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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. 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.

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

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    Incorporating evolution of transcription factor binding sites into annotated alignments. 841. J. Biosci. 32(5), August 2007. 1. Introduction. A majority of computational approaches that aim to predict transcription factor binding sites employ cross- species comparison to focus on conserved locations. Such a comparison helps in ...

  4. Social Network Sites as Educational Factors.

    Science.gov (United States)

    Ebrahimpour, Alireza; Rajabali, Farnaz; Yazdanfar, Fatemeh; Azarbad, Reza; Nodeh, Majid Rezaei; Siamian, Hasan; Vahedi, Mohammad

    2016-04-01

    in this present era, the technology development has established certain type of communication. Nowadays education as the fundamental principle in transferring cognition to the learners has found various methods. Recently the concept that social networks could be effective tool in easing the achievement to the educational goals has been under attention. Therefore, this investigation is trying to find out whether, the social networks could play role on the process of education among students? This cross sectional descriptive study was performed on 1000 students from 7 medical universities in 2015. The data collection tool was questionnaire that was approved Cronbach's alpha: was 0.85. Meanwhile its validity was confirmed too. The obtained data were analyzed by the descriptive statistic, ANOVA, Turkey and used X(2) SPSS-19. In this investigation, 940 subjects were under study. 85% used daily the social network. The highest usage was attributed to the Telegram. 52% preferred image suitable for transferring of information. Even though, 73% believed that these networks have significant effects on coordinating of students with in university charges. Considering the findings of the present study, it is proposed that the universities integrate the social networks in the education programs and recognize it as the awareness factor, therefore benefit it in the educational affairs.

  5. 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

  6. Delivery Site Preferences and Associated Factors among Married ...

    African Journals Online (AJOL)

    BACKGROUND: Efforts to reduce maternal mortality and morbidity must address societal and cultural factors that affect women's health and their access to services. There was no research conducted previously on delivery site preferences and associated factors among married women of child bearing age in the study area.

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

    African Journals Online (AJOL)

    Background: Surgical site infection (SSI) after cesarean section (CS) increases maternal morbidity, hospital stay and medical cost. However, in Ethiopia, limited evidence exists regarding the magnitude and risk factors of post-CS wound infection. The purpose of this study was to determine the prevalence of – and factors ...

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

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    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.

  9. Multiple criteria landfill site selection method incorporating the NIMBY factors

    Science.gov (United States)

    Salleh, Abdul Hakim; Ahamad, Mohd Sanusi S.; Yusoff, Mohd Suffian; Aziz, Hamidi Abdul

    2017-10-01

    Waste management and disposal issues one way or another need to be resolved correctly. Today, every developing country is facing the very common question of finding the best suitable site for a landfill. Relying on the technical factors alone would not solve the problem, but the best suitable sites for landfill need to consider the Not-In-My-Backyard (NIMBY) policy in resisting the pressure from unwanted development within the neighborhood or town. Therefore, the main objective of this paper is to propose a sustainable approach in finding and determining the best landfill site using GIS. A spatial analytical study is presented by applying various criteria derived from several types of spatial data available in the search for the most suitable landfill site in three (3) districts of Kuala Muda, Kulim and Baling, in Kedah. The results of the analysis have not only satisfied the technical factors but have also put into consideration the public opposition to the NIMBY issues.

  10. [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.

  11. Risk Factors of Surgical Site Infection at Muhimbili National Hospital ...

    African Journals Online (AJOL)

    Superficial SSI was the most commonly observed type, 54.8%. Overall HIV prevalence in this study was 16.9% with a 5 times risk of developing SSI. Conclusions: Surgical site infection has remained a major Nosocomial infection in developing countries. Factors shown to be associated with increased risk are wound class, ...

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

    African Journals Online (AJOL)

    It is recommended that preoperative hospital stay should be as short as possible and extra care/precautions taken when working on the elderly, using implants or requiring drainage. Keywords: Clean orthopaedic operations, risk factors, surgical site infection. Nigerian Journal of Clinical Practice • Oct-Dec 2013 • Vol 16 ...

  13. 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

  14. Structural Fingerprints of Transcription Factor Binding Site Regions

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    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.

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    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. Biophysical fitness landscapes for transcription factor binding sites.

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    Allan Haldane

    2014-07-01

    Full Text Available Phenotypic states and evolutionary trajectories available to cell populations are ultimately dictated by complex interactions among DNA, RNA, proteins, and other molecular species. Here we study how evolution of gene regulation in a single-cell eukaryote S. cerevisiae is affected by interactions between transcription factors (TFs and their cognate DNA sites. Our study is informed by a comprehensive collection of genomic binding sites and high-throughput in vitro measurements of TF-DNA binding interactions. Using an evolutionary model for monomorphic populations evolving on a fitness landscape, we infer fitness as a function of TF-DNA binding to show that the shape of the inferred fitness functions is in broad agreement with a simple functional form inspired by a thermodynamic model of two-state TF-DNA binding. However, the effective parameters of the model are not always consistent with physical values, indicating selection pressures beyond the biophysical constraints imposed by TF-DNA interactions. We find little statistical support for the fitness landscape in which each position in the binding site evolves independently, indicating that epistasis is common in the evolution of gene regulation. Finally, by correlating TF-DNA binding energies with biological properties of the sites or the genes they regulate, we are able to rule out several scenarios of site-specific selection, under which binding sites of the same TF would experience different selection pressures depending on their position in the genome. These findings support the existence of universal fitness landscapes which shape evolution of all sites for a given TF, and whose properties are determined in part by the physics of protein-DNA interactions.

  17. Biophysical fitness landscapes for transcription factor binding sites.

    Science.gov (United States)

    Haldane, Allan; Manhart, Michael; Morozov, Alexandre V

    2014-07-01

    Phenotypic states and evolutionary trajectories available to cell populations are ultimately dictated by complex interactions among DNA, RNA, proteins, and other molecular species. Here we study how evolution of gene regulation in a single-cell eukaryote S. cerevisiae is affected by interactions between transcription factors (TFs) and their cognate DNA sites. Our study is informed by a comprehensive collection of genomic binding sites and high-throughput in vitro measurements of TF-DNA binding interactions. Using an evolutionary model for monomorphic populations evolving on a fitness landscape, we infer fitness as a function of TF-DNA binding to show that the shape of the inferred fitness functions is in broad agreement with a simple functional form inspired by a thermodynamic model of two-state TF-DNA binding. However, the effective parameters of the model are not always consistent with physical values, indicating selection pressures beyond the biophysical constraints imposed by TF-DNA interactions. We find little statistical support for the fitness landscape in which each position in the binding site evolves independently, indicating that epistasis is common in the evolution of gene regulation. Finally, by correlating TF-DNA binding energies with biological properties of the sites or the genes they regulate, we are able to rule out several scenarios of site-specific selection, under which binding sites of the same TF would experience different selection pressures depending on their position in the genome. These findings support the existence of universal fitness landscapes which shape evolution of all sites for a given TF, and whose properties are determined in part by the physics of protein-DNA interactions.

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

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    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

  19. Scoring functions for transcription factor binding site prediction

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    Friberg Markus

    2005-04-01

    Full Text Available Abstract Background Transcription factor binding site (TFBS prediction is a difficult problem, which requires a good scoring function to discriminate between real binding sites and background noise. Many scoring functions have been proposed in the literature, but it is difficult to assess their relative performance, because they are implemented in different software tools using different search methods and different TFBS representations. Results Here we compare how several scoring functions perform on both real and semi-simulated data sets in a common test environment. We have also developed two new scoring functions and included them in the comparison. The data sets are from the yeast (S. cerevisiae genome. Our new scoring function LLBG (least likely under the background model performs best in this study. It achieves the best average rank for the correct motifs. Scoring functions based on positional bias performed quite poorly in this study. Conclusion LLBG may provide an interesting alternative to current scoring functions for TFBS prediction.

  20. Risk factors for surgical site infection after dermatological surgery.

    Science.gov (United States)

    Heal, Clare F; Buettner, Petra G; Drobetz, Herwig

    2012-07-01

      Surgical site infection (SSI) following minor surgery contributes to patient morbidity and compromises cosmetic outcomes. The purpose of this study was to determine the incidence of and risk factors for SSI after dermatological surgery in general practice.   A prospective, observational study which assessed infection among 972 patients was conducted in regional north Queensland, Australia. Consecutive patients presenting for minor skin excisions were invited to participate. Wounds were assessed for SSI at the time of removal of sutures. Infection occurred in 85 of the 972 excisions; thus, the overall incidence of infection was 8.7% (95% confidence interval 6.5-11.0). Excisions in the upper (Prisk factors for wound infection. The length of the excision (Prisk factors for infection. Diabetes was not found to be an independent risk factor for infection (P=0.891). Prophylactic antibiotics are probably prescribed excessively or inappropriately for dermatological surgery, and overall we wish to discourage their use. The results of this study may encourage the more judicial use of prophylactic antibiotics by defining high-risk procedures, such as excisions from the extremities, excision of BCC or SCC, and larger excisions, and patients who are at high risk for infection, such as ex-smokers. © 2012 The International Society of Dermatology.

  1. Surgical site infection following cesarean deliveries: trends and risk factors.

    Science.gov (United States)

    Krieger, Yuval; Walfisch, Asnat; Sheiner, Eyal

    2017-01-01

    To identify trends and risk factors for early surgical site infection (SSI) following cesarean delivery (CD). A population-based study comparing characteristics of women who have and have not developed post cesarean SSI was conducted. Deliveries occurred between the years 1988 and 2013 in a tertiary medical center. A multivariable logistic regression model, with backwards elimination, was used to control for confounders. Of the 41 375 cesarean deliveries performed during the study period, 1521 (3.7%) were complicated with SSI. SSI rates significantly deceased over the years, from 7.4% in 1988 to 1.5% in 2012. Using a multivariable regression model, the following independent risk factors for SSI were identified: obesity (OR 2.0; 95% CI, 1.6-2.5); previous CD (OR 1.8; 95% CI, 1.6-2.0); hypertensive disorders (OR 1.4; 95% CI, 1.2-1.6); premature rupture of membranes (OR 1.3; 95% CI, 1.1-1.6); gestational diabetes mellitus (GDM, OR 1.2; 95% CI, 1.1-1.4); and recurrent pregnancy losses (OR 1.2; 95% CI, 1.1-1.5). Independent risk factors for post-cesarean SSI include obesity, GDM, hypertensive disorders of pregnancy, premature rupture of membranes, and recurrent pregnancy losses. Information regarding higher rates of SSI and preventative measures should be provided to these high-risk women prior to surgery.

  2. Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites.

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    Timothy E Reddy

    2007-05-01

    Full Text Available Computational prediction of nucleotide binding specificity for transcription factors remains a fundamental and largely unsolved problem. Determination of binding positions is a prerequisite for research in gene regulation, a major mechanism controlling phenotypic diversity. Furthermore, an accurate determination of binding specificities from high-throughput data sources is necessary to realize the full potential of systems biology. Unfortunately, recently performed independent evaluation showed that more than half the predictions from most widely used algorithms are false. We introduce a graph-theoretical framework to describe local sequence similarity as the pair-wise distances between nucleotides in promoter sequences, and hypothesize that densely connected subgraphs are indicative of transcription factor binding sites. Using a well-established sampling algorithm coupled with simple clustering and scoring schemes, we identify sets of closely related nucleotides and test those for known TF binding activity. Using an independent benchmark, we find our algorithm predicts yeast binding motifs considerably better than currently available techniques and without manual curation. Importantly, we reduce the number of false positive predictions in yeast to less than 30%. We also develop a framework to evaluate the statistical significance of our motif predictions. We show that our approach is robust to the choice of input promoters, and thus can be used in the context of predicting binding positions from noisy experimental data. We apply our method to identify binding sites using data from genome scale ChIP-chip experiments. Results from these experiments are publicly available at http://cagt10.bu.edu/BSG. The graphical framework developed here may be useful when combining predictions from numerous computational and experimental measures. Finally, we discuss how our algorithm can be used to improve the sensitivity of computational predictions of

  3. 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.

  4. 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.

  5. The next generation of transcription factor binding site prediction.

    Directory of Open Access Journals (Sweden)

    Anthony Mathelier

    Full Text Available Finding where transcription factors (TFs bind to the DNA is of key importance to decipher gene regulation at a transcriptional level. Classically, computational prediction of TF binding sites (TFBSs is based on basic position weight matrices (PWMs which quantitatively score binding motifs based on the observed nucleotide patterns in a set of TFBSs for the corresponding TF. Such models make the strong assumption that each nucleotide participates independently in the corresponding DNA-protein interaction and do not account for flexible length motifs. We introduce transcription factor flexible models (TFFMs to represent TF binding properties. Based on hidden Markov models, TFFMs are flexible, and can model both position interdependence within TFBSs and variable length motifs within a single dedicated framework. The availability of thousands of experimentally validated DNA-TF interaction sequences from ChIP-seq allows for the generation of models that perform as well as PWMs for stereotypical TFs and can improve performance for TFs with flexible binding characteristics. We present a new graphical representation of the motifs that convey properties of position interdependence. TFFMs have been assessed on ChIP-seq data sets coming from the ENCODE project, revealing that they can perform better than both PWMs and the dinucleotide weight matrix extension in discriminating ChIP-seq from background sequences. Under the assumption that ChIP-seq signal values are correlated with the affinity of the TF-DNA binding, we find that TFFM scores correlate with ChIP-seq peak signals. Moreover, using available TF-DNA affinity measurements for the Max TF, we demonstrate that TFFMs constructed from ChIP-seq data correlate with published experimentally measured DNA-binding affinities. Finally, TFFMs allow for the straightforward computation of an integrated TF occupancy score across a sequence. These results demonstrate the capacity of TFFMs to accurately model DNA

  6. 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)

  7. 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.

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

    African Journals Online (AJOL)

    BACKGROUND: Surgical Site infections are the second most frequently reported infections of all nosocomial infections among hospital patients. Among surgical patients in obstetrics, Surgical Site Infections were the most common nosocomial infections and the rate is higher in sub-Saharan Africa. There has not been a ...

  9. 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.

  10. 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

  11. 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

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

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    Most current methods in this field adopt a multi-step ap proach that segregates the two aspects. Again, it is widely accepted that the ... In a simulated setting, we provide a proof of concept that the approach works given the ... We study how alignments and binding site predictions interplay at varying evolutionary distances ...

  15. 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....

  16. 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.

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

    African Journals Online (AJOL)

    This process of the N cycle can therefore be considered as the rate limiting step influencing tree growth. N mineralization is controlled by a complex interaction of various site factors, and numerous correlations and interactions between NH4 + mineralization (summer) and site factors are discussed. Statistical models were ...

  18. 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.)

  19. Risk factors for surgical site infection and association with infliximab administration during surgery for Crohn's disease.

    Science.gov (United States)

    Uchino, Motoi; Ikeuchi, Hiroki; Matsuoka, Hiroki; Bando, Toshihiro; Ichiki, Kaoru; Nakajima, Kazuhiko; Tomita, Naohiro; Takesue, Yoshio

    2013-10-01

    Preoperative infliximab treatment may influence postoperative infectious complications in patients with Crohn's disease. The aim of this study was to identify predictors of surgical site infection after surgery for Crohn's disease and evaluate the effects of preoperative infliximab administration. We performed a prospective surveillance and review of surgical site infections. This study was conducted in the Surgical Department of Hyogo College of Medicine. A total of 405 consecutive patients with Crohn's disease who underwent abdominal surgery between January 2008 and December 2011 were included. Infection was diagnosed by the infection control team. The possible risk factors were analyzed by using logistic regression analyses to determine their predictive significance. Within the patient population, 20% of patients received infliximab, and 60% had penetrating disease. The median duration from the last infliximab infusion to surgery was 43 days (range, 4-80). The overall incidence of surgical site infection was 27%. The incidence of incisional surgical site infection was 18%, and the organ/space surgical site infection rate was 8%. In the multivariate analysis, proctectomy was the highest risk factor for all surgical site infection (OR, 3.4-11.8; p risk factor for surgical site infection. By contrast, there was a significantly reduced risk of incisional surgical site infection in patients with penetrating disease who received infliximab (OR, 0.1; p risk factor for surgical site infection in patients with Crohn's disease. The administration of preoperative infliximab was not a risk factor for surgical site infection.

  20. Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.

    Science.gov (United States)

    Erb, Ionas; van Nimwegen, Erik

    2011-01-01

    The availability of sequence specificities for a substantial fraction of yeast's transcription factors and comparative genomic algorithms for binding site prediction has made it possible to comprehensively annotate transcription factor binding sites genome-wide. Here we use such a genome-wide annotation for comprehensively studying promoter architecture in yeast, focusing on the distribution of transcription factor binding sites relative to transcription start sites, and the architecture of TATA and TATA-less promoters. For most transcription factors, binding sites are positioned further upstream and vary over a wider range in TATA promoters than in TATA-less promoters. In contrast, a group of 6 'proximal promoter motifs' (GAT1/GLN3/DAL80, FKH1/2, PBF1/2, RPN4, NDT80, and ROX1) occur preferentially in TATA-less promoters and show a strong preference for binding close to the transcription start site in these promoters. We provide evidence that suggests that pre-initiation complexes are recruited at TATA sites in TATA promoters and at the sites of the other proximal promoter motifs in TATA-less promoters. TATA-less promoters can generally be classified by the proximal promoter motif they contain, with different classes of TATA-less promoters showing different patterns of transcription factor binding site positioning and nucleosome coverage. These observations suggest that different modes of regulation of transcription initiation may be operating in the different promoter classes. In addition we show that, across all promoter classes, there is a close match between nucleosome free regions and regions of highest transcription factor binding site density. This close agreement between transcription factor binding site density and nucleosome depletion suggests a direct and general competition between transcription factors and nucleosomes for binding to promoters.

  1. Leveraging cross-species transcription factor binding site patterns

    DEFF Research Database (Denmark)

    Claussnitzer, Melina; Dankel, Simon N; Klocke, Bernward

    2014-01-01

    Genome-wide association studies have revealed numerous risk loci associated with diverse diseases. However, identification of disease-causing variants within association loci remains a major challenge. Divergence in gene expression due to cis-regulatory variants in noncoding regions is central...... diabetes risk loci revealed a striking clustering of distinct homeobox TFBS. We identified the PRRX1 homeobox factor as a repressor of PPARG2 expression in adipose cells and demonstrate its adverse effect on lipid metabolism and systemic insulin sensitivity, dependent on the rs4684847 risk allele...

  2. 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.

  3. Kin, daytime associations, or preferred sleeping sites? Factors influencing sleep site selection in captive chimpanzees (Pan troglodytes).

    Science.gov (United States)

    Lock, Louise C; Anderson, James R

    2013-01-01

    Chimpanzee nesting behaviours and the factors that may influence these behaviours are rarely studied in captive settings. In the present study, the daytime associations, sleeping site selections and nesting groups of 11 zoo-housed chimpanzees over a 29-day period were analysed. Neither daytime associations nor presence of kin influenced sleeping site selection in females. Daytime associations did influence sleeping arrangements in males. Nighttime spatial arrangements and individual preferences for specific sleeping areas were broadly comparable to nesting patterns reported in free-living chimpanzee communities. In the interests of captive ape welfare, we conclude that exhibits should incorporate multilevel nesting areas and a choice of several potential sleeping sites. Copyright © 2013 S. Karger AG, Basel.

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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…

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

    Science.gov (United States)

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

    2017-10-01

    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 study is the first study to account for variation in donor behaviour across different collection sites. We applied a multilevel approach to data from Donor InSight, including 11 889 donors from 257 fixed and mobile collection sites in the Netherlands. The aim of the multilevel models was to account for variance at two levels, that is donors and collection sites. We estimated the likelihood of showing after invitation based on individual predictors, including demographics, donation history and attitude. At the collection site level, we included satisfaction with the blood bank aggregated from individual responses by donors who donate at this site, opening hours and collection site type, that is fixed/mobile. Most importantly, show behaviour varied considerably across collection sites and depended on characteristics of these sites. Moreover, women, older and more experienced donors had higher odds of showing after invitation than men, younger and less experienced donors. Donors higher on warm glow, self-efficacy and donor identity more likely showed after an invitation. Higher aggregate satisfaction and donating at fixed collection sites increased the odds of show. In addition to individual factors, collection site characteristics are important in explaining variation in donor show behaviour, thus presenting clues for blood bank policies and interventions to improve donor show. © 2017 International Society of Blood Transfusion.

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

    Energy Technology Data Exchange (ETDEWEB)

    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. 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

  12. Blood coagulation factor XIa binds specifically to a site on activated human platelets distinct from that for factor XI

    International Nuclear Information System (INIS)

    Sinha, D.; Seaman, F.S.; Koshy, A.; Knight, L.C.; Walsh, P.N.

    1984-01-01

    Binding of 125 I-Factor XIa to platelets required the presence of high molecular weight kininogen, was enhanced when platelets were stimulated with thrombin, and reached a plateau after 4-6 min of incubation at 37 degrees C. Factor XIa binding was specific: 50- to 100-fold molar excesses of unlabeled Factor XIa prevented binding, whereas Factor XI, prekallikrein, Factor XIIa, and prothrombin did not. When washed erythrocytes, added at concentrations calculated to provide an equivalent surface area to platelets, were incubated with Factor XIa, only a low level of nonspecific, nonsaturable binding was detected. Factor XIa binding to platelets was partially reversible and was saturable at concentrations of added Factor XIa of 0.2-0.4 microgram/ml (1.25-2.5 microM). The number of Factor XIa binding sites on activated platelets was estimated to be 225 per platelet (range, 110-450). We conclude that specific, high affinity, saturable binding sites for Factor XIa are present on activated platelets, are distinct from those previously demonstrated for Factor XI, and require the presence of high molecular weight kininogen

  13. 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.

  14. 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

  15. 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.

  16. 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...

  17. 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

  18. 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.

  19. 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...

  20. Morbidity and risk factors for surgical site infection following cesarean section in Guangdong Province, China.

    Science.gov (United States)

    Gong, Shi-Peng; Guo, Hong-Xia; Zhou, Hong-Zhen; Chen, Li; Yu, Yan-Hong

    2012-03-01

    To estimate the incidence of and identify the risk factors for a surgical site infection after a cesarean section. A survey of women who underwent a cesarean section was conducted in eight hospitals in Guangdong Province, China. The rate of surgical site infection was estimated and a nested case control study was then carried out to identify the risk factors. Among 13 798 women surveyed, 96 (0.7%) developed a surgical site infection after a cesarean section. Multivariate logistic regression analysis identified six factors independently associated with an increased risk of surgical site infection, which included obesity, premature rupture of membranes, lower preoperative hemoglobin, prolonged surgery, lack of prophylactic antibiotics and excessive anal examinations performed during hospitalization. Surgical site infection occurs in approximately 0.7% of cesarean section cases in the general obstetric population in China. Obesity, premature rupture of membranes, lower preoperative hemoglobin, prolonged surgery, lack of prophylactic antibiotics and excessive anal examinations during hospitalization are considered to be independent risk factors. © 2012 The Authors. Journal of Obstetrics and Gynaecology Research © 2012 Japan Society of Obstetrics and Gynecology.

  1. 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....

  2. A screening system to identify transcription factors that induce binding site-directed DNA demethylation.

    Science.gov (United States)

    Suzuki, Takahiro; Maeda, Shiori; Furuhata, Erina; Shimizu, Yuri; Nishimura, Hajime; Kishima, Mami; Suzuki, Harukazu

    2017-12-08

    DNA methylation is a fundamental epigenetic modification that is involved in many biological systems such as differentiation and disease. We and others recently showed that some transcription factors (TFs) are involved in the site-specific determination of DNA demethylation in a binding site-directed manner, although the reports of such TFs are limited. Here, we develop a screening system to identify TFs that induce binding site-directed DNA methylation changes. The system involves the ectopic expression of target TFs in model cells followed by DNA methylome analysis and overrepresentation analysis of the corresponding TF binding motif at differentially methylated regions. It successfully identified binding site-directed demethylation of SPI1, which is known to promote DNA demethylation in a binding site-directed manner. We extended our screening system to 15 master TFs involved in cellular differentiation and identified eight novel binding site-directed DNA demethylation-inducing TFs (RUNX3, GATA2, CEBPB, MAFB, NR4A2, MYOD1, CEBPA, and TBX5). Gene ontology and tissue enrichment analysis revealed that these TFs demethylate genomic regions associated with corresponding biological roles. We also describe the characteristics of binding site-directed DNA demethylation induced by these TFs, including the targeting of highly methylated CpGs, local DNA demethylation, and the overlap of demethylated regions between TFs of the same family. Our results show the usefulness of the developed screening system for the identification of TFs that induce DNA demethylation in a site-directed manner.

  3. Number of osteoporotic sites as a modifying factor for bone mineral density.

    Science.gov (United States)

    Lee, Jong Seok; Lee, Sungwha; Ryu, Ohk-Hyun; Choi, Moon-Gi; Kim, Youn Ji

    2015-11-01

    Discordance has been proposed as a new predictor of fracture risk that may affect fracture risk via bone mineral density (BMD). With an emphasis on better understanding the relationship between discordance and BMD, the aim of this study was to determine the effect of the number of osteoporotic sites, as an indicator of discordance, on BMD and to explore the clinical significance of BMD modification by this factor. This study was based on data obtained from the Korea National Health and Nutrition Examination Survey 2008-2011, which is a nationwide cross-sectional study. Among postmenopausal women aged 50 years or older, 3,849 women whose BMD was measured at three sites (lumbar spine, femoral neck, and total hip) were included in the study. The diagnosis was consistent across sites in only 39.2-59.0 % of cases. Lumbar spine T-score was reduced by 0.163 for two osteoporotic sites and by 0.462 for three osteoporotic sites, compared with having one osteoporotic site at the lumbar spine only. Femoral neck T-score was reduced by 0.609 for three osteoporotic sites compared with one or two osteoporotic sites. Using BMD adjusted for discordance, we found fracture risk probability changed significantly. Our results confirmed that BMD discordance was considerably high among Korean women in their 50s and older owing to site-dependent differences in the pattern of BMD reduction with age. Mean BMD decreased with increasing number of osteoporotic sites. Using a modified BMD adjusted for the number of osteoporotic sites may offer more accurate fracture risk assessment.

  4. Risk factors for surgical site infection following cesarean delivery: a retrospective cohort study.

    Science.gov (United States)

    Ketcheson, Felicia; Woolcott, Christy; Allen, Victoria; Langley, Joanne M

    2017-07-11

    The rate of cesarean delivery is increasing in North America. Surgical site infection following this operation can make it difficult to recover, care for a baby and return home. We aimed to determine the incidence of surgical site infection to 30 days following cesarean delivery, associated risk factors and whether risk factors differed for predischarge versus postdischarge infection. We identified a retrospective cohort in Nova Scotia by linking the provincial perinatal database to hospital admissions and physician billings databases to follow women for 30 days after they had given birth by cesarean delivery between Jan. 1, 1997 and Dec. 31, 2012. Logistic regression with generalized estimating equations was used to determine risk factors for infection. A total of 25 123 women had 33 991 cesarean deliveries over the study period. Of the 25 123, 923 had surgical site infections, giving an incidence rate of 2.7% (95% CI 2.54%-2.89%); the incidence decreased over time. Risk factors for infection (adjusted odds ratios ≥ 1.5) were prepregnancy weight 87.0 kg or more, gaining 30.0 kg or more during pregnancy, chorioamnionitis, maternal blood transfusion, anticoagulation therapy, alcohol or drug abuse, second stage of labour before surgery, delivery in 1997-2000 and delivery in a hospital performing 130-1249 cesarean deliveries annually. Women who gave birth earlier in the study period, those who gave birth in a hospital with 130-949 cesarean deliveries per year and those with more than 1 fetus were at a significantly higher risk for surgical site infection before discharge; women who smoked were at significantly higher risk for surgical site infection after discharge. Most risk factors are known before delivery, and some are potentially modifiable. Although the incidence of surgical site infection decreased over time, targeted clinical and infection prevention and control interventions could further reduce the burden of illness associated with this health

  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. Risk Factors for Puncture Site Complications After Endovascular Procedures in Patients With Peripheral Arterial Disease.

    Science.gov (United States)

    Hackl, Gerald; Gary, Thomas; Belaj, Klara; Hafner, Franz; Eller, Philipp; Brodmann, Marianne

    2015-10-01

    To compare femoral access site closure techniques and to highlight risk factors for puncture site complications after lower extremity endovascular procedures. This retrospective study included 787 patients. Procedures were performed according to a standardized protocol. Puncture site complications within 24 hours were regarded as study end points. Ninety (11.5%) puncture site complications were registered. Conventional manual compression (n = 87, 11.1%) was significantly associated with puncture site complications (odds ratio [OR] 2.08, P = .03). Body mass index > 25 kg/m(2) (OR 0.54, P = .01) and prothrombin time > 70% (OR 0.38, P = .04) were protective. All bleeding occurred in procedures >45 minutes. Blood pressure >200 mm Hg and below the knee (BTK) procedures were strong predictors for access site complications (OR 4.21, P = .01 and OR 3.33, P = .02). We observed an inferiority of conventional manual compression. Age, procedure duration > 45 minutes, BTK procedures, uncontrolled hypertension, and impaired coagulation were risk factors. © The Author(s) 2015.

  8. Understanding the factors that limit restoration success on a recreation-impacted subalpine site

    Science.gov (United States)

    Catherine Zabinski; David Cole

    2000-01-01

    Factors that limit successful revegetation of a subalpine site were studied through a combination of soil assays, greenhouse studies, and field manipulations. Campsite soils had higher available nitrogen, lower microbial community diversity, and lower seed bank density than undisturbed soils. In the greenhouse, there was no significant difference in plant growth on...

  9. AthaMap: from in silico data to real transcription factor binding sites.

    Science.gov (United States)

    Bülow, Lorenz; Steffens, Nils Ole; Galuschka, Claudia; Schindler, Martin; Hehl, Reinhard

    2006-01-01

    AthaMap generates a map for cis-regulatory sequences for the whole Arabidopsis thaliana genome. AthaMap was initially developed by matrix-based detection of putative transcription factor binding sites (TFBS) mostly determined from random binding site selection experiments. Now, also experimentally verified TFBS have been included for 48 different Arabidopsis thaliana transcription factors (TF). Based on these sequences, 89,416 very similar putative TFBS were determined within the genome of A. thaliana and annotated to AthaMap. Matrix- and single sequence-based binding sites can be included in colocalization analysis for the identification of combinatorial cis-regulatory elements. As an example, putative target genes of the WRKY18 transcription factor that is involved in plant-pathogen interaction were determined. New functions of AthaMap include descriptions for all annotated Arabidopsis thaliana genes and direct links to TAIR, TIGR and MIPS. Transcription factors used in the binding site determination are linked to TAIR and TRANSFAC databases. AthaMap is freely available at http://www.athamap.de.

  10. Soil-Site Factors Affecting Southern Upland Oak Managment and Growth

    Science.gov (United States)

    John K. Francis

    1980-01-01

    Soil supplies trees with physical support, moisture, oxygen, and nutrients. Amount of moisture most limits tree growth; and soil and topographic factors such as texture and aspect, which influence available soil moisture. are most useful in predicting growth. Equations that include soil and topographic variables can be used to predict site index. Foresters can also...

  11. 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.

  12. 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.

  13. 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.

  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. 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.

  16. 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.

  17. 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.

  18. MONKEY: Identifying conserved transcription-factor binding sitesin multiple alignments using a binding site-specific evolutionarymodel

    Energy Technology Data Exchange (ETDEWEB)

    Moses, Alan M.; Chiang, Derek Y.; Pollard, Daniel A.; Iyer, VenkyN.; Eisen, Michael B.

    2004-10-28

    We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit. Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function.

  19. 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

  20. 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.

  1. Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Crichlow, G.; Lubetsky, J; Leng, L; Bucala, R; Lolis, E

    2009-01-01

    Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic data indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.

  2. Patient, Surgery, and Hospital Related Risk Factors for Surgical Site Infections following Total Hip Arthroplasty

    Directory of Open Access Journals (Sweden)

    Georgios Triantafyllopoulos

    2015-01-01

    Full Text Available Surgical site infections (SSI following total hip arthroplasty (THA have a significantly adverse impact on patient outcomes and pose a great challenge to the treating surgeon. Therefore, timely recognition of those patients at risk for this complication is very important, as it allows for adopting measures to reduce this risk. This review discusses literature reported risk factors for SSI after THA. These can be classified into patient-related factors (age, gender, obesity, comorbidities, history of infection, primary diagnosis, and socioeconomic profile, surgery-related factors (allogeneic blood transfusion, DVT prophylaxis and coagulopathy, duration of surgery, antibiotic prophylaxis, bearing surface and fixation, bilateral procedures, NNIS index score, and anesthesia type, and hospital-related factors (duration of hospitalization, institution and surgeon volume, and admission from a healthcare facility. All these factors are discussed with respect to potential measures that can be taken to reduce their effect and consequently the overall risk for infection.

  3. 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.

  4. Shorebird roost-site selection at two temporal scales: Is human disturbance a factor?

    Science.gov (United States)

    Peters, K.A.; Otis, D.L.

    2007-01-01

    1. Roost-site selection in shorebirds is governed by ambient factors, including environmental conditions and human disturbance. Determination of the extent to which these factors affect roost use and the associated implications for shorebird habitat protection is important for conservation strategies and informed management of human recreational use of these habitats. Shorebird conservation as a whole is a high priority world-wide because a large proportion of shorebird species is in decline. However, little is understood about the consistency of roost use by different species, what conditions affect species-specific roost-site selection, and at what spatial and temporal scales conditions influence selection. 2. We studied high-tide roost-site selection by eight species of non-breeding shorebirds on a critically important stopover and wintering refuge. We calculated spatial and temporal variability in roost use for each species based on counts and consistency of incidence. We then examined roost-site selection in relation to structural, environmental and human disturbance factors, and how this varied across spatial and temporal scales. 3. Most roosts were used less than 50% of the time, although larger roosts were used more consistently. This varied among species, with red knot Calidris canutus tending to concentrate at a few roosts and American oystercatcher Haematopus palliatus, dowitcher Limnodromus griseus and Limnodromus scolopaceus and ruddy turnstone Arenaria interpres more diffusely distributed among roosts. 4. At an annual scale, the principal factors affecting shorebird presence at roosts were roost length (size), local region, substrate and aspect. The extent and direction of these effects varied among species. Among years, red knots avoided roosts that had high average boat activity within 1000 m, but disturbance did not appear to be a factor for other species. 5. Daily roost use was influenced primarily by wind speed and the ability of roosts to

  5. Effect of positional dependence and alignment strategy on modeling transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Quader Saad

    2012-07-01

    Full Text Available Abstract Background Many consensus-based and Position Weight Matrix-based methods for recognizing transcription factor binding sites (TFBS are not well suited to the variability in the lengths of binding sites. Besides, many methods discard known binding sites while building the model. Moreover, the impact of Information Content (IC and the positional dependence of nucleotides within an aligned set of TFBS has not been well researched for modeling variable-length binding sites. In this paper, we propose ML-Consensus (Mixed-Length Consensus: a consensus model for variable-length TFBS which does not exclude any reported binding sites. Methods We consider Pairwise Score (PS as a measure of positional dependence of nucleotides within an alignment of TFBS. We investigate how the prediction accuracy of ML-Consensus is affected by the incorporation of IC and PS with a particular binding site alignment strategy. We perform cross-validations for datasets of six species from the TRANSFAC public database, and analyze the results using ROC curves and the Wilcoxon matched-pair signed-ranks test. Results We observe that the incorporation of IC and PS in ML-Consensus results in statistically significant improvement in the prediction accuracy of the model. Moreover, the existence of a core region among the known binding sites (of any length is witnessed by the pairwise coexistence of nucleotides within the core length. Conclusions These observations suggest the possibility of an efficient multiple sequence alignment algorithm for aligning TFBS, accommodating known binding sites of any length, for optimal (or near-optimal TFBS prediction. However, designing such an algorithm is a matter of further investigation.

  6. Incidence and risk factors of surgical site infection following cesarean section at Dhulikhel Hospital.

    Science.gov (United States)

    Shrestha, S; Shrestha, R; Shrestha, B; Dongol, A

    2014-01-01

    Cesarean Section (CS) is one of the most commonly performed surgical procedures in obstetrical and gynecological department. Surgical site infection (SSI) after a cesarean section increases maternal morbidity prolongs hospital stay and medical costs. The aim of this study was to find out the incidence and associated risk factors of surgical site infection among cesarean section cases. A prospective, descriptive study was conducted at Dhulikhel Hospital, department of Obstetrics and Gynaecology from July 2013 to June 2014. Total of 648 women who underwent surgical procedure for delivery during study period were included in the study. Data was collected from patient using structred pro forma and examination of wound till discharge was done. Data was compared in terms of presence of surgical site infection and study variables. Wound was evaluated for the development of SSI on third day, and fifth post-operative day, and on the day of discharge. Total of 648 cases were studied. The mean age was 24±4.18. Among the studied cases 92% were literate and 8% were illiterate. Antenatal clinic was attended by 97.7%. The incidence rate of surgical site infection was 82 (12.6%). SSI was found to be common in women who had rupture of membrane before surgery (p=0.020), who underwent emergency surgery (p=0.0004), and the women who had vertical skin incision (p=0.0001) and interrupted skin suturing (p=0.0001) during surgery. Surgical site infection following caesarean section is common. Various modifiable risk factors were observed in this study. Development of SSI is related to multifactorial rather than one factor. Development and strict implementation of protocol by all the health care professionals could be effective to minimize and prevent the infection rate after caesarean section.

  7. Biophysical Models of Evolution: Application to Transcription Factor Binding Sites in Yeast

    Science.gov (United States)

    Manhart, Michael; Haldane, Allan; Morozov, Alexandre

    2012-02-01

    There has been growing interest in understanding the physical driving forces of evolution at the molecular scale, in particular how biophysics determines the fitness landscapes that shape the evolution of DNA and proteins. To that end we study a model of molecular evolution that explicitly incorporates the underlying biophysics. Using population genetics, we derive a steady-state distribution of monomorphic populations evolving on an arbitrary fitness landscape. Compared to previous studies, we find this result is universal for a large class of population models and fully incorporates both stochastic effects and strong natural selection. This distribution can then be used to infer the underlying fitness landscape from genomic data. This model can be applied to a variety of systems, but we focus on transcription factor binding sites, which play a crucial role in gene regulatory networks. Since these sites must be bound for successful gene regulation, we consider a simple thermodynamic model of fitness as a function of the free energy for binding a transcription factor at the site. Using empirical energy matrices and genome-wide sets of binding sites from the yeast Saccharomyces cerevisiae, we use this model to infer the role of DNA-protein interaction physics in evolution.

  8. An Empirical Examination of Factors Affecting Continuance Intention Towards Social Networking Sites

    OpenAIRE

    Abed, Salma,

    2016-01-01

    Part 3: Adoption and Diffusion; International audience; This study examines the factors that affect consumer continuance intention to use social networking sites as a business tool. Using the Technology Acceptance Model (TAM) as the theoretical framework, the researcher tested the research model and related hypotheses using structural equation modelling. The results from a survey of 304 Facebook users in Saudi Arabia indicate that trust, perceived usefulness, and perceived enjoyment had signi...

  9. Postdischarge surveillance following cesarean section: the incidence of surgical site infection and associated factors.

    Science.gov (United States)

    Cardoso Del Monte, Meire Celeste; Pinto Neto, Aarão Mendes

    2010-08-01

    The rate of surgical site infections (SSI) and their associated risk factors was identified by performing postdischarge surveillance following cesarean section at a public university teaching hospital in Brazil. The study was conducted at the Center for Women's Integrated Health Care in Brazil between May 2008 and March 2009. Women were contacted by telephone 15 and 30 days after cesarean section. During hospitalization, a form was completed on factors associated with post-cesarean SSI. The chi(2) test and Fisher exact test were used to analyze categorical variables and the Mann-Whitney test for numerical variables. Relative risks (RR) and their respective 95% confidence intervals (95% CI) were calculated for factors associated with SSI. P values cesarean section SSI. A 15-day postdischarge follow-up was shown to be sufficient. Hypertension was a factor associated with SSI. Copyright 2010 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

  10. Generation of a synthetic mammalian promoter library by modification of sequences spacing transcription factor binding sites

    DEFF Research Database (Denmark)

    Tornøe, Jens; Kusk, P.; Johansen, T.E.

    2002-01-01

    promoters. The JeT promoter was made by separating the included consensus boxes by the same distances in base pairs as found in the wild-type promoters, thus preserving transcription factor interaction. The resulting promoter was shown to drive reporter expression to high levels in enhanced green...... fluorescent protein and secreted alkaline phosphatase reporter assays. By replacing sequences separating the transcription factor binding sites with randomized sequences of the same length, sets of new promoters with different strengths, spanning a 10-fold range of transcriptional activity in cell culture...

  11. Site-directed enzymatic PEGylation of the human granulocyte colony-stimulating factor.

    Science.gov (United States)

    Maullu, Carlo; Raimondo, Domenico; Caboi, Francesca; Giorgetti, Alejandro; Sergi, Mauro; Valentini, Maria; Tonon, Giancarlo; Tramontano, Anna

    2009-11-01

    Poly(ethylene glycol) (PEG) is a widely used polymer employed to increase the circulating half-life of proteins in blood and to decrease their immunogenicity and antigenicity. PEG attaches to free amines, typically at lysine residues or at the N-terminal amino acid. This lack of selectivity can present problems when a PEGylated protein therapeutic is being developed, because predictability of activity and manufacturing reproducibility are needed for regulatory approval. Enzymatic modification of proteins is one route to overcome this limitation. Bacterial transglutaminases are enzyme candidates for site-specific modification, but they also have rather broad specificity. The need arises to be able to predict a priori potential PEGylation sites on the protein of interest and, especially, to be able to design mutants where unique PEGylation sites can be introduced when needed. We investigated the feasibility of a computational approach to the problem, using human granulocyte colony-stimulating factor as a test case. The selected protein is therapeutically relevant and represents a challenging problem, as it contains 17 potential PEGylation sites. Our results show that a combination of computational methods allows the identification of the specific glutamines that are substrates for enzymatic PEGylation by a microbial transglutaminase, and that it is possible to rationally modify the protein and introduce PEG moieties at desired sites, thus allowing the selection of regions that are unlikely to interfere with the biological activity of a therapeutic protein.

  12. 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/.

  13. 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.

  14. Contributing factors in restaurant-associated foodborne disease outbreaks, FoodNet sites, 2006 and 2007.

    Science.gov (United States)

    Gould, L Hannah; Rosenblum, Ida; Nicholas, David; Phan, Quyen; Jones, Timothy F

    2013-11-01

    An estimated 48 million cases of foodborne illness occur each year in the United States, resulting in approximately 128,000 hospitalizations and 3,000 deaths. Over half of all foodborne disease outbreaks reported to the Centers for Disease Control and Prevention are associated with eating in restaurants or delicatessens. We reviewed data from restaurant-associated foodborne disease outbreaks to better understand the factors that contribute to these outbreaks. Data on restaurant-associated foodborne disease outbreaks reported by sites participating in the Foodborne Diseases Active Surveillance Network (FoodNet) were analyzed to characterize contributing factors reported in foodborne disease outbreaks and the levels of evidence used to identify these factors. Of 457 foodborne disease outbreaks reported in 2006 and 2007 by FoodNet sites, 300 (66%) were restaurant associated, and of these 295 (98%) had at least one reported contributing factor. One to nine (with a median of two) contributing factors were reported per outbreak. Of the 257 outbreaks with a single etiology reported, contributing factors associated with food worker health and hygiene were reported for 165 outbreaks (64%), factors associated with food preparation practices within the establishment were reported for 88 outbreaks (34%), and factors associated with contamination introduced before reaching the restaurant were reported for 56 outbreaks (22%). The pronounced role of food workers in propagating outbreaks makes it clear that more work is needed to address prevention at the local level. Food workers should be instructed not to prepare food while ill to prevent the risk of transmitting pathogens.

  15. Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites.

    Science.gov (United States)

    Hosseini, Parsa; Ovcharenko, Ivan; Matthews, Benjamin F

    2013-04-11

    From initial seed germination through reproduction, plants continuously reprogram their transcriptional repertoire to facilitate growth and development. This dynamic is mediated by a diverse but inextricably-linked catalog of regulatory proteins called transcription factors (TFs). Statistically quantifying TF binding site (TFBS) abundance in promoters of differentially expressed genes can be used to identify binding site patterns in promoters that are closely related to stress-response. Output from today's transcriptomic assays necessitates statistically-oriented software to handle large promoter-sequence sets in a computationally tractable fashion. We present Marina, an open-source software for identifying over-represented TFBSs from amongst large sets of promoter sequences, using an ensemble of 7 statistical metrics and binding-site profiles. Through software comparison, we show that Marina can identify considerably more over-represented plant TFBSs compared to a popular software alternative. Marina was used to identify over-represented TFBSs in a two time-point RNA-Seq study exploring the transcriptomic interplay between soybean (Glycine max) and soybean rust (Phakopsora pachyrhizi). Marina identified numerous abundant TFBSs recognized by transcription factors that are associated with defense-response such as WRKY, HY5 and MYB2. Comparing results from Marina to that of a popular software alternative suggests that regardless of the number of promoter-sequences, Marina is able to identify significantly more over-represented TFBSs.

  16. 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.

  17. 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.

  18. Estimation of site-specific deposition velocities and mass interception factor using 7Be and the prediction of deposition pattern of radionuclides at Kaiga site (India)

    International Nuclear Information System (INIS)

    James, J. P.; Ravi, P. M.; Joshi, R. M.; Hegde, A. G.; Sarkar, P. K.

    2010-01-01

    Site-specific wet, dry deposition velocities and mass interception factors at Kaiga site, where three PHWR type power plants are operational, using 7 Be as a tracer are presented. Mean wet and dry deposition velocities for Kaiga site were found to be 7.4x10 -2 m s -1 and 3.0x10 -4 m s -1 , respectively. Mass interception factors for vegetation were found to be 0.7-5.6 m 2 kg -1 dry weight with a mean of 2.4 m 2 kg -1 dry weight. The site-specific data were used for the prediction of radionuclide distribution pattern in soil and vegetation in the case of a hypothetical air contamination. (authors)

  19. GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments.

    Science.gov (United States)

    Yevshin, Ivan; Sharipov, Ruslan; Valeev, Tagir; Kel, Alexander; Kolpakov, Fedor

    2017-01-04

    GTRD-Gene Transcription Regulation Database (http://gtrd.biouml.org)-is a database of transcription factor binding sites (TFBSs) identified by ChIP-seq experiments for human and mouse. Raw ChIP-seq data were obtained from ENCODE and SRA and uniformly processed: (i) reads were aligned using Bowtie2; (ii) ChIP-seq peaks were called using peak callers MACS, SISSRs, GEM and PICS; (iii) peaks for the same factor and peak callers, but different experiment conditions (cell line, treatment, etc.), were merged into clusters; (iv) such clusters for different peak callers were merged into metaclusters that were considered as non-redundant sets of TFBSs. In addition to information on location in genome, the sets contain structured information about cell lines and experimental conditions extracted from descriptions of corresponding ChIP-seq experiments. A web interface to access GTRD was developed using the BioUML platform. It provides: (i) browsing and displaying information; (ii) advanced search possibilities, e.g. search of TFBSs near the specified gene or search of all genes potentially regulated by a specified transcription factor; (iii) integrated genome browser that provides visualization of the GTRD data: read alignments, peaks, clusters, metaclusters and information about gene structures from the Ensembl database and binding sites predicted using position weight matrices from the HOCOMOCO database. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. 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.

  1. Human factors in environmental management: New directions from the Hanford Site

    Energy Technology Data Exchange (ETDEWEB)

    Wise, J.A.; Savage, S.F.

    1992-10-01

    Environmental management is the general term given to modern attempts to seek technological solutions to certain constrained environmental problems. it involves developing and applying new technologies that respond to changes in environmental policy. It does not eliminate the need for environmental ethics'' in society. Nor does it substitute for the fundamental changes in political and social structures that are needed for dealing with large-scale environmental issues. The scope of these issues can be illustrated by looking at the Hanford Site. Since 1943, the 560-square-mile Hanford Site in southeastern Washington state has been the production source of much of the nuclear weapons-grade radioactive materials for the United States. The legacy of 50 years of producing fissile materials has been an environmental cleanup problem of impressive proportions. In 1989, with the Cold War winding down, Secretary of Energy James Watkins established a new vision for Hanford as the flagship for waste management research.'' As plans and preparations for cleanup work proceed at the Hanford Site and around the world, the need for well-orchestrated environmental management methodologies has become increasingly apparent. In 1990, a Human Factors Engineering Group was established in the Technology Planning and Analysis Center at PNL to provide appropriate support for the Laboratory's research efforts. At an ever-increasing rate, these research efforts require integrating human performance into complex environmental technology systems. The endeavor of responding to the Laboratory's research needs has provided innovative opportunities for the application of the concept of Human Factors. Discussed are some of the major applications of Human Factors to environmental management.

  2. 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....... 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. METHODS: 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...

  3. 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

  4. Surgical site infection after cesarean delivery: incidence and risk factors at a US academic institution.

    Science.gov (United States)

    Moulton, Laura J; Munoz, Jessian L; Lachiewicz, Mark; Liu, Xiaobo; Goje, Oluwatosin

    2017-06-08

    To identify the rate of surgical site infection (SSI) after Cesarean delivery (CD) and determine risk factors predictive for infection at a large academic institution. This was a retrospective cohort study in women undergoing CD during 2013. SSIs were defined by Centers for Disease Control (CDC) criteria. Chi square and t-tests were used for bivariate analysis and multivariate logistic regression was used to identify SSI risk factors. In 2419 patients, the rate of SSI was 5.5% (n = 133) with cellulitis in 4.9% (n = 118), deep incisional infection in 0.6% (n = 15) and intra-abdominal infection in 0.3% (n = 7). On multivariate analysis, SSI was higher among CD for labor arrest (OR 2.4; 95%CI 1.6-3.5; p infection control interventions.

  5. An assessment of different atmospheric stability methods for annual atmospheric dispersion factors at a coastal site

    International Nuclear Information System (INIS)

    Bagavathsingh, A.; Rakesh, P.T.; Srinivas, C.V.; Baskaran, R.; Venkatraman, B.

    2018-01-01

    The meteorological data is used for routine radiological release consequence analysis, real time consequence assessments of accidental releases of radiological effluents and design basis accidental analysis in a nuclear plant site. For dispersion estimate, it is often required to specify the type of stability and/or turbulence conditions in which diffusion of pollutants would occur. Stability indicates the degree of turbulence and thus the atmospheric mixing. Intensity of turbulence and dispersion of pollutant releases in to the lower atmosphere are strongly dependent on the local winds as well as resistance of atmosphere to vertical mixing which is called atmospheric stability. Three different methods of atmospheric stability based on Standard deviation of wind direction (σθ), temperature gradient and Bulk Richardson (Rib) number are used to compute stability over Kalpakkam site using hourly meteorological data. All the three methods of estimating atmospheric stability are compared with M-O similarity based method. Different atmospheric stability methods were analyzed to estimate the annual average atmospheric dispersion factors at Kalpakkam coastal site for the year 2016

  6. 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.

  7. 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.

  8. 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.

  9. Ab initio identification of putative human transcription factor binding sites by comparative genomics

    Directory of Open Access Journals (Sweden)

    Provero P

    2005-05-01

    Full Text Available Abstract Background Understanding transcriptional regulation of gene expression is one of the greatest challenges of modern molecular biology. A central role in this mechanism is played by transcription factors, which typically bind to specific, short DNA sequence motifs usually located in the upstream region of the regulated genes. We discuss here a simple and powerful approach for the ab initio identification of these cis-regulatory motifs. The method we present integrates several elements: human-mouse comparison, statistical analysis of genomic sequences and the concept of coregulation. We apply it to a complete scan of the human genome. Results By using the catalogue of conserved upstream sequences collected in the CORG database we construct sets of genes sharing the same overrepresented motif (short DNA sequence in their upstream regions both in human and in mouse. We perform this construction for all possible motifs from 5 to 8 nucleotides in length and then filter the resulting sets looking for two types of evidence of coregulation: first, we analyze the Gene Ontology annotation of the genes in the set, searching for statistically significant common annotations; second, we analyze the expression profiles of the genes in the set as measured by microarray experiments, searching for evidence of coexpression. The sets which pass one or both filters are conjectured to contain a significant fraction of coregulated genes, and the upstream motifs characterizing the sets are thus good candidates to be the binding sites of the TF's involved in such regulation. In this way we find various known motifs and also some new candidate binding sites. Conclusion We have discussed a new integrated algorithm for the "ab initio" identification of transcription factor binding sites in the human genome. The method is based on three ingredients: comparative genomics, overrepresentation, different types of coregulation. The method is applied to a full-scan of the

  10. 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".

  11. 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

  12. 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

  13. Factors influencing clinical trial site selection in Europe: the Survey of Attitudes towards Trial sites in Europe (the SAT-EU Study).

    Science.gov (United States)

    Gehring, Marta; Taylor, Rod S; Mellody, Marie; Casteels, Brigitte; Piazzi, Angela; Gensini, Gianfranco; Ambrosio, Giuseppe

    2013-11-15

    Applications to run clinical trials in Europe fell 25% between 2007 and 2011. Costs, speed of approvals and shortcomings of European Clinical Trial Directive are commonly invoked to explain this unsatisfactory performance. However, no hard evidence is available on the actual weight of these factors or has it been previously investigated whether other criteria may also impact clinical trial site selection. The Survey of Attitudes towards Trial sites in Europe (SAT-EU Study) was an anonymous, cross-sectional web-based survey that systematically assessed factors impacting European clinical trial site selection. It explored 19 factors across investigator-driven, hospital-driven and environment-driven criteria, and costs. It also surveyed perceptions of the European trial environment. Clinical research organisations (CROs), academic clinical trial units (CTUs) and industry invited to respond. weight assigned to each factor hypothesised to impact trial site selection and trial incidence. Secondary outcome: desirability of European countries to run clinical trials. Responses were obtained from 485 professionals in 34 countries: 49% from BioPharma, 40% from CTUs or CROs. Investigator-dependent, environment-dependent and hospital-dependent factors were rated highly important, costs being less important (p<0.0001). Within environment-driven criteria, pool of eligible patients, speed of approvals and presence of disease-management networks were significantly more important than costs or government financial incentives (p<0.0001). The pattern of response was consistent across respondent groupings (CTU vs CRO vs industry). Considerable variability was demonstrated in the perceived receptivity of countries to undertake clinical trials, with Germany, the UK and the Netherlands rated the best trial markets (p<0.0001). Investigator-dependent factors and ease of approval dominate trial site selection, while costs appear less important. Fostering competitiveness of European clinical

  14. 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.

  15. 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

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

    Directory of Open Access Journals (Sweden)

    Li Wenhua

    2012-07-01

    Full Text Available Abstract Background To explore the outcomes and prognostic factors of ovarian metastasectomy intervention on overall survival from extragenital primary cancer. Methods 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. Results 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

  17. 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 ...

  18. Risk factors for cesarean surgical site infections at a Thai-Myanmar border hospital.

    Science.gov (United States)

    Assawapalanggool, Srisuda; Kasatpibal, Nongyao; Sirichotiyakul, Supatra; Arora, Rajin; Suntornlimsiri, Watcharin

    2016-09-01

    Cesarean surgical site infections (SSIs) are a major challenge in Thai-Myanmar border hospital settings. This study aimed to examine risk factors for SSIs after cesarean section. This was a prospective cohort study conducted in a Thai-Myanmar border hospital between January 2007 and December 2012. Data were collected from the medical record database by trained infection control nurses. Stepwise multivariable logistic regression was used for risk factor analysis and expressed as a risk ratio (RR). The cesarean SSI rate was 5.9% (293 SSIs in 4,988 cases). Of these, 17.1% were incisional SSIs (10.9% superficial and 6.2% deep incisional SSIs), and 82.9% were organ or space SSIs. Risk factors for cesarean organ-space SSIs included a wound class ≥3 (RR, 4.82; 95% confidence interval [CI], 3.41-6.83), ethnic minority (RR, 2.51; 95% CI, 1.61-3.92), hemoglobin Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

  19. Surgical Site Infection following Cesarean Delivery: Patient, Provider, and Procedure-Specific Risk Factors.

    Science.gov (United States)

    Shree, Raj; Park, Seo Young; Beigi, Richard H; Dunn, Shannon L; Krans, Elizabeth E

    2016-01-01

    This study aims to identify risk factors for cesarean delivery (CD) surgical site infection (SSI). study design: Retrospective analysis of 2,739 CDs performed at the University of Pittsburgh in 2011. CD SSIs were defined using National Healthcare Safety Network (NHSN) criteria. Chi-square test and t-test were used for bivariate analyses and multivariate logistic regression was used to identify SSI risk factors. Of 2,739 CDs, 178 (6.5%) were complicated by SSI. Patients with a SSI were more likely to have Medicaid, have resident physicians perform the CD, an American Society of Anesthesiologists (ASA) class of ≥ 3, chorioamnionitis, tobacco use, and labor before CD. In multivariable analysis, labor (odds ratio [OR], 2.35; 95% confidence interval [95% CI], 1.65-3.38), chorioamnionitis (OR, 2.24; 95% CI, 1.25-3.83), resident teaching service (OR, 2.15; 95% CI, 1.54-3.00), tobacco use (OR, 1.70; 95% CI, 1.04-2.70), ASA class ≥ 3 (OR, 1.61; 95% CI, 1.06-2.39), and CDs performed for nonreassuring fetal status (OR, 0.43; 95% CI, 0.26-0.67) were significantly associated with CD SSI. Multiple patient, provider, and procedure-specific risk factors contribute to CD SSI risk which may be targeted in infection-control efforts. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  20. Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis.

    Science.gov (United States)

    Hu, Jianqiang; Wang, Dongmei; Li, Jing; Jing, Gongchao; Ning, Kang; Xu, Jian

    2014-06-26

    Nannochloropsis spp. are a group of oleaginous microalgae that harbor an expanded array of lipid-synthesis related genes, yet how they are transcriptionally regulated remains unknown. Here a phylogenomic approach was employed to identify and functionally annotate the transcriptional factors (TFs) and TF binding-sites (TFBSs) in N. oceanica IMET1. Among 36 microalgae and higher plants genomes, a two-fold reduction in the number of TF families plus a seven-fold decrease of average family-size in Nannochloropsis, Rhodophyta and Chlorophyta were observed. The degree of similarity in TF-family profiles is indicative of the phylogenetic relationship among the species, suggesting co-evolution of TF-family profiles and species. Furthermore, comparative analysis of six Nannochloropsis genomes revealed 68 "most-conserved" TFBS motifs, with 11 of which predicted to be related to lipid accumulation or photosynthesis. Mapping the IMET1 TFs and TFBS motifs to the reference plant TF-"TFBS motif" relationships in TRANSFAC enabled the prediction of 78 TF-"TFBS motif" interaction pairs, which consisted of 34 TFs (with 11 TFs potentially involved in the TAG biosynthesis pathway), 30 TFBS motifs and 2,368 regulatory connections between TFs and target genes. Our results form the basis of further experiments to validate and engineer the regulatory network of Nannochloropsis spp. for enhanced biofuel production.

  1. 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.

  2. 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.

  3. 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.

  4. Prevalence of disability and associated factors in Dabat Health and Demographic Surveillance System site, northwest Ethiopia

    Directory of Open Access Journals (Sweden)

    Mulugeta Bayisa Chala

    2017-10-01

    Full Text Available Abstract Background Despite the high burden of disability in Ethiopia, little is known about it, particularly in the study area. Hence, this study aimed to investigate the prevalence and factors associated with disability at Dabat Health and Demographic Surveillance System (HDSS site, northwest Ethiopia. Method A population-based study was conducted from October to December 2014 at Dabat HDSS site. A total of 67,395 people were included in the study. The multivariable binary logistic regression analysis was employed to identify factors associated with disability. The Adjusted Odds Ratio (AOR with a 95% Confidence Interval (CI was estimated to show the strength of association. A p-value of <0.05 was used to declare statistical significance. Results One thousand two hundred twenty-eight individuals were reported to have a disability giving a prevalence rate of 1.82%, of which, about 39% was related to a vision disability. The high odds of disability were observed among the elderly (≥50 years [AOR: 4.49; 95% CI: 1.95, 10.33], severely food in-secured [AOR: 2.11; 95% CI: 1.59, 2.80], and separated marital status [AOR: 7.52; 95% CI: 1.18, 47.84]. While having a paid job [AOR: 0.46; 95% CI: 0.28, 0.77], being in the richest quintile [AOR: 0.55; 95% CI: 0.41, 0.75], and high engagement in work-related physical activities [AOR: 0.36; 95% CI: 0.27, 0.49] were inversely associated with the disability. Conclusion Disability is a major public health problem, and the burden is noticeable in the study area. Vision disability is the highest of all disabilities. Thus, efforts must be made on educating the public about disability and injury prevention. Measures that reduce disability should target the elderly, the poorer and the unemployed segment of the population.

  5. Prevalence of disability and associated factors in Dabat Health and Demographic Surveillance System site, northwest Ethiopia.

    Science.gov (United States)

    Chala, Mulugeta Bayisa; Mekonnen, Solomon; Andargie, Gashaw; Kebede, Yigzaw; Yitayal, Mezgebu; Alemu, Kassahun; Awoke, Tadesse; Wubeshet, Mamo; Azmeraw, Temesgen; Birku, Melkamu; Tariku, Amare; Gebeyehu, Abebaw; Shimeka, Alemayehu; Gizaw, Zemichael

    2017-10-02

    Despite the high burden of disability in Ethiopia, little is known about it, particularly in the study area. Hence, this study aimed to investigate the prevalence and factors associated with disability at Dabat Health and Demographic Surveillance System (HDSS) site, northwest Ethiopia. A population-based study was conducted from October to December 2014 at Dabat HDSS site. A total of 67,395 people were included in the study. The multivariable binary logistic regression analysis was employed to identify factors associated with disability. The Adjusted Odds Ratio (AOR) with a 95% Confidence Interval (CI) was estimated to show the strength of association. A p-value of <0.05 was used to declare statistical significance. One thousand two hundred twenty-eight individuals were reported to have a disability giving a prevalence rate of 1.82%, of which, about 39% was related to a vision disability. The high odds of disability were observed among the elderly (≥50 years) [AOR: 4.49; 95% CI: 1.95, 10.33], severely food in-secured [AOR: 2.11; 95% CI: 1.59, 2.80], and separated marital status [AOR: 7.52; 95% CI: 1.18, 47.84]. While having a paid job [AOR: 0.46; 95% CI: 0.28, 0.77], being in the richest quintile [AOR: 0.55; 95% CI: 0.41, 0.75], and high engagement in work-related physical activities [AOR: 0.36; 95% CI: 0.27, 0.49] were inversely associated with the disability. Disability is a major public health problem, and the burden is noticeable in the study area. Vision disability is the highest of all disabilities. Thus, efforts must be made on educating the public about disability and injury prevention. Measures that reduce disability should target the elderly, the poorer and the unemployed segment of the population.

  6. Membrane-associated transcription factor peptidase, site-2 protease, antagonizes ABA signaling in Arabidopsis.

    Science.gov (United States)

    Zhou, Shun-Fan; Sun, Le; Valdés, Ana Elisa; Engström, Peter; Song, Ze-Ting; Lu, Sun-Jie; Liu, Jian-Xiang

    2015-10-01

    Abscisic acid plays important roles in maintaining seed dormancy while gibberellins (GA) and other phytohormones antagonize ABA to promote germination. However, how ABA signaling is desensitized during the transition from dormancy to germination is still poorly understood. We functionally characterized the role of membrane-associated transcription factor peptidase, site-2 protease (S2P), in ABA signaling during seed germination in Arabidopsis. Genetic analysis showed that loss-of-function of S2P conferred high ABA sensitivity during seed germination, and expression of the activated form of membrane-associated transcription factor bZIP17, in which the transmembrane domain and endoplasmic reticulum (ER) lumen-facing C-terminus were deleted, in the S2P mutant rescued its ABA-sensitive phenotype. MYC and green fluorescent protein (GFP)-tagged bZIP17 were processed and translocated from the ER to the nucleus in response to ABA treatment. Furthermore, genes encoding negative regulators of ABA signaling, such as the transcription factor ATHB7 and its target genes HAB1, HAB2, HAI1 and AHG3, were up-regulated in seeds of the wild-type upon ABA treatment; this up-regulation was impaired in seeds of S2P mutants. Our results suggest that S2P desensitizes ABA signaling during seed germination through regulating the activation of the membrane-associated transcription factor bZIP17 and therefore controlling the expression level of genes encoding negative regulators of ABA signaling. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  7. 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.

  8. 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.

  9. Surgical site infection after liver transplantation: risk factors and association with graft loss or death.

    Science.gov (United States)

    Hellinger, Walter C; Crook, Julia E; Heckman, Michael G; Diehl, Nancy N; Shalev, Jefree A; Zubair, Abba C; Willingham, Darrin L; Hewitt, Winston R; Grewal, Hani P; Nguyen, Justin H; Hughes, Christopher B

    2009-05-15

    Risk factors for surgical site infection (SSI) after liver transplantation and outcomes associated with these infections have not been assessed using consensus surveillance and optimal analytic methods. A cohort study was performed of patients undergoing first liver transplantation at Mayo Clinic, Jacksonville, Florida, in 2003 and 2004. SSIs were identified by definitions and methods of the National Nosocomial Infections Surveillance System. Measures of known or suspected risk factors for SSI, graft loss, or death were collected on all patients. Associations of SSI with these factors and also with the primary composite endpoint of graft loss or death within 1 year of liver transplantation were examined using Cox proportional hazards models; relative risks (RRs) were estimated along with 95% confidence intervals (CIs). Of 370 patients, 66 (18%) had SSI and 57 (15%) died or sustained graft loss within 1 year after liver transplantation. Donor liver mass-to-recipient body mass ratio of less than 0.01 (RR 2.56; 95% CI 1.17-5.62; P=0.019) and increased operative time (RR 1.19 [1-hr increase]; 95% CI 1.03-1.37; P=0.018) were associated with increased SSI risk. SSI was associated with increased risk of death or graft loss within the first year after liver transplantation (RR 3.06; 95% CI 1.66-5.64; P<0.001). SSI is associated with increased risk of death or graft loss during the first year after liver transplantation. Increased operative time and decreased donor liver-to-recipient body mass ratio showed evidence of association with SSI.

  10. Surgical site infection rates and risk factors in orthopedic pediatric patients in Madrid, Spain.

    Science.gov (United States)

    Viqueira, Almudena Quintás; Caravaca, Gil Rodríguez; Quesada Rubio, José Antonio; Francés, Victoria Soler

    2014-07-01

    The objective of the study is to study surgical site infection (SSI) rates and risk factors in a pediatric population. We conducted a prospective cohort study to estimate the SSI rate at a national pediatric referral center, covering all patients managed at the Orthopedic Surgery Department of the Niño Jesús Children's University Teaching Hospital from January 2010 through December 2012. Risk factors and antibiotic prophylaxis were monitored. A comparison between Spanish and US data was performed, with a breakdown by National Nosocomial Infection Surveillance risk indices. We also conducted a comparative study of SSI rates from 2010 to 2012 to assess the impact of the epidemiologic surveillance system. The study population of 1079 patients had a SSI rate of 2.8%. SSI rates were calculated for spinal fusion and other musculoskeletal procedures according to the National Nosocomial Infection Surveillance risk index. In the case of other musculoskeletal procedures, our SSI rates were 0.8 times lower than the overall Spanish rate, but higher than US rates for all risk categories. For spinal fusion procedures, our SSI rates were 1.2 times higher than the Spanish rates and 3.5 times higher than National Nosocomial Infection Surveillance rates. This latter finding should be interpreted with caution because it was based on a small sample. The multivariate analysis indicated that the only predictive factors of SSI were American Society of Anesthesiologists score and age. The surveillance program showed that for clean procedures, SSI incidence decreased from 4% in 2010 to 3.2% in 2011 and to 2.4% in 2012.

  11. Surgical site infection after total en bloc spondylectomy: risk factors and the preventive new technology.

    Science.gov (United States)

    Hayashi, Hiroyuki; Murakami, Hideki; Demura, Satoru; Kato, Satoshi; Yoshioka, Katsuhito; Shinmura, Kazuya; Yokogawa, Noriaki; Ishii, Takayoshi; Fang, Xiang; Shirai, Toshiharu; Tsuchiya, Hiroyuki

    2015-01-01

    Surgical site infection (SSI) associated with instruments remains a serious and common complication in patients who undergo total en bloc spondylectomy (TES). It is very important that the risk factors for SSI are known to prevent it. The purpose of the study was to identify independent risk factors for SSI after TES and evaluate the positive effect of iodine-supported spinal instruments in the prevention of SSI after TES. This is a retrospective clinical study. One hundred twenty-five patients who underwent TES for vertebral tumor were evaluated. Incidence rate of SSI, risk factors for SSI after TES, and safety of iodine-supported spinal instruments were the outcome measures. Risk factors for SSI were analyzed using logistic regression. In recent 69 patients with iodine-supported spinal instruments, the thyroid hormone levels in the blood were examined to confirm if iodine from the implant influenced thyroid function. Postoperative radiological evaluations were performed regularly. The rate of SSI was 6.4% (8/125 patients). By multivariate logistic regression, combined anterior and posterior approach and nonuse of iodine-supported spinal instruments were associated with an increased risk of SSI. The rate of SSI without iodine-supported spinal instruments was 12.5%, whereas the rate with iodine-supported spinal instruments was 1.4%. This difference was statistically significant. There were no detected abnormalities of thyroid gland function with the use of iodine-supported instruments. Among the 69 patients with iodine-supported spinal instruments, 2 patients required additional surgery because of instrument failure. However, there were no obvious involvements with the use of iodine-supported spinal instruments. This study identified combined anterior and posterior approach and nonuse of iodine-supported spinal instruments to be independent risk factors for SSI after TES. Iodine-supported spinal instrument was extremely effective for prevention of SSI in patients

  12. Risk factors for surgical site infection after low transverse cesarean section.

    Science.gov (United States)

    Olsen, Margaret A; Butler, Anne M; Willers, Denise M; Devkota, Preetishma; Gross, Gilad A; Fraser, Victoria J

    2008-06-01

    Independent risk factors for surgical site infection (SSI) after cesarean section have not been well documented, despite the large number of cesarean sections performed and the relatively common occurrence of SSI. To determine independent risk factors for SSI after low transverse cesarean section. Retrospective case-control study. Barnes-Jewish Hospital, a 1,250-bed tertiary care hospital. A total of 1,605 women who underwent low transverse cesarean section during the period from July 1999 to June 2001. Using the International Classification of Diseases, Ninth Revision, Clinical Modification diagnosis codes for SSI or wound complication and/or data on antibiotic use during the surgical hospitalization or at readmission to the hospital or emergency department, we identified potential cases of SSI in a cohort of patients who underwent a low transverse cesarean section. Cases of SSI were verified by chart review using the definitions from the Centers for Disease Control and Prevention's National Nosocomial Infections Surveillance System. Control patients without SSI or endomyometritis were randomly selected from the population of patients who underwent cesarean section. Independent risk factors for SSI were determined by logistic regression. SSIs were identified in 81 (5.0%) of 1,605 women who underwent low transverse cesarean section. Independent risk factors for SSI included development of subcutaneous hematoma after the procedure (adjusted odds ratio [aOR], 11.6 [95% confidence interval [CI], 4.1-33.2]), operation performed by the university teaching service (aOR, 2.7 [95% CI, 1.4-5.2]), and a higher body mass index at admission (aOR, 1.1 [95% CI, 1.0-1.1]). Cephalosporin therapy before or after the operation was associated with a significantly lower risk of SSI (aOR, 0.2 [95% CI, 0.1-0.5]). Use of staples for skin closure was associated with a marginally increased risk of SSI. These independent risk factors should be incorporated into approaches for the prevention

  13. 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/.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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

  19. Crohn's disease but not diverticulitis is an independent risk factor for surgical site infections in colectomy.

    Science.gov (United States)

    Wideroff, Matthew; Xing, Yunfan; Liao, Junlin; Byrn, John C

    2014-10-01

    Surgical site infections (SSIs) after colectomy for colon cancer (CC), Crohn's disease (CD), and diverticulitis (DD) significantly impact both the immediate postoperative course and long-term disease-specific outcomes. We aim to profile the effect of diagnosis on SSI after segmental colectomy using the National Surgical Quality Improvement Program (NSQIP) data set. NSQIP data from 2006 to 2011 were investigated, and segmental colectomy procedures performed for the diagnoses of Crohn's disease, DD, and colon malignancy were included. SSI complications were compared by diagnosis using univariate and multivariate analysis. We included 35,557 colectomy cases in the analysis. CD had the highest rate of postoperative SSI (17 vs. 13% DD vs. 10% CC; p risk for acquiring at least one SSI (odds ratio (OR) = 1.38, p ≤ 0.001), deep incisional SSI (OR = 1.85, p = 0.03), and organ space SSI (OR = 1.51, p = 0.02). For patients undergoing segmental colectomy in the NSQIP data set, statistically significant increases in SSI are seen in CD, but not DD, when compared to CC, thus confirming CD as an independent risk factor for SSI.

  20. 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.

  1. 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.

  2. Embracing the emerging precision agriculture technologies for site-specific management of yield-limiting factors.

    Science.gov (United States)

    Melakeberhan, H

    2002-09-01

    Precision agriculture (PA) is providing an information revolution using Global Positioning (GPS) and Geographic Information (GIS) systems and Remote Sensing (RS). These technologies allow better decision making in the management of crop yield-limiting biotic and abiotic factors and their interactions on a site-specific (SSM) basis in a wide range of production systems. Characterizing the nature of the problem(s) and public education are among the challenges that scientists, producers, and industry face when adapting PA technologies. To apply SSM, spatio-temporal characteristics of the problem(s) need to be determined and variations within a field demonstrated. Spatio-temporal characteristics of a given pathogen or pest problem may be known but may not be the only or primary cause of the problem. Hence, exact cause-and-effect relationships need to be established by incorporating GIS, GPS, and RS-generated data as well as possible interactions. Exploiting the potential of PA technologies in sustainable ways depends on whether or not we first ask ''Are we doing the right thing?'' (strategic) as opposed to ''Are we doing it right?'' (tactical).

  3. 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

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

    International Nuclear Information System (INIS)

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

    1987-01-01

    New heterobifunctional photoaffinity cross-linking reagents, 6-maleimido-N-(4-benzoylphenyl)hexanamide, 12-maleimido-N-(4-benzoylphenyl)dodecanamide, and 12-[ 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 γ-polypeptide. Subsequent photolysis cross-links the γ-polypeptide covalently to α- and β-polypeptides. The cross-linkers prevent major movements of the γ-polypeptide with respect to the α- and β-polypeptides but are sufficiently long to permit some flexibility in the enzyme structure. When ∼ 50% of the γ-polypeptide was cross-linked to a α- and β-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 α- and β-polypeptides with respect to the γ-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

  5. The role of anthropic, ecological, and social factors in sleeping site choice by long-tailed macaques (Macaca fascicularis).

    Science.gov (United States)

    Brotcorne, Fany; Maslarov, Cindy; Wandia, I Nengah; Fuentes, Agustin; Beudels-Jamar, Roseline C; Huynen, Marie-Claude

    2014-12-01

    When choosing their sleeping sites, primates make adaptive trade-offs between various biotic and abiotic constraints. In human-modified environments, anthropic factors may play a role. We assessed the influence of ecological (predation), social (intergroup competition), and anthropic (proximity to human settlements) factors in sleeping site choice by long-tailed macaques (Macaca fascicularis) occupying a habitat at the interface of natural forests and human-modified zones in Bali Barat National Park, Indonesia. Over the course of 56 nights, we collected data relating to physical features of sleeping trees, patterns of the use of sleeping sites within the home range, pre-sleep behavior, diurnal ranging patterns and availability of natural and human food. Overall, the macaques used 17 sleeping sites with 37 sleeping trees. When the monkeys slept in forest zones, they selected sleeping trees that had larger trunks but were not significantly taller than surrounding trees. Though the macaques rarely re-used sleeping sites on consecutive nights, they frequently re-used four sites over the study period. The group favored sleeping within the core area of its home range, despite the occurrence of frequent agonistic intergroup encounters there. Macaques preferentially selected sleeping trees located within or near human-modified zones, especially when human food was abundant and natural food was scarce. These results partially support the hypothesis that long-tailed macaques choose their sleeping sites to avoid predation; proximity to human settlements appears to be the primary factor influencing sleeping site choice in this primate species. Our results reflect the strong influence that anthropic factors have on primates, which subsist in increasingly human-dominated landscapes. © 2014 Wiley Periodicals, Inc.

  6. 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.

  7. 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

  8. Surgical site infection and its associated factors following cesarean section: a cross sectional study from a public hospital in Ethiopia.

    Science.gov (United States)

    Gelaw, Kelemu Abebe; Aweke, Amlaku Mulat; Astawesegn, Feleke Hailemichael; Demissie, Birhanu Wondimeneh; Zeleke, Liknaw Bewket

    2017-01-01

    A cesarean section is a surgical procedure in which incisions are made through a woman's abdomen and uterus to deliver her baby. Surgical site infections are a common surgical complication among patients delivered with cesarean section. Further it caused to increase maternal morbidity, stay of hospital and the cost of treatment. Hospital based cross-sectional study was conducted to assess the magnitude of surgical site infection following cesarean Site Infections and its associated factors at Lemlem Karl hospital July 1, 2013 to June 30, 2016. Retrospective card review was done on 384 women who gave birth via cesarean section at Lemlem Karl hospital from July 1, 2013 to June 30, 2016. Systematic sampling technique was used to select patient medical cards. The data were entered by Epi info version 7.2 then analyzed using Statistical Package for Social Sciences windows version 20. Both bivariate and multivariate logistic regression was done to test association between predictors and dependent variables. P value of cesarean section, the magnitude of surgical site infection following cesarean section Infection was 6.8%. The identified independent risk factors for surgical site infections were the duration of labor AOR=3.48; 95%CI (1.25, 9.68), rupture of membrane prior to cesarean section AOR=3.678; 95%CI (1.13, 11.96) and the abdominal midline incision (AOR=5.733; 95%CI (2.05, 16.00). The magnitude of surgical site infection following cesarean section is low compare to other previous studies. The independent associated factors for surgical site infection after cesarean section in this study: Membranes rupture prior to cesarean section, duration of labor and sub umbilical abdominal incision. In addition to ensuring sterile environment and aseptic surgeries, use of WHO surgical safety checklist would appear to be a very important intervention to reduce surgical site infections.

  9. Identification of transcription factor AML-1 binding site upstream of human cytomegalovirus UL111A gene.

    Directory of Open Access Journals (Sweden)

    Xiaoqun Zheng

    Full Text Available Human cytomegalovirus (HCMV interleukin-10 (hcmvIL-10, encoded by HCMV UL111A gene, is a homolog of human IL-10. It exerts immunomodulatory effects that allow HCMV to evade host defense mechanisms. However, the exact mechanism underlying the regulation of hcmvIL-10 expression is not well understood. The transcription factor acute myeloid leukemia 1 (AML-1 plays an important role in the regulation of various genes involved in the differentiation of hematopoietic lineages. A putative AML-1 binding site is present within the upstream regulatory region (URR of UL111A gene. To provide evidence that AML-1 is involved in regulating UL111A gene expression, we examined the interaction of AML-1 with the URR of UL111A in HCMV-infected human monocytic THP-1 cells using a chromatin immunoprecipitation assay. HcmvIL-10 transcription was detected in differentiated THP-1 cells, but not in undifferentiated ones. Furthermore, the URR of UL111A showed a higher intensity of AML-1 binding, a higher level of histone H3 acetyl-K9, but a lower level of histone H3 dimethyl-K9 in differentiated THP-1 cells than undifferentiated cells. Down-regulation of AML1 by RNA interference decreased the expression of the UL111A gene. Our results suggest that AML-1 may contribute to the epigenetic regulation of UL111A gene via histone modification in HCMV-infected differentiated THP-1 cells. This finding could be useful for the development of new anti-viral therapies.

  10. Incidence and risk factors of surgical site infection and septic arthritis after elective arthroscopy in horses.

    Science.gov (United States)

    Brunsting, Julie Y; Pille, Frederik J; Oosterlinck, Maarten; Haspeslagh, Maarten; Wilderjans, Hans C

    2018-01-01

    To determine the incidence of infection and associated risk factors, after elective arthroscopy. Retrospective case study. Horses (n=1079) undergoing elective arthroscopy. Medical records of all horses that underwent elective arthroscopy between 2006 and 2013 were reviewed. Age, gender, breed, surgeon, number of joints operated, total anesthetic time, perioperative antimicrobial administration, and the presence and size of osteochondral fragments/subchondral lesions were recorded. For each operated joint, the development of postoperative infection (surgical site infection [SSI] and/or septic arthritis) and long-term outcome (>6 months) were recorded. Multivariate logistic regression was used to test for association between the independent variables and the dependent outcomes. A total of 1741 joints in 1079 horses underwent arthroscopy. SSI without septic arthritis occurred in 1 fetlock joint (0.14%), 1 tibiotarsal joint (0.19%), and 6 femoropatellar joints (1.67%). Thirteen joints (0.75%) were diagnosed with septic arthritis, including 1 fetlock joint (0.14%), 4 tibiotarsal joints (0.74%), and 8 femoropatellar joints (2.23%). The probability of postoperative SSI was higher when large lesions (>40 mm long) were treated, compared to medium (20-40 mm, P = .005) and small (septic arthritis (P septic arthritis rate (P = .028). Septic arthritis after elective arthroscopy was more likely in the presence of SSI and younger age. Horses with large lesions were at risk for SSI, which translated into a higher incidence of postoperative septic arthritis after femoropatellar arthroscopy. © 2017 The American College of Veterinary Surgeons.

  11. 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.

  12. Sterol regulation of human fatty acid synthase promoter I requires nuclear factor-Y- and Sp-1-binding sites.

    Science.gov (United States)

    Xiong, S; Chirala, S S; Wakil, S J

    2000-04-11

    To understand cholesterol-mediated regulation of human fatty acid synthase promoter I, we tested various 5'-deletion constructs of promoter I-luciferase reporter gene constructs in HepG2 cells. The reporter gene constructs that contained only the Sp-1-binding site (nucleotides -82 to -74) and the two tandem sterol regulatory elements (SREs; nucleotides -63 to -46) did not respond to cholesterol. Only the reporter gene constructs containing a nuclear factor-Y (NF-Y) sequence, the CCAAT sequence (nucleotides -90 to -86), an Sp-1 sequence, and the two tandem SREs responded to cholesterol. The NF-Y-binding site, therefore, is essential for cholesterol response. Mutating the SREs or the NF-Y site and inserting 4 bp between the Sp-1- and NF-Y-binding sites both resulted in a minimal cholesterol response of the reporter genes. Electrophoretic mobility-shift assays using anti-SRE-binding protein (SREBP) and anti-NF-Ya antibodies confirmed that these SREs and the NF-Y site bind the respective factors. We also identified a second Sp-1 site located between nucleotides -40 and -30 that can substitute for the mutated Sp-1 site located between nucleotides -82 and -74. The reporter gene expression of the wild-type promoter and the Sp-1 site (nucleotides -82 to -74) mutant promoter was similar when SREBP1a [the N-terminal domain of SREBP (amino acids 1-520)] was constitutively overexpressed, suggesting that Sp-1 recruits SREBP to the SREs. Under the same conditions, an NF-Y site mutation resulted in significant loss of reporter gene expression, suggesting that NF-Y is required to activate the cholesterol response.

  13. Problem list completeness in electronic health records: A multi-site study and assessment of success factors.

    Science.gov (United States)

    Wright, Adam; McCoy, Allison B; Hickman, Thu-Trang T; Hilaire, Daniel St; Borbolla, Damian; Bowes, Watson A; Dixon, William G; Dorr, David A; Krall, Michael; Malholtra, Sameer; Bates, David W; Sittig, Dean F

    2015-10-01

    To assess problem list completeness using an objective measure across a range of sites, and to identify success factors for problem list completeness. We conducted a retrospective analysis of electronic health record data and interviews at ten healthcare organizations within the United States, United Kingdom, and Argentina who use a variety of electronic health record systems: four self-developed and six commercial. At each site, we assessed the proportion of patients who have diabetes recorded on their problem list out of all patients with a hemoglobin A1c elevation>=7.0%, which is diagnostic of diabetes. We then conducted interviews with informatics leaders at the four highest performing sites to determine factors associated with success. Finally, we surveyed all the sites about common practices implemented at the top performing sites to determine whether there was an association between problem list management practices and problem list completeness. Problem list completeness across the ten sites ranged from 60.2% to 99.4%, with a mean of 78.2%. Financial incentives, problem-oriented charting, gap reporting, shared responsibility, links to billing codes, and organizational culture were identified as success factors at the four hospitals with problem list completeness at or near 90.0%. Incomplete problem lists represent a global data integrity problem that could compromise quality of care and put patients at risk. There was a wide range of problem list completeness across the healthcare facilities. Nevertheless, some facilities have achieved high levels of problem list completeness, and it is important to better understand the factors that contribute to success to improve patient safety. Problem list completeness varies substantially across healthcare facilities. In our review of EHR systems at ten healthcare facilities, we identified six success factors which may be useful for healthcare organizations seeking to improve the quality of their problem list

  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. 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)

  16. Inhibition of human immunodeficiency virus type 1 replication with artificial transcription factors targeting the highly conserved primer-binding site

    NARCIS (Netherlands)

    Eberhardy, Scott R.; Goncalves, Joao; Coelho, Sofia; Segal, David J.; Berkhout, Ben; Barbas, Carlos F.

    2006-01-01

    The human immunodeficiency virus type 1 (HIV-1) primer-binding site (PBS) is a highly conserved region in the HIV genome and represents an attractive target for the development of new anti-HIV therapies. In this study, we designed four artificial zinc finger transcription factors to bind at or

  17. CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting

    NARCIS (Netherlands)

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

    2004-01-01

    Prediction of transcription-factor target sites in promoters remains difficult due to the short length and degeneracy of the target sequences. Although the use of orthologous sequences and phylogenetic footprinting approaches may help in the recognition of conserved and potentially functional

  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. Decomposition of the factors that govern binding site preference in a multiple rotaxane.

    Science.gov (United States)

    Angelo, Joseph P; Sohlberg, Karl

    2009-06-18

    A particularly interesting class of multiple rotaxanes consists of complexes where one long shaft threads two rings. If the shaft contains three or more potential binding sites for the rings, multiple co-conformations are possible. Such a complex is a molecular topological analogue to an abacus. Here we address the question, how does strength of ring binding to the shaft vary with respect to position on the shaft? Previous studies have found that a shaft with three binding sites exhibits strongest ring binding at the center site. Here a five-binding-site shaft is studied. We employ a novel method to partition the total energy of the system into contributions from intercomponent binding and intracomponent distortion. The method uses the output of quantum mechanical electronic structure calculations to determine fitting parameters in a set of coupled equations. The solution of the equations yields the energy partitioning and reveals the influence of long-range intercomponent interactions.

  1. 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

  2. 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.

  3. 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.

  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 case-control study of risk factors for surgical site infection after cesarean delivery in eastern Burkina Faso.

    Science.gov (United States)

    Kaboré, Boezemwendé; Soudouem, Georges; Seck, Ibrahima; Millogo, Tieba; Evariste Yaméogo, Wambi Maurice; Kouanda, Seni

    2016-11-01

    To identify the risk factors for surgical site infection after cesarean delivery in a rural area in eastern Burkina Faso. A matched case-control study was conducted in Fada N'Gourma Regional Hospital Center and the Diapaga Medical Center with Surgical Antenna using data from 2011-2014. A total of 99 cases of surgical site infection after cesarean delivery were included in the study. Each case was matched with a control patient similar for age, admission date, and facility where the cesarean took place. Risk factors were identified using conditional logistic regression. Multivariate analysis identified hyperthermia at admission (OR 2.37; P=0.035), the presence of caput succedaneum in newborns (OR 7.07; P=0.001), and difficult delivery (OR 3.69; P=0. 019) as risk factors for surgical site infection. Provision of quality prenatal care, use of the partograph during labor, and the responsiveness of health workers during labor can reduce surgical site infection after cesarean delivery. Copyright © 2016. Published by Elsevier Ireland Ltd.

  6. 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

  7. 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

  8. 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

  9. Identification of a functional hepatocyte nuclear factor 4 binding site in the neutral ceramidase promoter

    DEFF Research Database (Denmark)

    Maltesen, Henrik R; Troelsen, Jesper T; Olsen, Jørgen

    2010-01-01

    in ceramide digestion. It was the purpose of the present work to experimentally verify the functional importance of a HNF-4a binding site predicted by bioinformatic analysis to be present in the Asah2 promoter. Using supershift analysis, HNF-4a overexpression, and HNF-4a knockdown experiments it was confirmed...... that the predicted HNF-4a binding site identified in the Asah2 promoter is functional. The results support the hypothesis that HNF-4a might be important for intestinal glycolipid metabolism....

  10. Supervision on Site: A Critical Factor in the Online Facilitated Internship

    Science.gov (United States)

    Dotson, Kaye B.; Bian, Hui

    2013-01-01

    Online education is increasingly prevalent in graduate schools of teacher education. Questions arise, however, as to the effectiveness of the online facilitated graduate internship. This article examines perspectives of librarian site supervisors within online supported internships. Perspectives in regard to program support and self-perceived…

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

    DEFF Research Database (Denmark)

    Sudzina, Frantisek; Pavlicek, Antonin

    2017-01-01

    . 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. 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.

  13. 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.

  14. 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)

  15. 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.

  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. Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Moses Alan M

    2009-12-01

    Full Text Available Abstract Background Although cis-regulatory changes play an important role in evolution, it remains difficult to establish the contribution of natural selection to regulatory differences between species. For protein coding regions, powerful tests of natural selection have been developed based on comparisons of synonymous and non-synonymous substitutions, and analogous tests for regulatory regions would be of great utility. Results Here, tests for natural selection on regulatory regions are proposed based on nucleotide substitutions that occur in characterized transcription factor binding sites (an important type functional element within regulatory regions. In the absence of selection, these substitutions will tend to reduce the strength of existing binding sites. On the other hand, purifying selection will act to preserve the binding sites in regulatory regions, while positive selection can act to create or destroy binding sites, as well as change their strength. Using standard models of binding site strength and molecular evolution in the absence of selection, this intuition can be used to develop statistical tests for natural selection. Application of these tests to two well-characterized regulatory regions in Drosophila provides evidence for purifying selection. Conclusion This demonstrates that it is possible to develop tests for selection on regulatory regions based on the specific functional constrains on these sequences.

  18. 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

  19. Contributing Factors in Restaurant-Associated Foodborne Disease Outbreaks, FoodNet Sites, 2006 and 2007†

    Science.gov (United States)

    GOULD, L. HANNAH; ROSENBLUM, IDA; NICHOLAS, DAVID; PHAN, QUYEN; JONES, TIMOTHY F.

    2015-01-01

    An estimated 48 million cases of foodborne illness occur each year in the United States, resulting in approximately 128,000 hospitalizations and 3,000 deaths. Over half of all foodborne disease outbreaks reported to the Centers for Disease Control and Prevention are associated with eating in restaurants or delicatessens. We reviewed data from restaurant-associated foodborne disease outbreaks to better understand the factors that contribute to these outbreaks. Data on restaurant-associated foodborne disease outbreaks reported by sites participating in the Foodborne Diseases Active Surveillance Network (FoodNet) were analyzed to characterize contributing factors reported in foodborne disease outbreaks and the levels of evidence used to identify these factors. Of 457 foodborne disease outbreaks reported in 2006 and 2007 by FoodNet sites, 300 (66%) were restaurant associated, and of these 295 (98%) had at least one reported contributing factor. One to nine (with a median of two) contributing factors were reported per outbreak. Of the 257 outbreaks with a single etiology reported, contributing factors associated with food worker health and hygiene were reported for 165 outbreaks (64%), factors associated with food preparation practices within the establishment were reported for 88 outbreaks (34%), and factors associated with contamination introduced before reaching the restaurant were reported for 56 outbreaks (22%). The pronounced role of food workers in propagating outbreaks makes it clear that more work is needed to address prevention at the local level. Food workers should be instructed not to prepare food while ill to prevent the risk of transmitting pathogens. PMID:24215683

  20. Injectable multiple sclerosis medications: a patient survey of factors associated with injection-site reactions.

    Science.gov (United States)

    Stewart, Thomas M; Tran, Zung Vu

    2012-01-01

    Although injection-site reactions (ISRs) occur with US Food and Drug Administration-approved injectable disease-modifying therapies (DMTs) for multiple sclerosis, there are currently few reports of real-world data on ISR management strategies or possible correlations between ISRs and patient demographics, disease characteristics, and missed injections. Patient-reported data on the use of DMTs, patient demographic and disease characteristics, missed injections, and ISR reduction strategies were collected via e-mail, a patient registry (www.ms-cam.org), and a Web-based survey. Of the 1380 respondents, 1201 (87%) indicated that they had used injectable DMTs, of whom 377 (31%) had used intramuscular (IM) interferon beta-1a (IFNβ-1a), 172 (14%) had used subcutaneous (SC) IFNβ-1a, 183 (15%) had used SC IFNβ-1b, and 469 (39%) had used glatiramer acetate (GA). The majority of respondents were older (73% were ≥40 years), female (79%), married or living with a partner (72%), white (94%), and nonsmoking (82%). Injection-site reaction incidence, grouped according to severity, varied among DMTs, with IM IFNβ-1a causing significantly (P ISRs than the other therapies. Female sex and younger age were significantly (P ISRs among users of IM IFNβ-1a, SC IFNβ-1b, and GA. Nonwhites reported severe ISRs more often than whites. For all DMTs injection-site massage and avoidance of sensitive sites were the most frequently used strategies to minimize ISRs. These data may help identify patients with characteristics associated with a higher risk for ISRs, allowing health-care professionals to provide anticipatory guidance to patients at risk for decreased adherence or discontinuation.

  1. Preoperative skin preparation with 2% chlorhexidine as a factor in the prevention of surgical site infection

    OpenAIRE

    Evelyn Solano Castro

    2014-01-01

    The results of secondary research that refers to preoperative skin preparation with antiseptic chlorhexidine 2% are presented. Surgical Site Infections are one of the most common complications in surgical procedures are associated with significant morbidity and mortality in the user and are the third -associated infection more frequent in the health care . Steps of clinical practice based on evidence were applied, considering in the first instance a question in PICO format, then a search for ...

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

    Energy Technology Data Exchange (ETDEWEB)

    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 (/sup 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 (/sup 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 (/sup 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.

  3. 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

    Transcription and pre-mRNA splicing are interdependent events. Although mechanisms governing the effects of transcription on splicing are becoming increasingly clear, the means by which splicing affects transcription remain elusive. Using cell lines stably expressing HIV-1 or β-globin mRNAs, harb...... a promoter-proximal 5′ splice site via its U1 snRNA interaction can feed back to stimulate transcription initiation by enhancing preinitiation complex assembly.......Transcription and pre-mRNA splicing are interdependent events. Although mechanisms governing the effects of transcription on splicing are becoming increasingly clear, the means by which splicing affects transcription remain elusive. Using cell lines stably expressing HIV-1 or β-globin mRNAs......, 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...

  4. 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

  5. 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

  6. 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

  7. Risk factors for surgical site infection following cesarean section in a Brazilian Women's Hospital: a case-control study.

    Science.gov (United States)

    Farret, Túlio Cícero Franco; Dallé, Jessica; Monteiro, Vinícius da Silva; Riche, Cezar Vinícius Würdig; Antonello, Vicente Sperb

    2015-01-01

    The present study evaluated patients with diagnosis of surgical site infection (SSI) following cesarean section and their controls to determinate risk factors and impact of antibiotic prophylaxis on this condition. All cesareans performed from January 2009 to December 2012 were evaluated for SSI, based on criteria established by CDC/NHSN. Control patients were determined after inclusion of case patients. Medical records of case and control patients were reviewed and compared regarding sociodemographic and clinical characteristics. Our study demonstrated an association following univariate analysis between post-cesarean SSI and number of internal vaginal examinations, time of membrane rupture, emergency cesarean and improper use of antibiotic prophylaxis. This same situation did not repeat itself in multivariate analysis with adjustment for risk factors, especially with regard to antibiotic prophylaxis, considering the emergency cesarean factor only. The authors of the present study not only question surgical antimicrobial prophylaxis use based on data presented here and in literature, but suggest that the prophylaxis is perhaps indicated primarily in selected groups of patients undergoing cesarean section. Further research with greater number of patients and evaluated risk factors are fundamental for better understanding of the causes and evolution of surgical site infection after cesarean delivery. Copyright © 2014. Published by Elsevier Editora Ltda.

  8. 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.

  9. 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.

  10. Airborne bacteria concentrations and related factors at university laboratories, hospital diagnostic laboratories and a biowaste site.

    Science.gov (United States)

    Hwang, Sung Ho; Park, Dong Uk; Ha, Kwon Chul; Cho, Hyun Woo; Yoon, Chung Sik

    2011-03-01

    To evaluate concentrations of airborne bacteria in university laboratories, hospital diagnostic laboratories, and a biowaste site in Seoul, Korea. To measure total airborne bacteria (TAB), the authors assessed sampling site, type of ventilation system, weather and detection of Gram-negative bacteria (GNB), indoors and outdoors. An Andersen one-stage sampler (Quick Take 30; SKC Inc) was used to sample air at a flow rate of 28.3 l/min for 5 min on nutrient medium in Petri dishes located on the impactor. A total of 236 samples (TAB, 109 indoor and nine outdoor; GNB, 109 indoor and nine outdoor) were collected three times in each spot from the 11 facilities to compare airborne bacteria concentrations. TAB concentrations ranged from undetectable to 3451 CFU/m³ (mean 384 CFU/m³), and GNB concentrations from undetectable to 394 CFU/m³ (mean 17 CFU/m³). TAB concentrations were high in window-ventilated facilities and facilities in which GNB were detected; concentrations were also high when it was rainy (all p values laboratories. It is recommended that special attention be given to regular control of indoor environments to improve the air quality of university and hospital laboratories.

  11. Prediction of transcription factor bindings sites affected by SNPs located at the osteopontin promoter.

    Science.gov (United States)

    Briones-Orta, Marco Antonio; Avendaño-Vázquez, S Eréndira; Ivette Aparicio-Bautista, Diana; Coombes, Jason D; Weber, Georg F; Syn, Wing-Kin

    2017-10-01

    This data contains information related to the research article entitled "Osteopontin splice variants and polymorphisms in Cancer Progression and Prognosis" [1]. Here, we describe an in silico analysis of transcription factors that could have altered binding to their DNA target sequence as a result of SNPs in the osteopontin gene promoter. We concentrated on SNPs associated with cancer risk and development. The analysis was performed with PROMO v3.0.2 software which incorporates TRANSFACT v6.4 of. We also present a figure depicting the putative transcription factor binding according to genotype.

  12. 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.

  13. MADS evolution : insights into evolutionary changes in transcription factors and their binding sites

    NARCIS (Netherlands)

    Bruijn, de Suze-Annigje

    2017-01-01

    Although most flowers follow a conserved 'bauplan' consisting of sepals, petals, stamens and carpels, there is a remarkable amount of morphological diversity. Interestingly, all flowers are specified by the conserved (A)BCE-model. Most of the transcription factors in this model belong to the

  14. 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

  15. Understory vegetation and site factors : implications for a managed Wisconsin landscape

    Science.gov (United States)

    K.D. Brosofske; J. Chen; Thomas R. Crow

    2001-01-01

    We investigated relationships between edaphic and environmental factors (soil, forest floor, topography, and canopy) and understory vegetation (composition, richness, and Shannon-Wiener diversity index, H')among 77 plots representing seven major patch types comprising a landscape in northern Wisconsin that has a long history of human management. Sampled patch...

  16. 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 ObjectivesShow 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

  17. Nutritional risk index as an independent predictive factor for the development of surgical site infection after pancreaticoduodenectomy.

    Science.gov (United States)

    Shinkawa, Hiroji; Takemura, Shigekazu; Uenishi, Takahiro; Sakae, Masayuki; Ohata, Kazunori; Urata, Yorihisa; Kaneda, Kazuhisa; Nozawa, Akinori; Kubo, Shoji

    2013-03-01

    Malnutrition has been considered a risk factor for the development of a surgical site infection (SSI). The aim of this study was to determine the relationship between preoperative nutritional screening scores and the development of SSI after pancreaticoduodenectomy. We examined 64 patients who had undergone pancreaticoduodenectomy. Their clinical data, nutritional risk index (NRI), and nutritional risk screening 2002 (NRS-2002) score were recorded. SSIs were diagnosed according to the definitions of wound infection established by the Center for Disease Control and Prevention and were confirmed by a microbiological examination. Data were analyzed using the Fisher exact probability method and a multivariate logistic regression analysis. SSIs developed in 21 patients (33 %). Eleven patients had wound infections, and 14 patients had an intra-abdominal abscess. A univariate analysis of perioperative factors revealed that a pancreatic fistula, the NRS-2002, and the NRI were significantly associated with the development of SSI (p NRI were independent risk factors for SSI. By analyzing the pre- and intra-operative factors after excluding the 11 patients with pancreatic fistulas, the NRI was still an independent risk factor for SSI. The present study showed the NRI to be an independent factor for predicting the risk of SSI after pancreaticoduodenectomy.

  18. Factors affecting oviposition site preference by Toxorhynchites splendens in the laboratory.

    Science.gov (United States)

    Benzon, G L; Apperson, C S; Clay, W

    1988-03-01

    In a series of laboratory oviposition assays, gravid Toxorhynchites splendens exhibited a preference for cups containing Aedes aegypti larval rearing water, but not for cups containing liquid cultures of bacteria, live Ae. aegypti in distilled water, Ae. aegypti larval holding water with reduced bacterial contamination, or methyl propionate at 0.1, 0.2 and 0.3% in distilled water. Preoviposition flight behavior was elicited by dark-colored containers, but few eggs were deposited if they contained no water. An invisible source of humidity placed in cups enhanced oviposition, but a reflective surface placed in dry cups did not. It is concluded that this species is strongly influenced by humidity and visual stimuli in the acceptance of a site for oviposition.

  19. 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...

  20. Vif is an auxiliary factor of the HIV-1 reverse transcriptase and facilitates abasic site bypass.

    Science.gov (United States)

    Cancio, Reynel; Spadari, Silvio; Maga, Giovanni

    2004-11-01

    The HIV-1 accessory protein Vif was found to modulate the RNA- and DNA-dependent DNA synthesis activity of the viral RT (reverse transcriptase) in two ways: (i) it stimulated the binding of the viral RT to the primer by increasing the association rate kcat/K(m) and by decreasing the thermodynamic barrier DeltaH([ES]) for complex formation, and (ii) it increased the polymerization rate of HIV-1 RT. A Vif mutant lacking the final 56 amino acids at the C-terminus failed to stimulate the viral RT. On the other hand, another Vif mutant lacking the first 43 amino acids at the N-terminus, which are involved in RNA binding and interaction with the viral protease, was able to stimulate RT activity. In addition, Vif was found to promote the bypass of an abasic site by HIV-1 RT.

  1. 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

  2. Risk factors for neurosurgical site infections after a neurosurgical procedure: a prospective observational study at Hospital Kuala Lumpur.

    Science.gov (United States)

    Buang, S S; Haspani, M S

    2012-08-01

    Surgical site infection (SSI) after craniotomy even though rare, poses a real risk of surgery and represents a substantial burden of disease for both patients and healthcare services in terms of morbidity, mortality and economic cost. The knowledge of risk factor for surgical site infection after craniotomy will allow the authority to implement specific preventive measures to reduce the infection rate. Therefore, the objectives of this study are to determine the incidence and the risk factors of surgical site infection after craniotomy. This study highlights an observational prospective study on adult patients who has undergone neurosurgical procedures in Hospital Kuala Lumpur (HKL) over a period of 2 years (June 2007 to June 2009). The neurosurgical procedures are craniectomy, craniotomy, cranioplasty and burrhole. A total of 390 cases fulfilled the requirements of inclusion and exclusion criteria were included in the study. Every patient in the study population was prospectively evaluated for development and risk factors for SSI. The follow-up cases were done by direct observation of the wound during their post-operative stay and ideally up to and including day 30 post-operatively, either as in-patients or through post discharge surveillance i.e. follow-up in the clinic 30 days post-operatively. SSIs were defined according to the Center for Disease Control definitions. Incidence was calculated per patient. Univariate Simple Logistic Regression analysis was used to analyse the association of the risk factors and SSI. A total of 30 post craniotomy surgical site infections (SSI) has been identified among 390 cases included in the study, resulting in an overall infection rate of 7.7%. This included 19 with superficial wound infection (63.3%), 9 with bone flap osteitis (30%) and 2 with organ/space infection (6.7%). Most of SSIs were detected during in patient cases accounting for 20 cases. The mean time between surgery and the onset of infection was 11.8 +/- 21.8 days

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. Preoperative skin preparation with 2% chlorhexidine as a factor in the prevention of surgical site infection

    Directory of Open Access Journals (Sweden)

    Evelyn Solano Castro

    2014-04-01

    Full Text Available The results of secondary research that refers to preoperative skin preparation with antiseptic chlorhexidine 2% are presented. Surgical Site Infections are one of the most common complications in surgical procedures are associated with significant morbidity and mortality in the user and are the third -associated infection more frequent in the health care . Steps of clinical practice based on evidence were applied, considering in the first instance a question in PICO format, then a search for information in databases recommended in the Course of Clinical Nursing Practice Evidence-Based, taught by the program for Collaborative Research in Evidence-Based Nursing of Costa Rica ( CIEBE -CR . The PubMed database and Cochrane LIBRARY was consulted, National Center for Biotechnology Information ( NCBI, Google Scholar, CINAHL (cummulative Index of Nursing and Allied Health Literature. SCIELO (Scientific Electronic Library on line www.Scielo.org . 22 documents were recovered, but only three were selected because had methodological rigor. For the critical analysis Critical Reading Sheets 2.0 ( FLC software was used. Was concluded that 2% chlorhexidine, is the best choice for preoperative skin preparation antiseptic, however, it is necessary to conduct further studies in order to determine which is the correct way in strength, frequency, technical and adverse effects in the pediatric population.

  8. 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.

  9. Epidemiology and risk factors associated with surgical site infection after different types of hepatobiliary and pancreatic surgery.

    Science.gov (United States)

    Morikane, Keita

    2017-10-01

    Surgical site infection (SSI) is one of the most common healthcare-associated infections (HAIs); however, SSI after hepatobiliary and pancreatic surgery (HBPS) has not been well investigated in a large cohort of patients. This study analyzed the factors associated with SSI following HBPS in Japan, using a Japanese national database. Data on HBPS performed between 2012 and 2014 were extracted from a national monitoring system for HAI: The Japan Nosocomial Infections Surveillance. Using multivariate logistic regression, I assessed the factors associated with SSI. The cumulative incidence of SSI following HBPS was 15.6% (2873/18,398). The incidence of SSI after pancreatoduodenectomy was 28.0%, which was significantly higher than that after liver resection and other types of HBPS (8.8 and 15.5%, respectively). Among the four traditional risk factors, the American Society of Anesthesiologists score was ineffective for predicting SSI in the final model of all three types of surgery. Additional risk factors were identified, including age and male gender. The incidence of and factors associated with SSI after the three types of HBPS analyzed differed significantly. To accurately compare hospital performance in relation to SSI following HBPS, the operative procedure category in the surveillance system must be divided into three types.

  10. High-resolution mapping of transcription factor binding sites on native chromatin

    Science.gov (United States)

    Kasinathan, Sivakanthan; Orsi, Guillermo A.; Zentner, Gabriel E.; Ahmad, Kami; Henikoff, Steven

    2014-01-01

    Sequence-specific DNA-binding proteins including transcription factors (TFs) are key determinants of gene regulation and chromatin architecture. Formaldehyde cross-linking and sonication followed by Chromatin ImmunoPrecipitation (X-ChIP) is widely used for profiling of TF binding, but is limited by low resolution and poor specificity and sensitivity. We present a simple protocol that starts with micrococcal nuclease-digested uncross-linked chromatin and is followed by affinity purification of TFs and paired-end sequencing. The resulting ORGANIC (Occupied Regions of Genomes from Affinity-purified Naturally Isolated Chromatin) profiles of Saccharomyces cerevisiae Abf1 and Reb1 provide highly accurate base-pair resolution maps that are not biased toward accessible chromatin, and do not require input normalization. We also demonstrate the high specificity of our method when applied to larger genomes by profiling Drosophila melanogaster GAGA Factor and Pipsqueak. Our results suggest that ORGANIC profiling is a widely applicable high-resolution method for sensitive and specific profiling of direct protein-DNA interactions. PMID:24336359

  11. Molecular imaging of nuclear factor-Y transcriptional activity maps proliferation sites in live animals.

    Science.gov (United States)

    Goeman, Frauke; Manni, Isabella; Artuso, Simona; Ramachandran, Balaji; Toietta, Gabriele; Bossi, Gianluca; Rando, Gianpaolo; Cencioni, Chiara; Germoni, Sabrina; Straino, Stefania; Capogrossi, Maurizio C; Bacchetti, Silvia; Maggi, Adriana; Sacchi, Ada; Ciana, Paolo; Piaggio, Giulia

    2012-04-01

    In vivo imaging involving the use of genetically engineered animals is an innovative powerful tool for the noninvasive assessment of the molecular and cellular events that are often targets of therapy. On the basis of the knowledge that the activity of the nuclear factor-Y (NF-Y) transcription factor is restricted in vitro to proliferating cells, we have generated a transgenic reporter mouse, called MITO-Luc (for mitosis-luciferase), in which an NF-Y-dependent promoter controls luciferase expression. In these mice, bioluminescence imaging of NF-Y activity visualizes areas of physiological cell proliferation and regeneration during response to injury. Using this tool, we highlight for the first time a role of NF-Y activity on hepatocyte proliferation during liver regeneration. MITO-Luc reporter mice should facilitate investigations into the involvement of genes in cell proliferation and provide a useful model for studying aberrant proliferation in disease pathogenesis. They should be also useful in the development of new anti/proproliferative drugs and assessment of their efficacy and side effects on nontarget tissues.

  12. 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

    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...... antibody (F1A2-mAb). No significant difference in binding efficacy between [18F]ASIS and ASIS could be detected. Furthermore, [18F]ASIS was relatively stable in vitro and in vivo in mice. In conclusion, [18F]ASIS has for the first time been successfully synthesized as a possible positron emission...

  13. 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.

  14. Contribution of factor VIII light-chain residues 2007-2016 to an activated protein C-interactive site.

    Science.gov (United States)

    Takeyama, Masahiro; Wakabayashi, Hironao; Fay, Philip J

    2013-02-01

    Although factor (F) VIIIa is inactivated by activated protein C (APC) through cleavages in the FVIII heavy chain-derived A1 (Arg(336)) and A2 subunits (Arg(562), the FVIII light chain (LC) contributes to catalysis by binding the enzyme. ELISA-based binding assays showed that FVIII and FVIII LC bound to immobilised active site-modified APC (DEGR-APC) (apparent K(d) ~270 nM and 1.0 μM, respectively). Fluid-phase binding studies using fluorescence indicated an estimated K(d) of ~590 nM for acrylodan-labelled LC binding to DEGR-APC. Furthermore, FVIII LC effectively competed with FVIIIa in blocking APC-catalysed cleavage at Arg(336) (K(i) = 709 nM). A binding site previously identified near the C-terminal end of the A3 domain (residues 2007-2016) of FVIII LC was subjected to Ala-scanning mutagenesis. FXa generation assays and western and dot blotting were employed to assess the contribution of these residues to FVIIIa interactions with APC. Virtually all variants tested showed reductions in the rates of APC-catalysed inactivation of the cofactor and cleavage at the primary inactivation site (Arg(336)), with maximal reductions in inactivation rates (~3-fold relative to WT) and cleavage rates (~3 to ~9-fold relative to WT) observed for the Met2010Ala, Ser2011Ala, and Leu2013Ala variants. Titration of FVIIIa substrate concentration monitoring cleavage by a dot blot assay indicated that these variants also showed ~3-fold increases relative to WT while a double mutant (Met2010Ala/Ser2011Ala) showed a >4-fold increase in K(m). These results show a contribution of a number of residues within the 2007-2016 sequence, and in particular residues Met2010, Ser2011, and Leu2013 to an APC-interactive site.

  15. Edaphic factors trigger diverse AM fungal communities associated to exotic camellias in closely located Lake Maggiore (Italy) sites.

    Science.gov (United States)

    Borriello, Roberto; Berruti, Andrea; Lumini, Erica; Della Beffa, Maria Teresa; Scariot, Valentina; Bianciotto, Valeria

    2015-05-01

    Camellia japonica L. is an acidophilic ornamental shrub of high economic value that has its center of origin in Japan and has been introduced in several European environmental niches. This exotic species forms arbuscular mycorrhizas (AM), known for their ability to positively affect plant growth. However, AM fungal communities associated to C. japonica in the field have never been characterized. For the first time, the AM fungal community naturally selected by C. japonica was screened in three sites located on the shores of Lake Maggiore (Italy), where specimens of this plant were introduced in the nineteenth century. Mycorrhizal levels were assessed, and the AM fungal communities associated to roots and soil were molecularly characterized based on the small subunit (SSU) rDNA region. The frequency of mycorrhizal roots was high in all sampled root systems (>90 %). Overall, 39 Operational Taxonomic Units (OTUs; 22 Glomerales, 9 Paraglomerales, 7 Archaeosporales, and 1 Diversisporales) were found in the root and soil samples. OTU richness did not significantly differ between the root and the soil niche (5.7 ± 0.6 and 8.0 ± 1.1 average OTUs per sample, respectively) and the three sites analyzed (7.5 ± 0.7, 5.2 ± 1.0, and 7.8 ± 1.5 average OTUs per sample in the three sites, respectively). The AM fungal community composition significantly differed between root-colonizing and soil-dwelling communities and among the three sites under study. Data show a major involvement of edaphic factors, such as available N sources, P, Mg, and K content in soil and soil compaction, in the structuring of the AM fungal communities.

  16. 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.

  17. Risk factors for incisional surgical site infections in elective surgery for colorectal cancer: focus on intraoperative meticulous wound management.

    Science.gov (United States)

    Itatsu, Keita; Sugawara, Gen; Kaneoka, Yuji; Kato, Takehito; Takeuchi, Eiji; Kanai, Michio; Hasegawa, Hiroshi; Arai, Toshiyuki; Yokoyama, Yukihiro; Nagino, Masato

    2014-07-01

    An incisional surgical site infection (I-SSI) is a frequently observed complication following colorectal surgery. Intraoperative wound management is one of the most important factors that determine the incidence of postoperative I-SSI. The purpose of this study was to assess the impact of the methods used for intraoperative wound management on the incidence of I-SSI following elective surgery for colorectal cancer. Between November 2009 and February 2011, the data of 1,980 consecutive patients who underwent elective colorectal resection for colorectal cancer were prospectively collected from 19 affiliated hospitals. The incidence of and risk factors for I-SSI were investigated. Overall, 233 I-SSIs were identified (11.7 %). Forty-two possible risk factors were analyzed. Using a multivariate analysis, the independent risk factors for I-SSI were identified to be a high body mass index, previous laparotomy, chronic liver disease, wound length, contaminated wound class, creation or closure of an ostomy, right hemicolectomy procedure, the suture material used for fascial closure and the incidence of organ/space SSI. To prevent I-SSI following elective colorectal surgery, it is crucial to avoid making large incisions and reduce fecal contamination whenever possible. A high quality randomized control trial is necessary to confirm the definitive intraoperative procedure(s) that can minimize the incidence of I-SSI.

  18. Site of deposition and factors affecting clearance of aerosolized solute from canine lungs

    International Nuclear Information System (INIS)

    Rizk, N.W.; Luce, J.M.; Hoeffel, J.M.; Price, D.C.; Murray, J.F.

    1984-01-01

    The influence of several factors on lung solute clearance using aerosolized /sup 99m/Tc-diethylenetriaminepentaacetate was determined. The authors used a jet nebulizer-plate separator-balloon system to generate particles with an activity median aerodynamic diameter of 1.1 μm, administered the aerosol in a standard fashion, and determined clearance half times (t/sub 1/2/) with a gamma-scintillation camera. The following serial studies were performed in five anesthetized, paralyzed, intubated, mechanically ventilated dogs: (1) control, with ventilatory frequency (f) = 15 breaths/min and tidal volume (V/sub T/) = 15 ml/kg during solute clearance; (2) repeat control, for reproducibility; (3) increased frequency, with f = 25 breaths/min and V/sub T/ = 10 ml/kg; (4) positive end-expiratory pressure (PEEP) of 10 cmH 2 O; (5) unilateral pulmonary arterial occlusion (PAO); and (6) bronchial arterial occlusion (BAO). Control t/sub 1/2/ was 25 +/- 5 min and did not change in the repeat control, increased frequency, or BAO experiments. PEEP markedly decreased t/sub 1/2/ to 13 +/- 3 min (P < 0.01), and PAO increased it to 37 +/- 6 min (P < 0.05). We conclude that clearance from the lungs by our method is uninfluenced by increased frequency, increases markedly with PEEP, and depends on pulmonary, not bronchial, blood flow

  19. 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.

  20. 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.

  1. 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.

  2. 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

    2017-01-01

    Full Text Available Background: Most of South Africa’s citizens who live in rural or underserved communities rely on the public health care sector to access quality health care. The value of rural exposure through clinical placements is well documented. Medical schools in South Africa have a responsibility to provide solutions that address the prevailing human resources challenges. Despite this commitment, medical students do not necessarily appreciate their role in resolving South Africa’s human resources challenges. This study aimed to assess the factors that influenced the choice of clinical learning sites in a self-selection process undertaken by Wits final year medical students for the compulsory 6-week integrated primary care block rotation.Methods: Qualitative data related to reasons for choice of service learning site were gathered from 524 pre-placement questionnaires completed by final year medical students entering the rotation over a 3-year period (2012–2014. Thematic analysis was performed using the MAXQDA software.Results: Eight themes emerged from the study indicating that the majority of participants were in favour of local urban underserved placement. Contextual factors, such as work commitments or family responsibilities, being compromised socially and losing academic standing were the main reasons for seeking urban placement. Good supervision, opportunistic learning, skills development and moral support were reasons for seeking rural placements. Previous voluntary exposure to rural practice or being of rural origin was a strong indicator for uptake of rural placement.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.

  3. 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

  4. 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.

  5. 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

  6. Factors limiting regeneration of Quercus alba and Cornus florida in formerly cultivated coastal plain sites, South Carolina.

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Joseph, M., Jr.; Jones, Robert, H.

    2003-01-01

    Riley, J.M. Jr., and R.H.Jones. 2003. Factors limiting regeneration of Quercus alba and Cornus florida in formerly cultivated coastal plain sites, South Carolina. For. Ecol., and Mgt. 177:571-586. To determine the extent that resources, conditions, and herbivoryy limit regeneration of Quercus alba L. and Cornus florida L. in formerly cultivated coastal plain uplands, we planted seedlings of the two species in two pine and one pine-hardwood forest understory and three adjacent clearcuts. Soil carbon and moisture, available nitrogen and phosphorous, and gap light index (GLI) were measured next to each seedling. Over two growing seasons, stem and leaf herbivory were estimated and survival was recorded. At the end of 2 years, all surviving stems were harvested to determine total leaf area and 2-year biomass growth. Survival to the end of the study was not significantly different between clearcuts and understories. However, clearcuts led to significantly greater biomass growth and leaf area for both Q. alba and C. florida. Soil moisture and available nutrients were also greater in the clearcuts. Using separate multiple linear (growth) or logistic (survival) regressions for each combination of three sites, two cutting treatments and two species, we found that soil moisture significantly affected survival in 12.5% and biomass growth in 8.3% of the regressions. Light availability significantly impacted biomass growth in 16.7% of the regressions. Stem and leaf herbivory had very little impact on survival (8.3%), but when combined, these two factors significantly impacted leaf area or biomass growth in 33.3% of the regressions. Seedling responses were highly variable, and no regression model accounted for more that 70.0% of this variation. In our study, stand-scalevariation in seedling responses (especially the difference between clearcut and understory) was much greater than within-stand variation. Of the within stand factors measured, herbivory was clearly the most

  7. 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

  8. Modulation of the nicotinic alpha-bungarotoxin site in chromaffin cells in culture by a factor(s) endogenous to neuronal tissue.

    Science.gov (United States)

    Quik, M; Fournier, S; Trifaró, J M

    1986-04-30

    An endogenous factor(s) which affects the in vitro binding of (alpha-BGT) to rat brain membranes has previously been found in brain supernatant. This fraction, as well as a partially purified preparation of this material from bovine brain, is here shown to affect the binding of alpha-BGT to chromaffin cell membranes. To study possible long term effects, the supernatant extract was added to adrenal medullary chromaffin cells in culture. The cells were incubated for several days and at the end of this time, the medium bathing the cells, which contained the endogenous factor(s), was removed and alpha-BGT binding to the cells measured. Binding to control cultures had shown that alpha-BGT bound to the chromaffin cells in a saturable manner, with high affinity (Kd = 1.5 nM) and the specificity of a nicotinic receptor ligand. After incubation of the cells with supernatant factor, a marked decline in the number of alpha-BGT binding sites was observed with no change in affinity. This does not appear to be due to a detrimental effect on the cells as cell number did not appear to be decreased in the cultures preincubated with the supernatant extract and the DNA and protein content were similar in the control and treated cultures. The possibility that there was some non-specific detrimental effect to the chromaffin cell membrane was considered; however, the stimulated release of noradrenaline from the cells was not affected by treatment of the cultures in the presence of the supernatant fractions. In addition, tyrosine hydroxylase activity was significantly increased in the treated cultures. D-Tubo-curarine, an antagonist at the acetylcholine receptor, caused an increase in alpha-BGT binding after 7 days of treatment, while the agonist nicotine and choline had no effect. These results suggest that in brain supernatant there may exist an endogenous factor(s), which may function in the regulation of the nicotinic-like alpha-BGT receptors in neuronal cell.

  9. 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.

  10. 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

    2015-01-01

    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. PMID:25918166

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

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    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.

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

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    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.

  13. 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

  14. Crystal Structure of the Cystic Fibrosis Transmembrane Conductance Regulator Inhibitory Factor Cif Reveals Novel Active-Site Features of an Epoxide Hydrolase Virulence Factor

    Energy Technology Data Exchange (ETDEWEB)

    Bahl, C.; Morisseau, C; Bomberger, J; Stanton, B; Hammock, B; O& apos; Toole, G; Madden, D

    2010-01-01

    Cystic fibrosis transmembrane conductance regulator (CFTR) inhibitory factor (Cif) is a virulence factor secreted by Pseudomonas aeruginosa that reduces the quantity of CFTR in the apical membrane of human airway epithelial cells. Initial sequence analysis suggested that Cif is an epoxide hydrolase (EH), but its sequence violates two strictly conserved EH motifs and also is compatible with other {alpha}/{beta} hydrolase family members with diverse substrate specificities. To investigate the mechanistic basis of Cif activity, we have determined its structure at 1.8-{angstrom} resolution by X-ray crystallography. The catalytic triad consists of residues Asp129, His297, and Glu153, which are conserved across the family of EHs. At other positions, sequence deviations from canonical EH active-site motifs are stereochemically conservative. Furthermore, detailed enzymatic analysis confirms that Cif catalyzes the hydrolysis of epoxide compounds, with specific activity against both epibromohydrin and cis-stilbene oxide, but with a relatively narrow range of substrate selectivity. Although closely related to two other classes of {alpha}/{beta} hydrolase in both sequence and structure, Cif does not exhibit activity as either a haloacetate dehalogenase or a haloalkane dehalogenase. A reassessment of the structural and functional consequences of the H269A mutation suggests that Cif's effect on host-cell CFTR expression requires the hydrolysis of an extended endogenous epoxide substrate.

  15. 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

  16. dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data

    Science.gov (United States)

    Chung, Dongjun; Park, Dan; Myers, Kevin; Grass, Jeffrey; Kiley, Patricia; Landick, Robert; Keleş, Sündüz

    2013-01-01

    Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) has been successfully used for genome-wide profiling of transcription factor binding sites, histone modifications, and nucleosome occupancy in many model organisms and humans. Because the compact genomes of prokaryotes harbor many binding sites separated by only few base pairs, applications of ChIP-Seq in this domain have not reached their full potential. Applications in prokaryotic genomes are further hampered by the fact that well studied data analysis methods for ChIP-Seq do not result in a resolution required for deciphering the locations of nearby binding events. We generated single-end tag (SET) and paired-end tag (PET) ChIP-Seq data for factor in Escherichia coli (E. coli). Direct comparison of these datasets revealed that although PET assay enables higher resolution identification of binding events, standard ChIP-Seq analysis methods are not equipped to utilize PET-specific features of the data. To address this problem, we developed dPeak as a high resolution binding site identification (deconvolution) algorithm. dPeak implements a probabilistic model that accurately describes ChIP-Seq data generation process for both the SET and PET assays. For SET data, dPeak outperforms or performs comparably to the state-of-the-art high-resolution ChIP-Seq peak deconvolution algorithms such as PICS, GPS, and GEM. When coupled with PET data, dPeak significantly outperforms SET-based analysis with any of the current state-of-the-art methods. Experimental validations of a subset of dPeak predictions from PET ChIP-Seq data indicate that dPeak can estimate locations of binding events with as high as to resolution. Applications of dPeak to ChIP-Seq data in E. coli under aerobic and anaerobic conditions reveal closely located promoters that are differentially occupied and further illustrate the importance of high resolution analysis of ChIP-Seq data. PMID:24146601

  17. Constraining the factor analytical solutions obtained from multiple-year receptor modeling of ambient PM2.5 data from five speciation sites in Ontario, Canada

    Science.gov (United States)

    Sofowote, Uwayemi M.; Su, Yushan; Dabek-Zlotorzynska, Ewa; Rastogi, Ankit K.; Brook, Jeff; Hopke, Philip K.

    2015-05-01

    Rotational ambiguity in factor analyses leads to solutions that are not always consistent with reality. The inherent non-negativity constraints in positive matrix factorization (PMF) help to prevent factor solutions from becoming overly unrealistic, but they are not sufficient to prevent unwanted rotations that could manifest in factors that should have similar compositions varying across multiple sites. The Canadian National Air Pollution Surveillance (NAPS) network operates five fine particulate matter (PM2.5) speciation sites in Ontario. Data from these sites from 2005 to 2010 were subjected to PMF to obtain factors representing sources of particulate matter. Eight factors were found to be common across these sites. These factors had profiles that varied greatly from one site to the other, suggesting that the PMF solutions were impacted by some rotational ambiguity. New features in the EPA PMF V5 program allow the use of a priori information to impose mathematical constraints that guide the evolution of the factor solutions. These constraints reduce the rotational space. In situations where major emissions sources are known and located in the neighborhood of receptors, or emissions inventories and literature source profiles exist, it is easy to use these profiles to force the factor solutions to conform to the expected signatures. In our case, reported source profiles were neither available nor applicable due to the large spatial span of potential sources and receptor sites. This work describes how such constraints can be generated and used in these complex situations. The fundamental principle explored in this work is the concept of 'stiffness' of PMF solutions to identify the desirable non-rotating factors.

  18. 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

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

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    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

  20. 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.

  1. 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.

  2. 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.

  3. Independent risk factors for surgical site infection after cesarean delivery in a rural tertiary care medical center.

    Science.gov (United States)

    Vallejo, Manuel C; Attaallah, Ahmed F; Shapiro, Robert E; Elzamzamy, Osama M; Mueller, Michael G; Eller, Warren S

    2017-02-01

    We aimed to determine the incidence of surgical site infection (SSI) after cesarean delivery (CD) and identify the risk factors in a rural population. We identified 218 SSI patients by International Classification of Disease codes and matched them with 3131 parturients (control) from the electronic record database in a time-matched retrospective quality assurance analysis. The incidence of SSI after CD was 7.0 %. Risk factors included higher body mass index (BMI) [40.30 ± 10.60 kg/m 2 SSI (95 % CI 38.73-41.87) vs 34.05 ± 8.24 kg/m 2 control (95 % CI 33.75-34.35, P < 0.001)], years of education [13.28 ± 2.44 years SSI (95 % CI 12.9-13.66) vs 14.07 ± 2.81 years control (95 % CI 13.96-14.18, P < 0.001)], number of prior births [2 (1-9) SSI vs 1 (1-11) control (P < 0.001)], tobacco use (OR 1.49; 95 % CI 1.06-2.09, P = 0.03), prior diagnosis of hypertension (OR 1.80; 95 % CI 1.34-2.42, P < 0.001), gestational diabetes (OR 1.59; 95 % CI 1.18-2.13, P = 0.003), and an emergency/STAT CD (OR 1.6; 95 % CI 1.1-2.3, P = 0.01). Risk factors for SSI after CD included higher BMI, less years of education, higher prior births, tobacco use, prior diagnosis of hypertension, gestational diabetes, and emergency/STAT CD. The presence of ruptured membranes was protective against SSI.

  4. 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.

  5. 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.

  6. Identification of novel sites of O-N-acetylglucosamine modification of serum response factor using quadrupole time-of-flight mass spectrometry.

    Science.gov (United States)

    Chalkley, Robert J; Burlingame, A L

    2003-03-01

    The addition of a single N-acetylglucosamine moiety O-linked to serine and threonine residues of nuclear and cytoplasmic proteins is a widespread post-translational modification. The conventional method for detecting and locating sites of modification is through a multistep radioactivity-based approach. We have recently shown that sites of O-GlcNAc modification can be determined using quadrupole time-of-flight tandem mass spectrometry (Chalkley, R. J., and Burlingame, A. L. (2001) Identification of GlcNAcylation sites of peptides and alpha-crystallin using Q-TOF mass spectrometry. J. Am. Soc. Mass Spectrom. 12, 1106-1113). In this work utilization of this new approach has revealed previously undetected sites of O-GlcNAc modification of the transcription factor serum response factor.

  7. BASELINE PARAMETER UPDATE FOR HUMAN HEALTH INPUT AND TRANSFER FACTORS FOR RADIOLOGICAL PERFORMANCE ASSESSMENTS AT THE SAVANNAH RIVER SITE

    Energy Technology Data Exchange (ETDEWEB)

    Coffield, T; Patricia Lee, P

    2007-01-31

    The purpose of this report is to update parameters utilized in Human Health Exposure calculations and Bioaccumulation Transfer Factors utilized at SRS for Performance Assessment modeling. The reason for the update is to utilize more recent information issued, validate information currently used and correct minor inconsistencies between modeling efforts performed in SRS contiguous areas of the heavy industrialized central site usage areas called the General Separations Area (GSA). SRS parameters utilized were compared to a number of other DOE facilities and generic national/global references to establish relevance of the parameters selected and/or verify the regional differences of the southeast USA. The parameters selected were specifically chosen to be expected values along with identifying a range for these values versus the overly conservative specification of parameters for estimating an annual dose to the maximum exposed individual (MEI). The end uses are to establish a standardized source for these parameters that is up to date with existing data and maintain it via review of any future issued national references to evaluate the need for changes as new information is released. These reviews are to be added to this document by revision.

  8. Coupling chemical transport model source attributions with positive matrix factorization: application to two IMPROVE sites impacted by wildfires.

    Science.gov (United States)

    Sturtz, Timothy M; Schichtel, Bret A; Larson, Timothy V

    2014-10-07

    Source contributions to total fine particle carbon predicted by a chemical transport model (CTM) were incorporated into the positive matrix factorization (PMF) receptor model to form a receptor-oriented hybrid model. The level of influence of the CTM versus traditional PMF was varied using a weighting parameter applied to an object function as implemented in the Multilinear Engine (ME-2). The methodology provides the ability to separate features that would not be identified using PMF alone, without sacrificing fit to observations. The hybrid model was applied to IMPROVE data taken from 2006 through 2008 at Monture and Sula Peak, Montana. It was able to separately identify major contributions of total carbon (TC) from wildfires and minor contributions from biogenic sources. The predictions of TC had a lower cross-validated RMSE than those from either PMF or CTM alone. Two unconstrained, minor features were identified at each site, a soil derived feature with elevated summer impacts and a feature enriched in sulfate and nitrate with significant, but sporadic contributions across the sampling period. The respective mean TC contributions from wildfires, biogenic emissions, and other sources were 1.18, 0.12, and 0.12 ugC/m(3) at Monture and 1.60, 0.44, and 0.06 ugC/m(3) at Sula Peak.

  9. Genome-wide analysis of p63 binding sites identifies AP-2 factors as co-regulators of epidermal differentiation.

    Science.gov (United States)

    McDade, Simon S; Henry, Alexandra E; Pivato, Geraldine P; Kozarewa, Iwanka; Mitsopoulos, Constantinos; Fenwick, Kerry; Assiotis, Ioannis; Hakas, Jarle; Zvelebil, Marketa; Orr, Nicholas; Lord, Christopher J; Patel, Daksha; Ashworth, Alan; McCance, Dennis J

    2012-08-01

    The p63 transcription factor (TP63) is critical in development, growth and differentiation of stratifying epithelia. This is highlighted by the severity of congenital abnormalities caused by TP63 mutations in humans, the dramatic phenotypes in knockout mice and de-regulation of TP63 expression in neoplasia altering the tumour suppressive roles of the TP53 family. In order to define the normal role played by TP63 and provide the basis for better understanding how this network is perturbed in disease, we used chromatin immunoprecipitation combined with massively parallel sequencing (ChIP-seq) to identify >7500 high-confidence TP63-binding regions across the entire genome, in primary human neonatal foreskin keratinocytes (HFKs). Using integrative strategies, we demonstrate that only a subset of these sites are bound by TP53 in response to DNA damage. We identify a role for TP63 in transcriptional regulation of multiple genes genetically linked to cleft palate and identify AP-2alpha (TFAP2A) as a co-regulator of a subset of these genes. We further demonstrate that AP-2gamma (TFAP2C) can bind a subset of these regions and that acute depletion of either TFAP2A or TFAP2C alone is sufficient to reduce terminal differentiation of organotypic epidermal skin equivalents, indicating overlapping physiological functions with TP63.

  10. 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.

  11. What Factors Coordinate the Optimal Position of a Single Monitoring Well Down Gradient of a Hazardous Site?

    Science.gov (United States)

    Bode, F.; Nowak, W.

    2013-12-01

    Drinking-water well catchments include many sources for potential contaminations like gas stations, roads, or fields used for agriculture. Additionally, there are many contaminated sites that need to be monitored inside and outside drinking water catchments. Finding optimal positions of monitoring wells for such purposes is challenging because there are various parameters (and their uncertainties) that influence the reliability and optimality of a suggested monitoring location. For example, there may be uncertainty in the exact position of the contamination, in the source volume, in the direction of the velocity field which can vary in angle and absolute value, and in other parameters that describe, e.g., dispersion and decay. Many national regulations and UN guidelines suggest monitoring as measure of risk control, but make no statements how to asses or design monitoring under the fact of uncertainty. To obtain optimal positions of monitoring wells, a large body of recent studies uses formal optimization approaches. Our goal is to obtain a better system understanding at a fundamental process level for the one-on-one situation of a single monitoring well for a single monitoring target. This knowledge can be used for a better understanding of the optimization results in complex situations, and also to better guide and restrict optimization procedures by newly obtained export knowledge. In order to obtain fundamental statements regardless of specific simulation settings, we use an analytical model based on the 2D steady-state advection-dispersion equation to predict contaminant transport from the monitoring target. Monte Carlo simulation techniques are applied to represent parametric uncertainty. Thus, we can obtain maps of contaminant detection probability for all possible placements of the monitoring well. The optimal position is defined by the highest detection probability. First findings show that uncertainty in the spill location pushes the optimal monitoring

  12. Activation of factor IX zymogen results in exposure of a binding site for low-density lipoprotein receptor-related protein.

    Science.gov (United States)

    Neels, J G; van Den Berg, B M; Mertens, K; ter Maat, H; Pannekoek, H; van Zonneveld, A J; Lenting, P J

    2000-11-15

    The interaction between the endocytic receptor low density lipoprotein receptor-related protein (LRP) and either coagulation factor IX or its active derivative factor IXa was studied. Purified factor IX was unable to associate with LRP when analyzed by surface plasmon resonance. By contrast, factor XIa-mediated conversion of factor IX into factor IXa resulted in reversible dose- and calcium-dependent binding to LRP. Active-site blocking of factor IXa did not affect binding to LRP, whereas LRP binding was efficiently inhibited in the presence of heparin or antibodies against factor IX or LRP. The factor IXa-LRP interaction could be described by a 2-site binding model with equilibrium dissociation constants of 27 nmol/L and 69 nmol/L. Consistent with this model, it was observed that factor IXa binds to 2 different recombinant receptor fragments of LRP (denoted cluster II and cluster IV) with equilibrium dissociation constants of 227 nmol/L and 53 nmol/L, respectively. The amount of factor IXa degraded by LRP-deficient cells was 35% lower than by LRP-expressing cells, demonstrating that LRP contributes to the transport of factor IXa to the intracellular degradation pathway. Because ligand binding to LRP is often preceded by binding to proteoglycans, the contribution of proteoglycans to the catabolism of factor IXa was addressed by employing proteoglycan-deficient cells. Degradation of factor IXa by proteoglycan-deficient cells proceeded at a 83% lower rate than wild-type cells. In conclusion, the data presented here indicate that both LRP and proteoglycans have the potential to contribute to the catabolism of factor IXa.

  13. Network, cluster and risk factor analyses for porcine reproductive and respiratory syndrome using data from swine sites participating in a disease control program.

    Science.gov (United States)

    Arruda, A G; Friendship, R; Carpenter, J; Hand, K; Poljak, Z

    2016-06-01

    The objectives of this study were to describe networks of Ontario swine sites and their service providers (including trucking, feed, semen, gilt and boar companies); to categorize swine sites into clusters based on site-level centrality measures, and to investigate risk factors for porcine reproductive and respiratory syndrome (PRRS) using information gathered from the above-mentioned analyses. All 816 sites included in the current study were enrolled in the PRRS area regional control and elimination projects in Ontario. Demographics, biosecurity and network data were collected using a standardized questionnaire and PRRS status was determined on the basis of available diagnostic tests and assessment by site veterinarians. Two-mode networks were transformed into one-mode dichotomized networks. Cluster and risk factor analyses were conducted separately for breeding and growing pig sites. In addition to the clusters obtained from cluster analyses, other explanatory variables of interest included: production type, type of animal flow, use of a shower facility, and number of neighboring swine sites within 3km. Unadjusted univariable analyses were followed by two types of adjusted models (adjusted for production systems): a generalizing estimation equation model (GEE) and a generalized linear mixed model (GLMM). Results showed that the gilt network was the most fragmented network, followed by the boar and truck networks. Considering all networks simultaneously, approximately 94% of all swine sites were indirectly connected. Unadjusted risk factor analyses showed significant associations between almost all predictors of interest and PRRS positivity, but these disappeared once production system was taken into consideration. Finally, the vast majority of the variation on PRRS status was explained by production system according to GLMM, which shows the highly correlated nature of the data, and raises the point that interventions at this level could potentially have high

  14. [Human coagulation factor IX gene therapy in murine hemophilia B by hydrodynamic delivery and site-specific genomic integration].

    Science.gov (United States)

    Zhang, Lei; Gu, Dong-Sheng; DU, Wei-Ting; Liu, Peng-Xia; Lu, Shi-Hong; Yang, Ren-Chi

    2010-05-01

    To investigate whether the plasmid bearing attB and human coagulation factor IX (hFIX) coding sequence could insert into hemophilia B mice genome and persistently express hFIX with co-injected integrase. The plasmid attB-hFIX-pIRES2-EGFP was constructed, which bore attB site and hFIX coding sequence and was proved in vitro to express hFIX. The plasmid and CMV-int expressing integrase was co-infused rapidly in a large-volume solution through tail vein of hemophilia B mice. Mice infused with the plasmid alone served as controls. ELISA was performed to determine serum hFIX level. Correction of coagulation defect in vivo by plasmid infusion was assessed by bleeding time. Genomic integration of the plasmid was determined by nested PCR. The plasmid attB-hFIX-pIRES2-EGFP was successfully constructed. The hemophilia B mice produced (1533 ± 239) ng/ml hFIX at 24 hour after infusion of the hFIX encoding plasmid and the bleeding diathesis of the hemophilia B mice was significantly corrected as measured by clotting assays. However, whether or not co-injected with CMV-int, the serum hFIX level decreased to background level in 10 days after infusion. Nested-PCR results indicated that the integrase phiC31 resulted in the integration of the plasmid in the mouse liver chromosomes. Integrase phiC31 can catalyze recombination of 34 bp attB and pseudo-attP. Human FIX driven by CMV promoter can be transiently and highly expressed after infusion, but rapidly silenced in vivo.

  15. 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

  16. 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.

  17. Factors associated with HIV virologic failure among patients on HAART for one year at three sentinel surveillance sites in China.

    Science.gov (United States)

    Wang, Xia; Yang, Liting; Li, Huiqin; Zuo, La; Liang, Shujia; Liu, Wei; Dong, Yonghui; Yang, Shaomin; Shang, Hong; Li, Jingyun; Kang, Laiyi; Zhong, Ping; Zheng, Wei; Liao, Lingjie; Xing, Hui; Chen, Ray Y; Ruan, Yuhua; Shao, Yiming

    2011-03-01

    Emerging HIV drug resistance (HIVDR) poses a growing threat to the long-term success and durability of highly active antiretroviral therapy (HAART). To understand the incidence of HIVDR and estimate the proportion of potential HIVDR and its associated risk factors among the patients on HAART for one year. Antiretroviral-naïve patients ≥ 18 years old were invited to participate in this one-year prospective study from seven clinics in Yunnan, Guangxi, and Xinjiang provinces. A questionnaire and blood draw were collected at baseline and 12 month follow-up. The protocol used was modified slightly from the WHO Protocol for Surveys of HIV Drug Resistance Emerging During Treatment and Related Program Factors in Sentinel ART Sites in Resource-limited Settings. 435 subjects were included in the final analysis, with median baseline CD4 cell count 139 cells/mm3. Of the total 417 patients who fall under WHO guidelines for 'Classification of outcomes based on endpoints' (on ART at 12 months, switch, lost to follow-up, and stop), 90 (21.6%) did not have any drug resistant mutations (potential HIVDR) and 17 (4.1%) did (HIVDR, Table 2). The remaining 310 (75.3%) had a viral load 1000 copies/ml.Patients who self-reported missing doses in the previous month were 6.2 fold (95% CI 2.5-15.7) more likely to fail than those who did not. and those from Xinjiang were 12.1 fold (95% CI 5.2-28.1) more likely to fail compared to those from Yunnan and Guangxi. Why Xinjiang was associated with virologic failure was not clear but may be related to the demographics of the participants from Xinjiang, being significantly more IDUs, poorer, and less adherent than those from Yunnan and Guangxi. Although successful virologic outcomes were seen in the vast majority (75.3%) of those treated at one year, virologic failure continues to be a problem particularly among those less adherent and from Xinjiang. Additional data are needed to understand the generalizability of these results, particularly those

  18. 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…

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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

  4. Burnout among the addiction counseling workforce: the differential roles of mindfulness and values-based processes and work-site factors.

    Science.gov (United States)

    Vilardaga, Roger; Luoma, Jason B; Hayes, Steven C; Pistorello, Jacqueline; Levin, Michael E; Hildebrandt, Mikaela J; Kohlenberg, Barbara; Roget, Nancy A; Bond, Frank

    2011-06-01

    Although work-site factors have been shown to be a consistent predictor of burnout, the importance of mindfulness and values-based processes among addiction counselors has been little examined. In this study, we explored how strongly experiential avoidance, cognitive fusion, and values commitment related to burnout after controlling for well-established work-site factors (job control, coworker support, supervisor support, salary, workload, and tenure). We conducted a cross-sectional survey among 699 addiction counselors working for urban substance abuse treatment providers in six states of the United States. Results corroborated the importance of work-site factors for burnout reduction in this specific population, but we found that mindfulness and values-based processes had a stronger and more consistent relationship with burnout as compared with work-site factors. We conclude that interventions that target experiential avoidance, cognitive fusion, and values commitment may provide a possible new direction for the reduction of burnout among addiction counselors. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. A retrospective analysis of the risk factors for surgical site infections and long-term follow-up after transpalpebral enucleation in horses

    NARCIS (Netherlands)

    Huppes, Tsjester; Hermans, Hanneke; Ensink, Jos M

    2017-01-01

    BACKGROUND: Implants are often used to improve the cosmetic appearance of horses after enucleation of the eye. When surgical site infection (SSI) occurs, the implant will almost always be lost. The aim of this study is to collect data on the risk factors for SSIs and report long-term follow-up

  6. Characteristics of and factors associated with dengue vector breeding sites in the City of Colombo, Sri Lanka.

    Science.gov (United States)

    Louis, Valérie R; Montenegro Quiñonez, Carlos Alberto; Kusumawathie, Pad; Palihawadana, Paba; Janaki, Sakoo; Tozan, Yesim; Wijemuni, Ruwan; Wilder-Smith, Annelies; Tissera, Hasitha A

    2016-03-01

    Dengue has emerged as a major public health problem in Sri Lanka. Vector control at community level is a frequent and widespread strategy for dengue control. The aim of the study was to assess Aedes mosquito breeding sites and the prevention practices of community members in a heavily urbanized part of Colombo. A cross-sectional entomological survey was conducted from April to June 2013 in 1469 premises located in a subdistrict of the City of Colombo. Types of breeding sites and, where found, their infestation with larvae or pupae were recorded. Furthermore, a questionnaire was administered to the occupants of these premises to record current practices of dengue vector control. The surveyed premises consisted of 1341 residential premises and 110 non-residential premises (11 schools, 99 work or public sites), 5 open lands, and 13 non-specified. In these 1469 premises, 15447 potential breeding sites suitable to host larvae of pupae were found; of these sites18.0% contained water. Among the 2775 potential breeding sites that contained water, 452 (16.3%) were positive for larvae and/or pupae. Schools were associated with the proportionally highest number of breeding sites; 85 out of 133 (63.9%) breeding sites were positive for larvae and/or pupae in schools compared with 338 out of 2288 (14.8%) in residential premises. The odds ratio (OR) for schools and work or public sites for being infested with larvae and/or pupae was 2.77 (95% CI 1.58, 4.86), when compared to residential premises. Occupants of 80.8% of the residential premises, 54.5% of the schools and 67.7% of the work or public sites reported using preventive measures. The main prevention practices were coverage of containers and elimination of mosquito breeding places. Occupants of residential premises were much more likely to practice preventive measures than were those of non-residential premises (OR 2.23; 1.49, 3.36). Schools and working sites were associated with the highest numbers of breeding sites and

  7. Risk factors for progression of atherosclerosis measured at multiple sites in the arterial tree - The Rotterdam Study

    NARCIS (Netherlands)

    van der Meer, IM; del Sol, AI; Hak, AE; Bots, ML; Hofman, A; Witteman, JCM

    2003-01-01

    Background and Purpose - Studies investigating determinants of atherosclerotic disease progression are relatively rare. Moreover, although atherosclerotic disease can be assessed noninvasively in different vascular beds, previous studies have not considered progression of atherosclerosis at >1 site.

  8. 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

  9. Genome-Wide Mapping of Binding Sites Reveals Multiple Biological Functions of the Transcription Factor Cst6p in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Liu, Guodong; Bergenholm, David; Nielsen, Jens

    2016-01-01

    In the model eukaryote Saccharomyces cerevisiae, the transcription factor Cst6p has been reported to play important roles in several biological processes. However, the genome-wide targets of Cst6p and its physiological functions remain unknown. Here, we mapped the genome-wide binding sites of Cst6p...... of transcription factors. In the model eukaryote Saccharomyces cerevisiae, the transcription factor Cst6p has been reported to regulate several biological processes, while its genome-wide targets remain unknown. Here, we mapped the genome-wide binding sites of Cst6p at high resolution. We show that the binding...... at high resolution. Cst6p binds to the promoter regions of 59 genes with various biological functions when cells are grown on ethanol but hardly binds to the promoter at any gene when cells are grown on glucose. The retarded growth of the CST6 deletion mutant on ethanol is attributed to the markedly...

  10. 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 :...

  11. Protein oxidation mediated by heme-induced active site conversion specific for heme-regulated transcription factor, iron response regulator.

    Science.gov (United States)

    Kitatsuji, Chihiro; Izumi, Kozue; Nambu, Shusuke; Kurogochi, Masaki; Uchida, Takeshi; Nishimura, Shin-ichiro; Iwai, Kazuhiro; O'Brian, Mark R; Ikeda-Saito, Masao; Ishimori, Koichiro

    2016-01-05

    The Bradyrhizobium japonicum transcriptional regulator Irr (iron response regulator) is a key regulator of the iron homeostasis, which is degraded in response to heme binding via a mechanism that involves oxidative modification of the protein. Here, we show that heme-bound Irr activates O2 to form highly reactive oxygen species (ROS) with the "active site conversion" from heme iron to non-heme iron to degrade itself. In the presence of heme and reductant, the ROS scavenging experiments show that Irr generates H2O2 from O2 as found for other hemoproteins, but H2O2 is less effective in oxidizing the peptide, and further activation of H2O2 is suggested. Interestingly, we find a time-dependent decrease of the intensity of the Soret band and appearance of the characteristic EPR signal at g = 4.3 during the oxidation, showing the heme degradation and the successive formation of a non-heme iron site. Together with the mutational studies, we here propose a novel "two-step self-oxidative modification" mechanism, during which O2 is activated to form H2O2 at the heme regulatory motif (HRM) site and the generated H2O2 is further converted into more reactive species such as ·OH at the non-heme iron site in the His-cluster region formed by the active site conversion.

  12. 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)

  13. The number of metastatic sites for stage IIIA endometrial carcinoma, endometrioid cell type, is a strong negative prognostic factor

    NARCIS (Netherlands)

    Jobsen, Jan J.; Naudin ten Cate, Lambert; Lybeert, Marnix L.M.; van der Steen-Banasik, Elzbieta M.; Scholten, A.M.; van der Palen, Jacobus Adrianus Maria; van der Palen, J.; Slot, Annerie; Stenfert Kroese, Marika C.; Schutter, Eltjo M.; Siesling, Sabine

    2010-01-01

    The aim of this study was to look at the impact of the number of sites with tumour involvement on outcome for patients with stage IIIA endometrioid-type endometrial carcinoma. Patients and methods: 141 patients stage IIIA were included. A central histopathological review was performed. Patients

  14. 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

  15. 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.

  16. Frequent chloroplast RNA editing in early-branching flowering plants: pilot studies on angiosperm-wide coexistence of editing sites and their nuclear specificity factors.

    Science.gov (United States)

    Hein, Anke; Polsakiewicz, Monika; Knoop, Volker

    2016-01-25

    RNA editing by cytidine-to-uridine conversions is an essential step of RNA maturation in plant organelles. Some 30-50 sites of C-to-U RNA editing exist in chloroplasts of flowering plant models like Arabidopsis, rice or tobacco. We now predicted significantly more RNA editing in chloroplasts of early-branching angiosperm genera like Amborella, Calycanthus, Ceratophyllum, Chloranthus, Illicium, Liriodendron, Magnolia, Nuphar and Zingiber. Nuclear-encoded RNA-binding pentatricopeptide repeat (PPR) proteins are key editing factors expected to coevolve with their cognate RNA editing sites in the organelles. With an extensive chloroplast transcriptome study we identified 138 sites of RNA editing in Amborella trichopoda, approximately the 3- to 4-fold of cp editing in Arabidopsis thaliana or Oryza sativa. Selected cDNA studies in the other early-branching flowering plant taxa furthermore reveal a high diversity of early angiosperm RNA editomes. Many of the now identified editing sites in Amborella have orthologues in ferns, lycophytes or hornworts. We investigated the evolution of CRR28 and RARE1, two known Arabidopsis RNA editing factors responsible for cp editing events ndhBeU467PL, ndhDeU878SL and accDeU794SL, respectively, all of which we now found conserved in Amborella. In a phylogenetically wide sampling of 65 angiosperm genomes we find evidence for only one single loss of CRR28 in chickpea but several independent losses of RARE1, perfectly congruent with the presence of their cognate editing sites in the respective cpDNAs. Chloroplast RNA editing is much more abundant in early-branching than in widely investigated model flowering plants. RNA editing specificity factors can be traced back for more than 120 million years of angiosperm evolution and show highly divergent patterns of evolutionary losses, matching the presence of their target editing events.

  17. Variation in transfer factor of radiocaesium in bank voles (Clethrionomys glareolus) in clear cut and mature forest sites after the Chernobyl accident

    Energy Technology Data Exchange (ETDEWEB)

    Palo, Thomas R. [Mid-Sweden University, Department of Natural Sciences, Holmgatan 10, 85170 Sundsvall (Sweden)]. E-mail: thomas.palo@miun.se

    2007-07-01

    Bank voles that were collected between 1986 and 2004 at sites in Chernobyl fallout areas of northern Sweden showed higher {sup 137}Cs activity concentrations at the mature forest sites compared to clear cuts. This difference was not attributed to differences in ground deposition between sites but to differences in aggregated transfer rates to voles. Differences in transfer between forest types were evident for all years 1986-2004 but the change occurred at different rates in the two habitats. The apparent transfer factor between bilberry (Vaccinium myrtillus) and voles was positively related and indicated that a biomagnification was about 1.5 from vegetation to these small mammalian herbivores. The aggregated transfer factor to bank voles measured in the forest habitat, although starting at higher levels declined faster with time than clear cut sites and the differences between the forest habitat and the clear cut areas diminished with time. After the Chernobyl accident in 1986 the mean level in bank vole was 514 Bq/kg fresh mass (SD = 505) that increased to 1485 Bq/kg (SD = 881) in 1988. The activity concentration declined thereafter. The bank voles collected in similar habitats in 2004 contained on average 1022 Bq/kg (SD = 723). Still 18 years after the radionuclide fallout over Sweden high activity concentrations in voles could be found.

  18. 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

  19. 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

  20. Analysis of factors associated with development of Bacille Calmette-Guérin inoculation site change in patients with Kawasaki disease.

    Science.gov (United States)

    Araki, Tooru; Kodera, Aya; Kitada, Kunimi; Fujiwara, Michimasa; Muraoka, Michiko; Abe, Yoshiko; Ikeda, Masanori; Tsukahara, Hirokazu

    2018-04-01

    Objective The present study was performed to identify factors associated with a Bacille Calmette-Guérin (BCG) inoculation site change in patients with Kawasaki disease (KD). Methods Among patients who had received BCG vaccination and treatment for KD at our hospital from 2005 through 2016, 177 patients born in 2005 through 2016 were enrolled. The patients were divided into those with (n = 83, change group) and without (n = 94, no-change group) a BCG site change, and the patient demographics, clinical severity, blood examination results, and echocardiographic findings were compared between the two groups. Results The change group was younger at onset and had a shorter interval from vaccination to onset. A BCG site change was observed in patients who developed the onset of KD symptoms from 31 to 806 days after BCG vaccination. Multivariate analysis showed that the interval from vaccination was closely and positively associated with the BCG site change (hazard ratio = 0.995, 95% confidence interval = 0.993-0.997). Conclusion A BCG site change in patients with KD is most closely associated with the interval from BCG vaccination to onset.

  1. 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.

  2. Methylation at a transcription factor-binding site on the 5-HT1A receptor gene correlates with negative symptom treatment response in first episode schizophrenia.

    Science.gov (United States)

    Tang, Hao; Dalton, Caroline F; Srisawat, Umarat; Zhang, Zhi Jun; Reynolds, Gavin P

    2014-04-01

    Individual variability and inadequate response of negative symptoms are major limitations of antipsychotic treatment in schizophrenia. A functional polymorphism, rs6295, in the 5-HT1A-receptor gene (HTR1A) contributes to this variability in negative symptom response. The DNA sequence containing rs6295 is rich in cytosine methylation (CpG) sites; CpG methylation is an epigenetic factor that, like rs6295, can modify transcriptional control. To investigate whether DNA methylation influences response to antipsychotic treatment, we determined methylation at CpG sites close to rs6295 in DNA from 82 Chinese subjects with a first psychotic episode. Methylation of one CpG site within a recognition sequence for HES transcriptional repressors was found to correlate with changes in total PANSS score (p = 0.006) and negative factor sub-score (p factor score (p = 0.019); the effect on symptom change remained after correction for this baseline score. An effect of rs6295 on negative symptom response was not seen in this sample, which may not have provided sufficient power for the pharmacogenetic association. These preliminary results indicate that epigenetic modification of transcriptional regulation by specific cytosine methylation may modulate HTR1A expression, resulting in effects on emotional dysfunction and negative symptom response to antipsychotic treatment.

  3. DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Silvis Remko

    2008-12-01

    Full Text Available Abstract Background A typical step in the analysis of gene expression data is the determination of clusters of genes that exhibit similar expression patterns. Researchers are confronted with the seemingly arbitrary choice between numerous algorithms to perform cluster analysis. Results We developed an exploratory application that benchmarks the results of clustering methods using functional annotations. In addition, a de novo DNA motif discovery algorithm is integrated in our program which identifies overrepresented DNA binding sites in the upstream DNA sequences of genes from the clusters that are indicative of sites of transcriptional control. The performance of our program was evaluated by comparing the original results of a time course experiment with the findings of our application. Conclusion DISCLOSE assists researchers in the prokaryotic research community in systematically evaluating results of the application of a range of clustering algorithms to transcriptome data. Different performance measures allow to quickly and comprehensively determine the best suited clustering approach for a given dataset.

  4. Temporal variations in gaseous elemental mercury concentrations at a contaminated site: Main factors affecting nocturnal maxima in daily cycles

    Science.gov (United States)

    Esbrí, José M.; Martínez-Coronado, Alba; Higueras, Pablo L.

    2016-01-01

    Mercury is considered to be a global pollutant and it has been globally transported as gaseous elemental mercury (GEM). International networks for the continuous monitoring of mercury, all of which are based on background sites, study the dispersion pattern of this metal and trends in its evolution in time and space. However, information about seasonal and daily cycling of polluted sites is scarce. The aim of the work described here was to cover this gap in knowledge. For this purpose, continuous (GEM) measurements were carried out in Almadén town from November 2011 to September 2013. Meteorological data were also collected during this time. GEM data show an average concentration during the sampling period (2011-2013) of 27.4 ng m-3, with a range of 0.8-686.9 ng m-3. The results highlighted seasonal and daily cycles of GEM in Almadén town, with seasonally higher levels in summer (686.9 ng m-3) and significantly daily higher levels during the night. A multiple linear regression model has established wind speed as the best GEM predictor in all seasons during the night, while the best predictor in winter is relative humidity, temperature in spring, solar radiation in summer and wind speed in autumn during the day. These results provide evidence that, in mining polluted sites like Almadén, photochemical reactions have a negligible impact on GEM levels during the daytime and that meteorological parameters are more relevant. Further studies on diurnal GEM cycling in polluted sites must be carried out to obtain a realistic local risk assessment, taking into account night GEM levels and their importance in each case study.

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

    OpenAIRE

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

    2015-01-01

    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 ...

  6. Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions.

    Science.gov (United States)

    Levitsky, Victor G; Ignatieva, Elena V; Ananko, Elena A; Turnaev, Igor I; Merkulova, Tatyana I; Kolchanov, Nikolay A; Hodgman, T C

    2007-12-19

    Reliable transcription factor binding site (TFBS) prediction methods are essential for computer annotation of large amount of genome sequence data. However, current methods to predict TFBSs are hampered by the high false-positive rates that occur when only sequence conservation at the core binding-sites is considered. To improve this situation, we have quantified the performance of several Position Weight Matrix (PWM) algorithms, using exhaustive approaches to find their optimal length and position. We applied these approaches to bio-medically important TFBSs involved in the regulation of cell growth and proliferation as well as in inflammatory, immune, and antiviral responses (NF-kappaB, ISGF3, IRF1, STAT1), obesity and lipid metabolism (PPAR, SREBP, HNF4), regulation of the steroidogenic (SF-1) and cell cycle (E2F) genes expression. We have also gained extra specificity using a method, entitled SiteGA, which takes into account structural interactions within TFBS core and flanking regions, using a genetic algorithm (GA) with a discriminant function of locally positioned dinucleotide (LPD) frequencies. To ensure a higher confidence in our approach, we applied resampling-jackknife and bootstrap tests for the comparison, it appears that, optimized PWM and SiteGA have shown similar recognition performances. Then we applied SiteGA and optimized PWMs (both separately and together) to sequences in the Eukaryotic Promoter Database (EPD). The resulting SiteGA recognition models can now be used to search sequences for BSs using the web tool, SiteGA. Analysis of dependencies between close and distant LPDs revealed by SiteGA models has shown that the most significant correlations are between close LPDs, and are generally located in the core (footprint) region. A greater number of less significant correlations are mainly between distant LPDs, which spanned both core and flanking regions. When SiteGA and optimized PWM models were applied together, this substantially reduced

  7. 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.

  8. 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.

  9. Simultaneous factor analysis of organic particle and gas mass spectra: AMS and PTR-MS measurements at an urban site

    Science.gov (United States)

    Slowik, J. G.; Vlasenko, A.; McGuire, M.; Evans, G. J.; Abbatt, J. P. D.

    2010-02-01

    During the winter component of the SPORT (Seasonal Particle Observations in the Region of Toronto) field campaign, particulate non-refractory chemical composition and concentration of selected volatile organic compounds (VOCs) were measured by an Aerodyne time-of-flight aerosol mass spectrometer (AMS) and a proton transfer reaction-mass spectrometer (PTR-MS), respectively. Sampling was performed in downtown Toronto ~15 m from a major road. The mass spectra from the AMS and PTR-MS were combined into a unified dataset, which was analysed using positive matrix factorization (PMF). The two instruments were given balanced weight in the PMF analysis by the application of a scaling factor to the uncertainties of each instrument. A residual based metric, Δsolid #000; color: #000;">esc, was used to evaluate the instrument relative weight within each solution. The PMF analysis yielded a 6-factor solution that included factors characteristic of regional transport, local traffic emissions, charbroiling and oxidative processing. The unified dataset provides information on emission sources (particle and VOC) and atmospheric processing that cannot be obtained from the datasets of the individual instruments: (1) apportionment of oxygenated VOCs to either direct emission sources or secondary reaction products; (2) improved correlation of oxygenated aerosol factors with photochemical age; and (3) increased detail regarding the composition of oxygenated organic aerosol factors. This analysis represents the first application of PMF to a unified AMS/PTR-MS dataset.

  10. 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

  11. 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.

  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

    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...... of complementary functional genomics filters, makes it possible to translate, for each TF, protein binding microarray data into a set of high-quality target genes. With this approach, we confirm NAC target genes reported from independent in vivo analyses. We emphasize that candidate target gene sets together...

  13. Factors influencing the atmospheric concentrations of PCBs at an abandoned e-waste recycling site in South China.

    Science.gov (United States)

    Wang, Yan; Wu, Xiaowei; Hou, Minmin; Zhao, Hongxia; Chen, Ruize; Luo, Chunling; Zhang, Gan

    2017-02-01

    The diurnal atmospheric concentrations of polychlorinated biphenyls (PCBs) were investigated at an abandoned e-waste recycling site in South China during winter and summer. Total PCB concentrations during winter and summer were 27.6-212 and 368-1704pg/m 3 in the particulate phase and 270-697 and 3000-15,500pg/m 3 in the gaseous phase, respectively. Both gaseous and particulate PCB concentrations and compositions exhibited significant difference between winter and summer samples, but no diurnal variations during the measurement period. The correlation analysis between PCB concentrations and meteorological conditions, including atmospheric temperature, humidity, and mixing layer height, suggested that the seasonal variability of atmospheric PCB concentrations was strongly temperature-dependent, while the diurnal variability was probably source-dependent. The temperature-driven variations can also be proved by the significant linear correlation between ln P and 1/T in the Clausius-Clapeyron plot. Although government has implemented controls to reduce e-waste pollution, both the relatively high concentrations of PCBs and the diurnal variation in the air suggested that emissions from occasional e-waste recycling activities may still exist in this recycling area. These results underline the importance of continuing e-waste recycling site management long after abandonment. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Solution structure of human insulin-like growth factor II; recognition sites for receptors and binding proteins.

    OpenAIRE

    Terasawa, H; Kohda, D; Hatanaka, H; Nagata, K; Higashihashi, N; Fujiwara, H; Sakano, K; Inagaki, F

    1994-01-01

    The three-dimensional structure of human insulin-like growth factor II was determined at high resolution in aqueous solution by NMR and simulated annealing based calculations. The structure is quite similar to those of insulin and insulin-like growth factor I, which consists of an alpha-helix followed by a turn and a strand in the B-region and two antiparallel alpha-helices in the A-region. However, the regions of Ala1-Glu6, Pro31-Arg40 and Thr62-Glu67 are not well-defined for lack of distanc...

  15. Do differences in risk factors, medical care seeking, or medical practices explain the geographic variation in campylobacteriosis in Foodborne Diseases Active Surveillance Network (FoodNet) sites?

    Science.gov (United States)

    Ailes, Elizabeth; Scallan, Elaine; Berkelman, Ruth L; Kleinbaum, David G; Tauxe, Robert V; Moe, Christine L

    2012-06-01

    In the United States, considerable geographic variation in the rates of culture-confirmed Campylobacter infection has been consistently observed among sites participating in the Foodborne Diseases Active Surveillance Network (FoodNet). We used data from the FoodNet Population Surveys and a FoodNet case-control study of sporadic infection to examine whether differences in medical care seeking, medical practices, or risk factors contributed to geographic variation in incidence. We found differences across the FoodNet sites in the proportion of persons seeking medical care for an acute campylobacteriosis-like illness (range, 24.9%-43.5%) and in the proportion of ill persons who submitted a stool sample (range, 18.6%-40.7%), but these differences were not statistically significant. We found no evidence of geographic effect modification of previously identified risk factors for campylobacteriosis in the case-control study analysis. The prevalence of some exposures varied among control subjects in the FoodNet sites, including the proportion of controls reporting eating chicken at a commercial eating establishment (18.2%-46.1%); contact with animal stool (8.9%-30.9%); drinking water from a lake, river, or stream (0%-5.1%); and contact with a farm animal (2.1%-12.7%). However, these differences do not fully explain the geographic variation in campylobacteriosis. Future studies that quantify Campylobacter contamination in poultry or variation in host immunity may be useful in identifying sources of this geographic variation in incidence.

  16. PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments

    Science.gov (United States)

    Zambelli, Federico; Pesole, Graziano; Pavesi, Giulio

    2013-01-01

    Chromatin immunoprecipitation followed by sequencing with next-generation technologies (ChIP-Seq) has become the de facto standard for building genome-wide maps of regions bound by a given transcription factor (TF). The regions identified, however, have to be further analyzed to determine the actual DNA-binding sites for the TF, as well as sites for other TFs belonging to the same TF complex or in general co-operating or interacting with it in transcription regulation. PscanChIP is a web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria. PscanChIP can successfully identify not only the actual binding sites for the TF investigated by a ChIP-Seq experiment but also secondary motifs corresponding to other TFs that tend to bind the same regions, and, if present, precise positional correlations among their respective sites. The web interface is free for use, and there is no login requirement. It is available at http://www.beaconlab.it/pscan_chip_dev. PMID:23748563

  17. 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...

  18. Determining the factors associated with seedling herbivory on afforested carbon sequestration sites in the Lower Mississippi Alluvial Valley: preliminary results

    Science.gov (United States)

    Daniel C. Sumerall; Donald L. Grebner; Jeanne C. Jones; Stephen C. Grado; Richard P. Maiers; Keith L. Belli

    2010-01-01

    One causal factor of failed afforestation attempts in the Lower Mississippi Alluvial Valley (LMAV) is mammalian herbivory. Herbivory of seedlings generally reduces growth and can also lead to seedling mortality. Seedlings were randomly selected for monitoring throughout the first growing season. Growth and survival data were recorded, as were signs of mammalian...

  19. Replication factor c recruits dna polymerase δ to sites of nucleotide excision repair but is not required for PCNA recruitment

    NARCIS (Netherlands)

    R.M. Overmeer (René); A.M. Gourdin (Audrey); G. Giglia-Mari (Giuseppina); H.J.M. Kool (Hanneke); A.B. Houtsmuller (Adriaan); T. Siegal (Tali); M.I. Fousteri (Maria); L.H.F. Mullenders (Leon); W. Vermeulen (Wim)

    2010-01-01

    textabstractNucleotide excision repair (NER) operates through coordinated assembly of repair factors into pre- and postincisioncomplexes. The postincision step of NER includes gap-filling DNA synthesis and ligation. However, the exact composition of this NER-associated DNA synthesis complex in vivo

  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. 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.

  2. Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites.

    Science.gov (United States)

    Radka, Christopher D; DeLucas, Lawrence J; Wilson, Landon S; Lawrenz, Matthew B; Perry, Robert D; Aller, Stephen G

    2017-07-01

    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. In Yersinia 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.

  3. 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.

  4. 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 ...

  5. 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.

  6. 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.

  7. Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites.

    Science.gov (United States)

    Liu, Ce Feng; Brandt, Gabriel S; Hoang, Quyen Q; Naumova, Natalia; Lazarevic, Vanja; Hwang, Eun Sook; Dekker, Job; Glimcher, Laurie H; Ringe, Dagmar; Petsko, Gregory A

    2016-10-25

    The transcription factor T-bet (Tbox protein expressed in T cells) is one of the master regulators of both the innate and adaptive immune responses. It plays a central role in T-cell lineage commitment, where it controls the T H 1 response, and in gene regulation in plasma B-cells and dendritic cells. T-bet is a member of the Tbox family of transcription factors; however, T-bet coordinately regulates the expression of many more genes than other Tbox proteins. A central unresolved question is how T-bet is able to simultaneously recognize distant Tbox binding sites, which may be located thousands of base pairs away. We have determined the crystal structure of the Tbox DNA binding domain (DBD) of T-bet in complex with a palindromic DNA. The structure shows a quaternary structure in which the T-bet dimer has its DNA binding regions splayed far apart, making it impossible for a single dimer to bind both sites of the DNA palindrome. In contrast to most other Tbox proteins, a single T-bet DBD dimer binds simultaneously to identical half-sites on two independent DNA. A fluorescence-based assay confirms that T-bet dimers are able to bring two independent DNA molecules into close juxtaposition. Furthermore, chromosome conformation capture assays confirm that T-bet functions in the direct formation of chromatin loops in vitro and in vivo. The data are consistent with a looping/synapsing model for transcriptional regulation by T-bet in which a single dimer of the transcription factor can recognize and coalesce distinct genetic elements, either a promoter plus a distant regulatory element, or promoters on two different genes.

  8. 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.

  9. 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 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.

  10. 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%, pgender 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. 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

  11. Calculation of site specific characterisation factors for metal ecotoxicity using decoupled multi species fate and exposure modelling

    DEFF Research Database (Denmark)

    Birkved, Morten; Strandesen, Maria; Larsen, HF

    2004-01-01

    Calculation of characterisation factors (CF’s) for metal ecotoxicity typically involves fate and exposure modelling of metals in multi-media models developed for assessment of organic compounds. Metals do not follow the fate patterns of organic chemicals, and the results will therefore most likely...... misrepresent the exposure concentration of metals. However, using multiple versions of such models for individual metal species within each model region and linking these to databases containing information on speciation pattern and fate properties of the individual metal species enables the assessment...... to the part of the metal species present as complexes which is very hard to account for in single species assessment. Preliminary results on the CF’s based on single species assessment and decoupled multi species assessment will be presented for 4 common metals....

  12. The DMI1 and DMI2 Early Symbiotic Genes of Medicago truncatula Are Required for a High-Affinity Nodulation Factor-Binding Site Associated to a Particulate Fraction of Roots1

    Science.gov (United States)

    Hogg, Bridget V.; Cullimore, Julie V.; Ranjeva, Raoul; Bono, Jean-Jacques

    2006-01-01

    The establishment of the legume-rhizobia symbiosis between Medicago spp. and Sinorhizobium meliloti is dependent on the production of sulfated lipo-chitooligosaccharidic nodulation (Nod) factors by the bacterial partner. In this article, using a biochemical approach to characterize putative Nod factor receptors in the plant host, we describe a high-affinity binding site (Kd = 0.45 nm) for the major Nod factor produced by S. meliloti. This site is termed Nod factor-binding site 3 (NFBS3). NFBS3 is associated to a high-density fraction prepared from roots of Medicago truncatula and shows binding specificity for lipo-chitooligosaccharidic structures. As for the previously characterized binding sites (NFBS1 and NFBS2), NFBS3 does not recognize the sulfate group on the S. meliloti Nod factor. Studies of Nod factor binding in root extracts of early symbiotic mutants of M. truncatula reveals that the new site is present in Nod factor perception and does not make infections 3 (dmi3) mutants but is absent in dmi1 and dmi2 mutants. Roots and cell cultures of all these mutants still contain sites similar to NFBS1 and NFBS2, respectively. These results suggest that NFBS3 is different from NFBS2 and NFBS1 and is dependent on the common symbiotic genes DMI1 and DMI2 required for establishment of symbioses with both rhizobia and arbuscular mycorrhizal fungi. The potential role of this site in the establishment of root endosymbioses is discussed. PMID:16377749

  13. 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.

  14. 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.

  15. Technical factors in the site selection for a radioactive wastes storage of low and intermediate level;Factores tecnicos en la seleccion del sitio para un almacen de desechos radioactivos de bajo y medio nivel

    Energy Technology Data Exchange (ETDEWEB)

    Badillo A, V. E.; Ramirez S, J. R.; Palacios H, J. C., E-mail: veronica.badillo@inin.gob.m [ININ, Carretera Mexico-Toluca s/n, 52750 Ocoyoacac, Estado de Mexico (Mexico)

    2009-10-15

    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)

  16. Host DNA damage response factors localize to merkel cell polyomavirus DNA replication sites to support efficient viral DNA replication.

    Science.gov (United States)

    Tsang, Sabrina H; Wang, Xin; Li, Jing; Buck, Christopher B; You, Jianxin

    2014-03-01

    Accumulating evidence indicates a role for Merkel cell polyomavirus (MCPyV) in the development of Merkel cell carcinoma (MCC), making MCPyV the first polyomavirus to be clearly associated with human cancer. With the high prevalence of MCPyV infection and the increasing amount of MCC diagnosis, there is a need to better understand the virus and its oncogenic potential. In this study, we examined the relationship between the host DNA damage response (DDR) and MCPyV replication. We found that components of the ATM- and ATR-mediated DDR pathways accumulate in MCPyV large T antigen (LT)-positive nuclear foci in cells infected with native MCPyV virions. To further study MCPyV replication, we employed our previously established system, in which recombinant MCPyV episomal DNA is autonomously replicated in cultured cells. Similar to native MCPyV infection, where both MCPyV origin and LT are present, the host DDR machinery colocalized with LT in distinct nuclear foci. Immunofluorescence in situ hybridization and bromodeoxyuridine (BrdU) incorporation analysis showed that these DDR proteins and MCPyV LT in fact colocalized at the actively replicating MCPyV replication complexes, which were absent when a replication-defective LT mutant or an MCPyV-origin mutant was introduced in place of wild-type LT or wild-type viral origin. Inhibition of DDR kinases using chemical inhibitors and ATR/ATM small interfering RNA (siRNA) knockdown reduced MCPyV DNA replication without significantly affecting LT expression or the host cell cycle. This study demonstrates that these host DDR factors are important for MCPyV DNA replication, providing new insight into the host machinery involved in the MCPyV life cycle. MCPyV is the first polyomavirus to be clearly associated with human cancer. However, the MCPyV life cycle and its oncogenic mechanism remain poorly understood. In this report, we show that, in cells infected with native MCPyV virions, components of the ATM- and ATR-mediated DDR

  17. 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.

  18. EBNA2 Drives Formation of New Chromosome Binding Sites and Target Genes for B-Cell Master Regulatory Transcription Factors RBP-jκ and EBF1.

    Science.gov (United States)

    Lu, Fang; Chen, Horng-Shen; Kossenkov, Andrew V; DeWispeleare, Karen; Won, Kyoung-Jae; Lieberman, Paul M

    2016-01-01

    Epstein-Barr Virus (EBV) transforms resting B-lymphocytes into proliferating lymphoblasts to establish latent infections that can give rise to malignancies. We show here that EBV-encoded transcriptional regulator EBNA2 drives the cooperative and combinatorial genome-wide binding of two master regulators of B-cell fate, namely EBF1 and RBP-jκ. Previous studies suggest that these B-cell factors are statically bound to target gene promoters. In contrast, we found that EBNA2 induces the formation of new binding for both RBP-jκ and EBF1, many of which are in close physical proximity in the cellular and viral genome. These newly induced binding sites co-occupied by EBNA2-EBF1-RBP-jκ correlate strongly with transcriptional activation of linked genes that are important for B-lymphoblast function. Conditional expression or repression of EBNA2 leads to a rapid alteration in RBP-jκ and EBF1 binding. Biochemical and shRNA depletion studies provide evidence for cooperative assembly at co-occupied sites. These findings reveal that EBNA2 facilitate combinatorial interactions to induce new patterns of transcription factor occupancy and gene programming necessary to drive B-lymphoblast growth and survival.

  19. EBNA2 Drives Formation of New Chromosome Binding Sites and Target Genes for B-Cell Master Regulatory Transcription Factors RBP-jκ and EBF1.

    Directory of Open Access Journals (Sweden)

    Fang Lu

    2016-01-01

    Full Text Available Epstein-Barr Virus (EBV transforms resting B-lymphocytes into proliferating lymphoblasts to establish latent infections that can give rise to malignancies. We show here that EBV-encoded transcriptional regulator EBNA2 drives the cooperative and combinatorial genome-wide binding of two master regulators of B-cell fate, namely EBF1 and RBP-jκ. Previous studies suggest that these B-cell factors are statically bound to target gene promoters. In contrast, we found that EBNA2 induces the formation of new binding for both RBP-jκ and EBF1, many of which are in close physical proximity in the cellular and viral genome. These newly induced binding sites co-occupied by EBNA2-EBF1-RBP-jκ correlate strongly with transcriptional activation of linked genes that are important for B-lymphoblast function. Conditional expression or repression of EBNA2 leads to a rapid alteration in RBP-jκ and EBF1 binding. Biochemical and shRNA depletion studies provide evidence for cooperative assembly at co-occupied sites. These findings reveal that EBNA2 facilitate combinatorial interactions to induce new patterns of transcription factor occupancy and gene programming necessary to drive B-lymphoblast growth and survival.

  20. 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

  1. 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.

  2. [Factors determining utilization of a Web site by parents in order to report side effects of vaccines].

    Science.gov (United States)

    Kimpton, Anne; Dubé, Eve; Sauvageau, Chantal; De Serres, Gaston

    2008-01-01

    Only a small percentage of adverse events following immunization (AEFI) are currently reported by physicians and nurses to the passive surveillance system. A solution to improve the sensitivity would be to involve parents in the reporting process via a Web-based platform. This exploratory study sought to explore and identify factors that would influence online parental reporting of AEFI. A total of 20 parents were recruited and interviewed individually during the first week of February 2007. Data were analyzed with the qualitative thematic content analysis method using qualitative software. Most parents were not aware of the existence of an AEFI surveillance system but they acknowledge the importance and would be interested in contributing to this surveillance. Compared to paper form, they considered online reporting more appealing because it is perceived as taking less time and being less cumbersome. Most interviewed parents have access to Internet. Parents indicated they would be more inclined to participate in online AEFI reporting if their vaccine provider endorsed the website, and if it were a secure, interactive environment that also provided useful information on vaccination. Parents seemed more inclined to report severe as opposed to mild expected AEFI. These middle-high class francophone parents identified no major obstacle to direct reporting of AEFI on a Website as long as this mode of reporting would be endorsed by their vaccine provider.

  3. 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

  4. 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.

  5. 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.

  6. 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 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.

  7. Survival of Manure-borne and Fecal Coliforms in Soil: Temperature Dependence as Affected by Site-Specific Factors.

    Science.gov (United States)

    Park, Yongeun; Pachepsky, Yakov; Shelton, Daniel; Jeong, Jaehak; Whelan, Gene

    2016-05-01

    Understanding pathogenic and indicator bacteria survival in soils is essential for assessing the potential of microbial contamination of water and produce. The objective of this work was to evaluate the effects of soil properties, animal source, experimental conditions, and the application method on temperature dependencies of manure-borne generic , O157:H7, and fecal coliforms survival in soils. A literature search yielded 151 survival datasets from 70 publications. Either one-stage or two-stage kinetics was observed in the survival datasets. We used duration and rate of the logarithm of concentration change as parameters of the first stage in the two-stage kinetics data. The second stage of the two-stage kinetics and the one-stage kinetics were simulated with the model to find the dependence of the inactivation rate on temperature. Classification and regression trees and linear regressions were applied to parameterize the kinetics. Presence or absence of two-stage kinetics was controlled by temperature, soil texture, soil water content, and for fine-textured soils by setting experiments in the field or in the laboratory. The duration of the first stage was predominantly affected by soil water content and temperature. In the model dependencies of inactivation rates on temperature, parameter estimates were significantly affected by the laboratory versus field conditions and by the application method, whereas inactivation rates at 20°C were significantly affected by all survival and management factors. Results of this work can provide estimates of coliform survival parameters for models of microbial water quality. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

  8. Distribution of virulence factors and association with emm polymorphism or isolation site among beta-hemolytic group G Streptococcus dysgalactiae subspecies equisimilis.

    Science.gov (United States)

    Lo, Hsueh-Hsia; Cheng, Wei-Shan

    2015-01-01

    Distribution of virulence factors and association with emm polymorphism or isolation site among beta-hemolytic group G Streptococcus dysgalactiae subspecies equisimilis. Streptococcus dysgalactiae subspecies equisimilis (SDSE), the dominant human pathogenic species among group G streptococci, is the causative agent of several invasive and non-invasive diseases worldwide. However, limited information is available about the distribution of virulence factors among SDSE isolates, or their association with emm types and the isolation sites. In this study, 246 beta-hemolytic group G SDSE isolates collected in central Taiwan between February 2007 and August 2011 were under investigation. Of these, 66 isolates were obtained from normally sterile sites and 180 from non-sterile sites. emm typing revealed 32 types, with the most prevalent one being stG10.0 (39.8%), followed by stG245.0 (15.4%), stG840.0 (12.2%), stG6.1 (7.7%), and stG652.0 (4.1%). The virulence genes lmb (encoding laminin-binding protein), gapC (glyceraldehyde 3-phosphate dehydrogenase), sagA (streptolysin S), and hylB (hyaluronidase) existed in all isolates. Also, 99.2% of the isolates possessed slo (streptolysin O) and scpA (C5a peptidase) genes. In addition, 72.8%, 14.6%, 9.4%, and 2.4% of the isolates possessed the genes ska (streptokinase), cbp (putative collagen-binding protein, SDEG_1781), fbp (putative fibronectin-binding protein, SDEG_0161), and sicG (streptococcal inhibitor of complement), respectively. The only superantigen gene detected was spegg (streptococcus pyrogenic exotoxin G(dys) ), which was possessed by 74.4% of the isolates; these isolates correlated with non-sterile sites. Positive correlations were observed between the following emm types and virulence genes: stG10.0 and stG840.0 with spegg, stG6.1 and stG652.0 with ska, and stG840.0 with cbp. On the other hand, negative correlations were observed between the following: stG245.0, stG6.1, and stG652.0 types with spegg, stG10.0 with ska

  9. Defining the DNA Binding Site Recognized by the Fission Yeast Zn2Cys6Transcription Factor Pho7 and Its Role in Phosphate Homeostasis.

    Science.gov (United States)

    Schwer, Beate; Sanchez, Ana M; Garg, Angad; Chatterjee, Debashree; Shuman, Stewart

    2017-08-15

    Fission yeast phosphate homeostasis entails transcriptional induction of genes encoding phosphate-mobilizing proteins under conditions of phosphate starvation. Transcription factor Pho7, a member of the Zn 2 Cys 6 family of fungal transcription regulators, is the central player in the starvation response. The DNA binding sites in the promoters of phosphate-responsive genes have not been defined, nor have any structure-function relationships been established for the Pho7 protein. Here we narrow this knowledge gap by (i) delineating an autonomous DNA-binding domain (DBD) within Pho7 that includes the Zn 2 Cys 6 module, (ii) deploying recombinant Pho7 DBD in DNase I footprinting and electrophoretic mobility shift assays (EMSAs) to map the Pho7 recognition sites in the promoters of the phosphate-regulated pho1 and tgp1 genes to a 12-nucleotide sequence motif [5'-TCG(G/C)(A/T)xxTTxAA], (iii) independently identifying the same motif as a Pho7 recognition element via in silico analysis of available genome-wide ChIP-seq data, (iv) affirming that mutations in the two Pho7 recognition sites in the pho1 promoter efface pho1 expression in vivo , and (v) establishing that the zinc-binding cysteines and a pair of conserved arginines in the DBD are essential for Pho7 activity in vivo IMPORTANCE Fungi respond to phosphate starvation by inducing the transcription of a set of phosphate acquisition genes that comprise a phosphate regulon. Pho7, a member of the Zn 2 Cys 6 family of fungal transcription regulators, is the central player in the phosphate starvation response in fission yeast. The present study identifies a 12-nucleotide Pho7 DNA binding motif [5'-TCG(G/C)(A/T)xxTTxAA] in the promoters of phosphate-regulated genes, pinpoints DNA and protein features important for Pho7 binding to DNA, and correlates them with Pho7-dependent gene expression in vivo The results highlight distinctive properties of Pho7 vis-a-vis other fungal zinc binuclear cluster transcription factors as

  10. Epidemiological profile of head and neck cancer patients in Western Uttar Pradesh and analysis of distributions of risk factors in relation to site of tumor

    Directory of Open Access Journals (Sweden)

    Mohammad Shadab Alam

    2017-01-01

    Results and Conclusion: HNC accounts for 21.2% of total body malignancy and 47% of all malignancies in males and 2.5% in females. Squamous cell carcinoma was the most common histological type (97%. Maximum incidence of HNC (>60% was in 40–60 year of age. Male:female ratio was 16:1. Oral cancers were most common HNC in patients below 40 year age group, whereas carcinoma oropharynx and larynx were more common in patients above 40 year age group. Tobacco smoking was a most prevalent risk factor for carcinoma oropharynx, larynx, and hypopharynx. Tobacco chewing was a most prevalent risk factor in females, young males, and carcinoma buccal mucosa patients. Habit of tobacco consumption in HNC patients was much higher than their normal counterpart. Alcohols drinking alone was observed in <1% patient as a risk factor. In oral tongue cancer, smoking and tobacco chewing were equally prevalent. Habit of tobacco chewing and alcohol were significantly higher in carcinoma buccal mucosa than other HNC suggesting synergistic effect specific to this site.

  11. The role of individual-media relationship and consumer personal factors on spanish teenagers´ mobile social networking sites usage

    OpenAIRE

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

    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 ...

  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. Risk factors for surgical site infections among 1,772 patients operated on for lumbar disc herniation: a multicentre observational registry-based study.

    Science.gov (United States)

    Habiba, Samer; Nygaard, Øystein P; Brox, Jens I; Hellum, Christian; Austevoll, Ivar M; Solberg, Tore K

    2017-06-01

    There are no previous studies evaluating risk factors for surgical site infections (SSIs) and the effectiveness of prophylactic antibiotic treatment (PAT), specifically for patients operated on for lumbar disc herniation. This observational multicentre study comprises a cohort of 1,772 consecutive patients operated on for lumbar disc herniation without laminectomy or fusion at 23 different surgical units in Norway. The patients were interviewed about SSIs according to a standardised questionnaire at 3 months' follow-up. Three months after surgery, 2.3% of the patients had an SSI. Only no PAT (OR = 5.3, 95% CI = 2.2-12.7, pdisc herniation. Senior surgeons assisting inexperienced colleagues to avoid prolonged duration of surgery could also reduce the occurrence of SSI.

  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. Magnitude and Factors Associated With Post-Cesarean Surgical Site Infection at Hawassa University Teaching and Referral Hospital, Southern Ethiopia: A Cross-sectional Study.

    Science.gov (United States)

    Wodajo, Samuel; Belayneh, Mehretu; Gebremedhin, Samson

    2017-05-01

    Surgical site infection (SSI) after cesarean section (CS) increases maternal morbidity, hospital stay and medical cost. However, in Ethiopia, limited evidence exists regarding the magnitude and risk factors of post-CS wound infection. The purpose of this study was to determine the prevalence of - and factors associated with the problem among mothers who gave birth in Hawassa University Teaching and Referral Hospital, Southern Ethiopia. Hospital based cross-sectional study was conducted based on the medical records of 592 women who underwent CS from June 2012 to May 2013. Data on the occurrence and factors associated with SSIs were extracted. Factors associated with SSI were identified using multivariate logistic regression analysis. The output of the analysis is presented using adjusted odds ratio (OR) with the corresponding 95% confidence interval (CI). The prevalence of SSI was 11.0% (95% CI: 8.6-13.8%). Mothers with prolonged labor (6.78, 95% CI: 2.54-18.00) and prolonged rupture of membrane (5.83, 95% CI: 2.14-15.89) had significantly increased odds of SSI. Compared to mothers who had no digital vaginal examination, those who had 1-4 and 5 or more examinations were at higher risk with OR of 2.91 (95% CI: 1.21-6.99) and 8.59 (95% CI: 1.74-42.23), respectively. Prolonged duration of surgery (12.32, 95% CI: 5.46-27.77), wound contamination class III (9.61, 95% CI: 1.84-50.06) and postoperative anemia (2.62, 95% CI: 1.21-5.69) were also significant predictors. CS conducted by junior practitioners is likely to be followed by infection. Post-CS SSI is relatively common in the hospital. Thus, it should be averted by implementing infection prevention techniques.

  18. 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 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.

  19. 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.

  20. Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in serum amyloid A gene promoter.

    Science.gov (United States)

    Tiwari, Prabha; Tripathi, Lokesh P; Nishikawa-Matsumura, Teppei; Ahmad, Shandar; Song, Soken-Nakazawa J; Isobe, Tomoyasu; Mizuguchi, Kenji; Yoshizaki, Kazuyuki

    2013-06-01

    We previously demonstrated that though the human SAA1 gene shows no typical STAT3 response element (STAT3-RE) in its promoter region, STAT3 and the nuclear factor (NF-κB) p65 first form a complex following interleukin IL-1 and IL-6 (IL-1+6) stimulation, after which STAT3 interacts with a region downstream of the NF-κB RE in the SAA1 promoter. In this study, we employed a computational approach based on indirect read outs of protein-DNA contacts to identify a set of candidates for non-consensus STAT3 transcription factor binding sites (TFBSs). The binding of STAT3 to one of the predicted non-consensus TFBSs was experimentally confirmed through a dual luciferase assay and DNA affinity chromatography. The present study defines a novel STAT3 non-consensus TFBS at nt -75/-66 downstream of the NF-κB RE in the SAA1 promoter region that is required for NF-κB p65 and STAT3 to activate SAA1 transcription in human HepG2 liver cells. Our analysis builds upon the current understanding of STAT3 function, suggesting a wider array of mechanisms of STAT3 function in inflammatory response, and provides a useful framework for investigating novel TF-target associations with potential therapeutic implications. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Development of long-acting ciliary neurotrophic factor by site-specific conjugation with different-sized polyethylene glycols and transferrin.

    Science.gov (United States)

    Zhang, Chun; Yu, Rong; Li, Zenglan; Feng, Cui; Wang, Qi; Liu, Yongdong; Su, Zhiguo

    2017-08-30

    To overcome the deficiency of rapid elimination from blood, the truncated human recombinant ciliary neurotrophic factor was formulated by site-specific attachment of different-sized PEG-maleimide or by cross-linking with human transferrin through a hetero-bi-functional PEG linker (NHS-PEG5k-MAL). The PEGylated CNTF was purified by a two-step chromatography procedure and the transferrin coupling CNTF conjugate was separated through an elegant protocol. The conjugation site on CNTF was identified by peptide mapping analysis and validated that the linkage of the conjugates was specifically happened to Cys17 residue. Although both PEGylated and transferrin coupling CNTF demonstrated decreased cell based residual activity, markedly enhanced pharmacokinetic behaviors in normal male Sprague-Dawley rats were observed, especially for the PEG40k-CNTF with approximately 58-times improvement compared with the unmodified counterpart. The evaluation of the in vivo potency of body weight-losing was performed with normal male C57BL6 mice and the results revealed that both PEGylation and transferrin coupling could achieve improved therapeutic benefits relative to that of CNTF. Besides, PEG20k/40k-CNTF demonstrated more effective than transferrin coupling CNTF (Tf-PEG5k-CNTF) despite that the later showed preferable pharmacokinetic profile and cell based residual activity compared with PEG20k-CNTF. Weekly subcutaneous administration of PEG40k-CNTF with 0.5mg/kg and 1.0mg/kg dose resulted in approximately 35% and 50% decrease in food intake during one interval period of injection, indicating that PEG40k-CNTF is the most potential anti-obese agent for therapeutics. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Localization and quantification of binding sites for follicle-stimulating hormone, luteinizing hormone, growth hormone, and insulin-like growth factor I in sheep ovarian follicles.

    Science.gov (United States)

    Eckery, D C; Moeller, C L; Nett, T M; Sawyer, H R

    1997-09-01

    In sheep, growth and development of ovarian follicles beyond 2 mm in diameter is acutely dependent on gonadotropin support. As a consequence, following hypophysectomy (HPX) or hypothalamic-pituitary stalk disconnection (HPD), growth of follicles beyond 2 mm is arrested and all follicles > 2 mm undergo atresia. Although administration of exogenous gonadotropins stimulates follicular growth and ovulation in HPD ewes, follicles in HPX ewes remain unresponsive unless growth hormone (GH) is also given. To determine whether the difference in follicular sensitivity to gonadotropins after HPD (gonadotropin sensitive) or HPX (gonadotropin insensitive) is related to the distribution and quantity of binding sites for FSH, LH, and/or insulin-like growth factor I (IGF-I), binding sites for these hormones were localized and quantified using topical autoradiography in healthy follicles from control (pituitary-intact), HPD, and HPX ewes. In addition, in situ hybridization was performed to localize mRNA for GH and FSH receptors. Irrespective of treatment, binding of FSH and mRNA for FSH receptor were greatest (p membrana granulosa; LH binding was greatest (p receptor was most abundant (p membrana granulosa and oocytes of small antral and preantral follicles. Compared to levels in controls and HPD ewes, the level of GH receptor mRNA was lower (p receptors for FSH, LH, or IGF-I. The observed reduction of mRNA for GH receptor in the membrana granulosa of follicles from HPX ewes provides evidence that GH may play an important role in early stages of folliculogenesis and that it is involved in the maintenance of sensitivity to gonadotropins.

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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)

  9. The ligand specificities of the insulin receptor and the insulin-like growth factor I receptor reside in different regions of a common binding site

    Energy Technology Data Exchange (ETDEWEB)

    Kjeldsen, T.; Andersen, A.S.; Wiberg, F.C.; Rasmussen, J.S.; Schaeffer, L.; Balschmidt, P.; Moller, K.B.; Moller, N.P.H. (Novo Nordisk, Bagsvaerd (Denmark))

    1991-05-15

    To identify the region(s) of the insulin receptor and the insulin-like growth factor I (IGF-I) receptor responsible for ligand specificity (high-affinity binding), expression vectors encoding soluble chimeric insulin/IGF-I receptors were prepared. The chimeric receptors were expressed in mammalian cells and partially purified. Binding studies revealed that a construct comprising an IGF-I receptor in which the 68 N-terminal amino acids of the insulin receptor {alpha}-subunit had replaced the equivalent IGF-I receptor segment displayed a markedly increased affinity for insulin. In contrast, the corresponding IGF-I receptor sequence is not critical for high-affinity IGF-I binding. It is shown that part of the cysteine-rich domain determines IGF-I specificity. The authors have previously shown that exchanging exons 1, 2, and 3 of the insulin receptor with the corresponding IGF-I receptor sequence results in loss of high affinity for insulin and gain of high affinity for IGF-I. Consequently, it is suggested that the ligand specificities of the two receptors (i.e., the sequences that discriminate between insulin and IGF-I) reside in different regions of a binding site with common features present in both receptors.

  10. 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

  11. 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

  12. 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.

  13. 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

  14. PM2.5 source apportionment in a French urban coastal site under steelworks emission influences using constrained non-negative matrix factorization receptor model.

    Science.gov (United States)

    Kfoury, Adib; Ledoux, Frédéric; Roche, Cloé; Delmaire, Gilles; Roussel, Gilles; Courcot, Dominique

    2016-02-01

    The constrained weighted-non-negative matrix factorization (CW-NMF) hybrid receptor model was applied to study the influence of steelmaking activities on PM2.5 (particulate matter with equivalent aerodynamic diameter less than 2.5 μm) composition in Dunkerque, Northern France. Semi-diurnal PM2.5 samples were collected using a high volume sampler in winter 2010 and spring 2011 and were analyzed for trace metals, water-soluble ions, and total carbon using inductively coupled plasma--atomic emission spectrometry (ICP-AES), ICP--mass spectrometry (ICP-MS), ionic chromatography and micro elemental carbon analyzer. The elemental composition shows that NO3(-), SO4(2-), NH4(+) and total carbon are the main PM2.5 constituents. Trace metals data were interpreted using concentration roses and both influences of integrated steelworks and electric steel plant were evidenced. The distinction between the two sources is made possible by the use Zn/Fe and Zn/Mn diagnostic ratios. Moreover Rb/Cr, Pb/Cr and Cu/Cd combination ratio are proposed to distinguish the ISW-sintering stack from the ISW-fugitive emissions. The a priori knowledge on the influencing source was introduced in the CW-NMF to guide the calculation. Eleven source profiles with various contributions were identified: 8 are characteristics of coastal urban background site profiles and 3 are related to the steelmaking activities. Between them, secondary nitrates, secondary sulfates and combustion profiles give the highest contributions and account for 93% of the PM2.5 concentration. The steelwork facilities contribute in about 2% of the total PM2.5 concentration and appear to be the main source of Cr, Cu, Fe, Mn, Zn. Copyright © 2015. Published by Elsevier B.V.

  15. Interaction of the 268-282 region of glycoprotein Ibalpha with the heparin-binding site of thrombin inhibits the enzyme activation of factor VIII.

    Science.gov (United States)

    De Cristofaro, R; De Filippis, V

    2003-01-01

    Activation of factor VIII (FVIII) by thrombin plays a fundamental role in the amplification of the coagulation cascade and takes place through specific proteolytic cleavages at Arg(372), Arg(740) and Arg(1689). Full FVIII activation requires cleavage at Arg(372), a process involving the alpha-thrombin exosite-II; referred to as heparin-binding site (HBS). The present study was aimed at investigating the effect of glycoprotein Ibalpha (GpIbalpha; 1-282 fragment) binding to thrombin HBS on FVIII activation. Similar experiments were also performed using a synthetic peptide modelled on the 268-282 sequence of GpIbalpha, and sulphated successfully at all tyrosine residues present along its sequence, at positions 276, 278 and 279. Both GpIbalpha 1-282 and the sulphated GpIb 268-282 peptides induced a progressive decrease (up to 70%) in activated FVIII generation, assessed by coagulation and FXa-generation assays. Furthermore, SDS/PAGE and Western-blot experiments showed that the specific appearance of the 44 kDa A2 domain on cleavage of the FVIII Arg(372)-Ser(373) peptide bond was delayed significantly in the presence of either GpIbalpha 1-282 or GpIb 268-282 peptide. Moreover, the effect of the latter on thrombin-mediated hydrolysis of a peptide having the sequence 341-376 of FVIII was investigated using reverse-phase HPLC. The k (cat)/ K (m) values of the FVIII 341-376 peptide hydrolysis by thrombin decreased linearly as a function of the GpIbalpha 268-282 peptide concentration, according to a competitive inhibition effect. Taken together, these experiments suggest that the sulphated 268-282 region of GpIbalpha binds to thrombin HBS, and is responsible for the inhibition of the Arg(372)-Ser(373) bond cleavage and activation of FVIII. PMID:12689334

  16. 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.

  17. Insulin-like growth factor-I feedback regulation of growth hormone and luteinizing hormone secretion in the pig: evidence for a pituitary site of action.

    Science.gov (United States)

    Barb, C R; Hausman, G J

    2009-06-01

    Three experiments (EXP) were conducted to determine the role of insulin-like growth factor-I (IGF-I) in the control of growth hormone (GH) and LH secretion. In EXP I, prepuberal gilts, 65 ± 6 kg body weight and 140 days of age received intracerebroventricular (ICV) injections of saline (n = 4), 25 μg (n = 4) or 75 μg (n = 4) IGF-I and jugular blood samples were collected. In EXP II, anterior pituitary cells in culture collected from 150-day-old prepuberal gilts (n = 6) were challenged with 0.1, 10 or 1000 nM [Ala15]-h growth hormone-releasing hormone-(1-29)NH2 (GHRH), or 0.01, 0.1, 1, 10, 30 nM IGF-I individually or in combinations with 1000 nM GHRH. Secreted GH was measured at 4 and 24 h after treatment. In EXP III, anterior pituitary cells in culture collected from 150-day-old barrows (n = 5) were challenged with 10, 100 or 1000 nM gonadotropin-releasing hormone (GnRH) or 0.01, 0.1, 1, 10, 30 nM IGF-I individually or in combinations with 100 nM GnRH. Secreted LH was measured at 4 h after treatment. In EXP I, serum GH and LH concentrations were unaffected by ICV IGF-I treatment. In EXP II, relative to control all doses of GHRH increased (P 0.1). In conclusion, under these experimental conditions the results suggest that the pituitary is the putative site for IGF-I modulation of GH and LH secretion. Further examination of the role of IGF-I on GH and LH secretion is needed to understand the inhibitory and stimulatory action of IGF-I on GH and LH secretion.

  18. Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants.

    Science.gov (United States)

    Peng, Fred Y; Hu, Zhiqiu; Yang, Rong-Cai

    2016-08-08

    Many genes involved in responses to photoperiod and vernalization have been characterized or predicted in Arabidopsis (Arabidopsis thaliana), Brachypodium (Brachypodium distachyon), wheat (Triticum aestivum) and barley (Hordeum vulgare). However, little is known about the transcription regulation of these genes, especially in the large, complex genomes of wheat and barley. We identified 68, 60, 195 and 61 genes that are known or postulated to control pathways of photoperiod (PH), vernalization (VE) and pathway integration (PI) in Arabidopsis, Brachypodium, wheat and barley for predicting transcription factor binding sites (TFBSs) in the promoters of these genes using the FIMO motif search tool of the MEME Suite. The initial predicted TFBSs were filtered to confirm the final numbers of predicted TFBSs to be 1066, 1379, 1528, and 789 in Arabidopsis, Brachypodium, wheat and barley, respectively. These TFBSs were mapped onto the PH, VE and PI pathways to infer about the regulation of gene expression in Arabidopsis and cereal species. The GC contents in promoters, untranslated regions (UTRs), coding sequences and introns were higher in the three cereal species than those in Arabidopsis. The predicted TFBSs were most abundant for two transcription factor (TF) families: MADS-box and CSD (cold shock domain). The analysis of publicly available gene expression data showed that genes with similar numbers of MADS-box and CSD TFBSs exhibited similar expression patterns across several different tissues and developmental stages. The intra-specific Tajima D-statistics of TFBS motif diversity showed different binding specificity among different TF families. The inter-specific Tajima D-statistics suggested faster TFBS divergence in TFBSs than in coding sequences and introns. Mapping TFBSs onto the PH, VE and PI pathways showed the predominance of MADS-box and CSD TFBSs in most genes of the four species, and the difference in the pathway regulations between Arabidopsis and the three

  19. 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...

  20. Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq

    Science.gov (United States)

    2013-01-01

    Background Two plant-specific transcription factors, NAC and YABBY, are involved in important plant developmental processes. However their molecular mechanisms, especially DNA binding sites and co-regulated genes, are largely unknown during soybean seedling development. Results In order to identify genome-wide binding sites of specific members of the NAC and YABBY transcription factors and co-regulated genes, we performed Chromatin Immunoprecipitation Sequencing (ChIP-Seq) and RNA Sequencing (RNA-Seq) using cotyledons from soybean seedling developmental stages. Our RNA-Seq data revealed that these particular NAC and YABBY transcription factors showed a clear pattern in their expression during soybean seedling development. The highest level of their expression was found in seedling developmental stage 4 when cotyledons undergo a physiological transition from non-photosynthetic storage tissue to a metabolically active photosynthetic tissue. Our ChIP-Seq data identified 72 genes potentially regulated by the NAC and 96 genes by the YABBY transcription factors examined. Our RNA-Seq data revealed highly differentially expressed candidate genes regulated by the NAC transcription factor include lipoxygense, pectin methyl esterase inhibitor, DEAD/DEAH box helicase and homeobox associated proteins. YABBY-regulated genes include AP2 transcription factor, fatty acid desaturase and WRKY transcription factor. Additionally, we have identified DNA binding motifs for the NAC and YABBY transcription factors. Conclusions Genome-wide determination of binding sites for NAC and YABBY transcription factors and identification of candidate genes regulated by these transcription factors will advance the understanding of complex gene regulatory networks during soybean seedling development. Our data imply that there is transcriptional reprogramming during the functional transition of cotyledons from non-photosynthetic storage tissue to metabolically active photosynthetic tissue. PMID:23865409

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. Evolution of human IgH3'EC duplicated structures: both enhancers HS1,2 are polymorphic with variation of transcription factor's consensus sites.

    Science.gov (United States)

    Giambra, Vincenzo; Fruscalzo, Alberto; Giufre', Maria; Martinez-Labarga, Cristina; Favaro, Marco; Rocchi, Mariano; Frezza, Domenico

    2005-02-14

    the 17-bp external element in hominids. The relevance of the polymorphisms in the HS1,2 enhancers is due to the variable number of binding sites for the transcription factors: NF-kappaB, CMYB, BSAP1/2, AP1/4, E47, MyoD and muE5 and thus to the possible influence of these variations on switch, production of Ig and on maturation of B cells.

  6. SUSTAINABLE TOURISM AS A DRIVING FACTOR FOR THE DEVELOPMENT OF CULTURAL HERITAGE SITES : Case Study: Lumbini - The Birthplace of Gautama Buddha

    OpenAIRE

    Pandey, Shiva

    2015-01-01

    The purpose of this thesis was to find out the role of sustainability for the development of cultural heritage sites. It was mainly targeted to know the importance of cultural heritage in tourism industry and its impact and ways to develop sustainable tourism in those sites. The case study of Lumbini (the birthplace of Gautama Buddha) was taken as the research project to analyze and interpret the significance and process of sustainability. The thesis suggested that tourism in cultural her...

  7. Allele variants in functional MicroRNA target sites of the neurotrophin-3 receptor gene (NTRK3) as susceptibility factors for anxiety disorders

    OpenAIRE

    Muiños Gimeno, Margarita; Guidi, Mònica; Kagerbauer, Birgit; Martín Santos, Rocío; Navinés, Ricard; Alonso, Pino; Menchón, José M.; Gratacós Mayora, Mònica; Estivill, Xavier, 1955-; Espinosa Parrilla, Yolanda

    2009-01-01

    Genetic and functional data indicate that variation in the expression of the neurotrophin-3 receptor gene (NTRK3) may have an impact on neuronal plasticity, suggesting a role for NTRK3 in the pathophysiology of anxiety disorders. MicroRNA (miRNA) posttranscriptional gene regulators act by base-pairing to specific sequence sites, usually at the 3'UTR of the target mRNA. Variants at these sites might result in gene expression changes contributing to disease susceptibility. We investigated genet...

  8. 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.

  9. Site assessment

    DEFF Research Database (Denmark)

    Villanueva, Héctor; Gómez Arranz, Paula

    This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed.......This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed....

  10. Site assessment

    DEFF Research Database (Denmark)

    Villanueva, Héctor; Vesth, Allan

    This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed......This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed...

  11. Shear Wave Velocity and Site Amplification Factors for 25 Strong-Motion Instrument Stations Affected by the M5.8 Mineral, Virginia, Earthquake of August 23, 2011

    Science.gov (United States)

    Kayen, Robert E.; Carkin, Brad A.; Corbett, Skye C.; Zangwill, Aliza; Estevez, Ivan; Lai, Lena

    2015-01-01

    Vertical one-dimensional shear wave velocity (Vs) profiles are presented for 25 strong-motion instrument sites along the Mid-Atlantic eastern seaboard, Piedmont region, and Appalachian region, which surround the epicenter of the M5.8 Mineral, Virginia, Earthquake of August 23, 2011. Testing was performed at sites in Pennsylvania, Maryland, West Virginia, Virginia, the District of Columbia, North Carolina, and Tennessee. The purpose of the study is to determine the detailed site velocity profile, the average velocity in the upper 30 meters of the profile (VS,30), the average velocity for the entire profile (VS,Z), and the National Earthquake Hazards Reduction Program (NEHRP) site classification. The Vs profiles are estimated using a non-invasive continuous-sine-wave method for gathering the dispersion characteristics of surface waves. A large trailer-mounted active source was used to shake the ground during the testing and produce the surface waves. Shear wave velocity profiles were inverted from the averaged dispersion curves using three independent methods for comparison, and the root-mean square combined coefficient of variation (COV) of the dispersion and inversion calculations are estimated for each site.

  12. Site Calibration

    DEFF Research Database (Denmark)

    Kock, Carsten Weber; Vesth, Allan

    This Site Calibration report is describing the results of a measured site calibration for a site in Denmark. The calibration is carried out by DTU Wind Energy in accordance with Ref.[3] and Ref.[4]. The measurement period is given. The site calibration is carried out before a power performance...... measurement on a given turbine to clarify the influence from the terrain on the ratio between the wind speed at the center of the turbine hub and at the met mast. The wind speed at the turbine is measured by a temporary mast placed at the foundation for the turbine. The site and measurement equipment...... is detailed described in [1] and [2]. All parts of the sensors and the measurement system have been installed by DTU Wind Energy....

  13. 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…

  14. 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

    for cells expressing kinase-negative receptor (A721). Moreover, tyrosine kinase activity of the Dc-123F receptor toward phospholipase C-gamma 1, compared to wild-type receptor, was reduced by 90%. Taken together, these results show that EGF receptor lacking five autophosphorylation sites functions similar...

  15. Factors Influencing the Effective Use of Technology for Teaching and Learning: Lessons Learned from the SEIR-TEC Intensive Site Schools. 2nd Edition.

    Science.gov (United States)

    Byrom, Elizabeth; Bingham, Margaret

    From 1995 to 2000, the SouthEast Initiatives Regional Technology in Education Consortium (SEIR-TEC) provided technical assistance and professional development to 12 schools, referred to as intensive sites. Typically, this effort entailed a member of the SEIR-TEC staff spending three or four days per month working with teachers and administrators…

  16. Nuclear facilities siting

    International Nuclear Information System (INIS)

    Kruger, P.

    1979-01-01

    A review of the status of requirements for the selection of sites for the facilities comprising the nuclear fuel cycle for electric power production. The report includes a summary of the legal and regulatory constraints that have resulted in complex and lengthy process for licensing of nuclear facilities. The nuclear fuel cycle, including the post-reactor operations of spent fuel reprocessing and waste disposal, is reviewed. Site evaluation factors for each major activity in the fuel cycle include geology, hydrology, demography, geography, meteorology, ecology, and institutional and social aspects. An analysis of current methods available for site evaluation are described. The report concludes with analysis of current issues affecting the ability of the nation's industry to license suitable sites for the many types of facility needed in the nuclear fuel cycle. The report should be of interest to civil engineers concerned with the resolution of technical problems of facility site selection. 36 refs

  17. 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

  18. 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

  19. 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...

  20. 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.

  1. 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.

  2. 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

  3. 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...

  4. 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.

  5. 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...

  6. 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 ...

  7. Integrated monitoring and evaluation and environmental risk factors for urogenital schistosomiasis and active trachoma in Burkina Faso before preventative chemotherapy using sentinel sites.

    Science.gov (United States)

    Koukounari, Artemis; Touré, Seydou; Donnelly, Christl A; Ouedraogo, Amadou; Yoda, Bernadette; Ky, Cesaire; Kaboré, Martin; Bosqué-Oliva, Elisa; Basáñez, María-Gloria; Fenwick, Alan; Webster, Joanne P

    2011-07-12

    Over 1 billion of the world's poorest inhabitants are afflicted by neglected tropical diseases (NTDs). Integrated control programmes aimed at tackling these debilitating NTDs have been recently initiated, mainly using preventative chemotherapy. Monitoring and evaluation (M&E) of these integrated programs presents particular challenges over and above those required for single disease vertical programmes. We used baseline data from the National NTD Control Programme in Burkina Faso in order to assess the feasibility of an integrated survey design, as well as to elucidate the contribution of environmental variables to the risk of either Schistosoma haematobium, trachoma, or both among school-aged children. S. haematobium infection was diagnosed by detecting eggs in urine. A trachoma case was defined by the presence of Trachomatous inflammation-Follicular (TF) and/or Trachomatous inflammation-Intense (TI) in either eye. Baseline data collected from 3,324 children aged 7-11 years in 21 sentinel sites across 11 regions of Burkina Faso were analyzed using simple and multivariable hierarchical binomial logistic regression models fitted by Markov Chain Monte Carlo estimation methods. Probabilities of the risk of belonging to each infection/disease category were estimated as a function of age, gender (individual level), and environmental variables (at sentinel site level, interpolated from national meteorological stations). Overall prevalence at the sentinel sites was 11.79% (95% CI: 10.70-12.89) for S. haematobium; 13.30% (12.14-14.45) for trachoma and 0.84% (0.53-1.15) for co-infections. The only significant predictor of S. haematobium infection was altitude. There were significant negative associations between the prevalence of active trachoma signs and minimum temperature, and air pressure. Conditional upon these predictors, these data are consistent with the two pathogens being independent. Urogenital schistosomiasis and trachoma constitute public health problems in

  8. Integrated monitoring and evaluation and environmental risk factors for urogenital schistosomiasis and active trachoma in Burkina Faso before preventative chemotherapy using sentinel sites

    Directory of Open Access Journals (Sweden)

    Bosqué-Oliva Elisa

    2011-07-01

    Full Text Available Abstract Background Over 1 billion of the world's poorest inhabitants are afflicted by neglected tropical diseases (NTDs. Integrated control programmes aimed at tackling these debilitating NTDs have been recently initiated, mainly using preventative chemotherapy. Monitoring and evaluation (M&E of these integrated programs presents particular challenges over and above those required for single disease vertical programmes. We used baseline data from the National NTD Control Programme in Burkina Faso in order to assess the feasibility of an integrated survey design, as well as to elucidate the contribution of environmental variables to the risk of either Schistosoma haematobium, trachoma, or both among school-aged children. Methods S. haematobium infection was diagnosed by detecting eggs in urine. A trachoma case was defined by the presence of Trachomatous inflammation-Follicular (TF and/or Trachomatous inflammation-Intense (TI in either eye. Baseline data collected from 3,324 children aged 7-11 years in 21 sentinel sites across 11 regions of Burkina Faso were analyzed using simple and multivariable hierarchical binomial logistic regression models fitted by Markov Chain Monte Carlo estimation methods. Probabilities of the risk of belonging to each infection/disease category were estimated as a function of age, gender (individual level, and environmental variables (at sentinel site level, interpolated from national meteorological stations. Results Overall prevalence at the sentinel sites was 11.79% (95% CI: 10.70-12.89 for S. haematobium; 13.30% (12.14-14.45 for trachoma and 0.84% (0.53-1.15 for co-infections. The only significant predictor of S. haematobium infection was altitude. There were significant negative associations between the prevalence of active trachoma signs and minimum temperature, and air pressure. Conditional upon these predictors, these data are consistent with the two pathogens being independent. Conclusions Urogenital

  9. Single base mismatches in the mRNA target site allow specific seed region-mediated off-target binding of siRNA targeting human coagulation factor 7.

    Science.gov (United States)

    Ravon, Morgane; Berrera, Marco; Ebeling, Martin; Certa, Ulrich

    2012-01-01

    We have analyzed the off-target activity of two siRNAs (F7-1, F7-2) that knock-down human blood coagulation factor 7 mRNA. F7-1 modulates a significant number of non-target transcripts while F7-2 shows high selectivity for the target transcript under various experimental conditions. The 3'-UTRs of all F7-1 off-target genes show statistically significant enrichment of the reverse complement of the F7-1 siRNA seed region located in the guide strand. Seed region enrichment was confirmed in off-target transcripts modulated by siRNA targeting the glucocorticoid receptor. To investigate how these sites contribute to off-target recognition of F7-1, we employed CXCL5 transcript as model system because it contains five F7-1 seed sequence motifs with single base mismatches. We show by transient transfection of reporter gene constructs into HEK293 cells that three out of five sites located in the 3'-UTR region are required for F7-1 off-target activity. For further mechanistic dissection, the sequences of these sites were synthesized and inserted either individually or joined in dimeric or trimeric constructs. Only the fusion constructs were silenced by F7-1 while the individual sites had no off-target activity. Based on F7-1 as a model, a single mismatch between the siRNA seed region and mRNA target sites is tolerated for target recognition and the CXCL5 data suggest a requirement for binding to multiple target sites in off-target transcripts.

  10. 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

  11. 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.

  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. 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)

  14. Malaria hotspot areas in a highland Kenya site are consistent in epidemic and non-epidemic years and are associated with ecological factors

    Directory of Open Access Journals (Sweden)

    Ernst Kacey C

    2006-09-01

    Full Text Available Abstract Background Malaria epidemics in highland areas of East Africa have caused considerable morbidity and mortality in the past two decades. Knowledge of "hotspot" areas of high malaria incidence would allow for focused preventive interventions in resource-poor areas, particularly if the hotspot areas can be discerned during non-epidemic periods and predicted by ecological factors. Methods To address this issue, spatial distribution of malaria incidence and the relationship of ecological factors to malaria incidence were assessed in the highland area of Kipsamoite, Kenya, from 2001–2004. Results Clustering of disease in a single geographic "hotspot" area occurred in epidemic and non-epidemic years, with a 2.6 to 3.2-fold increased risk of malaria inside the hotspot, as compared to outside the area (P Conclusion In this highland area, areas of high malaria risk are consistent in epidemic and non-epidemic years and are associated with specific ecological risk factors. Ongoing interventions in areas of ecological risk factors could be a cost-effective method of significantly reducing malaria incidence and blunting or preventing epidemics, even in the absence of malaria early warning systems. Further studies should be conducted to see if these findings hold true in varied highland settings.

  15. 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

  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. 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

  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. 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).

  20. 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.

  1. 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

  2. Site calibration

    DEFF Research Database (Denmark)

    Gómez Arranz, Paula; Georgieva Yankova, Ginka

    between the wind speed at the center of the turbine hub and at the met mast. The wind speed at the turbine is measured by a temporary mast placed at the foundation for the turbine. The site and measurement equipment is detailed described in [2]. The possible measurement sector for power performance...

  3. 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)

  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. 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

  6. 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....

  7. Site Practice

    DEFF Research Database (Denmark)

    Wahedi, Haseebullah

    2016-01-01

    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...... 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....... It is concluded that the drawings and the physical building play a vital role in relation to coordination within and across the various communities that are in play within the construction phas...

  8. Lunar Polar Landing Sites

    Science.gov (United States)

    Kamps, Oscar; Foing, Bernard H.; Flahaut, Jessica

    2016-07-01

    site to a PSR was chosen and used to do an automatic calculation for a rover traverse where the slope was assumed to be the limiting factor. Between the landing site and PSR a site of interest was chosen where temperature differences (Tmax-Tmin) is higher than 150K to study volatile migration processes. Eventually it is concluded that Amundsen is preferred above Rozhdestvesnkiy West because its flatter crater ground makes it easier to select landing sites. It contains more areas where volatile migration processes can studied and it is easier to rove.

  9. 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

  10. 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...... of a complex containing both Ste11 and Mat1-Mc. A single copy of this fragment was sufficient to activate a heterologous promoter in an M-specific fashion, suggesting that these two boxes act in a synergistic manner....

  11. The impact of non-monetary factors on the primary care utilization in Portugal. Finite mixture models applied to on-site and truncated samples

    OpenAIRE

    Lourenço, Óscar Domingos; Ferreira, Pedro Lopes

    2004-01-01

    In the Portuguese National Health Service (NHS) patients have to pay a co-payment of 2€ to visit a GP in the health centres. Therefore, the monetary price associated to each visit is low and, with a high probability, is not a factor that affects the utilization of consultations in health centres. On the other hand, in any health system in which the monetary cost to consume medical care is very low other kind of costs can emerge as determinants of medical care utilization. The Portuguese NHS s...

  12. Lethal factor VII deficiency due to novel mutations in the F7 promoter: functional analysis reveals disruption of HNF4 binding site.

    Science.gov (United States)

    Giansily-Blaizot, Muriel; Lopez, Estelle; Viart, Victoria; Chafa, Ouerdia; Tapon-Bretaudière, Jacqueline; Claustres, Mireille; Taulan, Magali

    2012-08-01

    Hereditary factor VII (FVII) deficiency is a rare autosomal recessive disorder. Deleterious mutations that prevent the synthesis of any amount of functional FVII have been associated with life-threatening haemorrhage in neonates. Here we report two infants, of Maghrebian origin, who suffered a fatal spontaneous cerebral haemorrhage. Investigation of the molecular basis for their severe FVII deficiency revealed novel mutations in a homozygous state within the F7 gene promoter: a single nucleotide substitution (c.-65G>C) and a 2bp deletion (c.-60_-59delTT). To determine whether these promoter variants were responsible for the FVII deficiency, computer-assisted sequence analyses were performed. The data predicted a disrupted binding of both HNF4 and COUP-TF transcription factors with each variant. Concordantly, experimental results revealed an altered HNF4-induced transactivation in the promoter mutated variants. The execution of functional tests is critical to ensuring a complete understanding of the effect of any promoter mutant on FVII deficiency. Only then can an accurate molecular diagnosis be made and further genetic counselling and prenatal diagnosis be offered.

  13. 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.

  14. 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

  15. Risk factors for extended spectrum β-lactamase-producing Escherichia coli versus susceptible E. coli in surgical site infections among cancer patients in Mexico.

    Science.gov (United States)

    Montes, Claudia V; Vilar-Compte, Diana; Velazquez, Consuelo; Golzarri, Maria Fernanda; Cornejo-Juarez, Patricia; Larson, Elaine L

    2014-10-01

    Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are of increasing concern as a cause of healthcare-associated infections. Using a matched case-control design, demographics, antibiotic use, and relevant surgical data were obtained for 173 cases (ESBL E. coli surgical site infections, [SSI]) and 173 controls (antibiotic-susceptible E. coli SSI) in an oncology hospital in Mexico City. Conditional logistic regression modeling was used to calculate odds ratios (OR). The mean age of patients was 53.6 years, 214 (62%) were female. Demographics and comorbidities were similar between groups. Although antibiotic prophylaxis was common among both cases and controls (84% and 89%), more than one-half of cases (53%) were given prophylaxis outside the recommended window or were exposed for more than 24 h in comparison to 29% of controls. Patients who received untimely (OR=3.13, 95% confidence interval [CI] 1.5-6.4) and discontinued inappropriately (OR 6.38, 95% CI=2.5-16.2) prophylaxis were more likely to develop an ESBL SSI. In addition, patients with an organ/space infection compared with superficial had a higher rate of a resistant infection (OR 4.2, 95% CI 1.3-13.9). Among patients not given timely or appropriately discontinued prophylaxis, post-operative cephalosporin use (OR 3.3, 95% CI 1.4-7.7) was associated with ESBL E. coli SSIs. The appropriate timing and duration of perioperative antimicrobial prophylaxis were associated with lower risk of ESBL E. coli in SSIs. Even though compliance to antimicrobial prophylaxis guidelines is of the utmost importance, reduced exposure to cephalosporins may also potentially decrease the risk of ESBL SSI.

  16. 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.

  17. 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.

  18. 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).

  19. Insight into PreImplantation Factor (PIF*) Mechanism for Embryo Protection and Development: Target Oxidative Stress and Protein Misfolding (PDI and HSP) through Essential RIPK Binding Site

    Science.gov (United States)

    Barnea, Eytan R.; Lubman, David M.; Liu, Yan-Hui; Absalon-Medina, Victor; Hayrabedyan, Soren; Todorova, Krassimira; Gilbert, Robert O.; Guingab, Joy; Barder, Timothy J.

    2014-01-01

    Background 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. Methods 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. Results 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 RIPK 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. Conclusion 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

  20. 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

  1. 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.

    Science.gov (United States)

    Patterson, Thomas L; Semple, Shirley J; Chavarin, Claudia V; Mendoza, Doroteo V; Santos, Lorena E; Chaffin, Mark; Palinkas, Lawrence A; Strathdee, Steffanie A; Aarons, Gregory A

    2012-10-29

    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). 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 intervention will be analyzed, and across CBOs

  2. Mutation of a nuclear respiratory factor 2 binding site in the 5' untranslated region of the ADSL gene in three patients with adenylosuccinate lyase deficiency.

    Science.gov (United States)

    Marie, S; Race, V; Nassogne, M-C; Vincent, M-F; Van den Berghe, G

    2002-07-01

    Adenylosuccinate lyase (ADSL; also called "adenylosuccinase") catalyzes two steps in the synthesis of purine nucleotides: (1) the conversion of succinylaminoimidazolecarboxamide ribotide into aminoimidazolecarboxamide ribotide and (2) the conversion of adenylosuccinate into adenosine monophosphate. ADSL deficiency, a recessively inherited disorder, causes variable-but most often severe-mental retardation, frequently accompanied by epilepsy and/or autism. It is characterized by the accumulation, in body fluids, of succinylaminoimidazolecarboxamide riboside and succinyladenosine, the dephosphorylated derivatives of the two substrates of the enzyme. Analysis of the ADSL gene of three unrelated patients with ADSL deficiency, in whom one of the ADSL alleles displayed a normal coding sequence, revealed a -49T-->C mutation in the 5' untranslated region of this allele. Measurements of the amount of mRNA transcribed from the latter allele showed that it was reduced to approximately 33% of that transcribed from the alleles mutated in their coding sequence. Further investigations showed that the -49T-->C mutation provokes a reduction to 25% of wild-type control of promoter function, as evaluated by luciferase activity and mRNA level in transfection experiments. The mutation also affects the binding of nuclear respiratory factor 2 (NRF-2), a known activator of transcription, as assessed by gel-shift studies. Our findings indicate that a mutation of a regulatory region of the ADSL gene might be an unusually frequent cause of ADSL deficiency, and they suggest a role for NRF-2 in the gene regulation of the purine biosynthetic pathway.

  3. 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

  4. Mutation of a Nuclear Respiratory Factor 2 Binding Site in the 5′ Untranslated Region of the ADSL Gene in Three Patients with Adenylosuccinate Lyase Deficiency

    Science.gov (United States)

    Marie, S.; Race, V.; Nassogne, M.-C.; Vincent, M.-F.; Van den Berghe, G.

    2002-01-01

    Adenylosuccinate lyase (ADSL; also called “adenylosuccinase”) catalyzes two steps in the synthesis of purine nucleotides: (1) the conversion of succinylaminoimidazolecarboxamide ribotide into aminoimidazolecarboxamide ribotide and (2) the conversion of adenylosuccinate into adenosine monophosphate. ADSL deficiency, a recessively inherited disorder, causes variable—but most often severe—mental retardation, frequently accompanied by epilepsy and/or autism. It is characterized by the accumulation, in body fluids, of succinylaminoimidazolecarboxamide riboside and succinyladenosine, the dephosphorylated derivatives of the two substrates of the enzyme. Analysis of the ADSL gene of three unrelated patients with ADSL deficiency, in whom one of the ADSL alleles displayed a normal coding sequence, revealed a −49T→C mutation in the 5′ untranslated region of this allele. Measurements of the amount of mRNA transcribed from the latter allele showed that it was reduced to ∼33% of that transcribed from the alleles mutated in their coding sequence. Further investigations showed that the −49T→C mutation provokes a reduction to 25% of wild-type control of promoter function, as evaluated by luciferase activity and mRNA level in transfection experiments. The mutation also affects the binding of nuclear respiratory factor 2 (NRF-2), a known activator of transcription, as assessed by gel-shift studies. Our findings indicate that a mutation of a regulatory region of the ADSL gene might be an unusually frequent cause of ADSL deficiency, and they suggest a role for NRF-2 in the gene regulation of the purine biosynthetic pathway. PMID:12016589

  5. 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

  6. Site Restoration

    International Nuclear Information System (INIS)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A.

    2002-01-01

    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

  7. 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.

  8. 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

  9. Self-absorption alpha particle factor in water: interest in the monitoring of specific military sites; Validation du facteur de correction de l'auto absorption des particules alpha dans une eau: application a la surveillance de sites specifiques de la defense

    Energy Technology Data Exchange (ETDEWEB)

    Cazoulat, A.; Lecompte, Y.; Bohand, S.; Gerasimo, P. [Bureau de Radioprotection Medicale, Service de Protection Radiologique des Armees, Lab. de Controle Radiotoxicologique, 92 - Clamart (France)

    2007-01-15

    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)

  10. 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.

  11. 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

  12. The Prevalence and Determinants of Chronic Non-Communicable Disease Risk Factors amongst Adults in the Dikgale Health Demographic and Surveillance System (HDSS Site, Limpopo Province of South Africa.

    Directory of Open Access Journals (Sweden)

    Eric Maimela

    Full Text Available The aim of the study was to determine the prevalence and determinants of chronic non-communicable disease (NCD risk factors in a rural community in the Limpopo Province of South Africa.This survey was conducted using the WHO "STEPwise approach to the surveillance of non-communicable diseases" (STEPS methodology. Participants were residents of the Dikgale HDSS site and standardised international protocols were used to measure behavioural risk factors (smoking, alcohol consumption, fruit and vegetable intake and, physical activity and physical characteristics (weight, height, waist and hip circumferences and blood pressure-BP. Fasting blood glucose, triglyceride, cholesterol and HDL-C were determined in 732 participants. Data were analysed using STATA 12 for Windows.The prevalence of current smokers amongst the participants was 13.7%, of which 81.3% were daily smokers. Alcohol was consumed by 16.3% of the participants. The majority of participants (88.6% had low daily intake of fruit and vegetables and low physical activity (66.5%. The prevalence of hypertension amongst the participants was 38.2%. Overweight, obesity and high waist circumference were prevalent in females. The cardio-metabolic risk profile was not significantly different between men and women. People who were older than 40 years, overweight or obese and those who consumed alcohol were more likely to be hypertensive. Smoking was associated significantly with older age, males, never married and divorced people. Alcohol consumption was associated with older age, males, low educational status and low income.High levels of risk factors for NCDs among adults in the Dikgale HDSS suggest an urgent need for health interventions to control these risk factors at the population level in order to reduce the prevalence of NCDs.

  13. 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

  14. 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

  15. 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

  16. Rh Factor Blood Test

    Science.gov (United States)

    ... June 3, 2015. Rh factor blood test About Advertisement Mayo Clinic does not endorse companies or products. ... a Job Site Map About This Site Twitter Facebook Google YouTube Pinterest Mayo Clinic is a not- ...

  17. Evidence that the requirements for ATP and wheat germ initiation factors 4A and 4F are affected by a region of satellite tobacco necrosis virus RNA that is 3' to the ribosomal binding site.

    Science.gov (United States)

    Browning, K S; Fletcher, L; Ravel, J M

    1988-06-15

    A cDNA containing the complete genome of satellite tobacco necrosis virus (STNV) RNA was constructed and cloned into a plasmid vector containing the T7 polymerase promotor. A second clone containing the first 54 nucleotides from the 5' end, which includes the ribosome binding site, was also constructed. RNAs were transcribed from these plasmids (pSTNV1239 and pSTNV54) and tested for their ability to bind to wheat germ 40 S ribosomal subunits in the presence of wheat germ initiation factors eIF-4A, eIF-4F, eIF-4G, eIF-3, eIF-2, Met-tRNA, ATP, and guanosine 5'-(beta, gamma-imino)triphosphate (GMP-PNP). Maximal binding of the STNV RNA transcribed from pSTNV1239 is obtained only in the presence of all the initiation factors and ATP. In contrast, close to maximal binding of STNV RNA transcribed from pSTNV54 is obtained in the absence of eIF-4A, eIF-4F, eIF-4G, and ATP. A series of deletion clones from the 3' end of the STNV cDNA was prepared, and the requirements for binding to 40 S ribosomal subunits were determined. STNV RNAs containing more than 134 nucleotides from the 5' end require eIF-4A, eIF-4F, eIF-4G, and ATP for maximal binding to 40 S ribosomal subunits, whereas STNV RNAs containing 86 nucleotides or less no longer require ATP and these factors. These findings indicate that a region 3' to the initiation codon affects the requirements for eIF-4A, eIF-4F, eIF-4G, and ATP.

  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. 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...

  20. 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.

  1. 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

  2. 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

  3. Common mental disorder in Nyanza province, Kenya in 2013 and its associated risk factors--an assessment of change since 2004, using a repeat household survey in a demographic surveillance site.

    Science.gov (United States)

    Jenkins, Rachel; Othieno, Caleb; Ongeri, Linnet; Sifuna, Peter; Ongecha, Michael; Kingora, James; Kiima, David; Omollo, Raymond; Ogutu, Bernhards

    2015-12-09

    Repeat household surveys are useful to assess change in prevalence over time, but there have been no repeat surveys of common mental disorder (CMD) in Kenya, or indeed sub-Saharan Africa. Therefore a repeat household survey of CMD and its associated risk factors was conducted in Maseno area, Kisumu county in Kenya, using a demographic surveillance site as the sample frame, in order to test the hypotheses that (a) the prevalence of CMD would increase between 2004 and 2013 due to the intervening political, social and economic pressures; (b) as in 2004, there would be no gender difference in prevalence of CMD. One thousand one hundred ninety households were selected, and 1158 adult participants consented to be interviewed with a structured epidemiological assessment while 32 refused to participate in the study interviews, giving a response rate of 97.3%. The study found that the overall prevalence of CMD in 2013 was 10.3%. However, there were significantly higher rates of having any CMD in 2013 if one was female (OR 6.2, p Common mental disorders continue to pose a significant public health burden in Kenya, and gender related vulnerability merits further research and is relevant for health worker training.

  4. 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.

  5. 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

  6. 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.

  7. 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)

  8. Abnormal secretion and function of recombinant human factor VII as the result of modification to a calcium binding site caused by a 15-base pair insertion in the F7 gene.

    Science.gov (United States)

    Peyvandi, F; Carew, J A; Perry, D J; Hunault, M; Khanduri, U; Perkins, S J; Mannucci, P M; Bauer, K A

    2001-02-15

    A case of a novel mutation in the F7 gene that results in factor VII coagulant activity (VII:c) of less than 1% and VII antigen (VII:Ag) levels of 10% is presented. DNA analysis revealed a homozygous 15-base pair (bp) in-frame insertion-type mutation at nucleotide 10554. This insertion consisted of a duplication of residues leucine (L)213 to aspartic acid (D)217 (leucine, serine, glutamic acid, histidine, and aspartic acid), probably arising by slipped mispairing between 2 copies of a direct repeat (GCGAGCACGAC) separated by 4 bp. Molecular graphic analyses showed that the insertion is located at the surface of the catalytic domain in an exposed loop stabilized by extensive salt-bridge and hydrogen bond formation at which the calcium binding site is located. The mutation probably interferes with protein folding during VII biosynthesis and/or diminishes functional activity through the loss of calcium binding. In vitro expression studies demonstrated that the levels of VII:Ag in lysates of cells transfected with wild type VII (VIIWT) were equivalent to those with mutant type VII (VIIMT), but the level of secreted VIIMT was 5% to 10% that of VIIWT. Pulse chase studies demonstrated that VIIMT did not accumulate intracellularly, and studies with inhibitors of protein degradation showed that recombinant VIIMT was partially degraded in the pre-Golgi compartment. Accordingly, only small amounts of VIIMT with undetectable procoagulant activity were secreted into conditioned media. These results demonstrate that a combination of secretion and functional defects is the mechanism whereby this insertion causes VII deficiency.

  9. 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

  10. 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.

  11. 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

  12. 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.)

  13. 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

  14. 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...

  15. 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...

  16. 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

  17. 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.

  18. 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.

  19. 10 CFR 100.21 - Non-seismic siting criteria.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Non-seismic siting criteria. 100.21 Section 100.21 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) REACTOR SITE CRITERIA Evaluation Factors for Stationary Power Reactor Site Applications on or After January 10, 1997 § 100.21 Non-seismic siting criteria. Applications...

  20. Accessibility Techniques for Museum Web Sites.

    Science.gov (United States)

    Anable, Susan; Alonzo, Adam

    Like other public institutions, museums strive to make their facilities accessible to people with disabilities, yet these same patrons may be hindered in their use of museum Web sites by electronic accessibility barriers. This presentation demonstrates that access was a primary design factor in the Virtual Museum Tour, part of the Web site of The…

  1. SITE SUITABILITY ANALYSIS AND ROUTE OPTIMIZATION FOR ...

    African Journals Online (AJOL)

    Fimba

    hence the application of GIS and Remote Sensing to waste disposal Site Suitability analysis and route optimization for solid waste in Yola town. Different factors or criteria were considered in relation to solid waste disposal sites. In order to achieve the aim of this paper, the Boolean logic was used, where suitable areas were ...

  2. 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.

  3. 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

  4. Site selection: Past and present

    International Nuclear Information System (INIS)

    Tilford, N.R.

    1994-01-01

    Site selection has been going on since the earliest times. The process has evolved through the Industrial Revolution to the present period of exploding population and environmental awareness. Now the work must be done both with increasing sophistication and greater transparency. Modern techniques for site selection have been developed during the last two decades or so, utilizing a teachable body of knowledge and a growing literature. Many firms and individuals have contributed to this growing field. The driving force has been the need for such a process in siting and licensing of critical facilities such as nuclear power plants. A list of crucial, documented steps for identifying social impacts and acceptability are provided. A recent innovation is the self-selection method developed by government. The Superconducting Supercollider serves as an example of this approach. Geological or geologically dependent factors often dominate the process. The role as engineering and environmental geoscientists is to provide responsible leadership, consultation, and communication to the effort

  5. Pesticide Use Site Index

    Science.gov (United States)

    The Pesticide Use Site Index will help a company (or other applicant) identify which data requirements are needed to register a pesticide product. It provides information on pesticide use sites and pesticide major use patterns.

  6. NPL Site Boundaries

    Data.gov (United States)

    U.S. Environmental Protection Agency — The National Priorities List (NPL) is a list published by EPA of Superfund sites. A site must be added to this list before remediation can begin under Superfund. The...

  7. Site Area Boundaries

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of site boundaries from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different times and...

  8. NPL Site Locations

    Data.gov (United States)

    U.S. Environmental Protection Agency — The National Priorities List (NPL) is a list published by EPA of Superfund sites. A site must be added to this list before remediation can begin under Superfund. The...

  9. Drupal 7 Multilingual Sites

    CERN Document Server

    Pol, Kristen

    2012-01-01

    A practical book with plenty of screenshots to guide you through the many features of multilingual Drupal. A demo ecommerce site is provided if you want to practice on a sample site, although you can apply the techniques learnt in the book directly to your site too. Any Drupal users who know the basics of building a Drupal site and are familiar with the Drupal UI, will benefit from this book. No previous knowledge of localization or internationalization is required.

  10. Site Calibration report

    DEFF Research Database (Denmark)

    Yordanova, Ginka; Vesth, Allan

    The report describes site calibration measurements carried out on a site in Denmark. The measurements are carried out in accordance to Ref. [1]. The site calibration is carried out before a power performance measurement on a given turbine to clarify the influence from the terrain on the ratio...

  11. Nuclear waste repository siting

    International Nuclear Information System (INIS)

    Soloman, B.D.; Cameron, D.M.

    1987-01-01

    This paper discusses the geopolitics of nuclear waste disposal in the USA. Constitutional choice and social equity perspectives are used to argue for a more open and just repository siting program. The authors assert that every potential repository site inevitably contains geologic, environmental or other imperfections and that the political process is the correct one for determining sites selected

  12. Site selection for new nuclear power plants

    International Nuclear Information System (INIS)

    Rizzo, Paul C.; Dubinsky, Melissa; Tastan, Erdem Onur; Miano, Sandra C.

    2015-01-01

    The current methodology for selecting the most advantageous site(s) for nuclear power plant (NPP) development is based on the latest evolution of protocols originally established in the 1990's by the Electric Power Research Institute (EPRI) and others for programs in the USA, and more recently by the International Atomic Energy Agency (IAEA), among others. The methodology includes protocols that account for lessons learned from both the Gen III projects and the catastrophic event at Fukushima, Japan. In general, the approach requires consideration of Exclusionary or 'fatal flaw' Criteria first, based on safety as well as significant impact to the environment or human health. Sites must meet all of these Exclusionary Criteria to be considered for NPP development. Next, the remaining sites are evaluated for Avoidance Criteria that affect primarily ease of construction and operations, which allow a ranking of sites best suited for NPP development. Finally, Suitability Criteria are applied to the potential sites to better differentiate between closely ranked sites. Generally, final selection of a Preferred and an Alternate Site will require balancing of factors, expert judgment, and client input, as sites being compared will differ in their scores associated with different Avoidance Criteria and Suitability Criteria. RIZZO Associates (RIZZO) offers in this paper a modification to this methodology for selecting the site for NPP development, which accords to the categories of Exclusionary, Avoidance and Suitability Criteria strict definitions which can be considered as Absolute Factors, Critical Factors, and Economic Factors for a more focused approach to site selection. Absolute Factors include all of the safety-related Exclusionary Criteria. Critical Factors are those that are difficult to overcome unless extraordinary mitigation measures are implemented; they have a significant impact on the ability of the project to be successful and may cause the

  13. General siting study 95. Siting of a deep repository for spent nuclear fuel

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-10-01

    General Siting Study 95 is a detailed description of the work carried out to put the siting of a deep repository in a national and regional context. The report is based on SKB`s siting factors, which have been applied on a national scale. Different factors of importance or of possible importance for the long-term radiological safety, technology, land and environment as well as society are described and evaluated. This report is the overall description on general siting studies which the government considered that SKB should report in connection with the RD and D Programme 95. 121 refs, 40 figs.

  14. General siting study 95. Siting of a deep repository for spent nuclear fuel

    International Nuclear Information System (INIS)

    1995-10-01

    General Siting Study 95 is a detailed description of the work carried out to put the siting of a deep repository in a national and regional context. The report is based on SKB's siting factors, which have been applied on a national scale. Different factors of importance or of possible importance for the long-term radiological safety, technology, land and environment as well as society are described and evaluated. This report is the overall description on general siting studies which the government considered that SKB should report in connection with the RD and D Programme 95. 121 refs, 40 figs

  15. Olkiluoto site description 2011

    International Nuclear Information System (INIS)

    2012-12-01

    This fourth version of the Olkiluoto Site Report, produced by the OMTF (Olkiluoto Modelling Task Force), updates the Olkiluoto Site Report 2008 with the data and knowledge obtained up to December 2010. A descriptive model of the site (the Site Descriptive Model, SDM), i.e. a model describing the geological and hydrogeological structure of the site, properties of the bedrock and the groundwater and its flow, and the associated interacting processes and mechanisms. The SDM is divided into six parts: surface system, geology, rock mechanics, hydrogeology, hydrogeochemistry and transport properties

  16. Site Environmental Report, 1993

    Energy Technology Data Exchange (ETDEWEB)

    1994-06-01

    The Site Environmental Report (SER) is prepared annually in accordance with DOE Order 5400.1, ``General Environmental Protection Program.`` This 1993 SER provides the general public as well as scientists and engineers with the results from the site`s ongoing Environmental Monitoring Program. Also included in this report is information concerning the site`s progress toward achieving full compliance with requirements set forth by DOE, US Environmental Protection Agency (USEPA), and Ohio EPA (OEPA). For some readers, the highlights provided in the Executive Summary may provide sufficient information. Many readers, however, may wish to read more detailed descriptions of the information than those which are presented here.

  17. Olkiluoto site description 2011

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-12-15

    This fourth version of the Olkiluoto Site Report, produced by the OMTF (Olkiluoto Modelling Task Force), updates the Olkiluoto Site Report 2008 with the data and knowledge obtained up to December 2010. A descriptive model of the site (the Site Descriptive Model, SDM), i.e. a model describing the geological and hydrogeological structure of the site, properties of the bedrock and the groundwater and its flow, and the associated interacting processes and mechanisms. The SDM is divided into six parts: surface system, geology, rock mechanics, hydrogeology, hydrogeochemistry and transport properties.

  18. Hanford Site Infrastructure Plan

    International Nuclear Information System (INIS)

    1990-01-01

    The Hanford Site Infrastructure Plan (HIP) has been prepared as an overview of the facilities, utilities, systems, and services that support all activities on the Hanford Site. Its purpose is three-fold: to examine in detail the existing condition of the Hanford Site's aging utility systems, transportation systems, Site services and general-purpose facilities; to evaluate the ability of these systems to meet present and forecasted Site missions; to identify maintenance and upgrade projects necessary to ensure continued safe and cost-effective support to Hanford Site programs well into the twenty-first century. The HIP is intended to be a dynamic document that will be updated accordingly as Site activities, conditions, and requirements change. 35 figs., 25 tabs

  19. Hanford Site Development Plan

    International Nuclear Information System (INIS)

    Hathaway, H.B.; Daly, K.S.; Rinne, C.A.; Seiler, S.W.

    1992-05-01

    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 a land use plan for the Hanford Site and presents a picture of what is currently known and anticipated in accordance with DOE Order 4320.1B. Site Development Planning. The HSDP wig be updated annually as future decisions further shape the mission and overall site development process. Further details about Hanford Site development are defined in individual area development plans

  20. Thematic report on community development and siting

    International Nuclear Information System (INIS)

    Vari, A.

    2002-01-01

    The paper analyses the Finnish spent fuel disposal facility siting from the perspective of community development, issues of fairness, and general factors of success. We found that anticipated positive impacts on host community development were the most important factors of local support. Second, the willingness of main stakeholders to adopt and combine several competing and changing concepts of fairness helped making legitimate decisions. Finally, we can conclude that in addition to important cultural factors which are unique in Finland, a number of siting elements have contributed to the success that are of cross-cultural nature. The paper summarises the lessons learned about the Finnish spent fuel disposal facility siting process regarding the issues of community development, fairness, and the transferability of siting approaches across cultures. It is largely based on information presented within the framework of the OECD Forum of Stakeholder Confidence Workshop held in Turku, Finland, on 15-16 November 2001. (author)

  1. Site characterization plan:

    International Nuclear Information System (INIS)

    1988-01-01

    The Yucca Mountain site in Nevada is one of three candidate sites for the first geologic repository for radioactive waste. On May 28, 1986, it was recommended for detailed study in a program of site characterization. This site characterization plan (SCP) has been prepared in accordance with the requirements of the Nuclear Waste Policy Act to summarize the information collected to date about the geologic conditions at the site;to describe the conceptual designs for the repository and the waste package;and to present the plans for obtaining the geologic information necessary to demonstrate the suitability of the site for repository, to design the repository and the waste package, to prepare an environmental impact statement, and to obtain from the US Nuclear Regulatory Commission (NRC) an authorization to construct the repository. This introduction begins with a brief section on the process for siting and developing a repository, followed by a discussion of the pertinent legislation and regulations. A description of site characterization is presented next;it describes the facilities to be constructed for the site