different. This presentation includes a brief description of each site, the methods used to perform radiological surveys, the logistics required to support the decontamination (including health physics and sample analysis), and the specific techniques used to reduce or remove the contamination

  9. Factors affecting the thermal environment of Agassiz’s Desert Tortoise (Gopherus agassizii) cover sites in the Central Mojave Desert during periods of temperature extremes

    Science.gov (United States)

    Mack, Jeremy S.; Berry, Kristin H.; Miller, David; Carlson, Andrea S.

    2015-01-01

    Agassiz's Desert Tortoises (Gopherus agassizii) spend >95% of their lives underground in cover sites that serve as thermal buffers from temperatures, which can fluctuate >40°C on a daily and seasonal basis. We monitored temperatures at 30 active tortoise cover sites within the Soda Mountains, San Bernardino County, California, from February 2004 to September 2006. Cover sites varied in type and structural characteristics, including opening height and width, soil cover depth over the opening, aspect, tunnel length, and surficial geology. We focused our analyses on periods of extreme temperature: in summer, between July 1 and September 1, and winter, between November 1 and February 15. With the use of multivariate regression tree analyses, we found cover-site temperatures were influenced largely by tunnel length and subsequently opening width and soil cover. Linear regression models further showed that increasing tunnel length increased temperature stability and dampened seasonal temperature extremes. Climate change models predict increased warming for southwestern North America. Cover sites that buffer temperature extremes and fluctuations will become increasingly important for survival of tortoises. In planning future translocation projects and conservation efforts, decision makers should consider habitats with terrain and underlying substrate that sustain cover sites with long tunnels and expanded openings for tortoises living under temperature extremes similar to those described here or as projected in the future.

  10. Hanford Site environmental setting data developed for the unit risk factor methodology in support of the Programmatic Environmental Impact Statement (PEIS)

    International Nuclear Information System (INIS)

    Schramke, J.A.; Glantz, C.S.; Holdren, G.R.

    1994-05-01

    This report describes the environmental settings identified for the Hanford Site in support of the US Department of Energy's (DOE's) Programmatic Environmental Impact Study (PEIS). The objective of the PEIS is to provide the public with information about the types of waste and contamination problems associated with major DOE facilities across the country and to assess the relative risks that these wastes pose to the public, onsite workers, and the environment. The environmental setting information consists of the site-specific data required to model (using the Multimedia Environmental Pollutant Assessment System) the atmospheric, groundwater, and surface-water transport of contaminants within the boundaries of the Hanford Site. The environmental setting data describes the climate, atmospheric dispersion, hydrogeology, and surface-water characteristics of the Site. The number of environmental settings developed for the Hanford Site was the fewest that could provide accurate results when used in the risk assessment modeling. Environmental settings for Hanford were developed in conjunction with local experts in the fields of meteorology, geology, hydrology, and geochemistry. Site experts participated in the initial development, fine-tuning, and final review of Hanford's PEIS environmental settings

  11. Site organization and site arrangement

    International Nuclear Information System (INIS)

    Boissonnet, B.; Macqueron, J.F.

    1976-01-01

    The present paper deals with criteria for the choice of a production unit or power plant site, the organization and development of a site in terms of its particular characteristics and takes into account personnel considerations in site organizations as well as the problem of integrating the architecture into the environment. (RW) [de

  12. Fear of falling as a risk factor of mobility disability in older people at five diverse sites of the IMIAS study.

    Science.gov (United States)

    Auais, Mohammad; Alvarado, Beatriz E; Curcio, Carmen-Lucia; Garcia, Angeles; Ylli, Alban; Deshpande, Nandini

    2016-01-01

    Fear of falling (FoF) is a common health problem among older adults. Although the relationship between FoF and limitation in daily activities has been reported, FoF's relationship to mobility disability, a transitional phase to end-stage disability, is not yet understood. We examined the relationship between FoF and mobility disability among community-dwelling older adults and explored the differences in this relationship among socio-culturally diverse sites. Cross-sectional study. Community. 1875 participants (65-74 years) were recruited from five sites and included in the analysis (Kingston, Canada: 394; St-Hyacinthe, Canada: 397; Tirana, Albania: 359; Manizales, Colombia: 341; and Natal, Brazil: 384). FoF was quantified using the Falls Efficacy Scale-International (FES-I, range: 16-64). Mobility disability was defined as difficulty climbing a flight of stairs or walking 400m without assistance. Overall, 21.5% of participants reported high FoF (FES-I>27). The average FoF scores were significantly different between the sites (pfive study sites (ranged from 19.8% at Kingston, Canada to 50.7% at Tirana, Albania, pfive sites. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  13. Site operations

    International Nuclear Information System (INIS)

    House, W.B.; Ebenhack, D.G.

    1989-01-01

    This chapter is a discussion of the management and operations practices used at the Barnwell Waste Management Facility in Barnwell, SC. The following topics are discussed: (1) Waste receiving and inspection, including manifest and certificates of compliance, radiological surveys, disposition of nonconforming items, and decontamination and disposition of secondary waste streams; (2) Waste disposal, including Title 10 CFR 61 requirements, disposal area evaluations, shipment offloading, container emplacement, and radiation protection; (3) Trench closure, including trench backfilling, trench capping, and permanent markers; (4) Site maintenance and stabilization, including trench maintenance, surface water management, and site closure activities; (5) Site monitoring programs, including operational monitoring, and environmental monitoring program; (6) Personnel training and qualifications, including basic training program, safety training program, special skills training, and physical qualifications; (7) Records management, including waste records, personnel training records, personnel dosimetry records, site monitoring records, trench qualification and construction records, and site drawings and stabilization records; (8) Site security; (9) Emergency response plans; and (10) Quality assurance

  14. Factor Structure of Content Preparation for E-Business Web Sites: Results of a Survey of 428 Industrial Employees in the People's Republic of China

    Science.gov (United States)

    Guo, Yinni; Salvendy, Gavriel

    2009-01-01

    To better fulfil customer satisfaction, a study of what content e-business web sites should contain is conducted. Based on background literature, a content preparation survey of 70 items was developed and completed by 428 white collar employees of an electronic company in mainland China. The survey aimed at examining the significant content…

  15. Estimation of PAHs dry deposition and BaP toxic equivalency factors (TEFs) study at Urban, Industry Park and rural sampling sites in central Taiwan, Taichung.

    Science.gov (United States)

    Fang, Guor-Cheng; Chang, Kuan-Foo; Lu, Chungsying; Bai, Hsunling

    2004-05-01

    The concentrations of polycyclic aromatic hydrocarbons (PAHs) in gas phase and particle bound were measured simultaneously at industrial (INDUSTRY), urban (URBAN), and rural areas (RURAL) in Taichung, Taiwan. And the PAH concentrations, size distributions, estimated PAHs dry deposition fluxes and health risk study of PAHs in the ambient air of central Taiwan were discussed in this study. Total PAH concentrations at INDUSTRY, URBAN, and RURAL sampling sites were found to be 1650 +/- 1240, 1220 +/- 520, and 831 +/- 427 ng/m3, respectively. The results indicated that PAH concentrations were higher at INDUSTRY and URBAN sampling sites than the RURAL sampling sites because of the more industrial processes, traffic exhausts and human activities. The estimation dry deposition and size distribution of PAHs were also studied. The results indicated that the estimated dry deposition fluxes of total PAHs were 58.5, 48.8, and 38.6 microg/m2/day at INDUSTRY, URBAN, and RURAL, respectively. The BaP equivalency results indicated that the health risk of gas phase PAHs were higher than the particle phase at three sampling sites of central Taiwan. However, compared with the BaP equivalency results to other studies conducted in factory, this study indicated the health risk of PAHs was acceptable in the ambient air of central Taiwan.

  16. Site-directed mutagenesis of Arg58 and Asp86 of elongation factor Tu from Escherichia coli: effects on the GTPase reaction and aminoacyl-tRNA binding

    DEFF Research Database (Denmark)

    Knudsen, Charlotte Rohde; Clark, Brian F. C.

    1996-01-01

    Elongation factor Tu from Escherichia coli was mutated separately at positions Asp86 and Arg58, in order to shed light both on the GTPase mechanism of elongation factor Tu and on the binding of aminoacyl-tRNA. In addition, the binding of guanine nucleotides was investigated by determination...

  17. A Computational Study of the Oligosaccharide Binding Sites in the Lectin-Like Domain of Tumor Necrosis Factor and the TNF-derived TIP Peptide

    Czech Academy of Sciences Publication Activity Database

    Dulebo, A.; Ettrich, Rüdiger; Lucas, R.; Kaftan, D.

    2012-01-01

    Roč. 18, č. 27 (2012), s. 4236-4243 ISSN 1381-6128 Institutional support: RVO:67179843 Keywords : lectin-like domain * tumor necrosis factor * TIP peptide * oligosaccharides * molecular docking * molecular dynamics simulation * alveolar liquid clearance Subject RIV: CE - Biochemistry Impact factor: 3.311, year: 2012

  18. Factor IX[sub Madrid 2]: A deletion/insertion in Facotr IX gene which abolishes the sequence of the donor junction at the exon IV-intron d splice site

    Energy Technology Data Exchange (ETDEWEB)

    Solera, J. (Unidades de Genetica Molecular, Madrid (Spain)); Magallon, M.; Martin-Villar, J. (Hemofilia Hospital, Madrid (Spain)); Coloma, A. (Departamento deBioquimica de la Facultad de Medicina de la Universidad Autonoma, Madrid (Spain))

    1992-02-01

    DNA from a patient with severe hemophilia B was evaluated by RFLP analysis, producing results which suggested the existence of a partial deletion within the factor IX gene. The deletion was further localized and characterized by PCR amplification and sequencing. The altered allele has a 4,442-bp deletion which removes both the donor splice site located at the 5[prime] end of intron d and the two last coding nucleotides located at the 3[prime] end of exon IV in the normal factor IX gene; this fragment has been inserted in inverted orientation. Two homologous sequences have been discovered at the ends of the deleted DNA fragment.

  19. Water Quality, Cyanobacteria, and Environmental Factors and Their Relations to Microcystin Concentrations for Use in Predictive Models at Ohio Lake Erie and Inland Lake Recreational Sites, 2013-14

    Science.gov (United States)

    Francy, Donna S.; Graham, Jennifer L.; Stelzer, Erin A.; Ecker, Christopher D.; Brady, Amie M. G.; Pam Struffolino,; Loftin, Keith A.

    2015-11-06

    Harmful cyanobacterial “algal” blooms (cyanoHABs) and associated toxins, such as microcystin, are a major water-quality issue for Lake Erie and inland lakes in Ohio. Predicting when and where a bloom may occur is important to protect the public that uses and consumes a water resource; however, predictions are complicated and likely site specific because of the many factors affecting toxin production. Monitoring for a variety of environmental and water-quality factors, for concentrations of cyanobacteria by molecular methods, and for algal pigments such as chlorophyll and phycocyanin by using optical sensors may provide data that can be used to predict the occurrence of cyanoHABs.

  20. The Italian reference sites of the European innovation partnership on active and healthy ageing: Progetto Mattone Internazionale as an enabling factor.

    Science.gov (United States)

    Illario, Maddalena; De Luca, Vincenzo; Tramontano, Giovanni; Menditto, Enrica; Iaccarino, Guido; Bertorello, Lorenzo; Palummeri, Ernesto; Romano, Valeria; Moda, Giuliana; Maggio, Marcello; Barbolini, Mirca; Leonardini, Lisa; Addis, Antonio

    2017-01-01

    Ageing population implies an increasing demand for health care services and resources, unsustainable according to current previsions. The European Commission is tackling this challenge throughout initiatives such as the European Innovation Partnership on Active and Healthy Ageing (EIP-AHA), where all the efforts are aligned to the common goal of adding two active and healthy years to the life of European Union (EU) citizens. We presented the collaborative efforts of Italian Reference Site Collaborative Network 2012-2015. Italian regions joined forces through the "Progetto Mattone Internazionale" of the Ministry of Health developing several national and international collaborations. Activities from all five Italian reference sites are presented with different good practices and scale-up approaches for improving health in ageing population. The simultaneous development of these activities allowed the strengthening of the coordination of Italian stakeholders in the European arena fostering collaboration and supporting the streamlining of the Italian regions still outside these projects.

  1. Shaft siting decision

    International Nuclear Information System (INIS)

    1987-08-01

    This study identifies and establishes relative guidelines to be used for siting of repository shafts. Weights were determined for the significant factors that impact the selection of shaft locations for a nuclear waste repository in salt. The study identified a total of 45 factors. A panel of experienced mining people utilized the Kepner-Tregoe (K-T) Decision Analysis Process to perform a structured evaluation of each significant shaft siting factor. The evaluation determined that 22 of the factors were absolute constraints and that the other 23 factors were desirable characteristics. The group established the relative weights for each of the 23 desirable characteristics by using a paired comparison method. 8 refs., 2 figs., 5 tabs

  2. To Kill, Stay or Flee: The Effects of Lions and Landscape Factors on Habitat and Kill Site Selection of Cheetahs in South Africa

    OpenAIRE

    Rostro-Garc?a, Susana; Kamler, Jan F.; Hunter, Luke T. B.

    2015-01-01

    Understanding how animals utilize available space is important for their conservation, as it provides insight into the ecological needs of the species, including those related to habitat, prey and inter and intraspecific interactions. We used 28 months of radio telemetry data and information from 200 kill locations to assess habitat selection at the 3rd order (selection of habitats within home ranges) and 4th order (selection of kill sites within the habitats used) of a reintroduced populatio...

  3. The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors

    Science.gov (United States)

    Cooper, Stacy; Guo, Hong; Friedman, Alan D.

    2015-01-01

    The murine Cebpa gene contains an evolutionarily conserved 453 bp enhancer located at +37 kb that, together with its promoter, directs expression to myeloid progenitors and to long-term hematopoietic stem cells in transgenic mice. In human acute myeloid leukemia cases, the enhancer lacks point mutations but binds the RUNX1-ETO oncoprotein. The enhancer contains the H3K4me1 and H3K27Ac histone modifications, denoting an active enhancer, at progressively increasing levels as long-term hematopoietic stem cells transition to granulocyte-monocyte progenitors. We previously identified four enhancer sites that bind RUNX1 and demonstrated that their integrity is required for maximal enhancer activity in 32Dcl3 myeloid cells. The +37 kb Cebpa enhancer also contains C/EBP, Ets factor, Myb, GATA, and E-box consensus sites conserved in the human +42 kb CEBPA enhancer. Mutation of the two C/EBP, seven Ets, one Myb, two GATA, or two E-box sites reduces activity of an enhancer-promoter reporter in 32Dcl3 cells. In 293T gel shift assays, exogenous C/EBPα binds both C/EBP sites, c-Myb binds the Myb site, PU.1 binds the second Ets site, PU.1, Fli-1, ERG, and Ets1 bind the sixth Ets site, GATA2 binds both GATA sites, and SCL binds the second E-box. Endogenous hematopoietic RUNX1, PU.1, Fli-1, ERG, C/EBPα, GATA2, and SCL were previously shown to bind the enhancer, and we find that endogenous PU.1 binds the second Ets site in 32Dcl3 cells. Using CRISPR/Cas9, we developed 32Dcl3 lines in which the wild-type enhancer alleles are replaced with a variant mutant in the seven Ets sites. These lines have 20-fold reduced Cebpa mRNA when cultured in IL-3 or G-CSF, demonstrating a critical requirement for enhancer integrity for optimal Cebpa expression. In addition, these results indicate that the +37 kb Cebpa enhancer is the focus of multiple regulatory transcriptional pathways that impact its expression during normal hematopoiesis and potentially during myeloid transformation. PMID:25938608

  4. Patient Factors But Not the Use of Novel Anticoagulants or Warfarin Are Associated With Internal Jugular Vein Access-Site Hematoma After Right Heart Catheterization.

    Science.gov (United States)

    Dasa, Osama; Shafiq, Qaiser; Ruzieh, Mohammed; Alhazmi, Luai; Al-Dabbas, Maen; Ammari, Zaid; Khouri, Samer; Moukarbel, George

    2017-12-01

    Right heart catheterization (RHC) is routinely performed to assess hemodynamics. Generally, anticoagulants are held prior to the procedure. At our center, anticoagulants are continued and ultrasound guidance is always used for internal jugular vein access. A micropuncture access kit is used to place a 5 or 6 Fr sheath using the modified Seldinger technique. Manual compression is applied for 10-15 min and the patient is observed for at least 2 hours after the procedure. In a retrospective analysis, we investigated the risk of bleeding complications associated with RHC via the internal jugular vein in patients with and without full anticoagulation. Our catheterization laboratory database was searched for adult patients who underwent RHC by a single operator between January 2012 and December 2015. A total of 571 patients were included in the analysis. Baseline characteristics, labs, relevant invasive hemodynamics, co-morbid conditions, and incidence of access-site hematoma are presented. Multivariable binary logistic regression was performed using IBM SPSS v. 23.0 software. Statistically significant associations with access-site hematoma were observed with body mass index (P=.02; 95% confidence interval [CI], 1.0-1.1), right atrial pressure (P=.03; 95% CI, 0.7-0.9), and dialysis dependence (P.99). The incidence of internal jugular vein access-site hematoma is small when using careful access techniques for RHC even with the continued use of novel oral anticoagulants and warfarin. Patient characteristics and co-morbid conditions are related to bleeding complications.

  5. Relation of periphyton and benthic invertebrate communities to environmental factors and land use at selected sites in part of the upper Mississippi River basin, 1996-98

    Science.gov (United States)

    ZumBerge, Jeremy Ryan; Lee, Kathy E.; Goldstein, Robert M.

    2003-01-01

    The Upper Mississippi River Basin is one of the hydrologic systems selected for study by the National Water-Quality Assessment (NAWQA) Program of the U.S. Geological Survey. NAWQA utilizes a multi-disciplinary approach to explain factors that affect water quality. Part of the NAWQA design addresses the relation of land use and environmental factors to periphyton and benthic invertebrate communities in streams.

  6. Superfund Sites

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This layer represents active Superfund Sites published by the Environmental Protection Agency (EPA). These data were extracted from the Superfund Enterprise...

  7. Site development

    International Nuclear Information System (INIS)

    Noack, J.

    1975-01-01

    The subject of this paper is a general view over all necessary considerations to develop the site after it has been chosen and before starting with the construction of a nuclear power plant. (orig./RW) [de

  8. Pre-operative urinary tract infection: is it a risk factor for early surgical site infection with hip fracture surgery? A retrospective analysis

    OpenAIRE

    Yassa, Rafik RD; Khalfaoui, Mahdi Y; Veravalli, Karunakar; Evans, D Alun

    2017-01-01

    Objective The aims of the current study were to determine whether pre-operative urinary tract infections in patients presenting acutely with neck of femur fractures resulted in a delay to surgery and whether such patients were at increased risk of developing post-operative surgical site infections. Design A retrospective review of all patients presenting with a neck of femur fracture, at a single centre over a one-year period. The hospital hip fracture database was used as the main source of ...

  9. On-site detection of Phytophthora spp.—single-stranded target DNA as the limiting factor to improve on-chip hybridization

    International Nuclear Information System (INIS)

    Schwenkbier, Lydia; Pollok, Sibyll; Popp, Jürgen; Weber, Karina; König, Stephan; Wagner, Stefan; Werres, Sabine; Weber, Jörg; Hentschel, Martin

    2014-01-01

    We report on a lab-on-a-chip approach for on-site detection of Phytophthora species that allows visual signal readout. The results demonstrate the significance of single-stranded DNA (ssDNA) generation in terms of improving the intensity of the hybridization signal and to improve the reliability of the method. Conventional PCR with subsequent heat denaturation, sodium hydroxide-based denaturation, lambda exonuclease digestion and two asymmetric PCR methods were investigated for the species P. fragariae, P. kernoviae, and P. ramorum. The positioning of the capture probe within the amplified yeast GTP-binding protein (YPT1) target DNA was also of interest because it significantly influences the intensity of the signal. Statistical tests were used to validate the impact of the ssDNA generation methods and the capture-target probe position. The single-stranded target DNA generated by Linear-After-The-Exponential PCR (LATE-PCR) was found to produce signal intensities comparable to post-PCR exonuclease treatment. The LATE-PCR is the best method for the on-site detection of Phytophthora because the enzymatic digestion after PCR is more laborious and time-consuming. (author)

  10. Disclosure of key stereoelectronic factors for efficient H2 binding and cleavage in the active site of [NiFe]-hydrogenases.

    Science.gov (United States)

    Bruschi, Maurizio; Tiberti, Matteo; Guerra, Alessandro; De Gioia, Luca

    2014-02-05

    A comparative analysis of a series of DFT models of [NiFe]-hydrogenases, ranging from minimal NiFe clusters to very large systems including both the first and second coordination sphere of the bimetallic cofactor, was carried out with the aim of unraveling which stereoelectronic properties of the active site of [NiFe]-hydrogenases are crucial for efficient H2 binding and cleavage. H2 binding to the Ni-SIa redox state is energetically favored (by 4.0 kcal mol(-1)) only when H2 binds to Ni, the NiFe metal cluster is in a low spin state, and the Ni cysteine ligands have a peculiar seesaw coordination geometry, which in the enzyme is stabilized by the protein environment. The influence of the Ni coordination geometry on the H2 binding affinity was then quantitatively evaluated and rationalized analyzing frontier molecular orbitals and populations. Several plausible reaction pathways leading to H2 cleavage were also studied. It turned out that a two-step pathway, where H2 cleavage takes place on the Ni-SIa redox state of the enzyme, is characterized by very low reaction barriers and favorable reaction energies. More importantly, the seesaw coordination geometry of Ni was found to be a key feature for facile H2 cleavage. The discovery of the crucial influence of the Ni coordination geometry on H2 binding and activation in the active site of [NiFe]-hydrogenases could be exploited in the design of novel biomimetic synthetic catalysts.

  11. Layered B-site cation ordering: A key factor in ferrimagnetism of Y{sub 2}MnCrO{sub 6}

    Energy Technology Data Exchange (ETDEWEB)

    Hao, Lin [Department of Physics, University of Science and Technology of China, Hefei, Anhui (China); Yang, Lei [Collaborative Innovation Center for Magnetoelectric Industry, China Three Gorges University, Yichang, Hubei (China); Lee, Ming-Hsien; Lin, Tseh-Hsing [Department of Physics, Tamkang University, Taipei, Taiwan (China); Zhang, ZhongFeng; Xie, XiangNan [Department of Physics, University of Science and Technology of China, Hefei, Anhui (China); Zhu, Hong, E-mail: zhuh@ustc.edu.cn [Department of Physics, University of Science and Technology of China, Hefei, Anhui (China)

    2014-07-15

    Highlights: • Rietveld refinement and first-principles calculations are performed for Y{sub 2}MnCrO{sub 6}. • The layered B-site cation ordering is a more reliable structure for Y{sub 2}MnCrO{sub 6}. • Y{sub 2}MnCrO{sub 6} has an insulating ferrimagnetism (0 0 1)-ordered ground state. • The layered ordered pattern plays a key role for the ferrimagnetism in Y{sub 2}MnCrO{sub 6}. - Abstract: We report the Rietveld refinement of powder X-ray diffraction (XRD) pattern and first-principles calculations for the half-Cr{sup 3+} doped YMnO{sub 3} compound. The Rietveld refinement results suggest that the compound has a monoclinic structure with the Mn{sup 3+}/Cr{sup 3+} layers alternately stacking along the [0 0 1] direction. The first-principles calculations show that the structure with layered B-site cation ordering has the lowest total energy; meanwhile, the insulating ferrimagnetic state is more favored compared to the ferromagnetic state, which is in agreement with the reported experimental results. Based upon Goodenough’s model of semi-covalent exchange, we argue that the anisotropic magnetic couplings between the Mn{sup 3+}/Cr{sup 3+} cations ordered in layered pattern play an important role for the ferrimagnetism in the compound.

  12. To kill, stay or flee: the effects of lions and landscape factors on habitat and kill site selection of cheetahs in South Africa.

    Directory of Open Access Journals (Sweden)

    Susana Rostro-García

    Full Text Available Understanding how animals utilize available space is important for their conservation, as it provides insight into the ecological needs of the species, including those related to habitat, prey and inter and intraspecific interactions. We used 28 months of radio telemetry data and information from 200 kill locations to assess habitat selection at the 3rd order (selection of habitats within home ranges and 4th order (selection of kill sites within the habitats used of a reintroduced population of cheetahs Acinonyx jubatus in Phinda Private Game Reserve, South Africa. Along with landscape characteristics, we investigated if lion Panthera leo presence affected habitat selection of cheetahs. Our results indicated that cheetah habitat selection was driven by a trade-off between resource acquisition and lion avoidance, and the balance of this trade-off varied with scale: more open habitats with high prey densities were positively selected within home ranges, whereas more closed habitats with low prey densities were positively selected for kill sites. We also showed that habitat selection, feeding ecology, and avoidance of lions differed depending on the sex and reproductive status of cheetahs. The results highlight the importance of scale when investigating a species' habitat selection. We conclude that the adaptability of cheetahs, together with the habitat heterogeneity found within Phinda, explained their success in this small fenced reserve. The results provide information for the conservation and management of this threatened species, especially with regards to reintroduction efforts in South Africa.

  13. To Kill, Stay or Flee: The Effects of Lions and Landscape Factors on Habitat and Kill Site Selection of Cheetahs in South Africa

    Science.gov (United States)

    Rostro-García, Susana; Kamler, Jan F.; Hunter, Luke T. B.

    2015-01-01

    Understanding how animals utilize available space is important for their conservation, as it provides insight into the ecological needs of the species, including those related to habitat, prey and inter and intraspecific interactions. We used 28 months of radio telemetry data and information from 200 kill locations to assess habitat selection at the 3rd order (selection of habitats within home ranges) and 4th order (selection of kill sites within the habitats used) of a reintroduced population of cheetahs Acinonyx jubatus in Phinda Private Game Reserve, South Africa. Along with landscape characteristics, we investigated if lion Panthera leo presence affected habitat selection of cheetahs. Our results indicated that cheetah habitat selection was driven by a trade-off between resource acquisition and lion avoidance, and the balance of this trade-off varied with scale: more open habitats with high prey densities were positively selected within home ranges, whereas more closed habitats with low prey densities were positively selected for kill sites. We also showed that habitat selection, feeding ecology, and avoidance of lions differed depending on the sex and reproductive status of cheetahs. The results highlight the importance of scale when investigating a species’ habitat selection. We conclude that the adaptability of cheetahs, together with the habitat heterogeneity found within Phinda, explained their success in this small fenced reserve. The results provide information for the conservation and management of this threatened species, especially with regards to reintroduction efforts in South Africa. PMID:25693067

  14. To kill, stay or flee: the effects of lions and landscape factors on habitat and kill site selection of cheetahs in South Africa.

    Science.gov (United States)

    Rostro-García, Susana; Kamler, Jan F; Hunter, Luke T B

    2015-01-01

    Understanding how animals utilize available space is important for their conservation, as it provides insight into the ecological needs of the species, including those related to habitat, prey and inter and intraspecific interactions. We used 28 months of radio telemetry data and information from 200 kill locations to assess habitat selection at the 3rd order (selection of habitats within home ranges) and 4th order (selection of kill sites within the habitats used) of a reintroduced population of cheetahs Acinonyx jubatus in Phinda Private Game Reserve, South Africa. Along with landscape characteristics, we investigated if lion Panthera leo presence affected habitat selection of cheetahs. Our results indicated that cheetah habitat selection was driven by a trade-off between resource acquisition and lion avoidance, and the balance of this trade-off varied with scale: more open habitats with high prey densities were positively selected within home ranges, whereas more closed habitats with low prey densities were positively selected for kill sites. We also showed that habitat selection, feeding ecology, and avoidance of lions differed depending on the sex and reproductive status of cheetahs. The results highlight the importance of scale when investigating a species' habitat selection. We conclude that the adaptability of cheetahs, together with the habitat heterogeneity found within Phinda, explained their success in this small fenced reserve. The results provide information for the conservation and management of this threatened species, especially with regards to reintroduction efforts in South Africa.

  15. Role of N-glycosylation sites and CXC motifs in trafficking of Medicago trunculata Nod Factor Perception protein to the plasma membrane.

    NARCIS (Netherlands)

    Lefebvre, B.; Klaus-Heisen, D.; Pietraszewska-Bogiel, A.; Hervé, M.; Camut, S.; Auriac, M.C.; Gasciolli, V.; Nurisso, A.; Gadella, T.W.; Cullimore, J.

    2012-01-01

    The lysin motif receptor like kinase, NFP, is a key protein in the legume Medicago truncatula for the perception of lipochitooligosaccharidic Nod Factors, which are secreted bacterial signals essential for establishing the nitrogen-fixing legume-rhizobia symbiosis. Predicted structural and genetic

  16. Factors causing spatial heterogeneity in soil properties, plant cover, and soil fauna in a non-reclaimed post-mining site

    Czech Academy of Sciences Publication Activity Database

    Frouz, J.; Kalčík, Jiří; Velichová, V.

    2011-01-01

    Roč. 37, č. 11 (2011), s. 1910-1913 ISSN 0925-8574 R&D Projects: GA MŠk 2B08023 Institutional research plan: CEZ:AV0Z60660521 Keywords : soil chemistry * vegetation * invertebrates Subject RIV: EH - Ecology, Behaviour Impact factor: 3.106, year: 2011

  17. The use of English in job advertisments on the Dutch job site Monsterboard.nl and factors on which it depends

    NARCIS (Netherlands)

    Meurs, F. van; Korzilius, H.P.L.M.; Hollander, Adriënne den

    2006-01-01

    Previous studies on the factors that determine the use of English in product advertising and print-medium job advertisements in non-English-speaking countries have overwhelmingly analysed English in product advertising. Drawing on the reasons suggested in such studies, the present contribution

  18. More Photos From Me to Thee : Factors Influencing the Intention to Continue Sharing Personal Photos on an Online Social Networking (OSN) Site among Young Adults in the Netherlands

    NARCIS (Netherlands)

    Beldad, Ardion Daroca; Hegner, Sabrina

    2017-01-01

    The current study investigated the factors influencing photo sharing continuance intention of Dutch Facebook users aged 18 to 25 years old. The focus was specifically on personal photos (those that include the person sharing), as their disclosure is expected to result in privacy-related issues for

  19. Phosphorylation of the Fas associated factor FAF1 by protein kinase CK2 and identification of serines 289 and 291 as the in vitro phosphorylation sites

    DEFF Research Database (Denmark)

    Jensen, H H; Hjerrild, M; Guerra, B

    2001-01-01

    We previously identified the human Fas associated factor (FAF1) as one of the interacting partners of protein kinase CK2 beta subunit. Since FAF1 is a phosphoprotein we investigated whether it is a substrate for CK2. Here, we report the full length human FAF1 cDNA sequence, expression of FAF1...

  20. Validating Domains of Patient Contextual Factors Essential to Preventing Contextual Errors: A Qualitative Study Conducted at Chicago Area Veterans Health Administration Sites.

    Science.gov (United States)

    Binns-Calvey, Amy E; Malhiot, Alex; Kostovich, Carol T; LaVela, Sherri L; Stroupe, Kevin; Gerber, Ben S; Burkhart, Lisa; Weiner, Saul J; Weaver, Frances M

    2017-09-01

    "Patient context" indicates patient circumstances and characteristics or states that are essential to address when planning patient care. Specific patient "contextual factors," if overlooked, result in an inappropriate plan of care, a medical error termed a "contextual error." The myriad contextual factors that constitute patient context have been grouped into broad domains to create a taxonomy of challenges to consider when planning care. This study sought to validate a previously identified list of contextual domains. This qualitative study used directed content analysis. In 2014, 19 Department of Veterans Affairs (VA) providers (84% female) and 49 patients (86% male) from two VA medical centers and four outpatient clinics in the Chicago area participated in semistructured interviews and focus groups. Topics included patient-specific, community, and resource-related factors that affect patients' abilities to manage their care. Transcripts were analyzed with a previously identified list of contextual domains as a framework. Analysis of responses revealed that patients and providers identified the same 10 domains previously published, plus 3 additional ones. Based on comments made by patients and providers, the authors created a revised list of 12 domains from themes that emerged. Six pertain to patient circumstances such as access to care and financial situation, and 6 to patient characteristics/states including skills, abilities, and knowledge. Contextual factors in patients' lives may be essential to address for effective care planning. The rubric developed can serve as a "contextual differential" for clinicians to consider when addressing challenges patients face when planning their care.

  1. Site development

    International Nuclear Information System (INIS)

    Gaynor, R.K.

    1989-01-01

    Development of a low-level radioactive waste land disposal facility is little different than any industrial development of similar scope. Consideration must be made for normal business and operations management, security, facility maintenance, traffic control and necessary amenities for personnel. The item specific to the low-level waste site is the handling of radioactive waste materials and the regulatory and environmental protection procedures that must be planned for and accomodated in the site design and development. Each of these elements and the facility as a whole must be designed to be compatible with local land use plans, available transportation and support services, and the social and economic goals of the local community. Plans should also be made for quality control and orderly construction. This chapter deals with those aspects of the facility, its design and construction which are integral parts to the overall performance of the site

  2. Study of methylation sites and factors in contaminated aquatic systems in the Amazon using an optimized radiochemical technique. Highlights and achievements

    International Nuclear Information System (INIS)

    Davee Guimaraes, Jean Remy

    2002-01-01

    Full text: Highlights and achievements: We confirmed that high methylation potentials (up to 22%) are found in roots of Paspalum repens and other floating macrophyte species such as Eichhomia crassipes and Ludwigia helmynthoryza during both phases of the hydrological cycle, with a tendency for higher values in the wet season, confirming findings of previous studies, and a strong intra and interlake variation. Hg methylation in macrophyte roots is carried out mainly in the root-associated periphyton a complex and variable assemblage of benthic microalgae, fungi, bacteria and organic and inorganic detritus. However, no significant correlation was found in the first campaign between Hg methylation in samples of Paspalum sp. roots and the amount of periphyton in these samples. We also verified that total plankton and phytoplankton are sites of a low 203 Hg; Basic infrastructure problems caused partial loss of samples in one of the campaigns. (author)

  3. Bioaugmentation of thiabendazole-contaminated soils from a wastewater disposal site: Factors driving the efficacy of this strategy and the diversity of the indigenous soil bacterial community.

    Science.gov (United States)

    Papadopoulou, Evangelia S; Genitsaris, Savvas; Omirou, Michalis; Perruchon, Chiara; Stamatopoulou, Anastasia; Ioannides, Ioannis; Karpouzas, Dimitrios G

    2018-02-01

    The application of the fungicide thiabendazole (TBZ) in fruit packaging plants (FPP) results in the production of effluents which are often disposed in adjacent field sites. These require remediation to prevent further environmental dispersal of TBZ. We assessed the bioaugmentation potential of a newly isolated TBZ-degrading bacterial consortium in a naturally contaminated soil (NCS) exhibiting a natural gradient of TBZ levels (12000, 400, 250 and 12 mg kg -1 ). The effect of aging on bioaugmentation efficacy was comparatively tested in a soil with similar physicochemical properties and soil microbiota, which was artificially, contaminated with the same TBZ levels (ACS). The impact of bioaugmentation and TBZ on the bacterial diversity in the NCS was explored via amplicon sequencing. Bioaugmentation effectively removed TBZ from both soils at levels up to 400 mg kg -1 but failed at the highest contamination level (12000 mg kg -1 ). Dissipation of TBZ in bioaugmented samples showed a concentration-dependent pattern, while aging of TBZ had a slight effect on bioaugmentation efficiency. Bioaugmentation had no impact on the soil bacterial diversity, in contrast to TBZ contamination. Soils from the hotspots of TBZ contamination (12000 mg kg -1 ) showed a drastically lower α-diversity driven by the dominance of β- and γ-proteobacteria at the expense of all other bacterial phyla, especially Actinobacteria. Overall, bioaugmentation with specialized microbial inocula could be an effective solution for the recovery of disposal sites contaminated with persistent chemicals like TBZ. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites

    Energy Technology Data Exchange (ETDEWEB)

    Radka, Christopher D.; DeLucas, Lawrence J.; Wilson, Landon S.; Lawrenz, Matthew B.; Perry, Robert D.; Aller, Stephen G.

    2017-06-30

    Gram-negative bacteria use siderophores, outer membrane receptors, inner membrane transporters and substrate-binding proteins (SBPs) to transport transition metals through the periplasm. The SBPs share a similar protein fold that has undergone significant structural evolution to communicate with a variety of differentially regulated transporters in the cell. InYersinia pestis, the causative agent of plague, YfeA (YPO2439, y1897), an SBP, is important for full virulence during mammalian infection. To better understand the role of YfeA in infection, crystal structures were determined under several environmental conditions with respect to transition-metal levels. Energy-dispersive X-ray spectroscopy and anomalous X-ray scattering data show that YfeA is polyspecific and can alter its substrate specificity. In minimal-media experiments, YfeA crystals grown after iron supplementation showed a threefold increase in iron fluorescence emission over the iron fluorescence emission from YfeA crystals grown from nutrient-rich conditions, and YfeA crystals grown after manganese supplementation during overexpression showed a fivefold increase in manganese fluorescence emission over the manganese fluorescence emission from YfeA crystals grown from nutrient-rich conditions. In all experiments, the YfeA crystals produced the strongest fluorescence emission from zinc and could not be manipulated otherwise. Additionally, this report documents the discovery of a novel surface metal-binding site that prefers to chelate zinc but can also bind manganese. Flexibility across YfeA crystal forms in three loops and a helix near the buried metal-binding site suggest that a structural rearrangement is required for metal loading and unloading.

  5. Site Practice

    DEFF Research Database (Denmark)

    Wahedi, Haseebullah

    2016-01-01

    different practices in the construction phase. The research is based on an ethnographic study of a case in Denmark. The empirical data were collected through direct observations and semi-structured interviews with site managers, contract managers, foremen and craftsmen. Findings revealed...... that the construction phase comprises several communities and practices, leading to various uses of the drawings. The results indicated that the craftsmen used drawings to position themselves in the correct location, and that the site managers and contract managers used them as management tools and legal documents...

  6. Microbial properties of soil aggregates created by earthworms and other factors: spherical and prismatic soil aggregates from unreclaimed post-mining sites

    Czech Academy of Sciences Publication Activity Database

    Frouz, J.; Krištůfek, Václav; Livečková, M.; van Loo, D.; Jacobs, P.; van Hoorebeke, L.

    2011-01-01

    Roč. 56, č. 1 (2011), s. 36-43 ISSN 0015-5632 R&D Projects: GA MŠk LC06066; GA MŠk 2B08023; GA AV ČR 1QS600660505 Institutional research plan: CEZ:AV0Z60660521 Keywords : microbial properties * earthworms * spherical and prismatic soil aggregates Subject RIV: EH - Ecology, Behaviour Impact factor: 0.677, year: 2011

  7. Sites involved in intra- and interdomain allostery associated with the activation of factor VIIa pinpointed by hydrogen-deuterium exchange and electron transfer dissociation mass spectrometry

    DEFF Research Database (Denmark)

    Song, Hongjian; Olsen, Ole H; Persson, Egon

    2014-01-01

    Factor VIIa (FVIIa) is a trypsin-like protease which plays an important role in initiating blood coagulation. Very limited structural information is available for the free, inactive form of FVIIa that circulates in the blood prior to vascular injury and the molecular details of its activity...... signal extends to the EGF1 domain in the light chain of FVIIa, underscoring a remarkable intra- and interdomain allosteric regulation of this trypsin-like protease....

  8. Site selection

    CERN Multimedia

    CERN PhotoLab

    1968-01-01

    To help resolve the problem of site selection for the proposed 300 GeV machine, the Council selected "three wise men" (left to right, J H Bannier of the Netherlands, A Chavanne of Switzerland and L K Boggild of Denmark).

  9. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A

    2001-04-01

    The objectives, the programme, and the achievements of the Site Restoration Department of SCK-CEN in 2000 are summarised. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and activities related to the management of decommissioning projects. The department provides consultancy and services to external organisations.

  10. Site Restoration

    International Nuclear Information System (INIS)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A.

    2001-01-01

    The objectives, the programme, and the achievements of the Site Restoration Department of SCK-CEN in 2000 are summarised. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and activities related to the management of decommissioning projects. The department provides consultancy and services to external organisations

  11. [Correlation between polymorphisms in the coagulation factor VII gene hypervariable region 4 site and the risk of coronary heart disease in population with different ethnic backgrounds: a Meta-analysis].

    Science.gov (United States)

    Wang, Li-li; Ma, Bin; Qian, Dun; Pang, Jun; Yao, Ya-li

    2013-12-01

    To assess the correlation between polymorphisms in the coagulation factor VII (F VII)gene hypervariable region 4 (HVR4)site and risk related to coronary heart disease (CHD)in different ethnic populations, especially the Asian populations. Publications up to April 2013, from CBM, CNKI, Wanfang Database,VIP, PubMed, Cochrane Library and Embase were searched to collect data from case-control studies related to F VII gene HVR4 site and CHD in populations from different ethnicities. Quality of studies was evaluated, available data extracted and both RevMan 5.1 and Stata 11.0 softwares were used for Meta-analysis. Fifteen case-control studies were included, involving 3167 cases with CHD group and 3168 cases in the control group. on this Meta-analysis showed that:a)polymorphism of the F VII gene HVR4 site H7/H6+H5 and CHD, b)H7H7/H6H6 + H7H6 and CHD were both slightly correlated between people with different ethnic backgrounds. However, the H6 allele versus H7+H5 allele and CHD showed different results-a high correlation seen in different ethnic groups. H5 allele versus H6+H7 allele and CHD did not appear significant difference(OR = 1.20, 95%CI:0.76-1.90, P = 0.43). Both F VII gene HVR4 polymorphisms H7 allele and the H7H7 genotype might have served as protective factors for CHD in different ethnic groups, H6 allele might serve as a risk factor for CHD, but H5 allele was likely not to be associated with CHD in different ethnic groups.

  12. Lifestyle factors and site-specific risk of hip fracture in community dwelling older women – a 13-year prospective population-based cohort study

    Science.gov (United States)

    2012-01-01

    Background Several risk factors are associated to hip fractures. It seems that different hip fracture types have different etiologies. In this study, we evaluated the lifestyle-related risk factors for cervical and trochanteric hip fractures in older women over a 13-year follow-up period. Methods The study design was a prospective, population-based study consisting of 1681 women (mean age 72 years). Seventy-three percent (n = 1222) participated in the baseline measurements, including medical history, leisure-time physical activity, smoking, and nutrition, along with body anthropometrics and functional mobility. Cox regression was used to identify the independent predictors of cervical and trochanteric hip fractures. Results During the follow-up, 49 cervical and 31 trochanteric fractures were recorded. The women with hip fractures were older, taller, and thinner than the women with no fractures (p trochanteric fractures (HR = 3.4, 95% CI 1.8-6.6, and HR = 5.3, 95% CI 2.5-11.4, respectively). Low baseline physical activity was associated with an increased risk of hip fracture, especially in the cervical region (HR = 2.5, 95% CI 1.3-4.9). A decrease in cervical fracture risk (p = 0.002) was observed with physically active individuals compared to their less active peers (categories: very low or low, moderate, and high). Moderate coffee consumption and hypertension decreased the risk of cervical fractures (HR = 0.4, 95% CI 0.2-0.8, for both), while smoking was a predisposing factor for trochanteric fractures (HR = 3.2, 95% CI 1.1-9.3). Conclusions Impaired functional mobility, physical inactivity, and low body mass may increase the risk for hip fractures with different effects at the cervical and trochanteric levels. PMID:22978821

  13. RNA Processing Factor 5 is required for efficient 5' cleavage at a processing site conserved in RNAs of three different mitochondrial genes in Arabidopsis thaliana.

    Science.gov (United States)

    Hauler, Aron; Jonietz, Christian; Stoll, Birgit; Stoll, Katrin; Braun, Hans-Peter; Binder, Stefan

    2013-05-01

    The 5' ends of many mitochondrial transcripts are generated post-transcriptionally. Recently, we identified three RNA PROCESSING FACTORs required for 5' end maturation of different mitochondrial mRNAs in Arabidopsis thaliana. All of these factors are pentatricopeptide repeat proteins (PPRPs), highly similar to RESTORERs OF FERTILTY (RF), that rescue male fertility in cytoplasmic male-sterile lines from different species. Therefore, we suggested a general role of these RF-like PPRPs in mitochondrial 5' processing. We now identified RNA PROCESSING FACTOR 5, a PPRP not classified as an RF-like protein, required for the efficient 5' maturation of the nad6 and atp9 mRNAs as well as 26S rRNA. The precursor molecules of these RNAs share conserved sequence elements, approximately ranging from positions -50 to +9 relative to mature 5' mRNA termini, suggesting these sequences to be at least part of the cis elements required for processing. The knockout of RPF5 has only a moderate influence on 5' processing of atp9 mRNA, whereas the generation of the mature nad6 mRNA and 26S rRNA is almost completely abolished in the mutant. The latter leads to a 50% decrease of total 26S rRNA species, resulting in an imbalance between the large rRNA and 18S rRNA. Despite these severe changes in RNA levels and in the proportion between the 26S and 18S rRNAs, mitochondrial protein levels appear to be unaltered in the mutant, whereas seed germination capacity is markedly reduced. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

  14. Environment of care: Is it time to reassess microbial contamination of the operating room air as a risk factor for surgical site infection in total joint arthroplasty?

    Science.gov (United States)

    Parvizi, Javad; Barnes, Sue; Shohat, Noam; Edmiston, Charles E

    2017-11-01

    In the modern operating room (OR), traditional surgical mask, frequent air exchanges, and architectural barriers are viewed as effective in reducing airborne microbial populations. Intraoperative sampling of airborne particulates is rarely performed in the OR because of technical difficulties associated with sampling methodologies and a common belief that airborne contamination is infrequently associated with surgical site infections (SSIs). Recent studies suggest that viable airborne particulates are readily disseminated throughout the OR, placing patients at risk for postoperative SSI. In 2017, virtually all surgical disciplines are engaged in the implantation of selective biomedical devices, and these implants have been documented to be at high risk for intraoperative contamination. Approximately 1.2 million arthroplasties are performed annually in the United States, and that number is expected to increase to 3.8 million by the year 2030. The incidence of periprosthetic joint infection is perceived to be low (<2.5%); however, the personal and fiscal morbidity is significant. Although the pharmaceutic and computer industries enforce stringent air quality standards on their manufacturing processes, there is currently no U.S. standard for acceptable air quality within the OR environment. This review documents the contribution of air contamination to the etiology of periprosthetic joint infection, and evidence for selective innovative strategies to reduce the risk of intraoperative microbial aerosols. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

  15. Influence of hydrologic factors on leaching of solidified low-level waste forms at an arid site field-scale lysimeter facility

    International Nuclear Information System (INIS)

    Jones, T.L.; Skaggs, R.L.

    1987-04-01

    Most of the precipitation at the Hanford Site arrives as winter snow; this contributes to a strong seasonal pattern in water storage and drainage observed in the lysimeters. This seasonal pattern in storage corresponds to an annual range in the volumetric soil water content of 11% in late winter to 7% in the late summer and early fall. Annual changes in drainage rates cause pore water velocities to vary annually by nearly two orders of magnitude. Rapid snowmelt and frozen soils in February 1985 caused runoff water from areas adjacent to the lysimeter facility to flood three of the lysimeters. This resulted in a temporary increase in soil water storage, and an additional 5 to 10 cm of drainage for these three lysimeters. Measurable quantities of tritium and cobalt-60 are being collected in lysimeter drainage water. Approximately 30% of the original tritium inventory has been leached from both lysimeters containing samples of this waste form. Cobalt-60 is consistently being leached from five lysimeters representing three of the five waste forms. Total cobalt-60 collected from each of the five lysimeters varies, but in each case is less than 0.1% of the original cobalt inventory of the waste sample. Comparisons of cobalt release among flooded and non-flooded lysimeters show no significant difference caused by the extra drainage

  16. The CCA-end of P-tRNA Contacts Both the Human RPL36AL and the A-site Bound Translation Termination Factor eRF1 at the Peptidyl Transferase Center of the Human 80S Ribosome.

    Science.gov (United States)

    Hountondji, Codjo; Bulygin, Konstantin; Créchet, Jean-Bernard; Woisard, Anne; Tuffery, Pierre; Nakayama, Jun-Ichi; Frolova, Ludmila; Nierhaus, Knud H; Karpova, Galina; Baouz, Soria

    2014-01-01

    We have demonstrated previously that the E-site specific protein RPL36AL present in human ribosomes can be crosslinked with the CCA-end of a P-tRNA in situ. Here we report the following: (i) We modeled RPL36AL into the structure of the archaeal ortholog RPL44E extracted from the known X-ray structure of the 50S subunit of Haloarcula marismortui. Superimposing the obtained RPL36AL structure with that of P/E tRNA observed in eukaryotic 80S ribosomes suggested that RPL36AL might in addition to its CCA neighbourhood interact with the inner site of the tRNA elbow similar to an interaction pattern known from tRNA•synthetase pairs. (ii) Accordingly, we detected that the isolated recombinant protein RPL36AL can form a tight binary complex with deacylated tRNA, and even tRNA fragments truncated at their CCA end showed a high affinity in the nanomolar range supporting a strong interaction outside the CCA end. (iii) We constructed programmed 80S complexes containing the termination factor eRF1 (stop codon UAA at the A-site) and a 2',3'-dialdehyde tRNA (tRNAox) analog at the P-site. Surprisingly, we observed a crosslinked ternary complex containing the tRNA, eRF1 and RPL36AL crosslinked both to the aldehyde groups of tRNAox at the 2'- and 3'-positions of the ultimate A. We also demonstrated that, upon binding to the ribosomal A-site, eRF1 induces an alternative conformation of the ribosome and/or the tRNA, leading to a novel crosslink of tRNAox to another large-subunit ribosomal protein (namely L37) rather than to RPL36AL, both ribosomal proteins being labeled in a mutually exclusive fashion. Since the human 80S ribosome in complex with P-site bound tRNAox and A-site bound eRF1 corresponds to the post-termination state of the ribosome, the results represent the first biochemical evidence for the positioning of the CCA-arm of the P-tRNA in close proximity to both RPL36AL and eRF1 at the end of the translation process.

  17. Lifestyle factors and site-specific risk of hip fracture in community dwelling older women – a 13-year prospective population-based cohort study

    Directory of Open Access Journals (Sweden)

    Määttä Mikko

    2012-09-01

    Full Text Available Abstract Background Several risk factors are associated to hip fractures. It seems that different hip fracture types have different etiologies. In this study, we evaluated the lifestyle-related risk factors for cervical and trochanteric hip fractures in older women over a 13-year follow-up period. Methods The study design was a prospective, population-based study consisting of 1681 women (mean age 72 years. Seventy-three percent (n = 1222 participated in the baseline measurements, including medical history, leisure-time physical activity, smoking, and nutrition, along with body anthropometrics and functional mobility. Cox regression was used to identify the independent predictors of cervical and trochanteric hip fractures. Results During the follow-up, 49 cervical and 31 trochanteric fractures were recorded. The women with hip fractures were older, taller, and thinner than the women with no fractures (p  Conclusions Impaired functional mobility, physical inactivity, and low body mass may increase the risk for hip fractures with different effects at the cervical and trochanteric levels.

  18. Factors to be Considered in Long-Term Monitoring of a Former Nuclear Test Site in a Geophysically Active and Water-rich Environment

    Science.gov (United States)

    Eichelberger, J.; Hill, G.; Patrick, M.; Freymueller, J.; Barnes, D.; Kelley, J.; Layer, P.

    2001-12-01

    The US Department of Energy (USDOE) is currently undertaking an ambitious program of environmental remediation of the surface of Amchitka Island in the western Aleutians, where three underground nuclear tests were conducted during 1963-1971. Among these tests was Cannikin, at approximately 5 megatons the largest nuclear device ever exploded underground by the United States and equivalent in seismic energy release to a magnitude 7 earthquake. The blast caused about 1 m of uplift of the Bering Sea coastline in the 3-km-wide fault-bounded block within which it was detonated. The impending final transfer of stewardship of this area to the US Fish and Wildlife Service as part of the Alaska Maritime National Wildlife Refuge raises anew the question of the potential for transport of radionuclides from the shot cavity, located at 1791 m depth in mafic laharic breccias, into the accessible environment. In particular, there is concern about whether such contaminants could become concentrated in the marine food chain that is used for subsistence by Alaskan Natives (and by the broader international community through the North Pacific and Bering Fisheries). Both possible transport pathways in the form of faults and transport medium in the form of abundant water are present. Since the pre-plate tectonics paradigm days of active testing, the scientific community's understanding of the tectonic context of the Aleutian Islands has grown tremendously. Recently, the first direct measurements of motion within the arc have been made. How this new understanding should guide plans for long-term monitoring of the site is an important question. Convergence due to subduction of the North Pacific plate beneath North America ranges from near-normal at the Alaska Peninsula and eastern Aleutian islands to highly oblique in the west. Amchitka itself can be seen as a subaerial portion of a 200-km-long Rat Island arc crest segment. This fragment has torn from the Andreanof Islands to the east at

  19. Microbial properties of soil aggregates created by earthworms and other factors: spherical and prismatic soil aggregates from unreclaimed post-mining sites

    Energy Technology Data Exchange (ETDEWEB)

    Frouz, J.; Kristufek, V.; Liveckova, M.; van Loo, D.; Jacobs, P.; Van Hoorebeke, L. [Charles University of Prague, Prague (Czech Republic). Inst. of Environmental Studies

    2011-01-15

    Soil aggregates between 2 and 5 mm from 35- and 45-year-old unreclaimed post-mining sites near Sokolov (Czech Republic) were divided into two groups: spherical and prismatic. X-ray tomography indicated that prismatic aggregates consisted of fragments of claystone bonded together by amorphous clay and roots while spherical aggregates consisted of a clay matrix and organic fragments of various sizes. Prismatic aggregates were presumed to be formed by plant roots and physical processes during weathering of Tertiary mudstone, while earthworms were presumed to contribute to the formation of spherical aggregates. The effects of drying and rewetting and glucose addition on microbial respiration, microbial biomass, and counts of bacteria in these aggregates were determined. Spherical aggregates contained a greater percentage of C and N and a higher C-to-N ratio than prismatic ones. The C content of the particulate organic matter was also higher in the spherical than in the prismatic aggregates. Although spherical aggregates had a higher microbial respiration and biomass, the growth of microbial biomass in spherical aggregates was negatively correlated with initial microbial biomass, indicating competition between bacteria. Specific respiration was negatively correlated with microbial biomass. Direct counts of bacteria were higher in spherical than in prismatic aggregates. Bacterial numbers were more stable in the center than in the surface layers of the aggregates. Transmission electron microscopy indicated that bacteria often occurred as individual cells in prismatic aggregates but as small clusters of cells in spherical aggregates. Ratios of colony forming units (cultivatable bacteria) to direct counts were higher in spherical than in prismatic aggregates. Spherical aggregates also contained faster growing bacteria.

  20. Using a minigene approach to characterize a novel splice site mutation in human F7 gene causing inherited factor VII deficiency in a Chinese pedigree.

    Science.gov (United States)

    Yu, T; Wang, X; Ding, Q; Fu, Q; Dai, J; Lu, Y; Xi, X; Wang, H

    2009-11-01

    Factor VII deficiency which transmitted as an autosomal recessive disorder is a rare haemorrhagic condition. The aim of this study was to identify the molecular genetic defect and determine its functional consequences in a Chinese pedigree with FVII deficiency. The proband was diagnosed as inherited coagulation FVII deficiency by reduced plasma levels of FVII activity (4.4%) and antigen (38.5%). All nine exons and their flanking sequence of F7 gene were amplified by polymerase chain reaction (PCR) for the proband and the PCR products were directly sequenced. The compound heterozygous mutations of F7 (NM_000131.3) c.572-1G>A and F7 (NM_000131.3) c.1165T>G; p.Cys389Gly were identified in the proband's F7 gene. To investigate the splicing patterns associated with F7 c.572-1G>A, ectopic transcripts in leucocytes of the proband were analyzed. F7 minigenes, spanning from intron 4 to intron 7 and carrying either an A or a G at position -1 of intron 5, were constructed and transiently transfected into human embryonic kidney (HEK) 293T cells, followed by RT-PCR analysis. The aberrant transcripts from the F7 c.572-1G>A mutant allele were not detected by ectopic transcription study. Sequencing of the RT-PCR products from the mutant transfectant demonstrated the production of an erroneously spliced mRNA with exon 6 skipping, whereas a normal splicing occurred in the wide type transfectant. The aberrant mRNA produced from the F7 c.572-1G>A mutant allele is responsible for the factor VII deficiency in this pedigree.

  1. NESHAP Dose-Release Factor Isopleths for Five Source-to-Receptor Distances from the Center of Site and H-Area for all Compass Sectors at SRS using CAP88-PC Version 4.0

    Energy Technology Data Exchange (ETDEWEB)

    Trimor, P. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2017-08-09

    The Environmental Protection Agency (EPA) requires the use of the computer model CAP88-PC to estimate the total effective doses (TED) for demonstrating compliance with 40 CFR 61, Subpart H (EPA 2006), the National Emission Standards for Hazardous Air Pollutants (NESHAP) regulations. As such, CAP88 Version 4.0 was used to calculate the receptor dose due to routine atmospheric releases at the Savannah River Site (SRS). For estimation, NESHAP dose-release factors (DRFs) have been supplied to Environmental Compliance and Area Closure Projects (EC&ACP) for many years. DRFs represent the dose to a maximum receptor exposed to 1 Ci of a specified radionuclide being released into the atmosphere. They are periodically updated to include changes in the CAP88 version, input parameter values, site meteorology, and location of the maximally exposed individual (MEI). This report presents the DRFs of tritium oxide released at two onsite locations, center-of-site (COS) and H-Area, at 0 ft. elevation to maximally exposed individuals (MEIs) located 1000, 3000, 6000, 9000, and 12000 meters from the release areas for 16 compass sectors. The analysis makes use of area-specific meteorological data (Viner 2014).

  2. Insight into PreImplantation Factor (PIF* mechanism for embryo protection and development: target oxidative stress and protein misfolding (PDI and HSP through essential RIKP [corrected] binding site.

    Directory of Open Access Journals (Sweden)

    Eytan R Barnea

    Full Text Available Endogenous PIF, upon which embryo development is dependent, is secreted only by viable mammalian embryos, and absent in non-viable ones. Synthetic PIF (sPIF administration promotes singly cultured embryos development and protects against their demise caused by embryo-toxic serum. To identify and characterize critical sPIF-embryo protein interactions novel biochemical and bio-analytical methods were specifically devised.FITC-PIF uptake/binding by cultured murine and equine embryos was examined and compared with scrambled FITC-PIF (control. Murine embryo (d10 lysates were fractionated by reversed-phase HPLC, fractions printed onto microarray slides and probed with Biotin-PIF, IDE and Kv1.3 antibodies, using fluorescence detection. sPIF-based affinity column was developed to extract and identify PIF-protein interactions from lysates using peptide mass spectrometry (LC/MS/MS. In silico evaluation examined binding of PIF to critical targets, using mutation analysis.PIF directly targets viable cultured embryos as compared with control peptide, which failed to bind. Multistep Biotin-PIF targets were confirmed by single-step PIF-affinity column based isolation. PIF binds protein disulfide isomerases a prolyl-4-hydroxylase β-subunit, (PDI, PDIA4, PDIA6-like containing the antioxidant thioredoxin domain. PIF also binds protective heat shock proteins (70&90, co-chaperone, BAG-3. Remarkably, PIF targets a common RIKP [corrected] site in PDI and HSP proteins. Further, single PIF amino acid mutation significantly reduced peptide-protein target bonding. PIF binds promiscuous tubulins, neuron backbones and ACTA-1,2 visceral proteins. Significant anti-IDE, while limited anti-Kv1.3b antibody-binding to Biotin-PIF positive lysates HPLC fractions were documented.Collectively, data identifies PIF shared targets on PDI and HSP in the embryo. Such are known to play a critical role in protecting against oxidative stress and protein misfolding. PIF-affinity-column is a

  3. Risk factors for the presence of dengue vector mosquitoes, and determinants of their prevalence and larval site selection in Dhaka, Bangladesh.

    Science.gov (United States)

    Paul, Kishor Kumar; Dhar-Chowdhury, Parnali; Haque, C Emdad; Al-Amin, Hasan Mohammad; Goswami, Doli Rani; Kafi, Mohammad Abdullah Heel; Drebot, Michael A; Lindsay, L Robbin; Ahsan, Gias Uddin; Brooks, W Abdullah

    2018-01-01

    Dengue viruses are responsible for over 100 million infections a year worldwide and are a public health concern in Bangladesh. Although risk of transmission is high, data on vector population characteristics are scanty in Bangladesh; therefore, a comprehensive prediction of the patterns of local virus transmission is not possible. Recognizing these gaps, multi-year entomological surveys were carried out in Dhaka, where the disease is most frequently reported. The specific objectives of the present study are threefold: i) to determine the risk factors for the presence of Aedes mosquitoes; ii) to identify the types of most productive and key containers; and iii) to estimate the effects of climatic factors on Aedes abundance in the city of Dhaka, Bangladesh. Entomological surveys were conducted in 12 out of 90 wards in Dhaka. These wards were selected using a probability proportional sampling procedure during the monsoon seasons in 2011, 2012 and 2013 and in the dry season in 2012. All containers inside and around sampled households were inspected for mosquito larvae and pupae, and containers were classified according to their relative size, use pattern, and materials of construction. During the study period (2011-2013), 12,680 larvae and pupae were collected. About 82% of the identified immature mosquitoes were Aedes aegypti, while the remainder were Ae. albopictus and other mosquito species. The largest number of immature mosquitoes was collected from tires and refrigerator trays during 2011 and 2012 monsoon seasons. Conversely, plastic drums were the most productive during the 2012 dry and 2013 monsoon season. Vehicle parts and discarded construction materials were the most efficient producers of Aedes mosquitoes in all surveys. The presence of Aedes mosquitoes was significantly (p Container location, presence of vegetation, and availability of shade for containers were also significantly associated with finding immature Aedes mosquitoes, based on multivariable

  4. Implementation of an efficacious intervention for high risk women in Mexico: protocol for a multi-site randomized trial with a parallel study of organizational factors

    Directory of Open Access Journals (Sweden)

    Patterson Thomas L

    2012-10-01

    Full Text Available Abstract Background Studies of implementation of efficacious human immunodeficiency virus (HIV prevention interventions are rare, especially in resource-poor settings, but important, because they have the potential to increase the impact of interventions by improving uptake and sustainability. Few studies have focused on provider and organizational factors that may influence uptake and fidelity to core intervention components. Using a hybrid design, we will study the implementation of an efficacious intervention to reduce sexually transmitted infections (STIs among female sex workers (FSWs in 12 cities across Mexico. Our protocol will test a ‘train-the-trainer’ implementation model for transporting the Mujer Segura (Healthy Woman intervention into community-based organizations (CBOs. Methods We have partnered with Mexican Foundation for Family Planning (Mexfam, a non-governmental organization that has CBOs throughout Mexico. At each CBO, trained ethnographers will survey CBO staff on characteristics of their organization and on their attitudes toward their CBO and toward the implementation of evidence-based interventions (EBIs. Then, after CBO staff recruit a sample of 80 eligible FSWs and deliver a standard-care, didactic intervention to 40 women randomly selected from that pool, a Mexfam staff person will be trained in the Mujer Segura intervention and will then train other counselors to deliver Mujer Segura to the 40 remaining participating FSWs. FSW participants will receive a baseline behavioral assessment and be tested for HIV and STIs (syphilis, gonorrhea, and chlamydia; they will be reassessed at six months post-intervention to measure for possible intervention effects. At the same time, both qualitative and quantitative data will be collected on the implementation process, including measures of counselors’ fidelity to the intervention model. After data collection at each CBO is complete, the relative efficacy of the Mujer Segura

  5. Activity concentration and transfer factor of 40K, from soil to plant and grass to milk/meat in Rajasthan Rawatbhata Site Environment

    International Nuclear Information System (INIS)

    Menaria, Tejpal; Tiwari, S.N.; Ravi, P.M.; Tripathi, R.M.

    2018-01-01

    Radionuclide uptake by plants is evaluated by transfer factor (TF) defined as the ratio between plant specific activity (Bqkg -1 fr.wt) and soil specific activity (Bqkg -1 fr.wt). It is widely used for calculating radiological human dose via the ingestion pathway. TF is regarded as one of the most important parameters in environmental safety assessment for nuclear facilities. The absorbance of radioactive substances by plants, man and animals can be direct and indirect. In the direct absorbance the plant, man and animals are directly incorporating the radioactive substances. Indirect presupposes the absorbance of radionuclides through the pathway soil - roots - plant -animal - man. The indirect way of intake is the most important and influences the food for greater period of time. Soil to plant transfer of various radionuclides are known to be affected by soil properties, organic matter content, variety of plant species, climatic condition and cultural practices. Study showed that absorption of 40 K by Cereals and Pulses are higher than vegetable because of smaller contiguity of 40 K with the carriers of the cellular membranes of the plant roots

  6. Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development.

    Science.gov (United States)

    Schmouth, Jean-François; Arenillas, David; Corso-Díaz, Ximena; Xie, Yuan-Yun; Bohacec, Slavita; Banks, Kathleen G; Bonaguro, Russell J; Wong, Siaw H; Jones, Steven J M; Marra, Marco A; Simpson, Elizabeth M; Wasserman, Wyeth W

    2015-07-24

    Nr2e1 (nuclear receptor subfamily 2, group e, member 1) encodes a transcription factor important in neocortex development. Previous work has shown that nuclear receptors can have hundreds of target genes, and bind more than 300 co-interacting proteins. However, recognition of the critical role of Nr2e1 in neural stem cells and neocortex development is relatively recent, thus the molecular mechanisms involved for this nuclear receptor are only beginning to be understood. Serial analysis of gene expression (SAGE), has given researchers both qualitative and quantitative information pertaining to biological processes. Thus, in this work, six LongSAGE mouse libraries were generated from laser microdissected tissue samples of dorsal VZ/SVZ (ventricular zone and subventricular zone) from the telencephalon of wild-type (Wt) and Nr2e1-null embryos at the critical development ages E13.5, E15.5, and E17.5. We then used a novel approach, implementing multiple computational methods followed by biological validation to further our understanding of Nr2e1 in neocortex development. In this work, we have generated a list of 1279 genes that are differentially expressed in response to altered Nr2e1 expression during in vivo neocortex development. We have refined this list to 64 candidate direct-targets of NR2E1. Our data suggested distinct roles for Nr2e1 during different neocortex developmental stages. Most importantly, our results suggest a possible novel pathway by which Nr2e1 regulates neurogenesis, which includes Lhx2 as one of the candidate direct-target genes, and SOX9 as a co-interactor. In conclusion, we have provided new candidate interacting partners and numerous well-developed testable hypotheses for understanding the pathways by which Nr2e1 functions to regulate neocortex development.

  7. DOE site performance assessment activities

    International Nuclear Information System (INIS)

    1990-07-01

    Information on performance assessment capabilities and activities was collected from eight DOE sites. All eight sites either currently dispose of low-level radioactive waste (LLW) or plan to dispose of LLW in the near future. A survey questionnaire was developed and sent to key individuals involved in DOE Order 5820.2A performance assessment activities at each site. The sites surveyed included: Hanford Site (Hanford), Idaho National Engineering Laboratory (INEL), Los Alamos National Laboratory (LANL), Nevada Test Site (NTS), Oak Ridge National Laboratory (ORNL), Paducah Gaseous Diffusion Plant (Paducah), Portsmouth Gaseous Diffusion Plant (Portsmouth), and Savannah River Site (SRS). The questionnaire addressed all aspects of the performance assessment process; from waste source term to dose conversion factors. This report presents the information developed from the site questionnaire and provides a comparison of site-specific performance assessment approaches, data needs, and ongoing and planned activities. All sites are engaged in completing the radioactive waste disposal facility performance assessment required by DOE Order 5820.2A. Each site has achieved various degrees of progress and have identified a set of critical needs. Within several areas, however, the sites identified common needs and questions

  8. Measurement of DNA adducts and strand breaks in dab (Limanda limanda) collected in the field: effects of biotic (age, sex) and abiotic (sampling site and period) factors on the extent of DNA damage

    Energy Technology Data Exchange (ETDEWEB)

    Akcha, F.; Leday, G.; Pfohl-Leszkowicz, A

    2004-08-18

    In the Eastern English Channel, the potential application of the comet assay and post-labelling technique in dab was evaluated for genotoxicity monitoring of the marine environment. The effects of biotic (age, sex) and abiotic (sampling site and period) factors on the extent of DNA lesions were also studied. Female and male dab of two class of size (juvenile and adult) were collected by trawling in different sites in Seine Bay and Somme Bay during September 2001. Single-strand breaks and adducts were, respectively, measured in erythrocytes and the liver. Results obtained for the adult female were compared with those collected during a first cruise in March 2001 [Akcha et al., Mutat Res. 534 (1-2) (2003) 21]. Significant effects of sex and age were demonstrated on the level of strand breaks. Moreover, a significant interaction between age and sex was shown that might indicate the complex influence of other factors on the extent of DNA damage (i.e. reproduction status). In the adult dab, the level of breaks is higher in the male than in the female, whereas the opposite trend was observed for the juvenile. Whatever the sex, the number of DNA breaks is higher in the adult than in the juvenile. For the female dab, significant differences were observed with the comet assay between the Seine Bay and the Somme Bay in March but not in September. This may be due to seasonal variations in the formation of DNA lesions related to variations in lipid content and levels of biotransformation activities and/or to spawning cycles. The presence of genotoxic substances in the study areas was also confirmed by the detection of DNA adducts in each sample analysed. Whereas no effect was shown on the total level of adducts for the tested biotic and abiotic factors, qualitative differences in adduct profiles were observed for each of these factors. For the female dab, comparison of adduct profiles obtained in March and September with one generated by hepatic microsomal activation in dab of

  9. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A

    2002-04-01

    The objectives, the programme, and the achievements of SCK-CEN's Site Restoration Department for 2001 are described. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and the management of spent fuel and the flow of dismantled materials and the recycling of materials from decommissioning activities based on the smelting of metallic materials in specialised foundries. The department provides consultancy and services to external organisations and performs R and D on new techniques including processes for the treatment of various waste components including the reprocessing of spent fuel, the treatment of tritium, the treatment of liquid alkali metals into cabonates through oxidation, the treatment of radioactive organic waste and the reconditioning of bituminised waste products.

  10. Mochovce site

    International Nuclear Information System (INIS)

    1997-01-01

    In Mochovce site the construction of four units of WWER 440 NPP with V-213 type of reactor is being carried out. The financing of Mochovce units completion was resolved in April 1996. The completion work commenced at the construction site under leadership of SKODA Prague, the general supplier. The completion work on building part and tests of constructional electric distributions and lightning constructors started. The revisions in technological part were finished, and final protocols from revisions are the basis for starting of completion work. The assembly of transport container anchorage,ventilation system in hermetic areas and hermetic coverage of pools for stored spent nuclear fuel is being carried out. The pre-completion tests of instrumentation and control of ventilation systems, individual dosimetric control in medical station, and tests of nuclear programme according to commissioning and assembling work schedule at the equipment for physical protection of the NPP area started. Inspection activities at Mochovce were performed in accordance with inspection plan for 1996. Evaluation of routine inspections was performed by means of quarterly protocols. Main findings from the inspections performed in Mochovce were in the following areas: (a) deficiencies in the knowledge of the respective regulation and conditions from the Resolution of the state regulatory body, concerning selected employees; (b) training of the selected employees; (c) aim of the measures imposes by inspectors is to eliminate deficiencies in preparation of programmes for pre-completion and completion testing. NRA SR assessment activities at Mochovce NPP were focused mainly on approving and inspecting of design modification to approving programmes for pre-completion and completion testing of system s and equipment and on approving quality assurance programmes. The suggestions of international missions, which reviewed Mochovce safety in the years, were taken into consideration in the programme

  11. Cell differentiation by interaction of two HMG-box proteins: Mat1-Mc activates M cell-specific genes in S.pombe by recruiting the ubiquitous transcription factor Ste11 to weak binding sites

    DEFF Research Database (Denmark)

    Kjaerulff, S; Dooijes, D; Clevers, H

    1997-01-01

    The Schizosaccharomyces pombe mfm1 gene is expressed in an M cell-specific fashion. This regulation requires two HMG-box proteins: the ubiquitous Ste11 transcription factor and the M cell-controlling protein Mat1-Mc. Here we report that the mfm1 promoter contains a single, weak Stell-binding site...... where we could not detect Mat1-Mc in the resulting protein-DNA complex. When we changed a single base in the mfm1 TR-box, such that it resembled those boxes found in ubiquitously expressed genes, Ste11 binding was enhanced, and in vivo the mfm1 gene also became expressed in P cells where Mat1-Mc...

  12. Investigating teachers’ exploration of a professional development website: An innovative approach to understanding the factors that motivate teachers to use Internet-based resources / Investigation de l’exploration par les enseignants d’un site Web

    Directory of Open Access Journals (Sweden)

    Pamela Beach

    2014-08-01

    Full Text Available This qualitative study examined an innovative methodology, combining screen capture technology and a retrospective think aloud, for exploring the use of Internet-based resources by elementary teachers. Pre-service and in-service teachers explored The Balanced Literacy Diet, a free, interactive, and evidenced-informed professional development website. As participants navigated through this complex site, each visual step was captured using Camtasia Studio, a screen recording computer software program developed by TechSmith. Immediately following their 10-minute exploration, participants revisited their online choices virtually and verbalized their thoughts while viewing their screen recording. Qualitative analysis confirmed the usefulness of the methodology and provided insights about the factors that motivate teachers to use professional development websites. Results of the analysis can contribute to the ongoing development of high quality online learning environments. Cette étude qualitative s’est penchée sur une méthodologie innovatrice combinant les technologies de saisie d’écran et la pensée rétrospective à voix haute pour l’exploration de l’utilisation des ressources dans Internet par les enseignants de l’élémentaire. Des enseignants en formation initiale et des enseignants sur place ont exploré The Balanced Literacy Diet, un site Web de perfectionnement professionnel gratuit, interactif et s’appuyant sur des données probantes. Tandis que les participants naviguaient dans ce site complexe, chaque étape visuelle était captée à l’aide de Camtasia Studio, un logiciel d’enregistrement de l’écran développé par TechSmith. Immédiatement après leur exploration de 10 minutes, les participants ont revisité virtuellement leurs choix en ligne et ont verbalisé leurs réflexions en regardant l’enregistrement de l’écran. L’analyse qualitative a confirmé l’utilité de la méthodologie et a fourni des

  13. YUCCA MOUNTAIN SITE DESCRIPTION

    International Nuclear Information System (INIS)

    Simmons, A.M.

    2004-01-01

    The ''Yucca Mountain Site Description'' summarizes, in a single document, the current state of knowledge and understanding of the natural system at Yucca Mountain. It describes the geology; geochemistry; past, present, and projected future climate; regional hydrologic system; and flow and transport within the unsaturated and saturated zones at the site. In addition, it discusses factors affecting radionuclide transport, the effect of thermal loading on the natural system, and tectonic hazards. The ''Yucca Mountain Site Description'' is broad in nature. It summarizes investigations carried out as part of the Yucca Mountain Project since 1988, but it also includes work done at the site in earlier years, as well as studies performed by others. The document has been prepared under the Office of Civilian Radioactive Waste Management quality assurance program for the Yucca Mountain Project. Yucca Mountain is located in Nye County in southern Nevada. The site lies in the north-central part of the Basin and Range physiographic province, within the northernmost subprovince commonly referred to as the Great Basin. The basin and range physiography reflects the extensional tectonic regime that has affected the region during the middle and late Cenozoic Era. Yucca Mountain was initially selected for characterization, in part, because of its thick unsaturated zone, its arid to semiarid climate, and the existence of a rock type that would support excavation of stable openings. In 1987, the United States Congress directed that Yucca Mountain be the only site characterized to evaluate its suitability for development of a geologic repository for high-level radioactive waste and spent nuclear fuel

  14. YUCCA MOUNTAIN SITE DESCRIPTION

    Energy Technology Data Exchange (ETDEWEB)

    A.M. Simmons

    2004-04-16

    The ''Yucca Mountain Site Description'' summarizes, in a single document, the current state of knowledge and understanding of the natural system at Yucca Mountain. It describes the geology; geochemistry; past, present, and projected future climate; regional hydrologic system; and flow and transport within the unsaturated and saturated zones at the site. In addition, it discusses factors affecting radionuclide transport, the effect of thermal loading on the natural system, and tectonic hazards. The ''Yucca Mountain Site Description'' is broad in nature. It summarizes investigations carried out as part of the Yucca Mountain Project since 1988, but it also includes work done at the site in earlier years, as well as studies performed by others. The document has been prepared under the Office of Civilian Radioactive Waste Management quality assurance program for the Yucca Mountain Project. Yucca Mountain is located in Nye County in southern Nevada. The site lies in the north-central part of the Basin and Range physiographic province, within the northernmost subprovince commonly referred to as the Great Basin. The basin and range physiography reflects the extensional tectonic regime that has affected the region during the middle and late Cenozoic Era. Yucca Mountain was initially selected for characterization, in part, because of its thick unsaturated zone, its arid to semiarid climate, and the existence of a rock type that would support excavation of stable openings. In 1987, the United States Congress directed that Yucca Mountain be the only site characterized to evaluate its suitability for development of a geologic repository for high-level radioactive waste and spent nuclear fuel.

  15. An analysis of the dispute process regarding high-level nuclear waste repository siting in Toyo-cho, Japan: Decisive factors in the dispute and roles of the governments and experts

    Energy Technology Data Exchange (ETDEWEB)

    Komatsuzaki, Shunsaku; Horii, Hideyuki (Dept. of Civil Engineering, Univ. of Tokyo (Japan)); Saigo, Takahiro (Mitsubishi Research Institute, Inc. (Japan))

    2010-09-15

    The siting policy of HLW repository in Japan was 'application-based' until 2007 and Toyo-cho is the only municipality which applied for the Literature Survey. In Toyo-cho, however, a serious antagonism among citizens occurred and the application was withdrawn after the mayor was replaced by election. Our detailed analysis of the process based on the methods of political science and psychology shows five decisive factors: 1) opposing activists both in the town and from outside successfully changed citizens' perceptions of HLW by rhetorical expressions, 2) the mayor lacks careful actions and effective policy adviser, 3) NUMO, an organization which runs HLW projects, didn't effectively coordinate Toyo-cho and stakeholders, 4) the municipal government and council exercised very limited influences on the dispute despite their political authority, and 5) the existence of grant adversely influenced the citizens since it causes criticism that Toyo-cho applies a repository for grant. We finally conclude that the substantial problems, caused by the five decisive factors, were the propagation of enthusiastic opposition and the lack of peaceful deliberation based on local governance. In order to avoid enthusiastic opposition and to realize responsible decision making, or negotiation, we suggest that A) active and prompt response of experts, especially political/administrative ones, to radical opposing activities, B) solution to the adverse influence of the grant by the government's agenda

  16. An analysis of the dispute process regarding high-level nuclear waste repository siting in Toyo-cho, Japan: Decisive factors in the dispute and roles of the governments and experts

    International Nuclear Information System (INIS)

    Komatsuzaki, Shunsaku; Horii, Hideyuki; Saigo, Takahiro

    2010-09-01

    The siting policy of HLW repository in Japan was 'application-based' until 2007 and Toyo-cho is the only municipality which applied for the Literature Survey. In Toyo-cho, however, a serious antagonism among citizens occurred and the application was withdrawn after the mayor was replaced by election. Our detailed analysis of the process based on the methods of political science and psychology shows five decisive factors: 1) opposing activists both in the town and from outside successfully changed citizens' perceptions of HLW by rhetorical expressions, 2) the mayor lacks careful actions and effective policy adviser, 3) NUMO, an organization which runs HLW projects, didn't effectively coordinate Toyo-cho and stakeholders, 4) the municipal government and council exercised very limited influences on the dispute despite their political authority, and 5) the existence of grant adversely influenced the citizens since it causes criticism that Toyo-cho applies a repository for grant. We finally conclude that the substantial problems, caused by the five decisive factors, were the propagation of enthusiastic opposition and the lack of peaceful deliberation based on local governance. In order to avoid enthusiastic opposition and to realize responsible decision making, or negotiation, we suggest that A) active and prompt response of experts, especially political/administrative ones, to radical opposing activities, B) solution to the adverse influence of the grant by the government's agenda

  17. The use of artificial spawning substrates in order to understand the factors influencing the spawning site selection, depth of egg strands deposition and hatching time of perch (Perca fluviatilis L.

    Directory of Open Access Journals (Sweden)

    Jan Kubečka

    2012-01-01

    Full Text Available The distribution of egg strands of perch Perca fluviatilis and factors affecting this distribution, in terms of spawning sites and spawning depths used, was studied in spring 2010 in Chabařovice Lake, Czech Republic, using areas with an artificial spawning substrate (A.S.S. and control areas outside the A.S.S. Perch significantly preferred a calm shore instead of a windward shore for spawning. The depths at which perch egg strands were found increased significantly during the spawning period in both A.S.S. areas and in areas outside the A.S.S. (on average from 4.9 m at the beginning to 12.3 m at the end of the spawning period. With increasing depth of deposition the size of the egg strands decreased significantly. The mean depth of egg strands on individual dates corresponded to the position of 10-12°C water layers. From the third week onward, however, egg strands were deposited in much deeper and colder water. A strong relationship was found between the depth at which egg strands were deposited and the duration of the daylight period, indicating that, at the end of the spawning season, perch do not react to the actual temperature of the water column but that they follow their inner clock, assuming that "normally" the shallower depth layers are too warm for successful embryo development. Factors influencing the depth distribution of egg strands were identified as waves, temperature and duration of the daylight period. Factors influencing the selection of spawning sites were identified as wind inducing current, internal seiches and temperature instability of the water column. The first perch larvae were present in the open water of Chabařovice Lake before mid-May, and the latest larvae not earlier than the beginning of July, since warming of the water in deeper layers was very slow. It appears that with prolonged spawning and hatching periods and with spawning occurring at various depths and temperatures, perch have evolved a powerful

  18. Sociality and the telencephalic distribution of corticotrophin-releasing factor, urocortin 3, and binding sites for CRF type 1 and type 2 receptors: A comparative study of eusocial naked mole-rats and solitary Cape mole-rats.

    Science.gov (United States)

    Coen, Clive W; Kalamatianos, Theodosis; Oosthuizen, Maria K; Poorun, Ravi; Faulkes, Christopher G; Bennett, Nigel C

    2015-11-01

    Various aspects of social behavior are influenced by the highly conserved corticotrophin-releasing factor (CRF) family of peptides and receptors in the mammalian telencephalon. This study has mapped and compared the telencephalic distribution of the CRF receptors, CRF1 and CRF2 , and two of their ligands, CRF and urocortin 3, respectively, in African mole-rat species with diametrically opposed social behavior. Naked mole-rats live in large eusocial colonies that are characterized by exceptional levels of social cohesion, tolerance, and cooperation in burrowing, foraging, defense, and alloparental care for the offspring of the single reproductive female. Cape mole-rats are solitary; they tolerate conspecifics only fleetingly during the breeding season. The telencephalic sites at which the level of CRF1 binding in naked mole-rats exceeds that in Cape mole-rats include the basolateral amygdaloid nucleus, hippocampal CA3 subfield, and dentate gyrus; in contrast, the level is greater in Cape mole-rats in the shell of the nucleus accumbens and medial habenular nucleus. For CRF2 binding, the sites with a greater level in naked mole-rats include the basolateral amygdaloid nucleus and dentate gyrus, but the septohippocampal nucleus, lateral septal nuclei, amygdalostriatal transition area, bed nucleus of the stria terminalis, and medial habenular nucleus display a greater level in Cape mole-rats. The results are discussed with reference to neuroanatomical and behavioral studies of various species, including monogamous and promiscuous voles. By analogy with findings in those species, we speculate that the abundance of CRF1 binding in the nucleus accumbens of Cape mole-rats reflects their lack of affiliative behavior. © 2015 Wiley Periodicals, Inc.

  19. Properties of the manganese(II) binding site in ternary complexes of Mnter dot ADP and Mnter dot ATP with chloroplast coupling factor 1: Magnetic field dependence of solvent sup 1 H and sup 2 H NMR relaxation rates

    Energy Technology Data Exchange (ETDEWEB)

    Haddy, A.E.; Frasch, W.D.; Sharp, R.R. (Univ. of Michigan, Ann Arbor (USA))

    1989-05-02

    The influence of the binding of ADP and ATP on the high-affinity Mn(II) binding site of chloroplast coupling factor 1 (CF{sub 1}) was studied by analysis of field-dependent solvent proton and deuteron spin-lattice relaxation data. In order to characterize metal-nucleotide complexes of CF{sub 1} under conditions similar to those of the NMR experiments, the enzyme was analyzed for bound nucleotides and Mn(II) after incubation with AdN and MnCl{sub 2} and removal of labile ligands by extensive gel filtration chromatography. In the field-dependent NMR experiments, the Mn(II) binding site of CF{sub 1} was studied for three mole ratios of added Mn(II) to CF{sub 1}, 0.5, 1.0, and 1.5, in the presence of an excess of either ADP or ATP. The results were extrapolated to zero Mn(II) concentration to characterize the environment of the first Mn(II) binding site of Cf{sub 1}. In the presence of both adenine nucleotides, pronounced changes in the Mn(II) environment relative to that in Mn(II)-CF{sub 1} were evident; the local relaxation rate maxima were more pronounced and shifted to higher field strengths, and the relaxation rate per bound Mn(II) increased at all field strengths. Analysis of the data revealed that the number of exchangeable water molecules liganded to bound Mn(II) increased from one in the binary Mn(II)-CF{sub 1} complex to three and two in the ternary Mn(II)-ADP-CF{sub 1} and Mn(II)-ATP-CF{sub 1} complexes, respectively; these results suggest that a water ligand to bound Mn(II) in the Mn(II)-ADP-CF{sub 1} complex is replaced by the {gamma}-phosphate of ATP in the Mn(II)-ATP-CF{sub 1} complex. A binding model is presented to account for these observations.

  20. KOMFORT catalogue (Katalog zur Erfassung Qrganisationaler und menschlicher Eaktoren bei Inspektionen vor Ort = Catalogue for recording organisational and human factors upon inspections at site) Revision 1 (state: 15 November 2005)

    International Nuclear Information System (INIS)

    2008-01-01

    The KOMFORT inspection instrument supports the collection of indicators in the personnel- organisational field within the scope of inspections at site. The continuous collection of information in the personnel-organisational field backs the long-term inspection and helps to identify negative developments and trends in this field in the sense of an early warning system. Improvements in the personnel-organisational area can be suggested and initiated during the annual talk with the licensee. Findings with safety-relevant meaning from the topics of the KOMFORT indicators can be ascertained in KOMFORT independent of the evaluation and documentation and can be communicated to the licensee and further observed. The indicator catalogue KOMFORT comprises the indicators: - Quality of written documents (frequency of indicator collection: 10 x per nuclear power plant unit and year); - Adherence to obligations (20 x); - Qualification and competencies (10 x); - Training (10 x); - Work load (20 x); - Seizing of leadership functions (10 x); - Cleanliness, tidiness and housekeeping of the plant (40 x); - Interaction with the authorities (40 x). Each indicator of the catalogue is divided into five sections: 1 - Definition: The scope of the indicator is outlined and defined as well as the aspects that are used to evaluate and assess the indicator. 2 - Reasons and evaluation tendency: Here it is shown how to evaluate the information of the indicators and how far they permit a statement on the personnel- organisational factors of a plant. 3 - Frequency of indicator collection: The frequency of indicator collection specifies how often an indicator is to be collected. 4 - Possibilities of indicator collection: In this section the methods are described that can be applied to collect an indicator. Besides, examples are given describing possible situations especially suited to collect an indicator. 5 - Evaluation support: The data collected are to be evaluated according to a four

  1. Contaminated Sites in Iowa

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — Sites contaminated by hazardous materials or wastes. These sites are those administered by the Contaminated Sites Section of Iowa DNR. Many are sites which are...

  2. G. Nuclear power plant siting

    International Nuclear Information System (INIS)

    1976-01-01

    The selection of a site for a nuclear power site is a complex process involving considerations of public health and safety, engineering design, economics, and environmental impact. Although policies adopted in various countries differ in some details, a common philosophy usually underlies the criteria employed. The author discusses the basic requirements, as they relate to New Zealand, under the headings: engineering and economics; health and safety; environmental factors

  3. SURGICAL SITE INFECTION: REVIEW

    Directory of Open Access Journals (Sweden)

    P. H. M. Bonai

    2016-07-01

    Full Text Available Nosocomial infection or nosocomial infection (NI is one of the factors that increase the cost of maintaining patients in the health system, even in processes that should safely occur, such as hospital patients and performing simple and routine surgical procedures surgical centers and clinics leading to complications resulting from these infections that prolong hospital stay and promote pain and suffering to the patient, resulting in the defense of the quality of services and influencing negatively the hospitals. Therefore, the aim of this study was to review the factors that result in surgical site infection, with the purpose of better understanding of the subject and the possibility of preventive actions to better treatment outcome of the patient.

  4. Bioremediation of contaminated sites

    International Nuclear Information System (INIS)

    Schneider, C.

    1996-01-01

    By volatilizing aromatic compounds through aeration, landfarming is a recognized approach to the bioremediation of hydrocarbon contaminated soil. With this method, the soil is cultivated and aided with fertilizer amendment to provide a nutrient source for the microbial population involved in the degradation of hydrocarbons. The effectiveness of bioremediation will depend on several factors, including topographic features, soil properties, and biochemistry. Since bioremediation is inhibited by anaerobic conditions, sites that are sloped or have trenches to collect runoff water are preferable. As for soil properties, the percentage of sand should not be too high, but aeration is essential to avoid anaerobic conditions. Addition of straw is generally beneficial, and fertilizers with nitrogen, phosphorous and potassium will help degrading hydrocarbons. Temperature, pH, and salt content are also important factors since they facilitate microbial activity. 3 refs

  5. Emotions as a site-related factor. The attitudes of the population towards energy policy and environmental protection; Emotionen als Standortfaktor. Die Einstellungen der Bevoelkerung zu Energiepolitik und Umweltschutz

    Energy Technology Data Exchange (ETDEWEB)

    Koecher, R. [Inst. fuer Demoskopie, Allensbach (Germany)

    1997-06-01

    For years, debate has been raging on the future competitiveness of Germany. The discussions focus on wages and incidental wage costs, working hours, the education and training system, technological changes, flexibilization and the fight against red tape as well as social consensus. But one site-related factor hardly crops up in public discussion and in economic-science textbook and expertises, although it quite essentially influences competitiveness, now even more than formerly: the mentality of the population. It includes priorities held by society, target concepts such as the openness of the population towards innovation and its attitude towards technology and technical progress as well as the way in which discussions are conducted in society and decisions taken, especially also people`s inclination to rationality or irrationality, and proneness to emotions or ideological thinking. (orig.) [Deutsch] Seit Jahren wird ueber die Zukunft des Standortes Deutschland diskutiert und gestritten. Im Mittelpunkt der Diskussion stehen Loehne und Lohnnebenkosten, Arbeitszeiten, das Bildungs- und Ausbildungssystem, technologische Veraenderungen, Flexibilisierung und Entbuerokratisierung und der soziale Frieden. Ein Standortfaktor kommt dagegen in der oeffentlichen Diskussion wie auch in den wirtschaftswissenschaftlichen Lehrbuechern und Expertisen kaum vor, obwohl er die Standortqualitaet ganz wesentlich beeinflusst, heute noch mehr als frueher: Die Mentalitaet der Bevoelkerung. Dazu gehoeren die gesellschaftlichen Prioritaeten und Zielvorstellungen wie die Innovationsoffenheit der Bevoelkerung, ihre Einstellung zu Technik und technischem Fortschritt wie die Art, gesellschaftliche Diskussionen zu fuehren und Entscheidungen zu treffen, besonders auch die Neigung zu Rationalitaet und Irrationalitaet, die Anfaelligkeit fuer Emotionen und Ideologisierung. (orig.)

  6. Siting guidelines and their role in repository site selection

    International Nuclear Information System (INIS)

    Hanlon, C.L.

    1985-01-01

    The first requirement of the Nuclear Waste Policy Act was for the Secretary of Energy to issue general guidelines for siting repositories. The guidelines were to specify detailed geologic considerations that would be the primary criteria for the selection of sites in various host rocks, as well as factors that would qualify or disqualify any site from development as a repository. These guidelines were clearly intended to provide not only the framework for the siting program but also the stimulus for establishing effective communication and consultation among the parties involved in the program. The Act further required that the guidelines be a factor in the development of all future decision documents of the Office of Civilian Radioactive Waste Management, including the environmental assessments that would accompany the nomination of sites for characterization, the site-characterization plans that are to be prepared before the sinking of exploratory shafts at any candidate site, and the environmental impact statement that is to support the recommendation of a site for development as a repository. More than two years after its passage, the intention of the Act for the guidelines has been realized. Concurred in by the Nuclear Regulatory Commission on June 22, 1984, and issued by the Department in November 1984, the guidelines include postclosure technical guidelines that apply to conditions governing the long-term performance of the repository system; preclosure technical guidelines that apply to conditions governing the siting, construction, operation, and closure of the repository; and system guidelines whose objective is to ensure that the regulatory requirements of the Environmental Protection Agency and the Nuclear Regulatory Commission are met

  7. Nuclear installations sites safety

    International Nuclear Information System (INIS)

    Barber, P.; Candes, P.; Duclos, P.; Doumenc, A.; Faure, J.; Hugon, J.; Mohammadioun, B.

    1988-11-01

    This report is divided into ten parts bearing: 1 Safety analysis procedures for Basis Nuclear Installations sites (BNI) in France 2 Site safety for BNI in France 3 Industrial and transport activities risks for BNI in France 4 Demographic characteristics near BNI sites in France 5 Meteorologic characteristics of BNI sites in France 6 Geological aspects near the BNI sites in France 7 Seismic studies for BNI sites in France 8 Hydrogeological aspects near BNI sites in France 9 Hydrological aspects near BNI sites in France 10 Ecological and radioecological studies of BNI sites in France [fr

  8. Social Media Sites

    Science.gov (United States)

    Media Sites Site Registration Contact Us Search AF.mil: Home > AF Sites > Social Media Sites Social Media Welcome to the Air Force social media directory! The directory is a one-stop shop of official Air Force social media pages across various social media sites. Social media is all about

  9. New Site Coefficients and Site Classification System Used in Recent Building Seismic Code Provisions

    Science.gov (United States)

    Dobry, R.; Borcherdt, R.D.; Crouse, C.B.; Idriss, I.M.; Joyner, W.B.; Martin, G.R.; Power, M.S.; Rinne, E.E.; Seed, R.B.

    2000-01-01

    Recent code provisions for buildings and other structures (1994 and 1997 NEHRP Provisions, 1997 UBC) have adopted new site amplification factors and a new procedure for site classification. Two amplitude-dependent site amplification factors are specified: Fa for short periods and Fv for longer periods. Previous codes included only a long period factor S and did not provide for a short period amplification factor. The new site classification system is based on definitions of five site classes in terms of a representative average shear wave velocity to a depth of 30 m (V?? s). This definition permits sites to be classified unambiguously. When the shear wave velocity is not available, other soil properties such as standard penetration resistance or undrained shear strength can be used. The new site classes denoted by letters A - E, replace site classes in previous codes denoted by S1 - S4. Site classes A and B correspond to hard rock and rock, Site Class C corresponds to soft rock and very stiff / very dense soil, and Site Classes D and E correspond to stiff soil and soft soil. A sixth site class, F, is defined for soils requiring site-specific evaluations. Both Fa and Fv are functions of the site class, and also of the level of seismic hazard on rock, defined by parameters such as Aa and Av (1994 NEHRP Provisions), Ss and S1 (1997 NEHRP Provisions) or Z (1997 UBC). The values of Fa and Fv decrease as the seismic hazard on rock increases due to soil nonlinearity. The greatest impact of the new factors Fa and Fv as compared with the old S factors occurs in areas of low-to-medium seismic hazard. This paper summarizes the new site provisions, explains the basis for them, and discusses ongoing studies of site amplification in recent earthquakes that may influence future code developments.

  10. The metal-ion-dependent adhesion site in the Von Willebrand factor-A domain of α2δ subunits is key to trafficking voltage-gated Ca2+ channels

    Science.gov (United States)

    Cantí, C.; Nieto-Rostro, M.; Foucault, I.; Heblich, F.; Wratten, J.; Richards, M. W.; Hendrich, J.; Douglas, L.; Page, K. M.; Davies, A.; Dolphin, A. C.

    2005-01-01

    All auxiliary α2δ subunits of voltage-gated Ca2+ (CaV) channels contain an extracellular Von Willebrand factor-A (VWA) domain that, in α2δ-1 and -2, has a perfect metal-ion-dependent adhesion site (MIDAS). Modeling of the α2δ-2 VWA domain shows it to be highly likely to bind a divalent cation. Mutating the three key MIDAS residues responsible for divalent cation binding resulted in a MIDAS mutant α2δ-2 subunit that was still processed and trafficked normally when it was expressed alone. However, unlike WT α2δ-2, the MIDAS mutant α2δ-2 subunit did not enhance and, in some cases, further diminished CaV1.2, -2.1, and -2.2 currents coexpressed with β1b by using either Ba2+ or Na+ as a permeant ion. Furthermore, expression of the MIDAS mutant α2δ-2 reduced surface expression and strongly increased the perinuclear retention of CaVα1 subunits at the earliest time at which expression was observed in both Cos-7 and NG108–15 cells. Despite the presence of endogenous α2δ subunits, heterologous expression of α2δ-2 in differentiated NG108–15 cells further enhanced the endogenous high-threshold Ca2+ currents, whereas this enhancement was prevented by the MIDAS mutations. Our results indicate that α2δ subunits normally interact with the CaVα1 subunit early in their maturation, before the appearance of functional plasma membrane channels, and an intact MIDAS motif in the α2δ subunit is required to promote trafficking of the α1 subunit to the plasma membrane by an integrin-like switch. This finding provides evidence for a primary role of a VWA domain in intracellular trafficking of a multimeric complex, in contrast to the more usual roles in binding extracellular ligands in other exofacial VWA domains. PMID:16061813

  11. Siting of geological disposal facilities

    International Nuclear Information System (INIS)

    1994-01-01

    Radioactive waste is generated from the production of nuclear energy and from the use of radioactive materials in industrial applications, research and medicine. The importance of safe management of radioactive waste for the protection of human health and the environment has long been recognized and considerable experience has been gained in this field. The Radioactive Waste Safety Standards (RADWASS) programme is the IAEA's contribution to establishing and promoting the basic safety philosophy for radioactive waste management and the steps necessary to ensure its implementation. This Safety Guide defines the process to be used and guidelines to be considered in selecting sites for deep geological disposal of radioactive wastes. It reflects the collective experience of eleven Member States having programmes to dispose of spent fuel, high level and long lived radioactive waste. In addition to the technical factors important to site performance, the Safety Guide also addresses the social, economic and environmental factors to be considered in site selection. 3 refs

  12. Quattor: managing (complex) grid sites

    International Nuclear Information System (INIS)

    Jouvin, M

    2008-01-01

    Quattor is a tool developed to efficiently manage fabrics with hundreds or thousands of Linux machines, while still being able to manage smaller clusters easily. It was originally developed inside the European Data Grid (EDG) project and is now in use at more than 50 grid sites running gLite middleware, ranging from small LCG T3s to very large sites like CERN. Quattor's ability to factorize and to reuse common parts of service configurations permitted the development of the QWG templates: a complete set of standard templates to configure the OS and gLite middleware. Any site can just import and customize the configuration without editing the bulk of the templates. Collaboration around these templates results in a very efficient sharing of installation and configuration information between those sites using them

  13. Storage of low-level radioactive wastes in the ground hydrogeologic and hydrochemical factors (with an appendix on the Maxey Flats, Kentucky, radioactive waste storage site: current knowledge and data needs for a quantitative hydrogeologic evaluation)

    International Nuclear Information System (INIS)

    Papadopulos, S.S.; Winograd, I.J.

    1974-01-01

    Hydrogeologic criteria presented by Cherry and others (1973) are adopted as a guideline to define the hydrogeologic and hydrochemical data needs for the evaluation of the suitability of proposed or existing low-level radioactive waste burial sites. Evaluation of the suitability of a site requires the prediction of flow patterns and of rates of nuclide transport in the regional hydrogeologic system. Such predictions can be made through mathematical simulation of flow and solute transport in porous media. The status of mathematical simulation techniques, as they apply to radioactive waste burial sites, is briefly reviewed, and hydrogeologic and hydrochemical data needs are listed in order of increasing difficulty and cost of acquisition. Predictive modeling, monitoring, and management of radionuclides dissolved and transported by ground water can best be done for sites in relatively simple hydrogeologic settings; namely, in unfaulted relatively flat-lying strata of intermediate permeability such as silt, siltstone and silty sandstone. In contrast, dense fractured or soluble media and poorly permeable porous media (aquitards) are not suitable for use as burial sites, first, because of media heterogeneity and difficulties of sampling, and consequently of predictive modeling, and, second, because in humid zones burial trenches in aquitards may overflow. A buffer zone several thousands of feet to perhaps several miles around existing or proposed sites is a mandatory consequence of the site selection criteria. As a specific example, the Maxey Flats, Kentucky low-level waste disposal site is examined. (U.S.)

  14. Ocean Disposal Site Monitoring

    Science.gov (United States)

    EPA is responsible for managing all designated ocean disposal sites. Surveys are conducted to identify appropriate locations for ocean disposal sites and to monitor the impacts of regulated dumping at the disposal sites.

  15. Promoting Your Web Site.

    Science.gov (United States)

    Raeder, Aggi

    1997-01-01

    Discussion of ways to promote sites on the World Wide Web focuses on how search engines work and how they retrieve and identify sites. Appropriate Web links for submitting new sites and for Internet marketing are included. (LRW)

  16. Particle Physics Education Sites

    Science.gov (United States)

    back to home page Particle Physics Education Sites quick reference Education and Information - National Laboratory Education Programs - Women and Minorities in Physics - Other Physics Sites - Physics Alliance - Accelerators at National Laboratories icon Particle Physics Education and Information sites: top

  17. Hanford Site Development Plan

    Energy Technology Data Exchange (ETDEWEB)

    Rinne, C.A.; Curry, R.H.; Hagan, J.W.; Seiler, S.W.; Sommer, D.J. (Westinghouse Hanford Co., Richland, WA (USA)); Yancey, E.F. (Pacific Northwest Lab., Richland, WA (USA))

    1990-01-01

    The Hanford Site Development Plan (Site Development Plan) is intended to guide the short- and long-range development and use of the Hanford Site. All acquisition, development, and permanent facility use at the Hanford Site will conform to the approved plan. The Site Development Plan also serves as the base document for all subsequent studies that involve use of facilities at the Site. This revision is an update of a previous plan. The executive summary presents the highlights of the five major topics covered in the Site Development Plan: general site information, existing conditions, planning analysis, Master Plan, and Five-Year Plan. 56 refs., 67 figs., 31 tabs.

  18. Hanford Site Development Plan

    International Nuclear Information System (INIS)

    Rinne, C.A.; Curry, R.H.; Hagan, J.W.; Seiler, S.W.; Sommer, D.J.; Yancey, E.F.

    1990-01-01

    The Hanford Site Development Plan (Site Development Plan) is intended to guide the short- and long-range development and use of the Hanford Site. All acquisition, development, and permanent facility use at the Hanford Site will conform to the approved plan. The Site Development Plan also serves as the base document for all subsequent studies that involve use of facilities at the Site. This revision is an update of a previous plan. The executive summary presents the highlights of the five major topics covered in the Site Development Plan: general site information, existing conditions, planning analysis, Master Plan, and Five-Year Plan. 56 refs., 67 figs., 31 tabs

  19. Realities of site investigation

    International Nuclear Information System (INIS)

    Beauheim, R.; Ben Benfahel, M.; Byrum, Ch.; Fedor, F.; Geier, J.; Nys, V.; Schelkes, K.; Selroos, J.O.; Szucs, I.; Whittaker, St.

    2007-01-01

    During the working session, Working Group C discussed the following questions proposed by the Scientific Programme Committee of AMIGO 2: - Provide a list of concrete examples of limitations and their reasons. In addressing these issues, consider the relation between what you can measure and what you would like to describe. - Can these limitations be handled by defensible uncertainty descriptions? - What has been your experience in predicting properties/responses and then making comparisons with subsequent measurements? How much 'after-fitting' was necessary? Did the exercise contribute to validation? What did it teach you about your abilities to characterise? - What are the realities of transferability of data between sites? What can actually be transferred (data, conceptual models, evaluation procedures) and what could not? - How have the experiences on possibilities and limitations influenced your investigation programme? - How are the limits in what can be achieved factored into safety assessment and engineering? (authors)

  20. Site Recommendation Subsurface Layout

    International Nuclear Information System (INIS)

    C.L. Linden

    2000-01-01

    The purpose of this analysis is to develop a Subsurface Facility layout that is capable of accommodating the statutory capacity of 70,000 metric tons of uranium (MTU), as well as an option to expand the inventory capacity, if authorized, to 97,000 MTU. The layout configuration also requires a degree of flexibility to accommodate potential changes in site conditions or program requirements. The objective of this analysis is to provide a conceptual design of the Subsurface Facility sufficient to support the development of the Subsurface Facility System Description Document (CRWMS M andO 2000e) and the ''Emplacement Drift System Description Document'' (CRWMS M andO 2000i). As well, this analysis provides input to the Site Recommendation Consideration Report. The scope of this analysis includes: (1) Evaluation of the existing facilities and their integration into the Subsurface Facility design. (2) Identification and incorporation of factors influencing Subsurface Facility design, such as geological constraints, thermal loading, constructibility, subsurface ventilation, drainage control, radiological considerations, and the Test and Evaluation Facilities. (3) Development of a layout showing an available area in the primary area sufficient to support both the waste inventories and individual layouts showing the emplacement area required for 70,000 MTU and, if authorized, 97,000 MTU

  1. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund) - NPL Sites

    Data.gov (United States)

    U.S. Environmental Protection Agency — National Priorities List (NPL) Sites - The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access...

  2. Superfund Site Information - Site Sampling Data

    Data.gov (United States)

    U.S. Environmental Protection Agency — This asset includes Superfund site-specific sampling information including location of samples, types of samples, and analytical chemistry characteristics of...

  3. Site Closure Strategy Model for Creosote Site

    International Nuclear Information System (INIS)

    Coll, F.R.; Gray, D.R.

    2009-01-01

    In conjunction with RCRA site corrective action at an active wood preserving facility, a risk-based site closure strategy was developed and incorporated the performance of a dense non-aqueous phase liquid (DNAPL) source recovery remedy, a monitored natural attenuation (MNA) remedy for dissolved phase groundwater, and institutional controls. Innovative creosote DNAPL source recovery has been undertaken at the Site since 1998. Pooled creosote DNAPL is present 90 feet below ground within a transmissive sand and gravel aquifer with a saturated thickness of approximately 80 feet. The creosote DNAPL source is situated on the property boundary of the site and has generated a 1/2 mile off-site dissolved phase plume, creating significant NAPL management and remedial technology verification issues. To date, over 120,000 gallons of creosote DNAPL have been recovered from the subsurface utilizing a modified circulation well technology. A mass discharge flux protocol was developed to serve as a major performance metrics for the continuation of source removal efforts and to support the application of monitored natural attenuation as an associated remedial technology for groundwater. The mass removal success has supported the MNA remedy for dissolved phase groundwater and the associated development of institutional controls. The enacted site management strategy outlines the current and future risk management activities for the Site and represents an appropriate site closure strategy for the Site. (authors)

  4. Site specific information in site selection

    International Nuclear Information System (INIS)

    Aeikaes, T.; Hautojaervi, A.

    1998-01-01

    The programme for the siting of a deep repository for final disposal of spent nuclear fuel was started already in 1983 and is carried out today by Posiva Oy which continues the work started by Teollisuuden Voima Oy. The programme aims at site selection by the end of the year 2000. The programme has progressed in successive interim stages with defined goals. After an early phase for site identification, five sites were selected in 1987 for preliminary site characterisation. Three of these were selected and judged to be best suited for the more detailed characterisation in 1992. An additional new site was included into the programme based on a separate feasibility study in the beginning of 1997. Since the year 1983 several safety assessments together with technical plans of the facility have been completed. When approaching the site selection the needs for more detailed consideration of the site specific properties in the safety assessment have been increased. The Finnish regulator STUK has published a proposal for general safety requirements for the final disposal of spent nuclear fuel in Finland. This set of requirements has been projected to be used in conjunction of the decision making by the end 2000. Based on the site evaluation all sites can provide a stable environment and there is evidence that the requirements for the longevity of the canister can be fulfilled at each site. In this manner the four candidate sites do not differ too much from each other. The main difference between the sites is in the salinity of the deep groundwater. The significance of differences in the salinity for the long-term safety cannot be defined yet. The differences may contribute to the discussion of the longevity of the bentonite buffer and also to the modelling of the groundwater flow and transport. The use of the geosphere as a transport barrier is basically culminated on the questions about sparse but fast flow routes and 'how bad channeling can be'. To answer these questions

  5. Hanford Site Development Plan

    International Nuclear Information System (INIS)

    Hathaway, H.B.; Daly, K.S.; Rinne, C.A.; Seiler, S.W.

    1993-05-01

    The Hanford Site Development Plan (HSDP) provides an overview of land use, infrastructure, and facility requirements to support US Department of Energy (DOE) programs at the Hanford Site. The HSDP's primary purpose is to inform senior managers and interested parties of development activities and issues that require a commitment of resources to support the Hanford Site. The HSDP provides an existing and future land use plan for the Hanford Site. The HSDP is updated annually in accordance with DOE Order 4320.1B, Site Development Planning, to reflect the mission and overall site development process. Further details about Hanford Site development are defined in individual area development plans

  6. Hanford Site environmental management specification

    International Nuclear Information System (INIS)

    Grygiel, M.L.

    1998-01-01

    The US Department of Energy, Richland Operations Office (RL) uses this Hanford Site Environmental Management Specification (Specification) to document top-level mission requirements and planning assumptions for the prime contractors involved in Hanford Site cleanup and infrastructure activities under the responsibility of the US Department of Energy, Office of Environmental Management. This Specification describes at a top level the activities, facilities, and infrastructure necessary to accomplish the cleanup of the Hanford Site and assigns this scope to Site contractors and their respective projects. This Specification also references the key National Environmental Policy Act of 1969 (NEPA), Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA), and safety documentation necessary to accurately describe the cleanup at a summary level. The information contained in this document reflects RL's application of values, priorities, and critical success factors expressed by those involved with and affected by the Hanford Site project. The prime contractors and their projects develop complete baselines and work plans to implement this Specification. These lower-level documents and the data that support them, together with this Specification, represent the full set of requirements applicable to the contractors and their projects. Figure 1-1 shows the relationship of this Specification to the other basic Site documents. Similarly, the documents, orders, and laws referenced in this specification represent only the most salient sources of requirements. Current and contractual reference data contain a complete set of source documents

  7. Hanford Site environmental management specification

    Energy Technology Data Exchange (ETDEWEB)

    Grygiel, M.L.

    1998-06-10

    The US Department of Energy, Richland Operations Office (RL) uses this Hanford Site Environmental Management Specification (Specification) to document top-level mission requirements and planning assumptions for the prime contractors involved in Hanford Site cleanup and infrastructure activities under the responsibility of the US Department of Energy, Office of Environmental Management. This Specification describes at a top level the activities, facilities, and infrastructure necessary to accomplish the cleanup of the Hanford Site and assigns this scope to Site contractors and their respective projects. This Specification also references the key National Environmental Policy Act of 1969 (NEPA), Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA), and safety documentation necessary to accurately describe the cleanup at a summary level. The information contained in this document reflects RL`s application of values, priorities, and critical success factors expressed by those involved with and affected by the Hanford Site project. The prime contractors and their projects develop complete baselines and work plans to implement this Specification. These lower-level documents and the data that support them, together with this Specification, represent the full set of requirements applicable to the contractors and their projects. Figure 1-1 shows the relationship of this Specification to the other basic Site documents. Similarly, the documents, orders, and laws referenced in this specification represent only the most salient sources of requirements. Current and contractual reference data contain a complete set of source documents.

  8. Region 9 NPL Sites (Superfund Sites 2013)

    Science.gov (United States)

    NPL site POINT locations for the US EPA Region 9. NPL (National Priorities List) sites are hazardous waste sites that are eligible for extensive long-term cleanup under the Superfund program. Eligibility is determined by a scoring method called Hazard Ranking System. Sites with high scores are listed on the NPL. The majority of the locations are derived from polygon centroids of digitized site boundaries. The remaining locations were generated from address geocoding and digitizing. Area covered by this data set include Arizona, California, Nevada, Hawaii, Guam, American Samoa, Northern Marianas and Trust Territories. Attributes include NPL status codes, NPL industry type codes and environmental indicators. Related table, NPL_Contaminants contains information about contaminated media types and chemicals. This is a one-to-many relate and can be related to the feature class using the relationship classes under the Feature Data Set ENVIRO_CONTAMINANT.

  9. Land Use Baseline Report Savannah River Site

    International Nuclear Information System (INIS)

    Noah, J.C.

    1995-01-01

    This document is to serve as a resource for Savannah River Site managers, planners, and SRS stakeholders by providing a general description of the site and land-use factors important to future use decisions and plans. The intent of this document is to be comprehensive in its review of SRS and the surrounding area

  10. Land Use Baseline Report Savannah River Site

    Energy Technology Data Exchange (ETDEWEB)

    Noah, J.C.

    1995-06-29

    This document is to serve as a resource for Savannah River Site managers, planners, and SRS stakeholders by providing a general description of the site and land-use factors important to future use decisions and plans. The intent of this document is to be comprehensive in its review of SRS and the surrounding area.

  11. Site remediation: The naked truth

    International Nuclear Information System (INIS)

    Calloway, J.M.

    1991-01-01

    The objective of any company faced with an environmental site remediation project is to perform the cleanup effectively at the lowest possible cost. Today, there are a variety of techniques being applied in the reme