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Sample records for high confidence protein

  1. Inferring high-confidence human protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Yu Xueping

    2012-05-01

    Full Text Available Abstract Background As numerous experimental factors drive the acquisition, identification, and interpretation of protein-protein interactions (PPIs, aggregated assemblies of human PPI data invariably contain experiment-dependent noise. Ascertaining the reliability of PPIs collected from these diverse studies and scoring them to infer high-confidence networks is a non-trivial task. Moreover, a large number of PPIs share the same number of reported occurrences, making it impossible to distinguish the reliability of these PPIs and rank-order them. For example, for the data analyzed here, we found that the majority (>83% of currently available human PPIs have been reported only once. Results In this work, we proposed an unsupervised statistical approach to score a set of diverse, experimentally identified PPIs from nine primary databases to create subsets of high-confidence human PPI networks. We evaluated this ranking method by comparing it with other methods and assessing their ability to retrieve protein associations from a number of diverse and independent reference sets. These reference sets contain known biological data that are either directly or indirectly linked to interactions between proteins. We quantified the average effect of using ranked protein interaction data to retrieve this information and showed that, when compared to randomly ranked interaction data sets, the proposed method created a larger enrichment (~134% than either ranking based on the hypergeometric test (~109% or occurrence ranking (~46%. Conclusions From our evaluations, it was clear that ranked interactions were always of value because higher-ranked PPIs had a higher likelihood of retrieving high-confidence experimental data. Reducing the noise inherent in aggregated experimental PPIs via our ranking scheme further increased the accuracy and enrichment of PPIs derived from a number of biologically relevant data sets. These results suggest that using our high-confidence

  2. A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.

    Science.gov (United States)

    Hosur, Raghavendra; Peng, Jian; Vinayagam, Arunachalam; Stelzl, Ulrich; Xu, Jinbo; Perrimon, Norbert; Bienkowska, Jadwiga; Berger, Bonnie

    2012-08-31

    Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-positive and false-negative rates. Coev2Net is easily applied to thousands of binary protein interactions and has superior predictive performance over existing methods. We experimentally validate selected high-confidence predictions in the human MAPK network and show that predicted interfaces are enriched for cancer -related or damaging SNPs. Coev2Net can be downloaded at http://struct2net.csail.mit.edu.

  3. Categorizing Biases in High-Confidence High-Throughput Protein-Protein Interaction Data Sets

    Science.gov (United States)

    2011-01-01

    Interactions Functional Diversity in Protein Interaction Data Sets—Al- though genomic-scale protein-protein interaction detection campaigns are by design...mapped out in Fig. 2 show that the different data sets covered distinct parts of the interaction space, with some FIG. 1. Functional diversity among

  4. A high confidence, manually validated human blood plasma protein reference set

    DEFF Research Database (Denmark)

    Schenk, Susann; Schoenhals, Gary J; de Souza, Gustavo

    2008-01-01

    sources, including the HUPO PPP dataset. CONCLUSION: Superior instrumentation combined with rigorous validation criteria gave rise to a set of 697 plasma proteins in which we have very high confidence, demonstrated by an exceptionally low false peptide identification rate of 0.29%.......BACKGROUND: The immense diagnostic potential of human plasma has prompted great interest and effort in cataloging its contents, exemplified by the Human Proteome Organization (HUPO) Plasma Proteome Project (PPP) pilot project. Due to challenges in obtaining a reliable blood plasma protein list...

  5. High Confidence Software and Systems Research Needs

    Data.gov (United States)

    Networking and Information Technology Research and Development, Executive Office of the President — This White Paper presents a survey of high confidence software and systems research needs. It has been prepared by the High Confidence Software and Systems...

  6. Hypercorrection of High Confidence Errors in Children

    Science.gov (United States)

    Metcalfe, Janet; Finn, Bridgid

    2012-01-01

    Three experiments investigated whether the hypercorrection effect--the finding that errors committed with high confidence are easier, rather than more difficult, to correct than are errors committed with low confidence--occurs in grade school children as it does in young adults. All three experiments showed that Grade 3-6 children hypercorrected…

  7. Hypercorrection of High Confidence Errors in Children

    Science.gov (United States)

    Metcalfe, Janet; Finn, Bridgid

    2012-01-01

    Three experiments investigated whether the hypercorrection effect--the finding that errors committed with high confidence are easier, rather than more difficult, to correct than are errors committed with low confidence--occurs in grade school children as it does in young adults. All three experiments showed that Grade 3-6 children hypercorrected…

  8. Asymptotically Honest Confidence Regions for High Dimensional

    DEFF Research Database (Denmark)

    Caner, Mehmet; Kock, Anders Bredahl

    While variable selection and oracle inequalities for the estimation and prediction error have received considerable attention in the literature on high-dimensional models, very little work has been done in the area of testing and construction of confidence bands in high-dimensional models. However...... develop an oracle inequality for the conservative Lasso only assuming the existence of a certain number of moments. This is done by means of the Marcinkiewicz-Zygmund inequality which in our context provides sharper bounds than Nemirovski's inequality. As opposed to van de Geer et al. (2014) we allow...

  9. High-Confidence Quantum Gate Tomography

    Science.gov (United States)

    Johnson, Blake; da Silva, Marcus; Ryan, Colm; Kimmel, Shelby; Donovan, Brian; Ohki, Thomas

    2014-03-01

    Debugging and verification of high-fidelity quantum gates requires the development of new tools and protocols to unwrap the performance of the gate from the rest of the sequence. Randomized benchmarking tomography[2] allows one to extract full information of the unital portion of the gate with high confidence. We report experimental confirmation of the technique's applicability to quantum gate tomography. We show that the method is robust to common experimental imperfections such as imperfect single-shot readout and state preparation. We also demonstrate the ability to characterize non-Clifford gates. To assist in the experimental implementation we introduce two techniques. ``Atomic Cliffords'' use phase ramping and frame tracking to allow single-pulse implementation of the full group of single-qubit Clifford gates. Domain specific pulse sequencers allow rapid implementation of the many thousands of sequences needed. This research was funded by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), through the Army Research Office contract no. W911NF-10-1-0324.

  10. Business confidence still high in Zimbabwe.

    Science.gov (United States)

    Amanor-wilks, D

    1995-12-01

    Business confidence has not been affected in Zimbabwe despite the AIDS epidemic in that country. An Australian mining company has recruited people to work at its platinum mine in Zimbabwe and also instituted an AIDS awareness program. The National Chamber of Commerce disclosed that semiskilled and unskilled workers who are the "easiest to replace" have been most affected by the epidemic. The impact of AIDS has not been as bad as had been predicted several years ago. By the end of the 1990s, however, there might be a skills shortage. The first AIDS case was detected in 1985 in Zimbabwe. By the end of 1995 a cumulative total of 38,500 cases had been reported, but the National AIDS Control Program believes that the true figure is over 100,000. The estimated number of HIV-infected people is about 1 million. The most economically productive age group (30-50) has the highest rates of infection. Transport is affected most, followed by mining and commercial farming. Infection rates among miners are estimated to be 20-30% and the rates are the highest at the mines on the major transport routes. The mining industry has not had any problems in recruiting labor, but, increasingly, deaths are AIDS-related. The growing sex industry at the mines has accelerated the spread of HIV. In addition, small mines do not have AIDS awareness programs in place. The National Employment Council runs a project for the transport industry, which seeks to intensify AIDS campaigns at truck stops. This also entails talks to drivers about AIDS; courses for police, nurses, and sex workers; and the distribution of condoms. In commercial farming, two-thirds of workers are unskilled casual laborers who live in squalid conditions that foster the spread of AIDS. At these farms there is also a growing number of orphans, whose number is estimated to rise to 60,000 by the late 1990s.

  11. Automated and high confidence protein phosphorylation site localization using complementary collision-activated dissociation and electron transfer dissociation tandem mass spectrometry

    DEFF Research Database (Denmark)

    Hansen, Thomas A; Sylvester, Marc; Jensen, Ole N

    2012-01-01

    -activated dissociation and electron transfer dissociation, an approach termed the Cscore. The scoring algorithm used in the Cscore was adapted from the widely used Ascore method. The analytical benefit of integrating the product ion information of both ETD and CAD data are evident by increased confidence in phospho...

  12. Distinguishing highly confident accurate and inaccurate memory: insights about relevant and irrelevant influences on memory confidence

    Science.gov (United States)

    Chua, Elizabeth F.; Hannula, Deborah E.; Ranganath, Charan

    2012-01-01

    It is generally believed that accuracy and confidence in one’s memory are related, but there are many instances when they diverge. Accordingly, it is important to disentangle the factors which contribute to memory accuracy and confidence, especially those factors that contribute to confidence, but not accuracy. We used eye movements to separately measure fluent cue processing, the target recognition experience, and relative evidence assessment on recognition confidence and accuracy. Eye movements were monitored during a face-scene associative recognition task, in which participants first saw a scene cue, followed by a forced-choice recognition test for the associated face, with confidence ratings. Eye movement indices of the target recognition experience were largely indicative of accuracy, and showed a relationship to confidence for accurate decisions. In contrast, eye movements during the scene cue raised the possibility that more fluent cue processing was related to higher confidence for both accurate and inaccurate recognition decisions. In a second experiment, we manipulated cue familiarity, and therefore cue fluency. Participants showed higher confidence for cue-target associations for when the cue was more familiar, especially for incorrect responses. These results suggest that over-reliance on cue familiarity and under-reliance on the target recognition experience may lead to erroneous confidence. PMID:22171810

  13. Distinguishing highly confident accurate and inaccurate memory: insights about relevant and irrelevant influences on memory confidence.

    Science.gov (United States)

    Chua, Elizabeth F; Hannula, Deborah E; Ranganath, Charan

    2012-01-01

    It is generally believed that accuracy and confidence in one's memory are related, but there are many instances when they diverge. Accordingly it is important to disentangle the factors that contribute to memory accuracy and confidence, especially those factors that contribute to confidence, but not accuracy. We used eye movements to separately measure fluent cue processing, the target recognition experience, and relative evidence assessment on recognition confidence and accuracy. Eye movements were monitored during a face-scene associative recognition task, in which participants first saw a scene cue, followed by a forced-choice recognition test for the associated face, with confidence ratings. Eye movement indices of the target recognition experience were largely indicative of accuracy, and showed a relationship to confidence for accurate decisions. In contrast, eye movements during the scene cue raised the possibility that more fluent cue processing was related to higher confidence for both accurate and inaccurate recognition decisions. In a second experiment we manipulated cue familiarity, and therefore cue fluency. Participants showed higher confidence for cue-target associations for when the cue was more familiar, especially for incorrect responses. These results suggest that over-reliance on cue familiarity and under-reliance on the target recognition experience may lead to erroneous confidence.

  14. Autism Spectrum Disorder and High Confidence Gene Factors

    OpenAIRE

    Mai, MOCHIZUKI

    2017-01-01

    Autism spectrum disorder (ASD) is a neurological developmental disorder whose mechanism isyet unclear. However, recent ASD studies, which employ exome- and genome-wide sequencing,have identified some high-confidence ASD genes. Those ASD studies have revealed that CHD8is likely associated with ASD. In this article, we highlight that CHD8 may regulate othercandidate ASD risk genes. Current research indicates that there exist some thousand autismsusceptibility candidate genes. Moreover, we sugge...

  15. Enabling high confidence detections of gravitational-wave bursts

    CERN Document Server

    Littenberg, Tyson B; Cornish, Neil J; Millhouse, Margaret

    2015-01-01

    With the advanced LIGO and Virgo detectors taking observations the detection of gravitational waves is expected within the next few years. Extracting astrophysical information from gravitational wave detections is a well-posed problem and thoroughly studied when detailed models for the waveforms are available. However, one motivation for the field of gravitational wave astronomy is the potential for new discoveries. Recognizing and characterizing unanticipated signals requires data analysis techniques which do not depend on theoretical predictions for the gravitational waveform. Past searches for short-duration un-modeled gravitational wave signals have been hampered by transient noise artifacts, or "glitches," in the detectors. In some cases, even high signal-to-noise simulated astrophysical signals have proven difficult to distinguish from glitches, so that essentially any plausible signal could be detected with at most 2-3 $\\sigma$ level confidence. We have put forth the BayesWave algorithm to differentiat...

  16. Inferring High-Confidence Human Protein-Protein Interactions

    Science.gov (United States)

    2012-01-01

    Similarly, the top-ranked interaction between L-threonine dehydrogenase ( TDH ) and aminoacetone synthetase (alias of GCAT) catalyzes the conversion of L...acetyltransferase TDH 2 L-threonine dehydrogenase 2 577.4 11.0 1328.0 CXCL16 4 Inducible T cell co-stimulator CXCR6 4 Inducible T cell co-stimulator

  17. Augmenting Chinese hamster genome assembly by identifying regions of high confidence.

    Science.gov (United States)

    Vishwanathan, Nandita; Bandyopadhyay, Arpan A; Fu, Hsu-Yuan; Sharma, Mohit; Johnson, Kathryn C; Mudge, Joann; Ramaraj, Thiruvarangan; Onsongo, Getiria; Silverstein, Kevin A T; Jacob, Nitya M; Le, Huong; Karypis, George; Hu, Wei-Shou

    2016-09-01

    Chinese hamster Ovary (CHO) cell lines are the dominant industrial workhorses for therapeutic recombinant protein production. The availability of genome sequence of Chinese hamster and CHO cells will spur further genome and RNA sequencing of producing cell lines. However, the mammalian genomes assembled using shot-gun sequencing data still contain regions of uncertain quality due to assembly errors. Identifying high confidence regions in the assembled genome will facilitate its use for cell engineering and genome engineering. We assembled two independent drafts of Chinese hamster genome by de novo assembly from shotgun sequencing reads and by re-scaffolding and gap-filling the draft genome from NCBI for improved scaffold lengths and gap fractions. We then used the two independent assemblies to identify high confidence regions using two different approaches. First, the two independent assemblies were compared at the sequence level to identify their consensus regions as "high confidence regions" which accounts for at least 78 % of the assembled genome. Further, a genome wide comparison of the Chinese hamster scaffolds with mouse chromosomes revealed scaffolds with large blocks of collinearity, which were also compiled as high-quality scaffolds. Genome scale collinearity was complemented with EST based synteny which also revealed conserved gene order compared to mouse. As cell line sequencing becomes more commonly practiced, the approaches reported here are useful for assessing the quality of assembly and potentially facilitate the engineering of cell lines.

  18. Determining confidence of predicted interactions between HIV-1 and human proteins using conformal method.

    Science.gov (United States)

    Nouretdinov, Ilia; Gammerman, Alex; Qi, Yanjun; Klein-Seetharaman, Judith

    2012-01-01

    Identifying protein-protein interactions (PPI's) is critical for understanding virtually all cellular molecular mechanisms. Previously, predicting PPI's was treated as a binary classification task and has commonly been solved in a supervised setting which requires a positive labeled set of known PPI's and a negative labeled set of non-interacting protein pairs. In those methods, the learner provides the likelihood of the predicted interaction, but without a confidence level associated with each prediction. Here, we apply a conformal prediction framework to make predictions and estimate confidence of the predictions. The conformal predictor uses a function measuring relative 'strangeness' interacting pairs to check whether prediction of a new example added to the sequence of already known PPI's would conform to the 'exchangeability' assumption: distribution of interacting pairs is invariant with any permutations of the pairs. In fact, this is the only assumption we make about the data. Another advantage is that the user can control a number of errors by providing a desirable confidence level. This feature of CP is very useful for a ranking list of possible interactive pairs. In this paper, the conformal method has been developed to deal with just one class - class interactive proteins - while there is not clearly defined of 'non-interactive'pairs. The confidence level helps the biologist in the interpretation of the results, and better assists the choices of pairs for experimental validation. We apply the proposed conformal framework to improve the identification of interacting pairs between HIV-1 and human proteins.

  19. High-confidence coding and noncoding transcriptome maps

    Science.gov (United States)

    2017-01-01

    The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. Here, we present a high-performing transcriptome assembly pipeline, called CAFE, that significantly improves the original assemblies, respectively assembled with stranded and/or unstranded RNA-seq data, by orienting unstranded reads using the maximum likelihood estimation and by integrating information about transcription start sites and cleavage and polyadenylation sites. Applying large-scale transcriptomic data comprising 230 billion RNA-seq reads from the ENCODE, Human BodyMap 2.0, The Cancer Genome Atlas, and GTEx projects, CAFE enabled us to predict the directions of about 220 billion unstranded reads, which led to the construction of more accurate transcriptome maps, comparable to the manually curated map, and a comprehensive lncRNA catalog that includes thousands of novel lncRNAs. Our pipeline should not only help to build comprehensive, precise transcriptome maps from complex genomes but also to expand the universe of noncoding genomes. PMID:28396519

  20. Preparation for high-acuity clinical placement: confidence levels of final-year nursing students

    Directory of Open Access Journals (Sweden)

    Porter J

    2013-04-01

    Full Text Available Joanne Porter, Julia Morphet, Karen Missen, Anita Raymond School of Nursing and Midwifery, Monash University, Churchill, VIC, Australia Aim: To measure final-year nursing students’ preparation for high-acuity placement with emphasis on clinical skill performance confidence. Background: Self-confidence has been reported as being a key component for effective clinical performance, and confident students are more likely to be more effective nurses. Clinical skill performance is reported to be the most influential source of self-confidence. Student preparation and skill acquisition are therefore important aspects in ensuring students have successful clinical placements, especially in areas of high acuity. Curriculum development should aim to assist students with their theoretical and clinical preparedness for the clinical environment. Method: A modified pretest/posttest survey design was used to measure the confidence of third-year undergraduate nursing students (n = 318 for placement into a high-acuity clinical setting. The survey comprised four questions related to clinical placement and prospect of participating in a cardiac arrest scenario, and confidence rating levels of skills related to practice in a high-acuity setting. Content and face validity were established by an expert panel (α = 0.90 and reliability was established by the pilot study in 2009. Comparisons were made between confidence levels at the beginning and end of semester. Results: Student confidence to perform individual clinical skills increased over the semester; however their feelings of preparedness for high-acuity clinical placement decreased over the same time period. Reported confidence levels improved with further exposure to clinical placement. Conclusion: There may be many external factors that influence students’ perceptions of confidence and preparedness for practice. Further research is recommended to identify causes of poor self-confidence in final-year nursing

  1. People’s Hypercorrection of High Confidence Errors: Did They Know it All Along?

    OpenAIRE

    Metcalfe, Janet; Finn, Bridgid

    2011-01-01

    This study investigated the ‘knew it all along’ explanation of the hypercorrection effect. The hypercorrection effect refers to the finding that when given corrective feedback, errors that are committed with high confidence are easier to correct than low confidence errors. Experiment 1 showed that people were more likely to claim that they ‘knew it all along,’ when they were given the answers to high confidence errors as compared to low confidence errors. Experiments 2 and 3 investigated whet...

  2. People's Hypercorrection of High-Confidence Errors: Did They Know It All Along?

    Science.gov (United States)

    Metcalfe, Janet; Finn, Bridgid

    2011-01-01

    This study investigated the "knew it all along" explanation of the hypercorrection effect. The hypercorrection effect refers to the finding that when people are given corrective feedback, errors that are committed with high confidence are easier to correct than low-confidence errors. Experiment 1 showed that people were more likely to…

  3. Common and specific brain regions in high- versus low-confidence recognition memory

    Science.gov (United States)

    Kim, Hongkeun; Cabeza, Roberto

    2009-01-01

    The goal of the present functional magnetic resonance imaging (fMRI) study was to investigate whether and to what extent brain regions involved in high-confidence recognition (HCR) versus low-confidence recognition (LCR) overlap or separate from each other. To this end, we performed conjunction analyses involving activations elicited during high-confidence hit, low-confidence hit, and high-confidence correct-rejection responses. The analyses yielded 3 main findings. First, sensory/perceptual and associated posterior regions were common to HCR and LCR, indicating contribution of these regions to both HCR and LCR activity. This finding may help explain why these regions are among the most common in functional neuroimaging studies of episodic retrieval. Second, medial temporal lobe (MTL) and associated midline regions were associated with HCR, possibly reflecting recollection-related processes, whereas specific prefrontal cortex (PFC) regions were associated with LCR, possibly reflecting executive control processes. This finding is consistent with the notion that the MTL and PFC networks play complementary roles during episodic retrieval. Finally, within posterior parietal cortex, a dorsal region was associated with LCR, possibly reflecting top-down attentional processes, whereas a ventral region was associated with HCR, possibly reflecting bottom-up attentional processes. This finding may help explain why functional neuroimaging studies have found diverse parietal effects during episodic retrieval. Taken together, our findings provide strong evidence that HCR versus LCR, and by implication, recollection versus familiarity processes, are represented in common as well as specific brain regions. PMID:19501072

  4. Understanding Parental Confidence in an Inclusive High School: A Pilot Survey

    Science.gov (United States)

    Morewood, Gareth D.; Bond, Caroline

    2012-01-01

    A questionnaire was developed and trialled in an inclusive high school with the aim of understanding factors that contribute to parental confidence in school provision for students with special educational needs and disabilities (SEND). Parents of all students at School Action, School Action Plus and those with Statements of special educational…

  5. Refutations in science texts lead to hypercorrection of misconceptions held with high confidence

    NARCIS (Netherlands)

    Van Loon, Mariëtte H.; Dunlosky, John; Van Gog, Tamara; Van Merriënboer, Jeroen J.g.; De Bruin, Anique B.h.

    2015-01-01

    Misconceptions about science are often not corrected during study when they are held with high confidence. However, when corrective feedback co-activates a misconception together with the correct conception, this feedback may surprise the learner and draw attention, especially when the misconception

  6. High-fidelity nursing simulation: impact on student self-confidence and clinical competence.

    Science.gov (United States)

    Blum, Cynthia A; Borglund, Susan; Parcells, Dax

    2010-01-01

    Development of safe nursing practice in entry-level nursing students requires special consideration from nurse educators. The paucity of data supporting high-fidelity patient simulation effectiveness in this population informed the development of a quasi-experimental, quantitative study of the relationship between simulation and student self-confidence and clinical competence. Moreover, the study reports a novel approach to measuring self-confidence and competence of entry-level nursing students. Fifty-three baccalaureate students, enrolled in either a traditional or simulation-enhanced laboratory, participated during their first clinical rotation. Student self-confidence and faculty perception of student clinical competence were measured using selected scale items of the Lasater Clinical Judgment Rubric. The results indicated an overall improvement in self-confidence and competence across the semester, however, simulation did not significantly enhance these caring attributes. The study highlights the need for further examination of teaching strategies developed to promote the transfer of self-confidence and competence from the laboratory to the clinical setting.

  7. Decision-making patterns and self-confidence in high school adolescents

    Directory of Open Access Journals (Sweden)

    Alejandro César Antonio Luna Bernal

    2014-07-01

    Full Text Available The present study aimed to analyse the factor structure of the Melbourne Decision Making Questionnaire (DMQ-II, and to examine the relationships between the factors identified and Self-confidence, in order to conceptualize the decision-making process in adolescents under the Conflict Model of Decision Making. Participants were 992 Mexican high-school students, aged between 15 and 19 years. The three factors were identified as decision-making patterns in adolescents: a Vigilance, b Hipervigilance/Procrastination and c Buck-passing. The Self-confidence showed a positive effect on Vigilance, and a negative effect on theother two patterns. Results are discussed considering the literature on decision making in adolescence.

  8. Data on electrical energy conservation using high efficiency motors for the confidence bounds using statistical techniques.

    Science.gov (United States)

    Shaikh, Muhammad Mujtaba; Memon, Abdul Jabbar; Hussain, Manzoor

    2016-09-01

    In this article, we describe details of the data used in the research paper "Confidence bounds for energy conservation in electric motors: An economical solution using statistical techniques" [1]. The data presented in this paper is intended to show benefits of high efficiency electric motors over the standard efficiency motors of similar rating in the industrial sector of Pakistan. We explain how the data was collected and then processed by means of formulas to show cost effectiveness of energy efficient motors in terms of three important parameters: annual energy saving, cost saving and payback periods. This data can be further used to construct confidence bounds for the parameters using statistical techniques as described in [1].

  9. Are Confidence Ratings Test- or Trait-Driven? Individual Differences among High, Average, and Low Comprehenders in Fourth Grade

    Science.gov (United States)

    Kasperski, Ronen; Katzir, Tami

    2013-01-01

    The aim of this study was to examine whether low, average, and high comprehenders (LC, AC, and HC, respectively) differed in their reading self-confidence and bias ratings, and whether confidence ratings were driven by reading ability or distributed evenly among diverse readers. Seventy fourth-graders with good decoding abilities were administered…

  10. Are Confidence Ratings Test- or Trait-Driven? Individual Differences among High, Average, and Low Comprehenders in Fourth Grade

    Science.gov (United States)

    Kasperski, Ronen; Katzir, Tami

    2013-01-01

    The aim of this study was to examine whether low, average, and high comprehenders (LC, AC, and HC, respectively) differed in their reading self-confidence and bias ratings, and whether confidence ratings were driven by reading ability or distributed evenly among diverse readers. Seventy fourth-graders with good decoding abilities were administered…

  11. A High-confidence Cyber-Physical Alarm System: Design and Implementation

    CERN Document Server

    Ma, Longhua; Xia, Feng; Xu, Ming; Yao, Jun; Shao, Meng

    2010-01-01

    Most traditional alarm systems cannot address security threats in a satisfactory manner. To alleviate this problem, we developed a high-confidence cyber-physical alarm system (CPAS), a new kind of alarm systems. This system establishes the connection of the Internet (i.e. TCP/IP) through GPRS/CDMA/3G. It achieves mutual communication control among terminal equipments, human machine interfaces and users by using the existing mobile communication network. The CPAS will enable the transformation in alarm mode from traditional one-way alarm to two-way alarm. The system has been successfully applied in practice. The results show that the CPAS could avoid false alarms and satisfy residents' security needs.

  12. Decreased memory confidence in obsessive-compulsive disorder for scenarios high and low on responsibility: is low still too high?

    Science.gov (United States)

    Moritz, Steffen; Jaeger, Anne

    2017-03-28

    Previous research suggests that patients with obsessive-compulsive disorder (OCD), particularly checkers, display an inflated sense of responsibility. For the present study, we tested whether memory confidence in OCD is reduced under conditions of heightened responsibility and/or reflects poor memory vividness. A computerized task designed to modulate perceived responsibility was administered to 26 OCD patients (12 checkers) and 21 healthy controls. In the experimental condition (high responsibility), participants had to allocate daily medications to ten fictive patients in a hospital emergency ward, whereas in the control condition (low responsibility) participants had to allocate bath essences for ten hotel guests. Participants' response time and accuracy were recorded as well as their memory confidence, memory vividness, and subjective success. Irrespective of the condition, OCD patients performed as accurately as healthy controls, but appraised their performance as worse than that of controls. Memory confidence was decreased in patients, particularly checkers. No group differences emerged on vividness, and none of the effects were moderated by the condition (high versus low responsibility). The relationship between responsibility and OCD behavior is complex. Results suggest metamemory problems in OCD checkers, even when induced responsibility is low. The findings speak against "cold" memory deficits in OCD, as patients did not differ from controls on accuracy, reaction time, or vividness. Future research should focus on idiosyncratic beliefs and scenarios that inflate responsibility and elicit cognitive biases.

  13. Iterative Non-m/z-sharing Rule for Confident and Sensitive Protein Identification of Non-shotgun Proteomics

    Institute of Scientific and Technical Information of China (English)

    YUN Dong; HE Fuchu; LU Haojie; WANG Haijian; ZHANG Yang; CHENG Gang; JIN Hong; YU Yanbao; XU Yawei; YANG Pengyuan

    2009-01-01

    Selecting reasonable matches from the database search results is crucial to mass spectrometry-based proteomics identification. However, the current score-based filter solution and decoy database methods are not effective enough to prevent all false positive and false negative selections. In this study, a systematic search strategy named iterative non-m/z-sharing (INMZS) analysis was proposed to address the problem. In the strategy, all search results were screened based on the share status of corresponding matched m/z, only the proteins that matched with exclusive m/z information were reserved for the confident matches. The researchers did further iterative search to improve the identification of minor components in a spot. Finally, identifications were confirmed by decoy database evaluation for the final phase of protein identification. Simulation and application tests of INMZS were implemented on a large human liver data set and standard protein cocktails. The result shows that INMZS plus decoy database evaluation is efficient in ensuring the confidence and sensitivity of 2-DE or similar non-shotgun based proteome identification.

  14. Gene expression correlation analysis predicts involvement of high- and low-confidence risk genes in different stages of prostate carcinogenesis.

    Science.gov (United States)

    Yano, Kojiro

    2010-12-01

    Whole genome association studies have identified many loci associated with the risk of prostate cancer (PC). However, very few of the genes associated with these loci have been related to specific processes of prostate carcinogenesis. Therefore I inferred biological functions associated with these risk genes using gene expression correlation analysis. PC risk genes reported in the literature were classified as having high (Plow (Phigh-confidence genes and other genes in the microarray dataset, whereas correlation between low-confidence genes and other genes in PC showed smaller decrease. Genes involved in developmental processes were significantly correlated with all risk gene categories. Ectoderm development genes, which may be related to squamous metaplasia, and genes enriched in fetal prostate stem cells (PSCs) showed strong association with the high-confidence genes. The association between the PSC genes and the low-confidence genes was weak, but genes related to neural system genes showed strong association with low-confidence genes. The high-confidence risk genes may be associated with an early stage of prostate carcinogenesis, possibly involving PSCs and squamous metaplasia. The low-confidence genes may be involved in a later stage of carcinogenesis. © 2010 Wiley-Liss, Inc.

  15. Quest-V: A Virtualized Multikernel for High-Confidence Systems

    CERN Document Server

    Li, Ye; West, Richard

    2011-01-01

    This paper outlines the design of `Quest-V', which is implemented as a collection of separate kernels operating together as a distributed system on a chip. Quest-V uses virtualization techniques to isolate kernels and prevent local faults from affecting remote kernels. This leads to a high-confidence multikernel approach, where failures of system subcomponents do not render the entire system inoperable. A virtual machine monitor for each kernel keeps track of shadow page table mappings that control immutable memory access capabilities. This ensures a level of security and fault tolerance in situations where a service in one kernel fails, or is corrupted by a malicious attack. Communication is supported between kernels using shared memory regions for message passing. Similarly, device driver data structures are shareable between kernels to avoid the need for complex I/O virtualization, or communication with a dedicated kernel responsible for I/O. In Quest-V, device interrupts are delivered directly to a kernel...

  16. Discovery of a high confidence soft lag from an X-ray flare of Markarian 421

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    We present the X-ray variability properties of the X-ray and TeV bright blazar Mrk 421 with a-60 ks long XMM-Newton observation performed on November 9-10,2005.The source experienced a pronounced flare,of which the inter-band time lags were determined with a very high confidence level.The soft(0.6-0.8 keV) X-ray variations lagged the hard(4-10 keV) ones by 1.09+0.11-0.12 ks,and the soft lag increases with increasing difference in the photon energy.The energy-dependent soft lags can be well fitted with the difference of the energy-dependent cooling timescales of the relativistic electron distribution responsible for the observed X-ray emission,which constrains the magnetic field strength and Doppler factor of the emitting region to be Bδ 1/3-1.78 Gauss.

  17. A Near-Term, High-Confidence Heavy Lift Launch Vehicle

    Science.gov (United States)

    Rothschild, William J.; Talay, Theodore A.

    2009-01-01

    The use of well understood, legacy elements of the Space Shuttle system could yield a near-term, high-confidence Heavy Lift Launch Vehicle that offers significant performance, reliability, schedule, risk, cost, and work force transition benefits. A side-mount Shuttle-Derived Vehicle (SDV) concept has been defined that has major improvements over previous Shuttle-C concepts. This SDV is shown to carry crew plus large logistics payloads to the ISS, support an operationally efficient and cost effective program of lunar exploration, and offer the potential to support commercial launch operations. This paper provides the latest data and estimates on the configurations, performance, concept of operations, reliability and safety, development schedule, risks, costs, and work force transition opportunities for this optimized side-mount SDV concept. The results presented in this paper have been based on established models and fully validated analysis tools used by the Space Shuttle Program, and are consistent with similar analysis tools commonly used throughout the aerospace industry. While these results serve as a factual basis for comparisons with other launch system architectures, no such comparisons are presented in this paper. The authors welcome comparisons between this optimized SDV and other Heavy Lift Launch Vehicle concepts.

  18. Visual Confidence.

    Science.gov (United States)

    Mamassian, Pascal

    2016-10-14

    Visual confidence refers to an observer's ability to judge the accuracy of her perceptual decisions. Even though confidence judgments have been recorded since the early days of psychophysics, only recently have they been recognized as essential for a deeper understanding of visual perception. The reluctance to study visual confidence may have come in part from obtaining convincing experimental evidence in favor of metacognitive abilities rather than just perceptual sensitivity. Some effort has thus been dedicated to offer different experimental paradigms to study visual confidence in humans and nonhuman animals. To understand the origins of confidence judgments, investigators have developed two competing frameworks. The approach based on signal decision theory is popular but fails to account for response times. In contrast, the approach based on accumulation of evidence models naturally includes the dynamics of perceptual decisions. These models can explain a range of results, including the apparently paradoxical dissociation between performance and confidence that is sometimes observed.

  19. Highly thermostable fluorescent proteins

    Science.gov (United States)

    Bradbury, Andrew M [Santa Fe, NM; Waldo, Geoffrey S [Santa Fe, NM; Kiss, Csaba [Los Alamos, NM

    2012-05-01

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  20. Highly thermostable fluorescent proteins

    Science.gov (United States)

    Bradbury, Andrew M.; Waldo, Geoffrey S.; Kiss, Csaba

    2011-03-22

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  1. Confidant Relations in Italy

    Directory of Open Access Journals (Sweden)

    Jenny Isaacs

    2015-02-01

    Full Text Available Confidants are often described as the individuals with whom we choose to disclose personal, intimate matters. The presence of a confidant is associated with both mental and physical health benefits. In this study, 135 Italian adults responded to a structured questionnaire that asked if they had a confidant, and if so, to describe various features of the relationship. The vast majority of participants (91% reported the presence of a confidant and regarded this relationship as personally important, high in mutuality and trust, and involving minimal lying. Confidants were significantly more likely to be of the opposite sex. Participants overall were significantly more likely to choose a spouse or other family member as their confidant, rather than someone outside of the family network. Familial confidants were generally seen as closer, and of greater value, than non-familial confidants. These findings are discussed within the context of Italian culture.

  2. Factors Related to Family Therapists' Breaking Confidence When Clients Disclose High-Risks-to-HIV/AIDS Sexual Behaviors.

    Science.gov (United States)

    Pais, Shobha; Piercy, Fred; Miller, JoAnn

    1998-01-01

    Through a national survey of marriage and family therapists, this study examines what therapists do when their HIV-positive clients disclose that they are engaging in high-risk sexual behavior. Participants (N=309) were more likely to break confidence when their clients were male, young, gay, or African American. Describes characteristic of…

  3. Factors Related to Family Therapists' Breaking Confidence When Clients Disclose High-Risks-to-HIV/AIDS Sexual Behaviors.

    Science.gov (United States)

    Pais, Shobha; Piercy, Fred; Miller, JoAnn

    1998-01-01

    Through a national survey of marriage and family therapists, this study examines what therapists do when their HIV-positive clients disclose that they are engaging in high-risk sexual behavior. Participants (N=309) were more likely to break confidence when their clients were male, young, gay, or African American. Describes characteristic of…

  4. Structuring high-protein foods

    NARCIS (Netherlands)

    Purwanti, N.

    2012-01-01

    Increased protein consumption gives rise to various health benefits. High-protein intake can lead to muscle development, body weight control and suppression of sarcopenia progression. However, increasing the protein content in food products leads to textural changes over time. These changes result i

  5. Confidence improvement of disosal safety bydevelopement of a safety case for high-level radioactive waste disposal

    Energy Technology Data Exchange (ETDEWEB)

    Baik, Min Hoon; Ko, Nak Youl; Jeong, Jong Tae; Kim, Kyung Su [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2016-12-15

    Many countries have developed a safety case suitable to their own countries in order to improve the confidence of disposal safety in deep geological disposal of high-level radioactive waste as well as to develop a disposal program and obtain its license. This study introduces and summarizes the meaning, necessity, and development process of the safety case for radioactive waste disposal. The disposal safety is also discussed in various aspects of the safety case. In addition, the status of safety case development in the foreign countries is briefly introduced for Switzerland, Japan, the United States of America, Sweden, and Finland. The strategy for the safety case development that is being developed by KAERI is also briefly introduced. Based on the safety case, we analyze the efforts necessary to improve confidence in disposal safety for high-level radioactive waste. Considering domestic situations, we propose and discuss some implementing methods for the improvement of disposal safety, such as construction of a reliable information database, understanding of processes related to safety, reduction of uncertainties in safety assessment, communication with stakeholders, and ensuring justice and transparency. This study will contribute to the understanding of the safety case for deep geological disposal and to improving confidence in disposal safety through the development of the safety case in Korea for the disposal of high-level radioactive waste.

  6. High-confidence software for safety-critical process-control systems

    Energy Technology Data Exchange (ETDEWEB)

    Bastani, F.B. [Univ. of Houston, TX (United States)

    1997-12-01

    Software for safety-critical systems, such as nuclear power plant control systems; avionic systems; and medical, defense, and manufacturing systems, must be highly reliable because failures can have catastrophic consequences. While existing methods, such as formal techniques, testing, and fault-tolerant software, can significantly enhance software reliability, they have some limitations in achieving ultrahigh reliability requirements. Formal methods are not able to cope with specification faults, testing is not cost-effective for high-assurance systems, and fault-tolerant software based on diverse designs is susceptible to common-mode failures.

  7. High School Students' Proficiency and Confidence Levels in Displaying Their Understanding of Basic Electrolysis Concepts

    Science.gov (United States)

    Sia, Ding Teng; Treagust, David F.; Chandrasegaran, A. L.

    2012-01-01

    This study was conducted with 330 Form 4 (grade 10) students (aged 15-16 years) who were involved in a course of instruction on electrolysis concepts. The main purposes of this study were (1) to assess high school chemistry students' understanding of 19 major principles of electrolysis using a recently developed 2-tier multiple-choice diagnostic…

  8. High School Students' Proficiency and Confidence Levels in Displaying Their Understanding of Basic Electrolysis Concepts

    Science.gov (United States)

    Sia, Ding Teng; Treagust, David F.; Chandrasegaran, A. L.

    2012-01-01

    This study was conducted with 330 Form 4 (grade 10) students (aged 15-16 years) who were involved in a course of instruction on electrolysis concepts. The main purposes of this study were (1) to assess high school chemistry students' understanding of 19 major principles of electrolysis using a recently developed 2-tier multiple-choice diagnostic…

  9. Assessment of risk to wildlife from ionising radiation: can initial screening tiers be used with a high level of confidence?

    Energy Technology Data Exchange (ETDEWEB)

    Beresford, N A; Barnett, C L [Centre for Ecology and Hydrology Lancaster, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP (United Kingdom); Hosseini, A; Brown, J E [Norwegian Radiation Protection Authority, Department of Emergency Preparedness and Environmental Radioactivity, Grini naeringspark 13 Postbox 55, NO-1332 Oesteraas (Norway); Cailes, C; Copplestone, D [Environment Agency, PO Box 12, Richard Fairclough House, Knutsford Road, Warrington WA4 1HG (United Kingdom); Beaugelin-Seiller, K, E-mail: nab@ceh.ac.u [Institut de Radioprotection et de Surete Nucleaire DEI/SECRE, CE Cadarache-Batiment 159, BP 3, 13115 Saint-Paul-lez-Durance (France)

    2010-06-15

    A number of models are being used to assess the potential environmental impact of releases of radioactivity. These often use a tiered assessment structure whose first tier is designed to be highly conservative and simple to use. An aim of using this initial tier is to identify sites of negligible concern and to remove them from further consideration with a high degree of confidence. In this paper we compare the screening assessment outputs of three freely available models. The outputs of these models varied considerably in terms of estimated risk quotient (RQ) and the radionuclide-organism combinations identified as being the most limiting. A number of factors are identified as contributing to this variability: values of transfer parameters (concentration ratios and K{sub d}) used; organisms considered; different input options and how these are utilised in the assessment; assumptions as regards secular equilibrium; geometries and exposure scenarios. This large variation in RQ values between models means that the level of confidence required by users is not achieved. We recommend that the factors contributing to the variation in screening assessments be subjected to further investigation so that they can be more fully understood and assessors (and those reviewing assessment outputs) can better justify and evaluate the results obtained.

  10. The Effects of Game-Based Learning on Mathematical Confidence and Performance: High Ability vs. Low Ability

    Science.gov (United States)

    Ku, Oskar; Chen, Sherry Y.; Wu, Denise H.; Lao, Andrew C. C.; Chan, Tak-Wai

    2014-01-01

    Many students possess low confidence toward learning mathematics, which, in turn, may lead them to give up pursuing more mathematics knowledge. Recently, game-based learning (GBL) is regarded as a potential means in improving students' confidence. Thus, this study tried to promote students' confidence toward mathematics by using GBL. In addition,…

  11. The Effects of Game-Based Learning on Mathematical Confidence and Performance: High Ability vs. Low Ability

    Science.gov (United States)

    Ku, Oskar; Chen, Sherry Y.; Wu, Denise H.; Lao, Andrew C. C.; Chan, Tak-Wai

    2014-01-01

    Many students possess low confidence toward learning mathematics, which, in turn, may lead them to give up pursuing more mathematics knowledge. Recently, game-based learning (GBL) is regarded as a potential means in improving students' confidence. Thus, this study tried to promote students' confidence toward mathematics by using GBL. In…

  12. Statistics with confidence confidence intervals and statistical guidelines

    CERN Document Server

    Altman, Douglas; Bryant, Trevor; Gardner, Stephen

    2013-01-01

    This highly popular introduction to confidence intervals has been thoroughly updated and expanded. It includes methods for using confidence intervals, with illustrative worked examples and extensive guidelines and checklists to help the novice.

  13. BCL::contact-low confidence fold recognition hits boost protein contact prediction and de novo structure determination.

    Science.gov (United States)

    Karakaş, Mert; Woetzel, Nils; Meiler, Jens

    2010-02-01

    Knowledge of all residue-residue contacts within a protein allows determination of the protein fold. Accurate prediction of even a subset of long-range contacts (contacts between amino acids far apart in sequence) can be instrumental for determining tertiary structure. Here we present BCL::Contact, a novel contact prediction method that utilizes artificial neural networks (ANNs) and specializes in the prediction of medium to long-range contacts. BCL::Contact comes in two modes: sequence-based and structure-based. The sequence-based mode uses only sequence information and has individual ANNs specialized for helix-helix, helix-strand, strand-helix, strand-strand, and sheet-sheet contacts. The structure-based mode combines results from 32-fold recognition methods with sequence information to a consensus prediction. The two methods were presented in the 6(th) and 7(th) Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments. The present work focuses on elucidating the impact of fold recognition results onto contact prediction via a direct comparison of both methods on a joined benchmark set of proteins. The sequence-based mode predicted contacts with 42% accuracy (7% false positive rate), while the structure-based mode achieved 45% accuracy (2% false positive rate). Predictions by both modes of BCL::Contact were supplied as input to the protein tertiary structure prediction program Rosetta for a benchmark of 17 proteins with no close sequence homologs in the protein data bank (PDB). Rosetta created higher accuracy models, signified by an improvement of 1.3 A on average root mean square deviation (RMSD), when driven by the predicted contacts. Further, filtering Rosetta models by agreement with the predicted contacts enriches for native-like fold topologies.

  14. Global high resolution versus Limited Area Model climate change projections over Europe: quantifying confidence level from PRUDENCE results

    Energy Technology Data Exchange (ETDEWEB)

    Deque, M. [Centre National de Recherches Meteorologiques, Meteo-France, Toulouse Cedex 01 (France); Jones, R.G.; Hassell, D.C. [Hadley Centre for Climate Prediction and Research, Met Office, Devon (United Kingdom); Wild, M.; Vidale, P.L. [Swiss Federal Institute of Technology, Institute for Atmospheric and Climate Science, ETH, Zurich (Switzerland); Giorgi, F.; Kucharski, F. [Abdus Salam International Centre for Theoretical Physics, Trieste (Italy); Christensen, J.H. [Danish Meteorological Institute, Copenhagen (Denmark); Rockel, B. [Institute of Coastal Research, GKSS Forschungszentrum Geesthacht GmbH, Geesthacht (Germany); Jacob, D. [Max-Planck-Institut fuer Meteorologie, Hamburg (Germany); Kjellstroem, E. [Swedish Meteorological and Hydrological Institute, Norrkoeping (Sweden); Castro, M. de. [Universidad de Castilla La Mancha, Dept. de Ciencias Ambientales, Toledo (Spain); Hurk, B. van den [KNMI, Postbus 201, AE De Bilt (Netherlands)

    2005-11-01

    Four high resolution atmospheric general circulation models (GCMs) have been integrated with the standard forcings of the PRUDENCE experiment: IPCC-SRES A2 radiative forcing and Hadley Centre sea surface temperature and sea-ice extent. The response over Europe, calculated as the difference between the 2071-2100 and the 1961-1990 means is compared with the same diagnostic obtained with nine Regional Climate Models (RCM) all driven by the Hadley Centre atmospheric GCM. The seasonal mean response for 2m temperature and precipitation is investigated. For temperature, GCMs and RCMs behave similarly, except that GCMs exhibit a larger spread. However, during summer, the spread of the RCMs - in particular in terms of precipitation - is larger than that of the GCMs. This indicates that the European summer climate is strongly controlled by parameterized physics and/or high-resolution processes. The temperature response is larger than the systematic error. The situation is different for precipitation. The model bias is twice as large as the climate response. The confidence in PRUDENCE results comes from the fact that the models have a similar response to the IPCC-SRES A2 forcing, whereas their systematic errors are more spread. In addition, GCM precipitation response is slightly but significantly different from that of the RCMs. (orig.)

  15. High-Protein Diets: Are They Safe?

    Science.gov (United States)

    Healthy Lifestyle Nutrition and healthy eating Are high-protein diets safe for weight loss? Answers from Katherine ... L.D. For most healthy people, a high-protein diet generally isn't harmful, particularly when followed ...

  16. High quality protein microarray using in situ protein purification

    Directory of Open Access Journals (Sweden)

    Fleischmann Robert D

    2009-08-01

    Full Text Available Abstract Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC. This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents

  17. High throughput recombinant protein production of fungal secreted proteins

    DEFF Research Database (Denmark)

    Vala, Andrea Lages Lino; Roth, Doris; Grell, Morten Nedergaard

    2011-01-01

    a high-throughput protein production system with a special focus on fungal secreted proteins. We use a ligation independent cloning to clone target genes into expression vectors for E. coli and P. pastoris and a small scale test expression to identify constructs producing soluble protein. Expressed...... interaction), between fungi of the order Entomophthorales and aphids (pathogenic interaction), and in the mycoparasitic interaction between the oomycetes Pythium oligandrum and P. ultimum. In general, the high-throughput protein production system can lead to a better understanding of fungal/host interactions...

  18. The Model Confidence Set

    DEFF Research Database (Denmark)

    Hansen, Peter Reinhard; Lunde, Asger; Nason, James M.

    The paper introduces the model confidence set (MCS) and applies it to the selection of models. A MCS is a set of models that is constructed such that it will contain the best model with a given level of confidence. The MCS is in this sense analogous to a confidence interval for a parameter. The M...

  19. Increasing Mobility Confidence

    Science.gov (United States)

    ... Español In Your Area NPF Shop Increasing Mobility Confidence To increase your confidence moving, you have to move! Make Text Smaller ... It might seem counterintuitive, but to increase your confidence moving, you have to move! Build physical activity ...

  20. The Effect of High-Fidelity Cardiopulmonary Resuscitation (CPR) Simulation on Athletic Training Student Knowledge, Confidence, Emotions, and Experiences

    Science.gov (United States)

    Tivener, Kristin Ann; Gloe, Donna Sue

    2015-01-01

    Context: High-fidelity simulation is widely used in healthcare for the training and professional education of students though literature of its application to athletic training education remains sparse. Objective: This research attempts to address a wide-range of data. This includes athletic training student knowledge acquisition from…

  1. The Effect of High-Fidelity Cardiopulmonary Resuscitation (CPR) Simulation on Athletic Training Student Knowledge, Confidence, Emotions, and Experiences

    Science.gov (United States)

    Tivener, Kristin Ann; Gloe, Donna Sue

    2015-01-01

    Context: High-fidelity simulation is widely used in healthcare for the training and professional education of students though literature of its application to athletic training education remains sparse. Objective: This research attempts to address a wide-range of data. This includes athletic training student knowledge acquisition from…

  2. Reader Accuracy and Confidence in Diagnosing Diffuse Lung Disease on High-Resolution Computed Tomography of the Lungs: Impact of Sampling Frequency

    Energy Technology Data Exchange (ETDEWEB)

    Sundaram, B.; Gross, B.H.; Oh, E.; Mueller, N.; Myles, J.D.; Kazerooni, E.A. (Dept. of Radiology, Michigan Institute for Clinical Health Research, Univ. of Michigan Health System, Ann Arbor, Michigan (United States))

    2008-10-15

    Background: The accuracy of the number of high-resolution computed tomography (HRCT) images necessary to diagnose diffuse lung disease (DLD) is not well established. Purpose: To evaluate the impact of HRCT sampling frequency on reader confidence and accuracy for diagnosing DLD. Material and Methods: HRCT images of 100 consecutive patients with proven DLD were reviewed. They were: 48 usual interstitial pneumonia, 22 sarcoidosis, six hypersensitivity pneumonitis, five each of desquamative interstitial pneumonitis, eosinophilic granulomatosis, and lymphangioleiomyomatosis, and nine others. Inspiratory images at 1-cm increments throughout the lungs and three specified levels formed complete and limited examinations. In random order, three experts (readers 1, 2, and 3) ranked their top three diagnoses and rated confidence for their top diagnosis, independently and blinded to clinical information. Results: Using the complete versus limited examinations for correct first-choice diagnosis, accuracy for reader 1 (R1) was 81% versus 80%, respectively, for reader 2 (R2) 70% versus 70%, and for reader 3 (R3) 64% versus 59%. Reader accuracy within their top three choices for complete versus limited examinations was: R1 91% versus 91% of cases, respectively, R2 84% versus 83%, and R3 79% versus 72% of cases. No statistically significant differences were found between the diagnosis methods (P=0.28 for first diagnosis and P=0.17 for top three choices). The confidence intervals for individual raters showed considerable overlap, and the point estimates are almost identical. The mean interreader agreement for complete versus limited HRCT for both top and top three diagnoses were the same (moderate and fair, respectively). The mean intrareader agreement between complete and limited HRCT for top and top three diagnoses were substantial and moderate, respectively. Conclusion: Overall reader accuracy and confidence in diagnosis did not significantly differ when fewer or more HRCT images

  3. High pressure effects on allergen food proteins.

    Science.gov (United States)

    Somkuti, Judit; Smeller, László

    2013-12-15

    There are several proteins, which can cause allergic reaction if they are inhaled or ingested. Our everyday food can also contain such proteins. Food allergy is an IgE-mediated immune disorder, a growing health problem of great public concern. High pressure is known to affect the structure of proteins; typically few hundred MPa pressure can lead to denaturation. That is why several trials have been performed to alter the structure of the allergen proteins by high pressure, in order to reduce its allergenicity. Studies have been performed both on simple protein solutions and on complex food systems. Here we review those allergens which have been investigated under or after high pressure treatment by methods capable of detecting changes in the secondary and tertiary structure of the proteins. We focus on those allergenic proteins, whose structural changes were investigated by spectroscopic methods under pressure in correlation with the observed allergenicity (IgE binding) changes. According to this criterion we selected the following allergen proteins: Mal d 1 and Mal d 3 (apple), Bos d 5 (milk), Dau c 1 (carrot), Gal d 2 (egg), Ara h 2 and Ara h 6 (peanut), and Gad m 1 (cod).

  4. Upsampling range camera depth maps using high-resolution vision camera and pixel-level confidence classification

    Science.gov (United States)

    Tian, Chao; Vaishampayan, Vinay; Zhang, Yifu

    2011-03-01

    We consider the problem of upsampling a low-resolution depth map generated by a range camera, by using information from one or more additional high-resolution vision cameras. The goal is to provide an accurate high resolution depth map from the viewpoint of one of the vision cameras. We propose an algorithm that first converts the low resolution depth map into a depth/disparity map through coordinate mappings into the coordinate frame of one vision camera, then classifies the pixels into regions according to whether the range camera depth map is trustworthy, and finally refine the depth values for the pixels in the untrustworthy regions. For the last refinement step, both a method based on graph cut optimization and that based on bilateral filtering are examined. Experimental results show that the proposed methods using classification are able to upsample the depth map by a factor of 10 x 10 with much improved depth details, with significantly better accuracy comparing to those without the classification. The improvements are visually perceptible on a 3D auto-stereoscopic display.

  5. Strengthening Public Confidence.

    Science.gov (United States)

    Herlihy, John J.

    Board members and administrators can build public confidence in their schools by taking every opportunity to communicate positive attitudes about the people in the schools. As leaders, they have the responsibility to use people power to promote the schools. If school employees feel good about their jobs, they will build confidence within the…

  6. Communicating Low-Probability High-Consequence Risk, Uncertainty and Expert Confidence: Induced Seismicity of Deep Geothermal Energy and Shale Gas.

    Science.gov (United States)

    Knoblauch, Theresa A K; Stauffacher, Michael; Trutnevyte, Evelina

    2017-08-10

    Subsurface energy activities entail the risk of induced seismicity including low-probability high-consequence (LPHC) events. For designing respective risk communication, the scientific literature lacks empirical evidence of how the public reacts to different written risk communication formats about such LPHC events and to related uncertainty or expert confidence. This study presents findings from an online experiment (N = 590) that empirically tested the public's responses to risk communication about induced seismicity and to different technology frames, namely deep geothermal energy (DGE) and shale gas (between-subject design). Three incrementally different formats of written risk communication were tested: (i) qualitative, (ii) qualitative and quantitative, and (iii) qualitative and quantitative with risk comparison. Respondents found the latter two the easiest to understand, the most exact, and liked them the most. Adding uncertainty and expert confidence statements made the risk communication less clear, less easy to understand and increased concern. Above all, the technology for which risks are communicated and its acceptance mattered strongly: respondents in the shale gas condition found the identical risk communication less trustworthy and more concerning than in the DGE conditions. They also liked the risk communication overall less. For practitioners in DGE or shale gas projects, the study shows that the public would appreciate efforts in describing LPHC risks with numbers and optionally risk comparisons. However, there seems to be a trade-off between aiming for transparency by disclosing uncertainty and limited expert confidence, and thereby decreasing clarity and increasing concern in the view of the public. © 2017 Society for Risk Analysis.

  7. High Protein Diet and Huntington's Disease.

    Directory of Open Access Journals (Sweden)

    Chiung-Mei Chen

    Full Text Available Huntington's disease (HD is a neurodegenerative disorder caused by the huntingtin (HTT gene with expanded CAG repeats. In addition to the apparent brain abnormalities, impairments also occur in peripheral tissues. We previously reported that mutant Huntingtin (mHTT exists in the liver and causes urea cycle deficiency. A low protein diet (17% restores urea cycle activity and ameliorates symptoms in HD model mice. It remains unknown whether the dietary protein content should be monitored closely in HD patients because the normal protein consumption is lower in humans (~15% of total calories than in mice (~22%. We assessed whether dietary protein content affects the urea cycle in HD patients. Thirty HD patients were hospitalized and received a standard protein diet (13.7% protein for 5 days, followed by a high protein diet (HPD, 26.3% protein for another 5 days. Urea cycle deficiency was monitored by the blood levels of citrulline and ammonia. HD progression was determined by the Unified Huntington's Disease Rating Scale (UHDRS. The HPD increased blood citrulline concentration from 15.19 μmol/l to 16.30 μmol/l (p = 0.0378 in HD patients but did not change blood ammonia concentration. A 2-year pilot study of 14 HD patients found no significant correlation between blood citrulline concentration and HD progression. Our results indicated a short period of the HPD did not markedly compromise urea cycle function. Blood citrulline concentration is not a reliable biomarker of HD progression.

  8. Protein Biophysics Explains Why Highly Abundant Proteins Evolve Slowly

    Directory of Open Access Journals (Sweden)

    Adrian W.R. Serohijos

    2012-08-01

    Full Text Available The consistent observation across all kingdoms of life that highly abundant proteins evolve slowly demonstrates that cellular abundance is a key determinant of protein evolutionary rate. However, other empirical findings, such as the broad distribution of evolutionary rates, suggest that additional variables determine the rate of protein evolution. Here, we report that under the global selection against the cytotoxic effects of misfolded proteins, folding stability (ΔG, simultaneous with abundance, is a causal variable of evolutionary rate. Using both theoretical analysis and multiscale simulations, we demonstrate that the anticorrelation between the premutation ΔG and the arising mutational effect (ΔΔG, purely biophysical in origin, is a necessary requirement for abundance–evolutionary rate covariation. Additionally, we predict and demonstrate in bacteria that the strength of abundance–evolutionary rate correlation depends on the divergence time separating reference genomes. Altogether, these results highlight the intrinsic role of protein biophysics in the emerging universal patterns of molecular evolution.

  9. High throughput protein-protein interaction data: clues for the architecture of protein complexes

    Directory of Open Access Journals (Sweden)

    Pang Chi

    2008-11-01

    Full Text Available Abstract Background High-throughput techniques are becoming widely used to study protein-protein interactions and protein complexes on a proteome-wide scale. Here we have explored the potential of these techniques to accurately determine the constituent proteins of complexes and their architecture within the complex. Results Two-dimensional representations of the 19S and 20S proteasome, mediator, and SAGA complexes were generated and overlaid with high quality pairwise interaction data, core-module-attachment classifications from affinity purifications of complexes and predicted domain-domain interactions. Pairwise interaction data could accurately determine the members of each complex, but was unexpectedly poor at deciphering the topology of proteins in complexes. Core and module data from affinity purification studies were less useful for accurately defining the member proteins of these complexes. However, these data gave strong information on the spatial proximity of many proteins. Predicted domain-domain interactions provided some insight into the topology of proteins within complexes, but was affected by a lack of available structural data for the co-activator complexes and the presence of shared domains in paralogous proteins. Conclusion The constituent proteins of complexes are likely to be determined with accuracy by combining data from high-throughput techniques. The topology of some proteins in the complexes will be able to be clearly inferred. We finally suggest strategies that can be employed to use high throughput interaction data to define the membership and understand the architecture of proteins in novel complexes.

  10. Confidence in Numerical Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Hemez, Francois M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-02-23

    This PowerPoint presentation offers a high-level discussion of uncertainty, confidence and credibility in scientific Modeling and Simulation (M&S). It begins by briefly evoking M&S trends in computational physics and engineering. The first thrust of the discussion is to emphasize that the role of M&S in decision-making is either to support reasoning by similarity or to “forecast,” that is, make predictions about the future or extrapolate to settings or environments that cannot be tested experimentally. The second thrust is to explain that M&S-aided decision-making is an exercise in uncertainty management. The three broad classes of uncertainty in computational physics and engineering are variability and randomness, numerical uncertainty and model-form uncertainty. The last part of the discussion addresses how scientists “think.” This thought process parallels the scientific method where by a hypothesis is formulated, often accompanied by simplifying assumptions, then, physical experiments and numerical simulations are performed to confirm or reject the hypothesis. “Confidence” derives, not just from the levels of training and experience of analysts, but also from the rigor with which these assessments are performed, documented and peer-reviewed.

  11. Trust vs. Confidence

    Science.gov (United States)

    2016-06-07

    defined. Although there are many different definitions of trust, our definition (Adams and Webb, 2003) is as follows: Trust is a psychological state...Judgments: Experiments on the Time to Determine Confidence. Journal of Experimental Psychology : Human Perception and Performance, 24(3), 929-945. BARANSKI...PETRUSIC, W. (2001). Testing Architectures of the Decision-Confidence Relation. Canadian Journal of Experimental Psychology , 55(3): 195-206. PETRUSIC, W

  12. Integrated process for high conversion and high yield protein PEGylation.

    Science.gov (United States)

    Pfister, David; Morbidelli, Massimo

    2016-08-01

    Over the past decades, PEGylation has become a powerful technique to increase the in vivo circulation half-life of therapeutic proteins while maintaining their activity. The development of new therapeutic proteins is likely to require further improvement of the PEGylation methods to reach even better selectivity and yield for reduced costs. The intensification of the PEGylation process was investigated through the integration of a chromatographic step in order to increase yield and conversion for the production of mono-PEGylated protein. Lysozyme was used as a model protein to demonstrate the feasibility of such approach. In the integrated reaction/separation process, chromatography was used as fractionation technique in order to isolate and recycle the unreacted protein from the PEGylated products. This allows operating the reactor with short reaction times so as to minimize the production of multi-PEGylated proteins (i.e., conjugated to more than one polymer). That is, the reaction is stopped before the desired product (i.e., the mono-PEGylated protein) can further react, thus leading to limited conversion but high yield. The recycling of the unreacted protein was then considered to drive the protein overall conversion to completion. This approach has great potential to improve processes whose yield is limited by the further reaction of the product leading to undesirable by-products. Biotechnol. Bioeng. 2016;113: 1711-1718. © 2016 Wiley Periodicals, Inc.

  13. Determination of red blood cell fatty acid profiles: Rapid and high-confident analysis by chemical ionization-gas chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Schober, Yvonne; Wahl, Hans Günther; Renz, Harald; Nockher, Wolfgang Andreas

    2017-01-01

    Cellular fatty acid (FA) profiles have been acknowledged as biomarkers in various human diseases. Nevertheless, common FA analysis by gas chromatography mass spectrometry (GC-MS) requires long analysis time. Hence, there is a need for feasible methods for high throughput analysis in clinical studies. FA was extracted from red blood cells (RBC) and derivatized to fatty acid methyl esters (FAME). A method using gas chromatography tandem mass spectrometry (GC-MS/MS) with ammonia-induced chemical ionization (CI) was developed for the analysis of FA profiles in human RBC. We compared this method with classical single GC-MS using electron impact ionization (EI). The FA profiles of 703 RBC samples were determined by GC-MS/MS. In contrast to EI ammonia-induced CI resulted in adequate amounts of molecular ions for further fragmentation of FAME. Specific fragments for confident quantification and fragmentation were determined for 45 FA. The GC-MS/MS method has a total run time of 9min compared to typical analysis times of up to 60min in conventional GC-MS. Intra and inter assay variations were <10% for all FA analyzed. Analysis of RBC FA composition revealed an age-dependent increase of the omega-3 eicosapentaenoic and docosahexaenoic acid, and a decline of the omega-6 linoleic acid with a corresponding rise of the omega-3 index. The combination of ammonia-induced CI and tandem mass spectrometry after GC separation allows for high-throughput, robust and confident analysis of FA profiles in the clinical laboratory. Copyright © 2016. Published by Elsevier B.V.

  14. Confidence and Construal Framing: When Confidence Increases versus Decreases Information Processing

    OpenAIRE

    Echo Wen Wan; Derek D. Rucker

    2013-01-01

    A large literature demonstrates that people process information more carefully in states of low compared to high confidence. This article presents an alternative hypothesis that either high or low confidence can increase or decrease information processing on the basis of how information is construed. Five experiments demonstrate two sets of findings supporting this alternative formulation. First, low confidence leads people to focus on concrete construals, whereas high confidence leads people...

  15. The Confidence Trick

    Directory of Open Access Journals (Sweden)

    Steve Keen

    2009-03-01

    Full Text Available This article reflects on the role that confidence plays in recovery from a financial crisis.The author reflects on lessons from the past – specifically The Great Crash of 1929 and on thework of economists Keynes and Fisher to apply to our current economic woes.The role of overconfidence in our current crisis is also examined.

  16. The Confidence Trick

    OpenAIRE

    2009-01-01

    This article reflects on the role that confidence plays in recovery from a financial crisis.The author reflects on lessons from the past – specifically The Great Crash of 1929 and on thework of economists Keynes and Fisher to apply to our current economic woes.The role of overconfidence in our current crisis is also examined.

  17. Confidence in Coastal Forecasts

    NARCIS (Netherlands)

    Baart, F.

    2013-01-01

    This thesis answers the question "How can we show and improve our confidence in coastal forecasts?", by providing four examples of common coastal forecasts. The first example shows how to improve the estimate of the one in ten thousand year storm-surge level. The three dimensional reconstruction,

  18. Adding Confidence to Knowledge

    Science.gov (United States)

    Goodson, Ludwika Aniela; Slater, Don; Zubovic, Yvonne

    2015-01-01

    A "knowledge survey" and a formative evaluation process led to major changes in an instructor's course and teaching methods over a 5-year period. Design of the survey incorporated several innovations, including: a) using "confidence survey" rather than "knowledge survey" as the title; b) completing an instructional…

  19. Raising Confident Kids

    Science.gov (United States)

    ... new skill and milestone, kids can develop increasing confidence. Parents can help by giving kids lots of opportunities to practice and master their skills, letting kids make mistakes and being there to boost their spirits so they keep trying. Respond with ...

  20. Resolving the Confidence Crisis

    Science.gov (United States)

    Apter, Terri

    2006-01-01

    As children approach adolescence, they often experience confusion and uncertainty as they attempt to appear more grown up than they really feel. Research on both girls and boys has documented that the buoyant self-confidence of younger children often gives way to self-consciousness as young adolescents become aware of the complexity and difficulty…

  1. Dynamics of a Highly Flexible Protein

    DEFF Research Database (Denmark)

    Andersen, Lisbeth

    Protein dynamics are important for protein function. Especially, dynamics plays an important role in ligand-binding where the induced fit and conformational selection binding mechanisms represent the extremes in a continuum of dynamic mechanisms. The difference between the mechanisms lies...... in the sequence of events; either the protein changes it conformation after initial binding of the ligand (induced fit) or before binding of the ligand (conformational selection). The nuclear co-activator binding domain (NCBD) interacts with many different binding partners to control gene transcription. High...... malleability are the subject of this defense. Using nuclear magnetic resonance (NMR) spectroscopy, the dynamics of NCBD have been investigated on timescales ranging from picoseconds to milliseconds using relaxation dispersion experiments, residual dipolar couplings and methyl group deuterium relaxation. From...

  2. Business Confidence Survey 2000

    Institute of Scientific and Technical Information of China (English)

    Guo Yan

    2009-01-01

    @@ In order to gain a better understanding about the depth and breadth of its effect on European companies'businesses,the new strategies they are adopting to cope with the crisis,and how their attitudes to towards China-including long-term plans-have changed in its aftermath,the European Union Chamber of Commerce in China today launches its sixth annual European Chamber Business Confidence Survey,which is published in partnership with Roland Berger Strategy Consultants in Beijing on June 30,2009.Drawing on the responses of more than 300 European companies active in China.the 2009 Survey highlights a European business community that remains bullish in China in most sectors and read to back up that confidence with continued investment in the local economy provided that Chinese government is committed to creating a more free,fair and competitive market.

  3. Varieties of Confidence Intervals.

    Science.gov (United States)

    Cousineau, Denis

    2017-01-01

    Error bars are useful to understand data and their interrelations. Here, it is shown that confidence intervals of the mean (CI M s) can be adjusted based on whether the objective is to highlight differences between measures or not and based on the experimental design (within- or between-group designs). Confidence intervals (CIs) can also be adjusted to take into account the sampling mechanisms and the population size (if not infinite). Names are proposed to distinguish the various types of CIs and the assumptions underlying them, and how to assess their validity is explained. The various CIs presented here are easily obtained from a succession of multiplicative adjustments to the basic (unadjusted) CI width. All summary results should present a measure of precision, such as CIs, as this information is complementary to effect sizes.

  4. We will be champions: Leaders' confidence in 'us' inspires team members' team confidence and performance.

    Science.gov (United States)

    Fransen, K; Steffens, N K; Haslam, S A; Vanbeselaere, N; Vande Broek, G; Boen, F

    2016-12-01

    The present research examines the impact of leaders' confidence in their team on the team confidence and performance of their teammates. In an experiment involving newly assembled soccer teams, we manipulated the team confidence expressed by the team leader (high vs neutral vs low) and assessed team members' responses and performance as they unfolded during a competition (i.e., in a first baseline session and a second test session). Our findings pointed to team confidence contagion such that when the leader had expressed high (rather than neutral or low) team confidence, team members perceived their team to be more efficacious and were more confident in the team's ability to win. Moreover, leaders' team confidence affected individual and team performance such that teams led by a highly confident leader performed better than those led by a less confident leader. Finally, the results supported a hypothesized mediational model in showing that the effect of leaders' confidence on team members' team confidence and performance was mediated by the leader's perceived identity leadership and members' team identification. In conclusion, the findings of this experiment suggest that leaders' team confidence can enhance members' team confidence and performance by fostering members' identification with the team. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  5. Cell-Dock: high-performance protein-protein docking.

    Science.gov (United States)

    Pons, Carles; Jiménez-González, Daniel; González-Álvarez, Cecilia; Servat, Harald; Cabrera-Benítez, Daniel; Aguilar, Xavier; Fernández-Recio, Juan

    2012-09-15

    The application of docking to large-scale experiments or the explicit treatment of protein flexibility are part of the new challenges in structural bioinformatics that will require large computer resources and more efficient algorithms. Highly optimized fast Fourier transform (FFT) approaches are broadly used in docking programs but their optimal code implementation leaves hardware acceleration as the only option to significantly reduce the computational cost of these tools. In this work we present Cell-Dock, an FFT-based docking algorithm adapted to the Cell BE processor. We show that Cell-Dock runs faster than FTDock with maximum speedups of above 200×, while achieving results of similar quality. The source code is released under GNU General Public License version 2 and can be downloaded from http://mmb.pcb.ub.es/~cpons/Cell-Dock. djimenez@ac.upc.edu or juanf@bsc.es Supplementary data are available at Bioinformatics online.

  6. Consumer confidence or the business cycle

    DEFF Research Database (Denmark)

    Møller, Stig Vinther; Nørholm, Henrik; Rangvid, Jesper

    2014-01-01

    Answer: The business cycle. We show that consumer confidence and the output gap both excess returns on stocks in many European countries: When the output gap is positive (the economy is doing well), expected returns are low, and when consumer confidence is high, expected returns are also low....... Consumer confidence and the output gap are also highly positively correlated. In fact, we find that consumer confidence does not contain independent information (i.e. information over and above that contained by the output gap) about expected returns. Our use of European data allows us to examine both...... aggregate European and local-country data on consumer confidence and output gaps. We find that even local-country consumer confidence does not contain independent information about expected returns. Our findings have asset pricing implication: We show taht the cross-country distribution of expected returns...

  7. High throughput recombinant protein production of fungal secreted proteins

    DEFF Research Database (Denmark)

    Vala, Andrea Lages Lino; Roth, Doris; Grell, Morten Nedergaard

    2011-01-01

    Secreted proteins are important for both symbiotic and pathogenic interactions between fungi and their hosts. Our research group uses screens and genomic mining to discover novel proteins involved in these processes. To efficiently study the large number of candidate proteins, we are establishing...

  8. Expenditure, Confidence, and Uncertainty: Identifying Shocks to Consumer Confidence Using Daily Data

    OpenAIRE

    Lachowska, Marta

    2013-01-01

    The importance of consumer confidence in stimulating economic activity is a disputed issue in macroeconomics. Do changes in confidence represent autonomous fluctuations in optimism, independent of information on economic fundamentals, or are they a reflection of economic news? I study this question by using high-frequency microdata on spending and consumer confidence, and I find that consumer confidence contains information relevant to predicting spending, independent from other indicators. T...

  9. Exceptional heat stability of high protein content dispersions containing whey protein particles

    NARCIS (Netherlands)

    Saglam, D.; Venema, P.; Vries, de R.J.; Linden, van der E.

    2014-01-01

    Due to aggregation and/or gelation during thermal treatment, the amount of whey proteins that can be used in the formulation of high protein foods e.g. protein drinks, is limited. The aim of this study was to replace whey proteins with whey protein particles to increase the total protein content and

  10. Alan Greenspan, the confidence strategy

    Directory of Open Access Journals (Sweden)

    Edwin Le Heron

    2006-12-01

    Full Text Available To evaluate the Greenspan era, we nevertheless need to address three questions: Is his success due to talent or just luck? Does he have a system of monetary policy or is he himself the system? What will be his legacy? Greenspan was certainly lucky, but he was also clairvoyant. Above all, he has developed a profoundly original monetary policy. His confidence strategy is clearly opposed to the credibility strategy developed in central banks and the academic milieu after 1980, but also inflation targeting, which today constitutes the mainstream monetary policy regime. The question of his legacy seems more nuanced. However, Greenspan will remain 'for a considerable period of time' a highly heterodox and original central banker. His political vision, his perception of an uncertain world, his pragmatism and his openness form the structure of a powerful alternative system, the confidence strategy, which will leave its mark on the history of monetary policy.

  11. Reclaim your creative confidence.

    Science.gov (United States)

    Kelley, Tom; Kelley, David

    2012-12-01

    Most people are born creative. But over time, a lot of us learn to stifle those impulses. We become warier of judgment, more cautious more analytical. The world seems to divide into "creatives" and "noncreatives," and too many people resign themselves to the latter category. And yet we know that creativity is essential to success in any discipline or industry. The good news, according to authors Tom Kelley and David Kelley of IDEO, is that we all can rediscover our creative confidence. The trick is to overcome the four big fears that hold most of us back: fear of the messy unknown, fear of judgment, fear of the first step, and fear of losing control. The authors use an approach based on the work of psychologist Albert Bandura in helping patients get over their snake phobias: You break challenges down into small steps and then build confidence by succeeding on one after another. Creativity is something you practice, say the authors, not just a talent you are born with.

  12. Interrelation of economic confidence with other types of confidence

    OpenAIRE

    Бонецький, Орест Олегович

    2013-01-01

    The paper gives the object and the subject of the study, which are used as a criterion allowing to separate the economic confidence from other types of confidence. The terms describing the psychological and sociological confidence are proposed. It was found that the economic confidence is interrelated with psychological confidence by motivation and advertising, sociological – by the results of activity of public organizations, state regulation of the economy. On the example of information-com...

  13. Regional Competition for Confidence: Features of Formation

    Directory of Open Access Journals (Sweden)

    Irina Svyatoslavovna Vazhenina

    2016-09-01

    Full Text Available The increase in economic independence of the regions inevitably leads to an increase in the quality requirements of the regional economic policy. The key to successful regional policy, both during its development and implementation, is the understanding of the necessity of gaining confidence (at all levels, and the inevitable participation in the competition for confidence. The importance of confidence in the region is determined by its value as a competitive advantage in the struggle for partners, resources and tourists, and attracting investments. In today’s environment the focus of governments, regions and companies on long-term cooperation is clearly expressed, which is impossible without a high level of confidence between partners. Therefore, the most important competitive advantages of territories are intangible assets such as an attractive image and a good reputation, which builds up confidence of the population and partners. The higher the confidence in the region is, the broader is the range of potential partners, the larger is the planning horizon of long-term concerted action, the better are the chances of acquiring investment, the higher is the level of competitive immunity of the territories. The article defines competition for confidence as purposeful behavior of a market participant in economic environment, aimed at acquiring specific intangible competitive advantage – the confidence of the largest possible number of other market actors. The article also highlights the specifics of confidence as a competitive goal, presents factors contributing to the destruction of confidence, proposes a strategy to fight for confidence as a program of four steps, considers the factors which integrate regional confidence and offers several recommendations for the establishment of effective regional competition for confidence

  14. Prediction Models of Retention Indices for Increased Confidence in Structural Elucidation during Complex Matrix Analysis: Application to Gas Chromatography Coupled with High-Resolution Mass Spectrometry.

    Science.gov (United States)

    Dossin, Eric; Martin, Elyette; Diana, Pierrick; Castellon, Antonio; Monge, Aurelien; Pospisil, Pavel; Bentley, Mark; Guy, Philippe A

    2016-08-02

    Monitoring of volatile and semivolatile compounds was performed using gas chromatography (GC) coupled to high-resolution electron ionization mass spectrometry, using both headspace and liquid injection modes. A total of 560 reference compounds, including 8 odd n-alkanes, were analyzed and experimental linear retention indices (LRI) were determined. These reference compounds were randomly split into training (n = 401) and test (n = 151) sets. LRI for all 552 reference compounds were also calculated based upon computational Quantitative Structure-Property Relationship (QSPR) models, using two independent approaches RapidMiner (coupled to Dragon) and ACD/ChromGenius software. Correlation coefficients for experimental versus predicted LRI values calculated for both training and test set compounds were calculated at 0.966 and 0.949 for RapidMiner and at 0.977 and 0.976 for ACD/ChromGenius, respectively. In addition, the cross-validation correlation was calculated at 0.96 from RapidMiner and the residual standard error value obtained from ACD/ChromGenius was 53.635. These models were then used to predict LRI values for several thousand compounds reported present in tobacco and tobacco-related fractions, plus a range of specific flavor compounds. It was demonstrated that using the mean of the LRI values predicted by RapidMiner and ACD/ChromGenius, in combination with accurate mass data, could enhance the confidence level for compound identification from the analysis of complex matrixes, particularly when the two predicted LRI values for a compound were in close agreement. Application of this LRI modeling approach to matrixes with unknown composition has already enabled the confirmation of 23 postulated compounds, demonstrating its ability to facilitate compound identification in an analytical workflow. The goal is to reduce the list of putative candidates to a reasonable relevant number that can be obtained and measured for confirmation.

  15. Simulation integration with confidence

    Science.gov (United States)

    Strelich, Tom; Stalcup, Bruce W.

    1999-07-01

    Current financial, schedule and risk constraints mandate reuse of software components when building large-scale simulations. While integration of simulation components into larger systems is a well-understood process, it is extremely difficult to do while ensuring that the results are correct. Illgen Simulation Technologies Incorporated and Litton PRC have joined forces to provide tools to integrate simulations with confidence. Illgen Simulation Technologies has developed an extensible and scaleable, n-tier, client- server, distributed software framework for integrating legacy simulations, models, tools, utilities, and databases. By utilizing the Internet, Java, and the Common Object Request Brokering Architecture as the core implementation technologies, the framework provides built-in scalability and extensibility.

  16. Whey protein particles modulate mechanical properties of gels at high protein concentrations

    NARCIS (Netherlands)

    Saglam, D.; Venema, P.; Vries, de R.J.; Berg, van den L.; Linden, van der E.

    2014-01-01

    We have studied the influence of dense whey protein particles on the mechanical properties of whey protein isolate (WPI) gels at high protein concentrations (16–22% (w/w)). Incorporation of dense whey protein particles in the gel, while keeping the total protein concentration constant, leads to a co

  17. The computation of Buehler confidence limits

    Institute of Scientific and Technical Information of China (English)

    FANG; Xiangzhong; CHEN; Jiading

    2005-01-01

    In medicine and industry, small sample size often arises owing to the high test cost. Then exact confidence inference is important. Buehler confidence limit is a kind of exact confidence limit for the function of parameters in a model. It can be always defined if the order in sample space is given. But the computing problem is often difficult, especially for the cases with high dimension parameter or with incomplete data. This paper presents an algorithm to compute the Buehler confidence limits by EM algorithm. This is the firsttime usage of EM algorithm on Buehler confidence limits, but the algorithm is often used for maximum likelihood estimate in literatures. Three computation examples are given to illustrate the method.

  18. Targeting protein-protein interactions with trimeric ligands: high affinity inhibitors of the MAGUK protein family.

    Directory of Open Access Journals (Sweden)

    Klaus B Nissen

    Full Text Available PDZ domains in general, and those of PSD-95 in particular, are emerging as promising drug targets for diseases such as ischemic stroke. We have previously shown that dimeric ligands that simultaneously target PDZ1 and PDZ2 of PSD-95 are highly potent inhibitors of PSD-95. However, PSD-95 and the related MAGUK proteins contain three consecutive PDZ domains, hence we envisioned that targeting all three PDZ domains simultaneously would lead to more potent and potentially more specific interactions with the MAGUK proteins. Here we describe the design, synthesis and characterization of a series of trimeric ligands targeting all three PDZ domains of PSD-95 and the related MAGUK proteins, PSD-93, SAP-97 and SAP-102. Using our dimeric ligands targeting the PDZ1-2 tandem as starting point, we designed novel trimeric ligands by introducing a PDZ3-binding peptide moiety via a cysteine-derivatized NPEG linker. The trimeric ligands generally displayed increased affinities compared to the dimeric ligands in fluorescence polarization binding experiments and optimized trimeric ligands showed low nanomolar inhibition towards the four MAGUK proteins, thus being the most potent inhibitors described. Kinetic experiments using stopped-flow spectrometry showed that the increase in affinity is caused by a decrease in the dissociation rate of the trimeric ligand as compared to the dimeric ligands, likely reflecting the lower probability of simultaneous dissociation of all three PDZ ligands. Thus, we have provided novel inhibitors of the MAGUK proteins with exceptionally high affinity, which can be used to further elucidate the therapeutic potential of these proteins.

  19. Identification of host cellular proteins that interact with the M protein of a highly pathogenic porcine reproductive and respiratory syndrome virus vaccine strain.

    Science.gov (United States)

    Wang, Qian; Li, Yanwei; Dong, Hong; Wang, Li; Peng, Jinmei; An, Tongqing; Yang, Xufu; Tian, Zhijun; Cai, Xuehui

    2017-02-22

    The highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) continues to pose one of the greatest threats to the swine industry. M protein is the most conserved and important structural protein of PRRSV. However, information about the host cellular proteins that interact with M protein remains limited. Host cellular proteins that interact with the M protein of HP-PRRSV were immunoprecipitated from MARC-145 cells infected with PRRSV HuN4-F112 using the M monoclonal antibody (mAb). The differentially expressed proteins were identified by LC-MS/MS. The screened proteins were used for bioinformatics analysis including Gene Ontology, the interaction network, and the enriched KEGG pathways. Some interested cellular proteins were validated to interact with M protein by CO-IP. The PRRSV HuN4-F112 infection group had 10 bands compared with the control group. The bands included 219 non-redundant cellular proteins that interact with M protein, which were identified by LC-MS/MS with high confidence. The gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) pathway bioinformatic analyses indicated that the identified proteins could be assigned to several different subcellular locations and functional classes. Functional analysis of the interactome profile highlighted cellular pathways associated with protein translation, infectious disease, and signal transduction. Two interested cellular proteins-nuclear factor of activated T cells 45 kDa (NF45) and proliferating cell nuclear antigen (PCNA)-that could interact with M protein were validated by Co-IP and confocal analyses. The interactome data between PRRSV M protein and cellular proteins were identified and contribute to the understanding of the roles of M protein in the replication and pathogenesis of PRRSV. The interactome of M protein will aid studies of virus/host interactions and provide means to decrease the threat of PRRSV to the swine industry in the future.

  20. Confidence and Cognitive Test Performance

    Science.gov (United States)

    Stankov, Lazar; Lee, Jihyun

    2008-01-01

    This article examines the nature of confidence in relation to abilities, personality, and metacognition. Confidence scores were collected during the administration of Reading and Listening sections of the Test of English as a Foreign Language Internet-Based Test (TOEFL iBT) to 824 native speakers of English. Those confidence scores were correlated…

  1. Confidence and Cognitive Test Performance

    Science.gov (United States)

    Stankov, Lazar; Lee, Jihyun

    2008-01-01

    This article examines the nature of confidence in relation to abilities, personality, and metacognition. Confidence scores were collected during the administration of Reading and Listening sections of the Test of English as a Foreign Language Internet-Based Test (TOEFL iBT) to 824 native speakers of English. Those confidence scores were correlated…

  2. Explorations in Statistics: Confidence Intervals

    Science.gov (United States)

    Curran-Everett, Douglas

    2009-01-01

    Learning about statistics is a lot like learning about science: the learning is more meaningful if you can actively explore. This third installment of "Explorations in Statistics" investigates confidence intervals. A confidence interval is a range that we expect, with some level of confidence, to include the true value of a population parameter…

  3. Microstructural Changes in High-Protein Nutrition Bars Formulated with Extruded or Toasted Milk Protein Concentrate.

    Science.gov (United States)

    Banach, J C; Clark, S; Lamsal, B P

    2016-02-01

    Milk protein concentrates with more than 80% protein (that is, MPC80) are underutilized as the primary protein source in high-protein nutrition bars as they impart crumbliness and cause hardening during storage. High-protein nutrition bar texture changes are often associated with internal protein aggregations and macronutrient phase separation. These changes were investigated in model high-protein nutrition bars formulated with MPC80 and physically modified MPC80s. High-protein nutrition bars formulated with extruded MPC80s hardened slower than those formulated with toasted or unmodified MPC80. Extruded MPC80 had reduced free sulfhydryl group exposure, whereas measurable increases were seen in the toasted MPC80. High-protein nutrition bar textural performance may be related to the number of exposed free sulfhydryl groups in MPC80. Protein aggregations resulting from ingredient modification and high-protein nutrition bar storage were studied with sodium dodecyl sulfate polyacrylamide gel electrophoresis. Disulfide-based protein aggregations and changes in free sulfhydryl concentration were not consistently relatable to high-protein nutrition bar texture change. However, the high-protein nutrition bars formulated with extruded MPC80 were less prone to phase separations, as depicted by confocal laser scanning microscopy, and underwent less texture change during storage than those formulated with toasted or unmodified MPC80.

  4. Fostering English Learners' Confidence

    Science.gov (United States)

    Bondie, Rhonda; Gaughran, Laurie; Zusho, Akane

    2014-01-01

    A teacher is doing something right when his high school students--kids with limited English, no less--form groups and begin discussing a lesson on quadratic equations at the start of class, without any teacher direction. Bondie, Gaughran, and Zusho describe "discussion routines" that teachers at International Community High School in the…

  5. Conversion of high and low pollen protein diets into protein in worker honey bees (Hymenoptera: Apidae).

    Science.gov (United States)

    Basualdo, M; Barragán, S; Vanagas, L; García, C; Solana, H; Rodríguez, E; Bedascarrasbure, E

    2013-08-01

    Adequate protein levels are necessary to maintain strong honey bee [Apis mellifera (L.)] colonies. The aim of this study was to quantify how pollens with different crude protein contents influence protein stores within individual honey bees. Caged bees were fed one of three diets, consisting of high-protein-content pollen, low-protein-content pollen, or protein-free diet as control; measurements were made based on protein content in hemolymph and fat body, fat body weight, and body weight. Vitellogenin in hemolymph was also measured. Bees fed with high crude protein diet had significantly higher levels of protein in hemolymph and fat bodies. Caged bees did not increase pollen consumption to compensate for the lower protein in the diet, and ingesting approximately 4 mg of protein per bee could achieve levels of 20 microg/microl protein in hemolymph. Worker bees fed with low crude protein diet took more time in reaching similar protein content of the bees that were fed with high crude protein diet. The data showed that fat bodies and body weight were not efficient methods of measuring the protein status of bees. The determination of total protein or vitellogenin concentration in the hemolymph from 13-d-old bees and protein concentration of fat bodies from 9-d-old bees could be good indicators of nutritional status of honey bees.

  6. Is a malleable protein necessarily highly dynamic?

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Poulsen, Flemming Martin; Teilum, Kaare

    2012-01-01

    core of NCBD in the ligand-free state and in a well-folded complex with the ligand activator for thyroid hormone and retinoid receptors using multiple NMR methods including methyl chemical shifts, coupling constants, and methyl order parameters. From all NMR measures, the aliphatic side chains...... in the hydrophobic core are slightly more dynamic in the free protein than in the complex, but have mobility comparable to the hydrophobic cores of average folded proteins. Urea titration monitored by NMR reveals that all parts of the protein, including the side-chain packing in the hydrophobic core, denatures...... in a single cooperative process. The molten globule characteristics of NCBD are thus restricted to a slowly fluctuating tertiary structure. Consequently, the conformational plasticity of the protein is most likely related to its low overall stability rather than an intrinsically flexible protein structure...

  7. High Mobility Group Proteins and Their Post-Translational Modifications

    OpenAIRE

    Zhang, Qingchun; Wang, Yinsheng

    2008-01-01

    The high mobility group (HMG) proteins, including HMGA, HMGB and HMGN, are abundant and ubiquitous nuclear proteins that bind to DNA, nucleosome and other multi-protein complexes in a dynamic and reversible fashion to regulate DNA processing in the context of chromatin. All HMG proteins, like histone proteins, are subjected to extensive post-translational modifications (PTMs), such as lysine acetylation, arginine/lysine methylation and serine/threonine phosphorylation, to modulate their inter...

  8. Explicit representation of confidence informs future value-based decisions

    DEFF Research Database (Denmark)

    Folke, Tomas; Jacobsen, Catrine; Fleming, Stephen M.

    2016-01-01

    Humans can reflect on decisions and report variable levels of confidence. But why maintain an explicit representation of confidence for choices that have already been made and therefore cannot be undone? Here we show that an explicit representation of confidence is harnessed for subsequent changes...... of mind. Specifically, when confidence is low, participants are more likely to change their minds when the same choice is presented again, an effect that is most pronounced in participants with greater fidelity in their confidence reports. Furthermore, we show that choices reported with high confidence...... of confidence has a positive impact on the quality of future value-based decisions....

  9. Highly viscous dough-forming properties of marama protein.

    Science.gov (United States)

    Amonsou, Eric O; Taylor, John R N; Naushad Emmambux, M; Gyebi Duodu, K; Minnaar, Amanda

    2012-10-01

    Marama bean is an indigenous southern African oilseed legume with an unusual protein composition. Hence, its rheological properties were studied. Marama protein formed a highly viscous and extensible dough when compared to soya and gluten. With a dough of 38% moisture, marama protein extensibility was very high (304% of its original length), twice that of gluten and soya, and this increased considerably (>3-fold) when the moisture content was increased to 45%. With added peroxidase, the storage modulus (G') of marama protein dough increased with time, suggesting the formation of new and strong protein networks. Dityrosine crosslinks were detected in the doughs. Marama protein showed a single transition with a denaturation temperature higher than soya glycinin. Marama protein was more hydrophobic and contained more β-sheet structure than did soya. Thus, the highly viscous and extensible rheological behaviour of marama protein is probably related to its high β-sheet conformation, hydrophobic interactions and tyrosine crosslinks.

  10. US outlook and German confidence : does the confidence channel work?

    OpenAIRE

    Horn, Gustav Adolf

    2003-01-01

    One channel of business cycle shock transmission which gained attraction only recently is the confidence channel. The aim of the paper is to find out whether the confidence channel is actually working between the US and Germany. This is analysed using times series methods. In contrast to other studies the direct informational content of leading US indicators for German producer confidence and the significance of asymmetric reactions is tested. The results show that there is a relationship bet...

  11. Confidence intervals for the MMPI-2.

    Science.gov (United States)

    Munley, P H

    1991-08-01

    The confidence intervals for the Minnesota Multiphasic Personality Inventory (MMPI-2) clinical scales were investigated. Based on the clinical scale reliabilities published in the MMPI-2 manual, estimated true scores, standard errors of measurement for estimated true scores, and 95% confidence intervals centered around estimated true scores were calculated at 5-point MMPI-2 T-score intervals. The relationships between obtained T-scores, estimated true T-scores, scale reliabilities, and confidence intervals are discussed. The possible role of error measurement in defining scale high point and code types is noted.

  12. Weighting Mean and Variability during Confidence Judgments

    Science.gov (United States)

    de Gardelle, Vincent; Mamassian, Pascal

    2015-01-01

    Humans can not only perform some visual tasks with great precision, they can also judge how good they are in these tasks. However, it remains unclear how observers produce such metacognitive evaluations, and how these evaluations might be dissociated from the performance in the visual task. Here, we hypothesized that some stimulus variables could affect confidence judgments above and beyond their impact on performance. In a motion categorization task on moving dots, we manipulated the mean and the variance of the motion directions, to obtain a low-mean low-variance condition and a high-mean high-variance condition with matched performances. Critically, in terms of confidence, observers were not indifferent between these two conditions. Observers exhibited marked preferences, which were heterogeneous across individuals, but stable within each observer when assessed one week later. Thus, confidence and performance are dissociable and observers’ confidence judgments put different weights on the stimulus variables that limit performance. PMID:25793275

  13. Better Confidence Intervals for Importance Sampling

    OpenAIRE

    HALIS SAK; WOLFGANG HÖRMANN; JOSEF LEYDOLD

    2010-01-01

    It is well known that for highly skewed distributions the standard method of using the t statistic for the confidence interval of the mean does not give robust results. This is an important problem for importance sampling (IS) as its final distribution is often skewed due to a heavy tailed weight distribution. In this paper, we first explain Hall's transformation and its variants to correct the confidence interval of the mean and then evaluate the performance of these methods for two numerica...

  14. High Caloric Diet for ALS Patients: High Fat, High Carbohydrate or High Protein

    Directory of Open Access Journals (Sweden)

    Sarvin Sanaie

    2015-01-01

    Full Text Available ALS is a fatal motor neurodegenerative disease characterized by muscle atrophy and weakness, dysarthria, and dysphagia. The mean survival of ALS patients is three to five years, with 50% of those diagnosed dying within three years of onset (1. A multidisciplinary approach is crucial to set an appropriate plan for metabolic and nutritional support in ALS. Nutritional management incorporates a continuous assessment and implementation of dietary modifications throughout the duration of the disease. The nutritional and metabolic approaches to ALS should start when the diagnosis of ALS is made and should become an integral part of the continuous care to the patient, including nutritional surveillance, dietary counseling, management of dysphagia, and enteral nutrition when needed. Malnutrition and lean body mass loss are frequent findings in ALS patients necessitating comprehensive energy requirement assessment for these patients. Malnutrition is an independent prognostic factor for survival in ALS with a 7.7 fold increase in risk of death. Malnutrition is estimated to develop in one quarter to half of people with ALS (2. Adequate calorie and protein provision would diminish muscle loss in this vulnerable group of patients. Although appropriate amount of energy to be administered is yet to be established, high calorie diet is expected to be effective for potential improvement of survival; ALS patients do not normally receive adequate  intake of energy. A growing number of clinicians suspect that a high calorie diet implemented early in their disease may help people with ALS meet their increased energy needs and extend their survival. Certain high calorie supplements appear to be safe and well tolerated by people with ALS according to studies led by Universitäts klinikum Ulm's and, appear to stabilize body weight within 3 months. In a recent study by Wills et al., intake of high-carbohydrate low-fat supplements has been recommended in ALS patients (3

  15. Targeting Protein-Protein Interactions with Trimeric Ligands: High Affinity Inhibitors of the MAGUK Protein Family

    DEFF Research Database (Denmark)

    Nissen, Klaus B; Kedström, Linda Maria Haugaard; Wilbek, Theis S

    2015-01-01

    PDZ domains in general, and those of PSD-95 in particular, are emerging as promising drug targets for diseases such as ischemic stroke. We have previously shown that dimeric ligands that simultaneously target PDZ1 and PDZ2 of PSD-95 are highly potent inhibitors of PSD-95. However, PSD-95...... of trimeric ligands targeting all three PDZ domains of PSD-95 and the related MAGUK proteins, PSD-93, SAP-97 and SAP-102. Using our dimeric ligands targeting the PDZ1-2 tandem as starting point, we designed novel trimeric ligands by introducing a PDZ3-binding peptide moiety via a cysteine-derivatized NPEG...

  16. Dynamics of a Highly Flexible Protein

    DEFF Research Database (Denmark)

    Andersen, Lisbeth

    Protein dynamics are important for protein function. Especially, dynamics plays an important role in ligand-binding where the induced fit and conformational selection binding mechanisms represent the extremes in a continuum of dynamic mechanisms. The difference between the mechanisms lies......-resolution structures of NCBD in complex with four binding partners are currently known and while three of them are practically identical and resemble the major conformation in the unbound ensemble, one shows NCBD adopting an alternative and markedly different conformation. The mechanisms underlying this conformational...

  17. Assessing Undergraduate Students' Conceptual Understanding and Confidence of Electromagnetics

    Science.gov (United States)

    Leppavirta, Johanna

    2012-01-01

    The study examines how students' conceptual understanding changes from high confidence with incorrect conceptions to high confidence with correct conceptions when reasoning about electromagnetics. The Conceptual Survey of Electricity and Magnetism test is weighted with students' self-rated confidence on each item in order to infer how strongly…

  18. Confidence Estimation in Structured Prediction

    CERN Document Server

    Mejer, Avihai

    2011-01-01

    Structured classification tasks such as sequence labeling and dependency parsing have seen much interest by the Natural Language Processing and the machine learning communities. Several online learning algorithms were adapted for structured tasks such as Perceptron, Passive- Aggressive and the recently introduced Confidence-Weighted learning . These online algorithms are easy to implement, fast to train and yield state-of-the-art performance. However, unlike probabilistic models like Hidden Markov Model and Conditional random fields, these methods generate models that output merely a prediction with no additional information regarding confidence in the correctness of the output. In this work we fill the gap proposing few alternatives to compute the confidence in the output of non-probabilistic algorithms.We show how to compute confidence estimates in the prediction such that the confidence reflects the probability that the word is labeled correctly. We then show how to use our methods to detect mislabeled wor...

  19. Bayesian estimation of keyword confidence in Chinese continuous speech recognition

    Institute of Scientific and Technical Information of China (English)

    HAO Jie; LI Xing

    2003-01-01

    In a syllable-based speaker-independent Chinese continuous speech recognition system based on classical Hidden Markov Model (HMM), a Bayesian approach of keyword confidence estimation is studied, which utilizes both acoustic layer scores and syllable-based statistical language model (LM) score. The Maximum a posteriori (MAP) confidence measure is proposed, and the forward-backward algorithm calculating the MAP confidence scores is deduced. The performance of the MAP confidence measure is evaluated in keyword spotting application and the experiment results show that the MAP confidence scores provide high discriminability for keyword candidates. Furthermore, the MAP confidence measure can be applied to various speech recognition applications.

  20. Total protein or high-abundance protein: Which offers the best loading control for Western blotting?

    Science.gov (United States)

    Thacker, Jonathan S; Yeung, Derrick H; Staines, W Richard; Mielke, John G

    2016-03-01

    Western blotting routinely involves a control for variability in the amount of protein across immunoblot lanes. Normalizing a target signal to one found for an abundantly expressed protein is widely regarded as a reliable loading control; however, this approach is being increasingly questioned. As a result, we compared blotting for two high-abundance proteins (actin and glyceraldehyde 3-phosphate dehydrogenase [GAPDH]) and two total protein membrane staining methods (Ponceau and Coomassie Brilliant Blue) to determine the best control for loading variability. We found that Ponceau staining optimally balanced accuracy and precision, and we suggest that this approach be considered as an alternative to normalizing with a high-abundance protein.

  1. Confidence scores for prediction models

    DEFF Research Database (Denmark)

    Gerds, Thomas Alexander; van de Wiel, MA

    2011-01-01

    modelling strategy is applied to different training sets. For each modelling strategy we estimate a confidence score based on the same repeated bootstraps. A new decomposition of the expected Brier score is obtained, as well as the estimates of population average confidence scores. The latter can be used...... to distinguish rival prediction models with similar prediction performances. Furthermore, on the subject level a confidence score may provide useful supplementary information for new patients who want to base a medical decision on predicted risk. The ideas are illustrated and discussed using data from cancer...

  2. APPLICATION OF ECONOMIC CONFIDENCE ESTIMATION

    Directory of Open Access Journals (Sweden)

    Valeriy S. Ayzatullen

    2013-01-01

    Full Text Available The socio-economic category of “trust” is studied in the article. The analysis of the existing views about the term “trust” was conducted. A model of the interaction of “Power - Business - People”, using the concept of “trust”, was made. The application and the structure of confidence estimations in economy and politics are studied. The accumulated experience of application of confidence estimations in the macroeconomics of the major countries of the world was showed. The current weaknesses of the confidence indexes are reflected.

  3. Manufacture and application of high milk protein powder

    OpenAIRE

    Mistry, Vikram

    2002-01-01

    International audience; A procedure was developed for the production of a high milk protein powder that was rich in both milk proteins, casein and whey proteins, and free of lactose. The method utilized ultrafiltration and diafiltration with no pH adjustment and a relatively low temperature. Spray drying was conducted at low temperatures (120 to 125 °C inlet air temperature, 75 to 80 °C outlet air temperature). The resulting powder contained at least 84% total protein (casein and whey protein...

  4. Contrasting Academic Behavioural Confidence in Mexican and European Psychology Students

    Science.gov (United States)

    Ochoa, Alma Rosa Aguila; Sander, Paul

    2012-01-01

    Introduction: Research with the Academic Behavioural Confidence scale using European students has shown that students have high levels of confidence in their academic abilities. It is generally accepted that people in more collectivist cultures have more realistic confidence levels in contrast to the overconfidence seen in individualistic European…

  5. Confidence and the business cycle

    OpenAIRE

    Sylvain Leduc

    2010-01-01

    The idea that business cycle fluctuations may stem partly from changes in consumer and business confidence is controversial. One way to test the idea is to use professional economic forecasts to measure confidence at specific points in time and correlate the results with future economic activity. Such an analysis suggests that changes in expectations regarding future economic performance are important drivers of economic fluctuations. Moreover, periods of heightened optimism are followed by a...

  6. Regaining confidence in confidence intervals for the mean treatment effect.

    Science.gov (United States)

    O'Gorman, Thomas W

    2014-09-28

    In many experiments, it is necessary to evaluate the effectiveness of a treatment by comparing the responses of two groups of subjects. This evaluation is often performed by using a confidence interval for the difference between the population means. To compute the limits of this confidence interval, researchers usually use the pooled t formulas, which are derived by assuming normally distributed errors. When the normality assumption does not seem reasonable, the researcher may have little confidence in the confidence interval because the actual one-sided coverage probability may not be close to the nominal coverage probability. This problem can be avoided by using the Robbins-Monro iterative search method to calculate the limits. One problem with this iterative procedure is that it is not clear when the procedure produces a sufficiently accurate estimate of a limit. In this paper, we describe a multiple search method that allows the user to specify the accuracy of the limits. We also give guidance concerning the number of iterations that would typically be needed to achieve a specified accuracy. This multiple iterative search method will produce limits for one-sided and two-sided confidence intervals that maintain their coverage probabilities with non-normal distributions.

  7. Identification of highly active flocculant proteins in bovine blood.

    Science.gov (United States)

    Piazza, George J; Nuñez, Alberto; Garcia, Rafael A

    2012-03-01

    Synthetic polymeric flocculants are used extensively for wastewater remediation, soil stabilization, and reduction in water leakage from unlined canals. Sources of highly active, inexpensive, renewable flocculants are needed to replace synthetic flocculants. High kaolin flocculant activity was documented for bovine blood (BB) and blood plasma with several anticoagulant treatments. BB serum also had high flocculant activity. To address the hypothesis that some blood proteins have strong flocculating activity, the BB proteins were separated by SEC. Then, the major proteins of the flocculant-active fractions were separated by SDS-PAGE. Identity of the major protein components was determined by tryptic digestion and peptide analysis by MALDI TOF MS. The sequence of selected peptides was confirmed using TOF/TOF-MS/MS fragmentation. Hemoglobin dimer (subunits α and β) was identified as the major protein component of the active fraction in BB; its high flocculation activity was confirmed by testing a commercial sample of hemoglobin. In the same manner, three proteins from blood plasma (fibrinogen, γ-globulin, α-2-macroglobulin) were found to be highly active flocculants, but bovine serum albumin, α-globulin, and β-globulin were not flocculants. On a mass basis, hemoglobin, γ-globulin, α-2-macroglobulin were as effective as anionic polyacrylamide (PAM), a widely used synthetic flocculant. The blood proteins acted faster than PAM, and unlike PAM, the blood proteins flocculants did not require calcium salts for their activity.

  8. Optimizing high performance computing workflow for protein functional annotation.

    Science.gov (United States)

    Stanberry, Larissa; Rekepalli, Bhanu; Liu, Yuan; Giblock, Paul; Higdon, Roger; Montague, Elizabeth; Broomall, William; Kolker, Natali; Kolker, Eugene

    2014-09-10

    Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding. Newly sequenced bacterial genomes alone contain over 7.5 million proteins. The rate of data generation has far surpassed that of protein annotation. The volume of protein data makes manual curation infeasible, whereas a high compute cost limits the utility of existing automated approaches. In this work, we present an improved and optmized automated workflow to enable large-scale protein annotation. The workflow uses high performance computing architectures and a low complexity classification algorithm to assign proteins into existing clusters of orthologous groups of proteins. On the basis of the Position-Specific Iterative Basic Local Alignment Search Tool the algorithm ensures at least 80% specificity and sensitivity of the resulting classifications. The workflow utilizes highly scalable parallel applications for classification and sequence alignment. Using Extreme Science and Engineering Discovery Environment supercomputers, the workflow processed 1,200,000 newly sequenced bacterial proteins. With the rapid expansion of the protein sequence universe, the proposed workflow will enable scientists to annotate big genome data.

  9. Effects of High Fidelity Simulation on Knowledge Acquisition, Self-Confidence, and Satisfaction with Baccalaureate Nursing Students Using the Solomon-Four Research Design

    Science.gov (United States)

    Hall, Rachel Mattson

    2013-01-01

    High Fidelity Simulation is a teaching strategy that is becoming well-entrenched in the world of nursing education and is rapidly expanding due to the challenges and demands of the health care environment. The problem addressed in this study is the conflicting research results regarding the effectiveness of HFS for students' knowledge acquisition…

  10. A Quantitative Assessment of Gender and Career Decision-Making Confidence Levels of High School Seniors in a School-to-Work Program Using the Career Decision Scale.

    Science.gov (United States)

    Fawcett, Mary; Maycock, George

    This study measured differences in the levels of career indecision for urban male and female high school seniors who had varying levels of experience in vocational programs or job related activities through school-to-work (STW) vocational programs. The 113 students, of whom 44% were male and 56% were female, completed the Career Decision Scale…

  11. High dietary protein intake, reducing or eliciting insulin resistance?

    NARCIS (Netherlands)

    Rietman, A.; Schwarz, J.; Tome, D.; Kok, F.J.; Mensink, M.R.

    2014-01-01

    Dietary proteins have an insulinotropic effect and thus promote insulin secretion, which indeed leads to enhanced glucose clearance from the blood. In the long term, however, a high dietary protein intake is associated with an increased risk of type 2 diabetes. Moreover, branched-chain amino acids (

  12. High dietary protein intake, reducing or eliciting insulin resistance?

    NARCIS (Netherlands)

    Rietman, A.; Schwarz, J.; Tome, D.; Kok, F.J.; Mensink, M.R.

    2014-01-01

    Dietary proteins have an insulinotropic effect and thus promote insulin secretion, which indeed leads to enhanced glucose clearance from the blood. In the long term, however, a high dietary protein intake is associated with an increased risk of type 2 diabetes. Moreover, branched-chain amino acids

  13. The role of confidence in world-class sport performance.

    Science.gov (United States)

    Hays, Kate; Thomas, Owen; Maynard, Ian; Bawden, Mark

    2009-09-01

    In this study, we examined the role of confidence in relation to the cognitive, affective, and behavioural responses it elicits, and identified the factors responsible for debilitating confidence within the organizational subculture of world-class sport. Using Vealey's (2001) integrative model of sport confidence as a broad conceptual base, 14 athletes (7 males, 7 females) were interviewed in response to the research aims. Analysis indicated that high sport confidence facilitated performance through its positive effect on athletes' thoughts, feelings, and behaviours. However, the athletes participating in this study were susceptible to factors that served to debilitate their confidence. These factors appeared to be associated with the sources from which they derived their confidence and influenced to some extent by gender. Thus, the focus of interventions designed to enhance sport confidence must reflect the individual needs of the athlete, and might involve identifying an athlete's sources and types of confidence, and ensuring that these are intact during competition preparation phases.

  14. 农村初中英语学困生自信心的干预研究%Interference Study on the Confidence of Students with Learning Difficulties in English in Rural Junior High School

    Institute of Scientific and Technical Information of China (English)

    徐伟; 苏静

    2012-01-01

    We categorized 28 students with learning difficuhies in English from a rural junior high school into experimental and control group randomly, and carried out group guidance for nine times, and measured their confidence before and after the group guid- ance, to explore if the confidence intervention - oriented group guidance have a positive impact on the academic achievements of students with learning difficulties in rural junior school. After the group guidance, the confidence of the experimental group has been improved obviously, and students has made certain progress in English. So, the confidence intervention - oriented group guidance has positive intervention effect on rural junior school students with learning difficulties in English.%我们将某农村中学28名英语学困生随机分为实验组与对照组,并对实验组进行9次团体辅导,在实施团体辅导前后采用自信心量表进行测量,探讨以自信心干预为主的团体辅导是否对农村初中英语学困生的成绩有积极影响。团体辅导后,实验组被试的自信心水平显著提高,且英语学习成绩取得一定的进步。所以,以自信心干预为主的团体辅导对农村初中英语学困生具有积极的干预效果。

  15. Increasing the Confidence in Student's $t$ Interval

    OpenAIRE

    Goutis, Constantinos; Casella, George

    1992-01-01

    The usual confidence interval, based on Student's $t$ distribution, has conditional confidence that is larger than the nominal confidence level. Although this fact is known, along with the fact that increased conditional confidence can be used to improve a confidence assertion, the confidence assertion of Student's $t$ interval has never been critically examined. We do so here, and construct a confidence estimator that allows uniformly higher confidence in the interval and is closer (than $1 ...

  16. Increasing the Confidence in Student's $t$ Interval

    OpenAIRE

    Goutis, Constantinos; Casella, George

    1992-01-01

    The usual confidence interval, based on Student's $t$ distribution, has conditional confidence that is larger than the nominal confidence level. Although this fact is known, along with the fact that increased conditional confidence can be used to improve a confidence assertion, the confidence assertion of Student's $t$ interval has never been critically examined. We do so here, and construct a confidence estimator that allows uniformly higher confidence in the interval and is closer (than $1 ...

  17. Professional confidence: a concept analysis.

    Science.gov (United States)

    Holland, Kathlyn; Middleton, Lyn; Uys, Leana

    2012-03-01

    Professional confidence is a concept that is frequently used and or implied in occupational therapy literature, but often without specifying its meaning. Rodgers's Model of Concept Analysis was used to analyse the term "professional confidence". Published research obtained from a federated search in four health sciences databases was used to inform the concept analysis. The definitions, attributes, antecedents, and consequences of professional confidence as evidenced in the literature are discussed. Surrogate terms and related concepts are identified, and a model case of the concept provided. Based on the analysis, professional confidence can be described as a dynamic, maturing personal belief held by a professional or student. This includes an understanding of and a belief in the role, scope of practice, and significance of the profession, and is based on their capacity to competently fulfil these expectations, fostered through a process of affirming experiences. Developing and fostering professional confidence should be nurtured and valued to the same extent as professional competence, as the former underpins the latter, and both are linked to professional identity.

  18. PhenoMeter: a metabolome database search tool using statistical similarity matching of metabolic phenotypes for high-confidence detection of functional links

    Directory of Open Access Journals (Sweden)

    Adam James Carroll

    2015-07-01

    Full Text Available This article describes PhenoMeter, a new type of metabolomics database search that accepts metabolite response patterns as queries and searches the MetaPhen database of reference patterns for responses that are statistically significantly similar or inverse for the purposes of detecting functional links. To identify a similarity measure that would detect functional links as reliably as possible, we compared the performance of four statistics in correctly top-matching metabolic phenotypes of Arabidopsis thaliana metabolism mutants affected in different steps of the photorespiration metabolic pathway to reference phenotypes of mutants affected in the same enzymes by independent mutations. The best performing statistic, the PhenoMeter Score (PM Score, was a function of both Pearson correlation and Fisher’s Exact Test of directional overlap. This statistic outperformed Pearson correlation, biweight midcorrelation and Fisher’s Exact Test used alone. To demonstrate general applicability, we show that the PhenoMeter reliably retrieved the most closely functionally-linked response in the database when queried with responses to a wide variety of environmental and genetic perturbations. Attempts to match metabolic phenotypes between independent studies were met with varying success and possible reasons for this are discussed. Overall, our results suggest that integration of pattern-based search tools into metabolomics databases will aid functional annotation of newly recorded metabolic phenotypes analogously to the way sequence similarity search algorithms have aided the functional annotation of genes and proteins. PhenoMeter is freely available at MetabolomeExpress (https://www.metabolome-express.org/phenometer.php.

  19. A highly efficient pipeline for protein expression in Leishmania tarentolae using infrared fluorescence protein as marker

    Directory of Open Access Journals (Sweden)

    Mueller-Roeber Bernd

    2010-05-01

    . The facile in-cell and in-gel detection tools built on IFP make Leishmania amenable for high-throughput expression of proteins from plant and animal sources.

  20. Targeting Low Career Confidence Using the Career Planning Confidence Scale

    Science.gov (United States)

    McAuliffe, Garrett; Jurgens, Jill C.; Pickering, Worth; Calliotte, James; Macera, Anthony; Zerwas, Steven

    2006-01-01

    The authors describe the development and validation of a test of career planning confidence that makes possible the targeting of specific problem issues in employment counseling. The scale, developed using a rational process and the authors' experience with clients, was tested for criterion-related validity against 2 other measures. The scale…

  1. The fallacy of placing confidence in confidence intervals

    NARCIS (Netherlands)

    Morey, Richard D.; Hoekstra, Rink; Rouder, Jeffrey N.; Lee, Michael D.; Wagenmakers, Eric-Jan

    2016-01-01

    Interval estimates – estimates of parameters that include an allowance for sampling uncertainty – have long been touted as a key component of statistical analyses. There are several kinds of interval estimates, but the most popular are confidence intervals (CIs): intervals that contain the true

  2. The fallacy of placing confidence in confidence intervals

    NARCIS (Netherlands)

    Morey, R.D.; Hoekstra, R.; Rouder, J.N.; Lee, M.D.; Wagenmakers, E.-J.

    Interval estimates – estimates of parameters that include an allowance for sampling uncertainty – have long been touted as a key component of statistical analyses. There are several kinds of interval estimates, but the most popular are confidence intervals (CIs): intervals that contain the true

  3. Minimax confidence intervals in geomagnetism

    Science.gov (United States)

    Stark, Philip B.

    1992-01-01

    The present paper uses theory of Donoho (1989) to find lower bounds on the lengths of optimally short fixed-length confidence intervals (minimax confidence intervals) for Gauss coefficients of the field of degree 1-12 using the heat flow constraint. The bounds on optimal minimax intervals are about 40 percent shorter than Backus' intervals: no procedure for producing fixed-length confidence intervals, linear or nonlinear, can give intervals shorter than about 60 percent the length of Backus' in this problem. While both methods rigorously account for the fact that core field models are infinite-dimensional, the application of the techniques to the geomagnetic problem involves approximations and counterfactual assumptions about the data errors, and so these results are likely to be extremely optimistic estimates of the actual uncertainty in Gauss coefficients.

  4. Automated High Throughput Protein Crystallization Screening at Nanoliter Scale and Protein Structural Study on Lactate Dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Li, Fenglei [Iowa State Univ., Ames, IA (United States)

    2006-08-09

    The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by lysozyme crystallization screening. Secondly, we developed a new crystallization method with high screening efficiency, low protein consumption and compatibility with automation and high throughput. In this crystallization method, a gas permeable membrane is employed to achieve the gentle evaporation required by protein crystallization. Protein consumption is significantly reduced to nanoliter scale for each condition and thus permits exploring more conditions in a phase diagram for given amount of protein. In addition

  5. Filtering high-throughput protein-protein interaction data using a combination of genomic features

    Directory of Open Access Journals (Sweden)

    Patil Ashwini

    2005-04-01

    Full Text Available Abstract Background Protein-protein interaction data used in the creation or prediction of molecular networks is usually obtained from large scale or high-throughput experiments. This experimental data is liable to contain a large number of spurious interactions. Hence, there is a need to validate the interactions and filter out the incorrect data before using them in prediction studies. Results In this study, we use a combination of 3 genomic features – structurally known interacting Pfam domains, Gene Ontology annotations and sequence homology – as a means to assign reliability to the protein-protein interactions in Saccharomyces cerevisiae determined by high-throughput experiments. Using Bayesian network approaches, we show that protein-protein interactions from high-throughput data supported by one or more genomic features have a higher likelihood ratio and hence are more likely to be real interactions. Our method has a high sensitivity (90% and good specificity (63%. We show that 56% of the interactions from high-throughput experiments in Saccharomyces cerevisiae have high reliability. We use the method to estimate the number of true interactions in the high-throughput protein-protein interaction data sets in Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens to be 27%, 18% and 68% respectively. Our results are available for searching and downloading at http://helix.protein.osaka-u.ac.jp/htp/. Conclusion A combination of genomic features that include sequence, structure and annotation information is a good predictor of true interactions in large and noisy high-throughput data sets. The method has a very high sensitivity and good specificity and can be used to assign a likelihood ratio, corresponding to the reliability, to each interaction.

  6. High dietary protein decreases fat deposition induced by high-fat and high-sucrose diet in rats

    NARCIS (Netherlands)

    Chaumontet, C.; Schwarz, J.; Even, P.C.; Simonin-Foucault, A.; Piedcoq, J.; Fromentin, G.; Azzout-Marniche, D.; Tome, D.

    2015-01-01

    High-protein diets are known to reduce adiposity in the context of high carbohydrate and Western diets. However, few studies have investigated the specific high-protein effect on lipogenesis induced by a high-sucrose (HS) diet or fat deposition induced by high-fat feeding. We aimed to determine the

  7. Reverse Phase Protein Arrays for High-Throughput Protein Measurements in Mammospheres

    DEFF Research Database (Denmark)

    Pedersen, Marlene Lemvig; Block, Ines; List, Markus

    Protein Array (RPPA)-based readout format integrated into robotic siRNA screening. This technique would allow post-screening high-throughput quantification of protein changes. Recently, breast cancer stem cells (BCSCs) have attracted much attention, as a tumor- and metastasis-driving subpopulation...

  8. Haptoglobin-related protein is a high-affinity hemoglobin-binding plasma protein

    DEFF Research Database (Denmark)

    Nielsen, Marianne Jensby; Petersen, Steen Vang; Jacobsen, Christian

    2006-01-01

    Haptoglobin-related protein (Hpr) is a primate-specific plasma protein associated with apolipoprotein L-I (apoL-I)-containing high-density lipoprotein (HDL) particles shown to be a part of the innate immune defense. Despite the assumption hitherto that Hpr does not bind to hemoglobin, the present...

  9. Robust misinterpretation of confidence intervals

    NARCIS (Netherlands)

    Hoekstra, Rink; Morey, Richard; Rouder, Jeffrey N.; Wagenmakers, Eric-Jan

    2014-01-01

    Null hypothesis significance testing (NHST) is undoubtedly the most common inferential technique used to justify claims in the social sciences. However, even staunch defenders of NHST agree that its outcomes are often misinterpreted. Confidence intervals (CIs) have frequently been proposed as a more

  10. Robust misinterpretation of confidence intervals

    NARCIS (Netherlands)

    Hoekstra, R.; Morey, R.D.; Rouder, J.N.; Wagenmakers, E.-J.

    2014-01-01

    Null hypothesis significance testing (NHST) is undoubtedly the most common inferential technique used to justify claims in the social sciences. However, even staunch defenders of NHST agree that its outcomes are often misinterpreted. Confidence intervals (CIs) have frequently been proposed as a more

  11. Assessment of cartilage-dedicated sequences at ultra-high-field MRI: comparison of imaging performance and diagnostic confidence between 3.0 and 7.0 T with respect to osteoarthritis-induced changes at the knee joint

    Energy Technology Data Exchange (ETDEWEB)

    Stahl, Robert [University of California, Musculoskeletal and Quantitative Imaging Group, Department of Radiology, San Francisco, CA (United States); University Hospitals - Campus Grosshadern, Ludwig Maximilians University of Munich, Department of Clinical Radiology, Munich (Germany); Krug, Roland; Zuo, Jin; Majumdar, Sharmila; Link, Thomas M. [University of California, Musculoskeletal and Quantitative Imaging Group, Department of Radiology, San Francisco, CA (United States); Kelley, Douglas A.C. [General Electrics Healthcare Technologies, San Francisco, CA (United States); Ma, C.B. [University of California, Department of Orthopedic Surgery, San Francisco, CA (United States)

    2009-08-15

    The objectives of the study were to optimize three cartilage-dedicated sequences for in vivo knee imaging at 7.0 T ultra-high-field (UHF) magnetic resonance imaging (MRI) and to compare imaging performance and diagnostic confidence concerning osteoarthritis (OA)-induced changes at 7.0 and 3.0 T MRI. Optimized MRI sequences for cartilage imaging at 3.0 T were tailored for 7.0 T: an intermediate-weighted fast spin-echo (IM-w FSE), a fast imaging employing steady-state acquisition (FIESTA) and a T1-weighted 3D high-spatial-resolution volumetric fat-suppressed spoiled gradient-echo (SPGR) sequence. Three healthy subjects and seven patients with mild OA were examined. Signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), diagnostic confidence in assessing cartilage abnormalities, and image quality were determined. Abnormalities were assessed with the whole organ magnetic resonance imaging score (WORMS). Focal cartilage lesions and bone marrow edema pattern (BMEP) were also quantified. At 7.0 T, SNR was increased (p<0.05) for all sequences. For the IM-w FSE sequence, limitations with the specific absorption rate (SAR) required modifications of the scan parameters yielding an incomplete coverage of the knee joint, extensive artifacts, and a less effective fat saturation. CNR and image quality were increased (p<0.05) for SPGR and FIESTA and decreased for IM-w FSE. Diagnostic confidence for cartilage lesions was highest (p<0.05) for FIESTA at 7.0 T. Evaluation of BMEP was decreased (p < 0.05) at 7.0 T due to limited performance of IM-w FSE. Gradient echo-based pulse sequences like SPGR and FIESTA are well suited for imaging at UHF which may improve early detection of cartilage lesions. However, UHF IM-w FSE sequences are less feasible for clinical use. (orig.)

  12. Autopilot: an online data acquisition control system for the enhanced high-throughput characterization of intact proteins.

    Science.gov (United States)

    Durbin, Kenneth R; Fellers, Ryan T; Ntai, Ioanna; Kelleher, Neil L; Compton, Philip D

    2014-02-04

    The ability to study organisms by direct analysis of their proteomes without digestion via mass spectrometry has benefited greatly from recent advances in separation techniques, instrumentation, and bioinformatics. However, improvements to data acquisition logic have lagged in comparison. Past workflows for Top Down Proteomics (TDPs) have focused on high throughput at the expense of maximal protein coverage and characterization. This mode of data acquisition has led to enormous overlap in the identification of highly abundant proteins in subsequent LC-MS injections. Furthermore, a wealth of data is left underutilized by analyzing each newly targeted species as unique, rather than as part of a collection of fragmentation events on a distinct proteoform. Here, we present a major advance in software for acquisition of TDP data that incorporates a fully automated workflow able to detect intact masses, guide fragmentation to achieve maximal identification and characterization of intact protein species, and perform database search online to yield real-time protein identifications. On Pseudomonas aeruginosa, the software combines fragmentation events of the same precursor with previously obtained fragments to achieve improved characterization of the target form by an average of 42 orders of magnitude in confidence. When HCD fragmentation optimization was applied to intact proteins ions, there was an 18.5 order of magnitude gain in confidence. These improved metrics set the stage for increased proteome coverage and characterization of higher order organisms in the future for sharply improved control over MS instruments in a project- and lab-wide context.

  13. Integrated and comparative proteomics of high-oil and high-protein soybean seeds.

    Science.gov (United States)

    Xu, Xiu Ping; Liu, Hui; Tian, Lihong; Dong, Xiang Bai; Shen, Shi Hua; Qu, Le Qing

    2015-04-01

    We analysed the global protein expression in seeds of a high-oil soybean cultivar (Jiyu 73, JY73) by proteomics. More than 700 protein spots were detected and 363 protein spots were successfully identified. Comparison of the protein profile of JY73 with that of a high-protein cultivar (Zhonghuang 13, ZH13) revealed 40 differentially expressed proteins, including oil synthesis, redox/stress, hydrolysis and storage-related proteins. All redox/stress proteins were less or not expressed in JY73, whereas the expression of the major storage proteins, nitrogen and carbon metabolism-related proteins was higher in ZH13. Biochemical analysis of JY73 revealed that it was in a low oxidation state, with a high content of polyunsaturated fatty acids and vitamin E. Vitamin E was more active than antioxidant enzymes and protected the soybean seed in a lower oxidation state. The characteristics of high oil and high protein in soybean, we revealed, might provide a reference for soybean nutrition and soybean breeding.

  14. Potential interaction between warfarin and high dietary protein intake.

    Science.gov (United States)

    Hornsby, Lori B; Hester, E Kelly; Donaldson, Amy R

    2008-04-01

    A 55-year-old Caucasian man was receiving warfarin therapy after undergoing aortic valve replacement. His international normalized ratio (INR) was stabilized with warfarin 95 mg/week for 5 weeks. Commencement of a low-carbohydrate, high-protein diet resulted in a series of subtherapeutic INRs that led to a 16% increase in the dosage requirement to maintain therapeutic INRs. After the patient discontinued the diet, his INR increased, and several dosage reductions were required until his INR stabilized with his original dosage of 95 mg/week. Two additional case reports have described a possible interaction between warfarin and a high-protein diet. The potential for increased dietary protein intake to raise serum albumin levels and/or cytochrome P450 activity has been postulated as mechanisms for the resulting decrease in INRs. Given the available animal and human data that demonstrate alterations in drug metabolism in the presence of altered dietary protein intake, an increase in warfarin metabolism due to cytochrome P450 activation appears to be the most likely cause. In addition to the previously reported cases, this case indicates a potential interaction between warfarin and a high-protein diet. Because of the popularity of high-protein diets and because of the risks associated with inadequate or excessive warfarin anticoagulation, patients and health care providers should be aware of this interaction to ensure appropriate monitoring when warranted.

  15. Perceived Sources of Team Confidence in Soccer and Basketball.

    Science.gov (United States)

    Fransen, Katrien; Vanbeselaere, Norbert; De Cuyper, Bert; Vande Broek, Gert; Boen, Filip

    2015-07-01

    Although it is generally accepted that team confidence is beneficial for optimal team functioning and performance, little is known about the predictors of team confidence. The present study was aimed to shed light on the precursors of both high and low team confidence in two different sports. A distinction is made between sources of process-oriented team confidence (i.e., collective efficacy) and sources of outcome-oriented team confidence (i.e., team outcome confidence), which have often been confounded in previous research. In a first step, two qualitative studies were conducted to identify all possible sources of team confidence in basketball and in soccer. In a second step, three quantitative studies were conducted to further investigate the sources of team outcome confidence in soccer (N = 1028) and in basketball (N = 867), and the sources of collective efficacy in basketball (N = 825). Players perceived high-quality performance as the most important factor for their team outcome confidence. With regard to collective efficacy, team enthusiasm was perceived as most predictive determinant. Positive coaching emerged as second most decisive factor for both types of team confidence. In contrast, negative communication and expression by the players or the coach was perceived as the most decisive predictor of low levels of team confidence. At item level, all studies pointed to the importance of team confidence expression by the athlete leaders (i.e., leader figures within the team) and the coach. The present manuscript sheds light on the precursors of high and low levels of team confidence. Athlete leaders and the coach emerged as key triggers of both upward and downward spirals of team confidence, thereby contaminating all team members.

  16. High-resolution mapping of protein sequence-function relationships.

    Science.gov (United States)

    Fowler, Douglas M; Araya, Carlos L; Fleishman, Sarel J; Kellogg, Elizabeth H; Stephany, Jason J; Baker, David; Fields, Stanley

    2010-09-01

    We present a large-scale approach to investigate the functional consequences of sequence variation in a protein. The approach entails the display of hundreds of thousands of protein variants, moderate selection for activity and high-throughput DNA sequencing to quantify the performance of each variant. Using this strategy, we tracked the performance of >600,000 variants of a human WW domain after three and six rounds of selection by phage display for binding to its peptide ligand. Binding properties of these variants defined a high-resolution map of mutational preference across the WW domain; each position had unique features that could not be captured by a few representative mutations. Our approach could be applied to many in vitro or in vivo protein assays, providing a general means for understanding how protein function relates to sequence.

  17. High-Confidence Predictions under Adversarial Uncertainty

    CERN Document Server

    Drucker, Andrew

    2011-01-01

    We study the setting in which the bits of an unknown infinite binary sequence x are revealed sequentially to an observer. We show that very limited assumptions about x allow one to make successful predictions about unseen bits of x. First, we study the problem of successfully predicting a single 0 from among the bits of x. In our model we have only one chance to make a prediction, but may do so at a time of our choosing. We describe and motivate this as the problem of a frog who wants to cross a road safely. Letting N_t denote the number of 1s among the first t bits of x, we say that x is "eps-weakly sparse" if lim inf (N_t/t) 0, we give a randomized forecasting algorithm S_eps that, given sequential access to a binary sequence x, makes a predi ction of the form: "A p fraction of the next N bits will be 1s." (The algorithm gets to choose p, N, and the time of the prediction.) For any fixed sequence x, the forecast fraction p is accurate to within +-eps with probability 1 - eps.

  18. Global Geometric Affinity for Revealing High Fidelity Protein Interaction Network

    Science.gov (United States)

    Fang, Yi; Benjamin, William; Sun, Mengtian; Ramani, Karthik

    2011-01-01

    Protein-protein interaction (PPI) network analysis presents an essential role in understanding the functional relationship among proteins in a living biological system. Despite the success of current approaches for understanding the PPI network, the large fraction of missing and spurious PPIs and a low coverage of complete PPI network are the sources of major concern. In this paper, based on the diffusion process, we propose a new concept of global geometric affinity and an accompanying computational scheme to filter the uncertain PPIs, namely, reduce the spurious PPIs and recover the missing PPIs in the network. The main concept defines a diffusion process in which all proteins simultaneously participate to define a similarity metric (global geometric affinity (GGA)) to robustly reflect the internal connectivity among proteins. The robustness of the GGA is attributed to propagating the local connectivity to a global representation of similarity among proteins in a diffusion process. The propagation process is extremely fast as only simple matrix products are required in this computation process and thus our method is geared toward applications in high-throughput PPI networks. Furthermore, we proposed two new approaches that determine the optimal geometric scale of the PPI network and the optimal threshold for assigning the PPI from the GGA matrix. Our approach is tested with three protein-protein interaction networks and performs well with significant random noises of deletions and insertions in true PPIs. Our approach has the potential to benefit biological experiments, to better characterize network data sets, and to drive new discoveries. PMID:21559288

  19. Beyond hypercorrection: remembering corrective feedback for low-confidence errors.

    Science.gov (United States)

    Griffiths, Lauren; Higham, Philip A

    2017-07-01

    Correcting errors based on corrective feedback is essential to successful learning. Previous studies have found that corrections to high-confidence errors are better remembered than low-confidence errors (the hypercorrection effect). The aim of this study was to investigate whether corrections to low-confidence errors can also be successfully retained in some cases. Participants completed an initial multiple-choice test consisting of control, trick and easy general-knowledge questions, rated their confidence after answering each question, and then received immediate corrective feedback. After a short delay, they were given a cued-recall test consisting of the same questions. In two experiments, we found high-confidence errors to control questions were better corrected on the second test compared to low-confidence errors - the typical hypercorrection effect. However, low-confidence errors to trick questions were just as likely to be corrected as high-confidence errors. Most surprisingly, we found that memory for the feedback and original responses, not confidence or surprise, were significant predictors of error correction. We conclude that for some types of material, there is an effortful process of elaboration and problem solving prior to making low-confidence errors that facilitates memory of corrective feedback.

  20. Combinatorial synthesis with high throughput discovery of protein-resistant membrane surfaces.

    Science.gov (United States)

    Gu, Minghao; Vegas, Arturo J; Anderson, Daniel G; Langer, Robert S; Kilduff, James E; Belfort, Georges

    2013-08-01

    Using combinatorial methods, we synthesized a series of new vinyl amide monomers and graft-polymerized them to light-sensitive poly(ether sulfone) (PES) porous films for protein resistance. To increase the discovery rate and statistical confidence, we developed high throughput surface modification methods (HTP) that allow synthesis, screening and selection of desirable monomers from a large library in a relatively short time (days). A series of amide monomers were synthesized by amidation of methacryloyl chloride with amines and grafted onto commercial poly(ether sulfone) (PES) membranes using irradiation from atmospheric pressure plasma (APP). The modified PES membrane surfaces were then tested and screened for static protein adhesion using HTP. Hydroxyl amide monomers N-(3-hydroxypropyl)methacrylamide (A3), N-(4-hydroxybutyl)methacrylamide (A4), and N-(4-hydroxybutyl)methacrylamide (A6), ethylene glycol (EG) monomer N-(3-methoxypropyl)methacrylamide (A7), and N-(2-(dimethylamino)ethyl)-N-methylmethacrylamide (A8), and N-(2-(diethylamino)ethyl)-N-methylmethacrylamide (A9) all terminated with tertiary amines and were shown to have protein resistance. The PES membranes modified with these monomers exhibited both low protein adhesion (i.e. membrane plugging or fouling) and high flux. Their performance is comparable with previously identified best performing PEG and zwitterionic monomers, i.e. the so-called gold-standard for protein resistance. Combining a Hansen solubility parameter (HSP) analysis of the amide monomers and the HTP filtration results, we conclude that monomer solubility in water correlates with protein-resistant surfaces, presumably through its effects on surface-water interactions.

  1. Self-Confidence & Social Interactions

    OpenAIRE

    Bénabou, Roland; Tirole, Jean

    2000-01-01

    This paper studies the interactions between an individual's self-esteem and his social environment - in the workplace, at school, and in personal relationships. Because a person generally has only imperfect knowledge of his own abilities, people who derive benefits from his performance (parent, spouse, friend, teacher, manager, etc.) have incentives to manipulate his self--confidence. We first study situations where an informed principal chooses an incentive structure, such as offering paymen...

  2. The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.

    Science.gov (United States)

    Bastian, Frederic B; Chibucos, Marcus C; Gaudet, Pascale; Giglio, Michelle; Holliday, Gemma L; Huang, Hong; Lewis, Suzanna E; Niknejad, Anne; Orchard, Sandra; Poux, Sylvain; Skunca, Nives; Robinson-Rechavi, Marc

    2015-01-01

    Biocuration has become a cornerstone for analyses in biology, and to meet needs, the amount of annotations has considerably grown in recent years. However, the reliability of these annotations varies; it has thus become necessary to be able to assess the confidence in annotations. Although several resources already provide confidence information about the annotations that they produce, a standard way of providing such information has yet to be defined. This lack of standardization undermines the propagation of knowledge across resources, as well as the credibility of results from high-throughput analyses. Seeded at a workshop during the Biocuration 2012 conference, a working group has been created to address this problem. We present here the elements that were identified as essential for assessing confidence in annotations, as well as a draft ontology--the Confidence Information Ontology--to illustrate how the problems identified could be addressed. We hope that this effort will provide a home for discussing this major issue among the biocuration community. Tracker URL: https://github.com/BgeeDB/confidence-information-ontology Ontology URL: https://raw.githubusercontent.com/BgeeDB/confidence-information-ontology/master/src/ontology/cio-simple.obo

  3. Confidence-Based Feature Acquisition

    Science.gov (United States)

    Wagstaff, Kiri L.; desJardins, Marie; MacGlashan, James

    2010-01-01

    Confidence-based Feature Acquisition (CFA) is a novel, supervised learning method for acquiring missing feature values when there is missing data at both training (learning) and test (deployment) time. To train a machine learning classifier, data is encoded with a series of input features describing each item. In some applications, the training data may have missing values for some of the features, which can be acquired at a given cost. A relevant JPL example is that of the Mars rover exploration in which the features are obtained from a variety of different instruments, with different power consumption and integration time costs. The challenge is to decide which features will lead to increased classification performance and are therefore worth acquiring (paying the cost). To solve this problem, CFA, which is made up of two algorithms (CFA-train and CFA-predict), has been designed to greedily minimize total acquisition cost (during training and testing) while aiming for a specific accuracy level (specified as a confidence threshold). With this method, it is assumed that there is a nonempty subset of features that are free; that is, every instance in the data set includes these features initially for zero cost. It is also assumed that the feature acquisition (FA) cost associated with each feature is known in advance, and that the FA cost for a given feature is the same for all instances. Finally, CFA requires that the base-level classifiers produce not only a classification, but also a confidence (or posterior probability).

  4. Feature Augmentation for Learning Confidence Measure in Stereo Matching.

    Science.gov (United States)

    Kim, Sunok; Min, Dongbo; Kim, Seungryong; Sohn, Kwanghoon

    2017-09-08

    Confidence estimation is essential for refining stereo matching results through a post-processing step. This problem has recently been studied using a learning-based approach, which demonstrates a substantial improvement on conventional simple non-learning based methods. However, the formulation of learning-based methods that individually estimates the confidence of each pixel disregards spatial coherency that might exist in the confidence map, thus providing a limited performance under challenging conditions. Our key observation is that the confidence features and resulting confidence maps are smoothly varying in the spatial domain, and highly correlated within the local regions of an image. We present a new approach that imposes spatial consistency on the confidence estimation. Specifically, a set of robust confidence features is extracted from each superpixel decomposed using the Gaussian mixture model (GMM), and then these features are concatenated with pixel-level confidence features. The features are then enhanced through adaptive filtering in the feature domain. In addition, the resulting confidence map, estimated using the confidence features with a random regression forest, is further improved through K-nearest neighbor (K-NN) based aggregation scheme on both pixel-and superpixel-level. To validate the proposed confidence estimation scheme, we employ cost modulation or ground control points (GCPs) based optimization in stereo matching. Experimental results demonstrate that the proposed method outperforms state-of-the-art approaches on various benchmarks including challenging outdoor scenes.

  5. Social media sentiment and consumer confidence

    OpenAIRE

    Piet J.H. Daas; Puts, Marco J.H.

    2014-01-01

    Changes in the sentiment of Dutch public social media messages were compared with changes in monthly consumer confidence over a period of three-and-a-half years, revealing that both were highly correlated (up to r = 0.9) and that both series cointegrated. This phenomenon is predominantly affected by changes in the sentiment of all Dutch public Facebook messages. The inclusion of various selections of public Twitter messages improved this association and the response to changes in sentiment. G...

  6. High-resolution protein structure determination by serial femtosecond crystallography.

    Science.gov (United States)

    Boutet, Sébastien; Lomb, Lukas; Williams, Garth J; Barends, Thomas R M; Aquila, Andrew; Doak, R Bruce; Weierstall, Uwe; DePonte, Daniel P; Steinbrener, Jan; Shoeman, Robert L; Messerschmidt, Marc; Barty, Anton; White, Thomas A; Kassemeyer, Stephan; Kirian, Richard A; Seibert, M Marvin; Montanez, Paul A; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M; Philipp, Hugh T; Tate, Mark W; Hromalik, Marianne; Koerner, Lucas J; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y; Hunter, Mark S; Johansson, Linda C; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C H; Chapman, Henry N; Schlichting, Ilme

    2012-07-20

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

  7. Characterization of seed storage proteins in high protein genotypes of cowpea [Vigna unguiculata (L.) Walp].

    Science.gov (United States)

    Gupta, Prachi; Singh, Rohtas; Malhotra, S; Boora, K S; Singal, H R

    2010-01-01

    Twenty one genotypes and two check varieties viz. CS-88 and V-240 of cowpea [Vigna unguiculata (L.) Walp. ] were screened for total proteins. The total protein content ranged from 22.4 (HC-3) to 27.9 % (HC-98-64) in 21 genotypes whereas in check varieties it was 25.6 (V-240) and 26.0 % (CS-88). Seven genotypes viz. HC-6, HC-5, CP-21, LST-II-C-12, CP-16, COVU-702 and HC-98-64 having high protein content (26.7 to 27.9 %) were selected for further characterization of their seed storage proteins. Globulins were the major protein fraction ranging from 55.6 (LST-II-C-12) to 58.8 % (CP-16 and HC-6) of total protein. Glutelins was the second major fraction ranging from 14.4 to 15.6 % followed by albumins (8.2 to 11.9 %) and prolamins (2.3 to 5.0 %). Content of free amino acids also showed variations amongst genotypes with COVU-702 having maximum and LST-II-C-12 having minimum content. Essential amino acid analysis revealed that S-amino acids (cysteine and methionine) were the first limiting amino acids followed by tryptophan. From the results presented here it could be suggested that two genotypes viz. LST-II-C-12 and HC-5 be used in breeding programmes aimed at developing high protein moth bean varieties with good quality.

  8. Exploring novel food proteins and processing technologies : a case study on quinoa protein and high pressure –high temperature processing

    NARCIS (Netherlands)

    Avila Ruiz, Geraldine

    2016-01-01

    Foods rich in protein are nowadays high in demand worldwide. To ensure a sustainable supply and a high quality of protein foods, novel food proteins and processing technologies need to be explored to understand whether they can be used for the development of high-quality protein foods. Therefore, th

  9. Castration alters protein balance after high-frequency muscle contraction.

    Science.gov (United States)

    Steiner, Jennifer L; Fukuda, David H; Rossetti, Michael L; Hoffman, Jay R; Gordon, Bradley S

    2017-02-01

    Resistance exercise increases muscle mass by shifting protein balance in favor of protein accretion. Androgens independently alter protein balance, but it is unknown whether androgens alter this measure after resistance exercise. To answer this, male mice were subjected to sham or castration surgery 7-8 wk before undergoing a bout of unilateral, high-frequency, electrically induced muscle contractions in the fasted or refed state. Puromycin was injected 30 min before euthanasia to measure protein synthesis. The tibialis anterior was analyzed 4 h postcontraction. In fasted mice, neither basal nor stimulated rates of protein synthesis were affected by castration despite lower phosphorylation of mechanistic target of rapamycin in complex 1 (mTORC1) substrates [p70S6K1 (Thr389) and 4E-BP1 (Ser65)]. Markers of autophagy (LC3 II/I ratio and p62 protein content) were elevated by castration, and these measures remained elevated above sham values after contractions. Furthermore, in fasted mice, the protein content of Regulated in Development and DNA Damage 1 (REDD1) was correlated with LC3 II/I in noncontracted muscle, whereas phosphorylation of uncoordinated like kinase 1 (ULK1) (Ser757) was correlated with LC3 II/I in the contracted muscle. When mice were refed before contractions, protein synthesis and mTORC1 signaling were not affected by castration in either the noncontracted or contracted muscle. Conversely, markers of autophagy remained elevated in the muscles of refed, castrated mice even after contractions. These data suggest the castration-mediated elevation in baseline autophagy reduces the absolute positive shift in protein balance after muscle contractions in the refed or fasted states.

  10. Understanding the structural ensembles of a highly extended disordered protein.

    Science.gov (United States)

    Daughdrill, Gary W; Kashtanov, Stepan; Stancik, Amber; Hill, Shannon E; Helms, Gregory; Muschol, Martin; Receveur-Bréchot, Véronique; Ytreberg, F Marty

    2012-01-01

    Developing a comprehensive description of the equilibrium structural ensembles for intrinsically disordered proteins (IDPs) is essential to understanding their function. The p53 transactivation domain (p53TAD) is an IDP that interacts with multiple protein partners and contains numerous phosphorylation sites. Multiple techniques were used to investigate the equilibrium structural ensemble of p53TAD in its native and chemically unfolded states. The results from these experiments show that the native state of p53TAD has dimensions similar to a classical random coil while the chemically unfolded state is more extended. To investigate the molecular properties responsible for this behavior, a novel algorithm that generates diverse and unbiased structural ensembles of IDPs was developed. This algorithm was used to generate a large pool of plausible p53TAD structures that were reweighted to identify a subset of structures with the best fit to small angle X-ray scattering data. High weight structures in the native state ensemble show features that are localized to protein binding sites and regions with high proline content. The features localized to the protein binding sites are mostly eliminated in the chemically unfolded ensemble; while, the regions with high proline content remain relatively unaffected. Data from NMR experiments support these results, showing that residues from the protein binding sites experience larger environmental changes upon unfolding by urea than regions with high proline content. This behavior is consistent with the urea-induced exposure of nonpolar and aromatic side-chains in the protein binding sites that are partially excluded from solvent in the native state ensemble.

  11. Effects of high external electric fields on protein conformation

    Science.gov (United States)

    Pompa, Pier Paolo; Bramanti, Alessandro; Maruccio, Giuseppe; del Mercato, Loretta Laureana; Chiuri, Rocco; Cingolani, Roberto; Rinaldi, Ross

    2005-06-01

    Resistance of biomolecules to high electric fields is a main concern for nanobioelectronics/nanobiosensing applications, and it is also a relevant issue from a fundamental perspective, to understand the dielectric properties and structural dynamics of proteins. In nanoscale devices, biomolecules may experience electric fields as high as 107 V/m in order to elicit charge transport/transfer. Understanding the effects of such fields on their structural integrity is thus crucial to assess the reliability of biomolecular devices. In this study, we show experimental evidence for the retention of native-like fold pattern by proteins embedded in high electric fields. We have tested the metalloprotein azurin, deposited onto SiO2 substrates in air with proper electrode configuration, by applying high static electric fields (up to 106-107 V/m). The effects on the conformational properties of protein molecules have been determined by means of intrinsic fluorescence measurements. Experimental results indicate that no significant field-induced conformational alteration occurs. This behavior is also discussed and supported by theoretical predictions of the intrinsic intra-protein electric fields. As the general features of such inner fields are not peculiar of azurin, the conclusions presented here should have general validity.

  12. High pressure-low temperature processing of food proteins.

    Science.gov (United States)

    Dumay, Eliane; Picart, Laetitia; Regnault, Stéphanie; Thiebaud, Maryse

    2006-03-01

    High pressure-low temperature (HP-LT) processing is of interest in the food field in view of: (i) obtaining a "cold" pasteurisation effect, the level of microbial inactivation being higher after pressurisation at low or sub-zero than at ambient temperature; (ii) limiting the negative impact of atmospheric pressure freezing on food structures. The specific effects of freezing by fast pressure release on the formation of ice I crystals have been investigated on oil in water emulsions stabilized by proteins, and protein gels, showing the formation of a high number of small ice nuclei compared to the long needle-shaped crystals obtained by conventional freezing at 0.1 MPa. It was therefore of interest to study the effects of HP-LT processing on unfolding or dissociation/aggregation phenomena in food proteins, in view of minimizing or controlling structural changes and aggregation reactions, and/or of improving protein functional properties. In the present studies, the effects of HP-LT have been investigated on protein models such as (i) beta-lactoglobulin, i.e., a whey protein with a well known 3-D structure, and (ii) casein micelles, i.e., the main milk protein components, the supramolecular structure of which is not fully elucidated. The effects of HP-LT processing was studied up to 300 MPa at low or sub-zero temperatures and after pressure release, or up to 200 MPa by UV spectroscopy under pressure, allowing to follow reversible structural changes. Pressurisation of approximately 2% beta-lactoglobulin solutions up to 300 MPa at low/subzero temperatures minimizes aggregation reactions, as measured after pressure release. In parallel, such low temperature treatments enhanced the size reduction of casein micelles.

  13. Formation of truncated proteins and high-molecular-mass aggregates upon soft illumination of photosynthetic proteins

    DEFF Research Database (Denmark)

    Rinalducci, Sara; Campostrini, Natascia; Antonioli, Paolo

    2005-01-01

    Different spot profiles were observed in 2D gel electrophoresis of thylakoid membranes performed either under complete darkness or by leaving the sample for a short time to low visible light. In the latter case, a large number of new spots with lower molecular masses, ranging between 15,000 and 25......,000 Da, were observed, and high-molecular-mass aggregates, seen as a smearing in the upper part of the gel, appeared in the region around 250 kDa. Identification of protein(s) contained in these new spots by MS/MS revealed that most of them are simply truncated proteins deriving from native ones......, fragments, or aggregates. This resulted from the formation of extremely reactive oxygen species (ROS) that can derive by the exposure of chlorophyll binding proteins of photosynthetic apparatus to low-intensity light during laboratory manipulation of sample for electrophoresis runs....

  14. Predicting protein-protein interactions from sequence using correlation coefficient and high-quality interaction dataset.

    Science.gov (United States)

    Shi, Ming-Guang; Xia, Jun-Feng; Li, Xue-Ling; Huang, De-Shuang

    2010-03-01

    Identifying protein-protein interactions (PPIs) is critical for understanding the cellular function of the proteins and the machinery of a proteome. Data of PPIs derived from high-throughput technologies are often incomplete and noisy. Therefore, it is important to develop computational methods and high-quality interaction dataset for predicting PPIs. A sequence-based method is proposed by combining correlation coefficient (CC) transformation and support vector machine (SVM). CC transformation not only adequately considers the neighboring effect of protein sequence but describes the level of CC between two protein sequences. A gold standard positives (interacting) dataset MIPS Core and a gold standard negatives (non-interacting) dataset GO-NEG of yeast Saccharomyces cerevisiae were mined to objectively evaluate the above method and attenuate the bias. The SVM model combined with CC transformation yielded the best performance with a high accuracy of 87.94% using gold standard positives and gold standard negatives datasets. The source code of MATLAB and the datasets are available on request under smgsmg@mail.ustc.edu.cn.

  15. High Pressure Cryocooling of Protein Crystals: The Enigma of Water

    Science.gov (United States)

    Gruner, Sol M.

    2010-03-01

    A novel high-pressure cryocooling technique for preparation biological samples for x-ray analysis is described. The method, high-pressure cryocooling, involves cooling samples to cryogenic temperatures (e.g., 100 K) in high-pressure Helium gas (up to 200 MPa). It bears both similarities and differences to high-pressure cooling methods that have been used to prepare samples for electron microscopy, and has been especially useful for cryocooling of macromolecular crystals for x-ray diffraction. Examples will be given where the method has been effective in providing high quality crystallographic data for difficult samples, such as cases where ligands needed to be stabilized in binding sites to be visualized, or where very high resolution data were required. The talk concludes with a discussion of data obtained by high-pressure cryocooling that pertains to two of the most important problems in modern science: the enigma of water and how water affects the activity of proteins.

  16. Confidence sets for network structure

    CERN Document Server

    Airoldi, Edoardo M; Wolfe, Patrick J

    2011-01-01

    Latent variable models are frequently used to identify structure in dichotomous network data, in part because they give rise to a Bernoulli product likelihood that is both well understood and consistent with the notion of exchangeable random graphs. In this article we propose conservative confidence sets that hold with respect to these underlying Bernoulli parameters as a function of any given partition of network nodes, enabling us to assess estimates of 'residual' network structure, that is, structure that cannot be explained by known covariates and thus cannot be easily verified by manual inspection. We demonstrate the proposed methodology by analyzing student friendship networks from the National Longitudinal Survey of Adolescent Health that include race, gender, and school year as covariates. We employ a stochastic expectation-maximization algorithm to fit a logistic regression model that includes these explanatory variables as well as a latent stochastic blockmodel component and additional node-specific...

  17. RIASEC Interest and Confidence Cutoff Scores: Implications for Career Counseling

    Science.gov (United States)

    Bonitz, Verena S.; Armstrong, Patrick Ian; Larson, Lisa M.

    2010-01-01

    One strategy commonly used to simplify the joint interpretation of interest and confidence inventories is the use of cutoff scores to classify individuals dichotomously as having high or low levels of confidence and interest, respectively. The present study examined the adequacy of cutoff scores currently recommended for the joint interpretation…

  18. nigerian students' self-confidence in responding to statements of ...

    African Journals Online (AJOL)

    Temechegn

    The goal of the study was to find out the self-confidence and confidence level of senior ... Specifically, chemistry teachers ask students this question when an ... high school students from connecting with scientific principles in the way ... chemical reaction, ability to identify factors that affect equilibrium reactions and ability to.

  19. Highly Branched Pentasaccharide-Bearing Amphiphiles for Membrane Protein Studies

    DEFF Research Database (Denmark)

    Ehsan, Muhammad; Du, Yang; Scull, Nicola J

    2016-01-01

    structural and functional analysis feasible. Although a number of novel agents have been developed to overcome the limitations of conventional detergents, most have traditional head groups such as glucoside or maltoside. In this study, we introduce a class of amphiphiles, the PSA/Es with a novel highly...... branched pentasaccharide hydrophilic group. The PSA/Es conferred markedly increased stability to a diverse range of membrane proteins compared to conventional detergents, indicating a positive role for the new hydrophilic group in maintaining the native protein integrity. In addition, PDCs formed by PSA....../Es were smaller and more suitable for electron microscopic analysis than those formed by DDM, indicating that the new agents have significant potential for the structure-function studies of membrane proteins....

  20. Rheological properties of highly concentrated protein-stabilized emulsions.

    Science.gov (United States)

    Dimitrova, Tatiana D; Leal-Calderon, Fernando

    2004-05-20

    We prepared concentrated quasi monodisperse hexadecane-in-water emulsions stabilized by various proteins and investigated their rheological properties. Some protein-stabilized emulsions possess remarkably high elasticity and at the same time they are considerably fragile--they exhibit coalescence at yield strain and practically do not flow. The elastic storage modulus G' and the loss modulus G" of the emulsions were determined for different oil volume fractions above the random close packing. Surprisingly, the dimensionless elastic moduli G'/(sigma/a), sigma being the interfacial tension, and a being the mean drop radius, obtained for emulsions stabilized by different proteins do not collapse on a single master curve. They are almost always substantially higher than the corresponding values obtained for equivalent Sodium Dodecyl Sulfate (SDS)-stabilized emulsions. The unusually high elasticity cannot be attributed to a specificity of the continuous phase, because the osmotic equation of state of our emulsions is found identical to the one obtained for samples stabilized by classical surfactants. In parallel, we mimicked the thin films that separate the droplets in the concentrated emulsion and found that the protein adsorption layers contain a substantial number of sticky surface aggregates. These severely obstruct local rearrangements of individual drops in respect to their neighbors which leads to coalescence at yield strain. Furthermore, we found that G'/(sigma/a) is correlated (for a given oil volume fraction) to the dilatational elastic modulus, of the protein layer adsorbed on the droplets. The intrinsic elasticity of the protein layers, together with the blocked local rearrangements are considered as the main factors determining the unusual bulk elasticity of the studied emulsions.

  1. Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein

    Science.gov (United States)

    Vestergaard, Mike; Chan, Siu Hung Joshua; Jensen, Peter Ruhdal

    2016-11-01

    An increasing population and their increased demand for high-protein diets will require dramatic changes in the food industry, as limited resources and environmental issues will make animal derived foods and proteins, gradually more unsustainable to produce. To explore alternatives to animal derived proteins, an economic model was built around the genome-scale metabolic network of E. coli to study the feasibility of recombinant protein production as a food source. Using a novel model, we predicted which microbial production strategies are optimal for economic return, by capturing the tradeoff between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used to explore the feasibility of recombinant Bovine Alpha Lactalbumin production coupled with market prices of utilized materials. We found that recombinant protein production could be a feasible food source and an alternative to traditional sources.

  2. High dietary protein decreases fat deposition induced by high-fat and high-sucrose diet in rats.

    Science.gov (United States)

    Chaumontet, Catherine; Even, Patrick C; Schwarz, Jessica; Simonin-Foucault, Angélique; Piedcoq, Julien; Fromentin, Gilles; Azzout-Marniche, Dalila; Tomé, Daniel

    2015-10-28

    High-protein diets are known to reduce adiposity in the context of high carbohydrate and Western diets. However, few studies have investigated the specific high-protein effect on lipogenesis induced by a high-sucrose (HS) diet or fat deposition induced by high-fat feeding. We aimed to determine the effects of high protein intake on the development of fat deposition and partitioning in response to high-fat and/or HS feeding. A total of thirty adult male Wistar rats were assigned to one of the six dietary regimens with low and high protein, sucrose and fat contents for 5 weeks. Body weight (BW) and food intake were measured weekly. Oral glucose tolerance tests and meal tolerance tests were performed after 4th and 5th weeks of the regimen, respectively. At the end of the study, the rats were killed 2 h after ingestion of a calibrated meal. Blood, tissues and organs were collected for analysis of circulating metabolites and hormones, body composition and mRNA expression in the liver and adipose tissues. No changes were observed in cumulative energy intake and BW gain after 5 weeks of dietary treatment. However, high-protein diets reduced by 20 % the adiposity gain induced by HS and high-sucrose high-fat (HS-HF) diets. Gene expression and transcriptomic analysis suggested that high protein intake reduced liver capacity for lipogenesis by reducing mRNA expressions of fatty acid synthase (fasn), acetyl-CoA carboxylase a and b (Acaca and Acacb) and sterol regulatory element binding transcription factor 1c (Srebf-1c). Moreover, ketogenesis, as indicated by plasma β-hydroxybutyrate levels, was higher in HS-HF-fed mice that were also fed high protein levels. Taken together, these results suggest that high-protein diets may reduce adiposity by inhibiting lipogenesis and stimulating ketogenesis in the liver.

  3. Habituation to low or high protein intake does not modulate basal or postprandial muscle protein synthesis rates: a randomized trial

    NARCIS (Netherlands)

    Gorissen, S.H.; Horstman, Astrid; Franssen, Rinske; Kouw, I.W.; Wall, B.T.; Burd, N.A.; Groot, de C.P.G.M.; Loon, van L.J.C.

    2017-01-01

    Background: Muscle mass maintenance is largely regulated by basal muscle protein synthesis rates and the ability to increase muscle protein synthesis after protein ingestion. To our knowledge, no previous studies have evaluated the impact of habituation to either low protein intake (LOW PRO) or high

  4. Sterile Filtration of Highly Concentrated Protein Formulations: Impact of Protein Concentration, Formulation Composition, and Filter Material.

    Science.gov (United States)

    Allmendinger, Andrea; Mueller, Robert; Huwyler, Joerg; Mahler, Hanns-Christian; Fischer, Stefan

    2015-10-01

    Differences in filtration behavior of concentrated protein formulations were observed during aseptic drug product manufacturing of biologics dependent on formulation composition. The present study investigates filtration forces of monoclonal antibody formulations in a small-scale set-up using polyvinylidene difluoride (PVDF) or polyethersulfone (PES) filters. Different factors like formulation composition and protein concentration related to differences in viscosity, as well as different filtration rates were evaluated. The present study showed that filtration behavior was influenced by the presence or absence of a surfactant in the formulation, which defines the interaction between filter membrane and surface active formulation components. This can lead to a change in filter resistance (PES filter) independent on the buffer system used. Filtration behavior was additionally defined by rheological non-Newtonian flow behavior. The data showed that high shear rates resulting from small pore sizes and filtration pressure up to 1.0 bar led to shear-thinning behavior for highly concentrated protein formulations. Differences in non-Newtonian behavior were attributed to ionic strength related to differences in repulsive and attractive interactions. The present study showed that the interplay of formulation composition, filter material, and filtration rate can explain differences in filtration behavior/filtration flux observed for highly concentrated protein formulations thus guiding filter selection.

  5. High Mobility Group Box Protein-1 in Wound Repair

    Directory of Open Access Journals (Sweden)

    Mauro Patrone

    2012-09-01

    Full Text Available High-mobility group box 1 protein (HMGB1, a member of highly conserved non-histone DNA binding protein family, has been studied as transcription factor and growth factor. Secreted extracellularly by activated monocytes and macrophages or passively released by necrotic or damaged cells, extracellular HMGB1 is a potent mediator of inflammation. Extracellular HMGB1 has apparently contrasting biological actions: it sustains inflammation (with the possible establishment of autoimmunity or of self-maintaining tissue damage, but it also activates and recruits stem cells, boosting tissue repair. Here, we focus on the role of HMGB1 in physiological and pathological responses, the mechanisms by which it contributes to tissue repair and therapeutic strategies base on targeting HMGB1.

  6. Reverse Phase Protein Arrays for High-throughput Toxicity Screening

    DEFF Research Database (Denmark)

    Pedersen, Marlene Lemvig; Block, Ines; List, Markus

    High-throughput screening is extensively applied for identification of drug targets and drug discovery and recently it found entry into toxicity testing. Reverse phase protein arrays (RPPAs) are used widespread for quantification of protein markers. We reasoned that RPPAs also can be utilized...... beneficially in automated high-throughput toxicity testing. An advantage of using RPPAs is that, in addition to the baseline toxicity readout, they allow testing of multiple markers of toxicity, such as inflammatory responses, which do not necessarily cumulate in cell death. We used transfection of si...... a robotic screening platform. Furthermore, we automated sample tracking and data analysis by developing a bundled bioinformatics tool named “MIRACLE”. Automation and RPPA-based viability/toxicity readouts enable rapid testing of large sample numbers, while granting the possibility for flexible consecutive...

  7. Properties of frequentist confidence levels derivatives

    CERN Document Server

    Martínez, Miriam Lucio; Dettori, Francesco

    2016-01-01

    In high energy physics, results from searches for new particles or rare processes are often reported using a modified frequentist approach, known as $\\rm{CL_s}$ method. In this paper, we study the properties of the derivatives of $\\rm{CL_s}$ and $\\rm{CL_{s+b}}$ as signal strength estimators if the confidence levels are interpreted as credible intervals. Our approach allows obtaining best fit points and $\\chi^2$ functions which can be used for phenomenology studies. In addition, this approach can be used to incorporate $\\rm{CL_s}$ results into Bayesian combinations.

  8. High-throughput protein analysis integrating bioinformatics and experimental assays.

    Science.gov (United States)

    del Val, Coral; Mehrle, Alexander; Falkenhahn, Mechthild; Seiler, Markus; Glatting, Karl-Heinz; Poustka, Annemarie; Suhai, Sandor; Wiemann, Stefan

    2004-01-01

    The wealth of transcript information that has been made publicly available in recent years requires the development of high-throughput functional genomics and proteomics approaches for its analysis. Such approaches need suitable data integration procedures and a high level of automation in order to gain maximum benefit from the results generated. We have designed an automatic pipeline to analyse annotated open reading frames (ORFs) stemming from full-length cDNAs produced mainly by the German cDNA Consortium. The ORFs are cloned into expression vectors for use in large-scale assays such as the determination of subcellular protein localization or kinase reaction specificity. Additionally, all identified ORFs undergo exhaustive bioinformatic analysis such as similarity searches, protein domain architecture determination and prediction of physicochemical characteristics and secondary structure, using a wide variety of bioinformatic methods in combination with the most up-to-date public databases (e.g. PRINTS, BLOCKS, INTERPRO, PROSITE SWISSPROT). Data from experimental results and from the bioinformatic analysis are integrated and stored in a relational database (MS SQL-Server), which makes it possible for researchers to find answers to biological questions easily, thereby speeding up the selection of targets for further analysis. The designed pipeline constitutes a new automatic approach to obtaining and administrating relevant biological data from high-throughput investigations of cDNAs in order to systematically identify and characterize novel genes, as well as to comprehensively describe the function of the encoded proteins.

  9. Robust misinterpretation of confidence intervals.

    Science.gov (United States)

    Hoekstra, Rink; Morey, Richard D; Rouder, Jeffrey N; Wagenmakers, Eric-Jan

    2014-10-01

    Null hypothesis significance testing (NHST) is undoubtedly the most common inferential technique used to justify claims in the social sciences. However, even staunch defenders of NHST agree that its outcomes are often misinterpreted. Confidence intervals (CIs) have frequently been proposed as a more useful alternative to NHST, and their use is strongly encouraged in the APA Manual. Nevertheless, little is known about how researchers interpret CIs. In this study, 120 researchers and 442 students-all in the field of psychology-were asked to assess the truth value of six particular statements involving different interpretations of a CI. Although all six statements were false, both researchers and students endorsed, on average, more than three statements, indicating a gross misunderstanding of CIs. Self-declared experience with statistics was not related to researchers' performance, and, even more surprisingly, researchers hardly outperformed the students, even though the students had not received any education on statistical inference whatsoever. Our findings suggest that many researchers do not know the correct interpretation of a CI. The misunderstandings surrounding p-values and CIs are particularly unfortunate because they constitute the main tools by which psychologists draw conclusions from data.

  10. Scalable photonic crystal chips for high sensitivity protein detection.

    Science.gov (United States)

    Liang, Feng; Clarke, Nigel; Patel, Parth; Loncar, Marko; Quan, Qimin

    2013-12-30

    Scalable microfabrication technology has enabled semiconductor and microelectronics industries, among other fields. Meanwhile, rapid and sensitive bio-molecule detection is increasingly important for drug discovery and biomedical diagnostics. In this work, we designed and demonstrated that photonic crystal sensor chips have high sensitivity for protein detection and can be mass-produced with scalable deep-UV lithography. We demonstrated label-free detection of carcinoembryonic antigen from pg/mL to μg/mL, with high quality factor photonic crystal nanobeam cavities.

  11. Anti-Viral Antibody Profiling by High Density Protein Arrays

    Science.gov (United States)

    Bian, Xiaofang; Wiktor, Peter; Kahn, Peter; Brunner, Al; Khela, Amritpal; Karthikeyan, Kailash; Barker, Kristi; Yu, Xiaobo; Magee, Mitch; Wasserfall, Clive H.; Gibson, David; Rooney, Madeleine E; Qiu, Ji; LaBaer, Joshua

    2015-01-01

    Viral infections elicit anti-viral antibodies and have been associated with various chronic diseases. Detection of these antibodies can facilitate diagnosis, treatment of infection and understanding of the mechanisms of virus associated diseases. In this work, we assayed anti-viral antibodies using a novel high density-nucleic acid programmable protein array (HD-NAPPA) platform. Individual viral proteins were expressed in situ directly from plasmids encoding proteins in an array of microscopic reaction chambers. Quality of protein display and serum response was assured by comparing intra- and inter- array correlation within or between printing batches with average correlation coefficients of 0.91 and 0.96, respectively. HD-NAPPA showed higher signal to background (S/B) ratio compared with standard NAPPA on planar glass slides and ELISA. Antibody responses to 761 antigens from 25 different viruses were profiled among patients with juvenile idiopathic arthritis (JIA) and type 1 diabetes (T1D). Common as well as unique antibody reactivity patterns were detected between patients and healthy controls. We believe HD-viral-NAPPA will enable the study of host-pathogen interactions at unprecedented dimensions and elucidate the role of pathogen infections in disease development. PMID:25758251

  12. Highly Flexible Protein-Peptide Docking Using CABS-Dock.

    Science.gov (United States)

    Ciemny, Maciej Paweł; Kurcinski, Mateusz; Kozak, Konrad Jakub; Kolinski, Andrzej; Kmiecik, Sebastian

    2017-01-01

    Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the capabilities and features of the CABS-dock server for flexible protein-peptide docking. CABS-dock allows highly efficient modeling of full peptide flexibility and significant flexibility of a protein receptor. During CABS-dock docking, the peptide folding and binding process is explicitly simulated and no information about the peptide binding site or its structure is used. This chapter presents a successful CABS-dock use for docking a potentially therapeutic peptide to a protein target. Moreover, simulation contact maps, a new CABS-dock feature, are described and applied to the docking test case. Finally, a tutorial for running CABS-dock from the command line or command line scripts is provided. The CABS-dock web server is available from http://biocomp.chem.uw.edu.pl/CABSdock/ .

  13. Metabolic responses to high protein diet in Korean elite bodybuilders with high-intensity resistance exercise

    Directory of Open Access Journals (Sweden)

    Choue Ryowon

    2011-07-01

    Full Text Available Abstract Background High protein diet has been known to cause metabolic acidosis, which is manifested by increased urinary excretion of nitrogen and calcium. Bodybuilders habitually consumed excessive dietary protein over the amounts recommended for them to promote muscle mass accretion. This study investigated the metabolic response to high protein consumption in the elite bodybuilders. Methods Eight elite Korean bodybuilders within the age from 18 to 25, mean age 21.5 ± 2.6. For data collection, anthropometry, blood and urinary analysis, and dietary assessment were conducted. Results They consumed large amounts of protein (4.3 ± 1.2 g/kg BW/day and calories (5,621.7 ± 1,354.7 kcal/day, as well as more than the recommended amounts of vitamins and minerals, including potassium and calcium. Serum creatinine (1.3 ± 0.1 mg/dl and potassium (5.9 ± 0.8 mmol/L, and urinary urea nitrogen (24.7 ± 9.5 mg/dl and creatinine (2.3 ± 0.7 mg/dl were observed to be higher than the normal reference ranges. Urinary calcium (0.3 ± 0.1 mg/dl, and phosphorus (1.3 ± 0.4 mg/dl were on the border of upper limit of the reference range and the urine pH was in normal range. Conclusions Increased urinary excretion of urea nitrogen and creatinine might be due to the high rates of protein metabolism that follow high protein intake and muscle turnover. The obvious evidence of metabolic acidosis in response to high protein diet in the subjects with high potassium intake and intensive resistance exercise were not shown in this study results. However, this study implied that resistance exercise with adequate mineral supplementation, such as potassium and calcium, could reduce or offset the negative effects of protein-generated metabolic changes. This study provides preliminary information of metabolic response to high protein intake in bodybuilders who engaged in high-intensity resistance exercise. Further studies will be needed to determine the effects of the intensity

  14. Highly Charged Protein Ions: The Strongest Organic Acids to Date.

    Science.gov (United States)

    Zenaidee, Muhammad A; Leeming, Michael G; Zhang, Fangtong; Funston, Toby T; Donald, William A

    2017-07-10

    The basicity of highly protonated cytochrome c (cyt c) and myoglobin (myo) ions were investigated using tandem mass spectrometry, ion-molecule reactions (IMRs), and theoretical calculations as a function of charge state. Surprisingly, highly charged protein ions (HCPI) can readily protonate non-polar molecules and inert gases, including Ar, O2 , and N2 in thermal IMRs. The most HCPIs that can be observed are over 130 kJ mol(-1) less basic than the least basic neutral organic molecules known (tetrafluoromethane and methane). Based on theoretical calculations, it is predicted that protonated cyt c and myo ions should spontaneously lose a proton to vacuum for charge states in which every third residue is protonated. In this study, HCPIs are formed where every fourth residue on average is protonated. These results indicate that protein ions in higher charge states can be formed using a low-pressure ion source to reduce proton-transfer reactions between protein ions and gases from the atmosphere. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Confidence rating of marine eutrophication assessments

    DEFF Research Database (Denmark)

    Murray, Ciarán; Andersen, Jesper Harbo; Kaartokallio, Hermanni

    2011-01-01

    This report presents the development of a methodology for assessing confidence in eutrophication status classifications. The method can be considered as a secondary assessment, supporting the primary assessment of eutrophication status. The confidence assessment is based on a transparent scoring...

  16. A Mathematical Framework for Statistical Decision Confidence.

    Science.gov (United States)

    Hangya, Balázs; Sanders, Joshua I; Kepecs, Adam

    2016-09-01

    Decision confidence is a forecast about the probability that a decision will be correct. From a statistical perspective, decision confidence can be defined as the Bayesian posterior probability that the chosen option is correct based on the evidence contributing to it. Here, we used this formal definition as a starting point to develop a normative statistical framework for decision confidence. Our goal was to make general predictions that do not depend on the structure of the noise or a specific algorithm for estimating confidence. We analytically proved several interrelations between statistical decision confidence and observable decision measures, such as evidence discriminability, choice, and accuracy. These interrelationships specify necessary signatures of decision confidence in terms of externally quantifiable variables that can be empirically tested. Our results lay the foundations for a mathematically rigorous treatment of decision confidence that can lead to a common framework for understanding confidence across different research domains, from human and animal behavior to neural representations.

  17. Comparison of high protein and high fiber weight-loss diets in women with risk factors for the metabolic syndrome: a randomized trial

    Directory of Open Access Journals (Sweden)

    Williams Sheila M

    2011-04-01

    Full Text Available Abstract Background Studies have suggested that moderately high protein diets may be more appropriate than conventional low-fat high carbohydrate diets for individuals at risk of developing the metabolic syndrome and type 2 diabetes. However in most such studies sources of dietary carbohydrate may not have been appropriate and protein intakes may have been excessively high. Thus, in a proof-of-concept study we compared two relatively low-fat weight loss diets - one high in protein and the other high in fiber-rich, minimally processed cereals and legumes - to determine whether a relatively high protein diet has the potential to confer greater benefits. Methods Eighty-three overweight or obese women, 18-65 years, were randomized to either a moderately high protein (30% protein, 40% carbohydrate diet (HP or to a high fiber, relatively high carbohydrate (50% carbohydrate, > 35 g total dietary fiber, 20% protein diet (HFib for 8 weeks. Energy intakes were reduced by 2000 - 4000 kJ per day in order to achieve weight loss of between 0.5 and 1 kg per week. Results Participants on both diets lost weight (HP: -4.5 kg [95% confidence interval (CI:-3.7, -5.4 kg] and HFib: -3.3 kg [95% CI: -4.2, -2.4 kg], and reduced total body fat (HP: -4.0 kg [5% CI:-4.6, -3.4 kg] and HFib: -2.5 kg [95% CI: -3.5, -1.6 kg], and waist circumference (HP: -5.4 cm [95% CI: -6.3, -4.5 cm] and HFib: -4.7 cm [95% CI: -5.8, -3.6 cm], as well as total and LDL cholesterol, triglycerides, fasting plasma glucose and blood pressure. However participants on HP lost more body weight (-1.3 kg [95% CI: -2.5, -0.1 kg; p = 0.039] and total body fat (-1.3 kg [95% CI: -2.4, -0.1; p = 0.029]. Diastolic blood pressure decreased more on HP (-3.7 mm Hg [95% CI: -6.2, -1.1; p = 0.005]. Conclusions A realistic high protein weight-reducing diet was associated with greater fat loss and lower blood pressure when compared with a high carbohydrate, high fiber diet in high risk overweight and obese women.

  18. High Throughput Screening for Drugs that Modulate Intermediate Filament Proteins

    Science.gov (United States)

    Sun, Jingyuan; Groppi, Vincent E.; Gui, Honglian; Chen, Lu; Xie, Qing; Liu, Li

    2016-01-01

    Intermediate filament (IF) proteins have unique and complex cell and tissue distribution. Importantly, IF gene mutations cause or predispose to more than 80 human tissue-specific diseases (IF-pathies), with the most severe disease phenotypes being due to mutations at conserved residues that result in a disrupted IF network. A critical need for the entire IF-pathy field is the identification of drugs that can ameliorate or cure these diseases, particularly since all current therapies target the IF-pathy complication, such as diabetes or cardiovascular disease, rather than the mutant IF protein or gene. We describe a high throughput approach to identify drugs that can normalize disrupted IF proteins. This approach utilizes transduction of lentivirus that expresses green-fluorescent-protein-tagged keratin 18 (K18) R90C in A549 cells. The readout is drug ‘hits’ that convert the dot-like keratin filament distribution, due to the R90C mutation, to a wildtype-like filamentous array. A similar strategy can be used to screen thousands of compounds and can be utilized for practically any IF protein with a filament-disrupting mutation, and could therefore potentially target many IF-pathies. ‘Hits’ of interest require validation in cell culture then using in vivo experimental models. Approaches to study the mechanism of mutant-IF normalization by potential drugs of interest are also described. The ultimate goal of this drug screening approach is to identify effective and safe compounds that can potentially be tested for clinical efficacy in patients. PMID:26795471

  19. Fluorescent biosensors for high throughput screening of protein kinase inhibitors.

    Science.gov (United States)

    Prével, Camille; Pellerano, Morgan; Van, Thi Nhu Ngoc; Morris, May C

    2014-02-01

    High throughput screening assays aim to identify small molecules that interfere with protein function, activity, or conformation, which can serve as effective tools for chemical biology studies of targets involved in physiological processes or pathways of interest or disease models, as well as templates for development of therapeutics in medicinal chemistry. Fluorescent biosensors constitute attractive and powerful tools for drug discovery programs, from high throughput screening assays, to postscreen characterization of hits, optimization of lead compounds, and preclinical evaluation of candidate drugs. They provide a means of screening for inhibitors that selectively target enzymatic activity, conformation, and/or function in vitro. Moreover, fluorescent biosensors constitute useful tools for cell- and image-based, multiplex and multiparametric, high-content screening. Application of fluorescence-based sensors to screen large and complex libraries of compounds in vitro, in cell-based formats or whole organisms requires several levels of optimization to establish robust and reproducible assays. In this review, we describe the different fluorescent biosensor technologies which have been applied to high throughput screens, and discuss the prerequisite criteria underlying their successful application. Special emphasis is placed on protein kinase biosensors, since these enzymes constitute one of the most important classes of therapeutic targets in drug discovery.

  20. ROCS: a Reproducibility Index and Confidence Score for Interaction Proteomics Studies

    Directory of Open Access Journals (Sweden)

    Dazard Jean-Eudes

    2012-06-01

    Full Text Available Abstract Background Affinity-Purification Mass-Spectrometry (AP-MS provides a powerful means of identifying protein complexes and interactions. Several important challenges exist in interpreting the results of AP-MS experiments. First, the reproducibility of AP-MS experimental replicates can be low, due both to technical variability and the dynamic nature of protein interactions in the cell. Second, the identification of true protein-protein interactions in AP-MS experiments is subject to inaccuracy due to high false negative and false positive rates. Several experimental approaches can be used to mitigate these drawbacks, including the use of replicated and control experiments and relative quantification to sensitively distinguish true interacting proteins from false ones. Methods To address the issues of reproducibility and accuracy of protein-protein interactions, we introduce a two-step method, called ROCS, which makes use of Indicator Prey Proteins to select reproducible AP-MS experiments, and of Confidence Scores to select specific protein-protein interactions. The Indicator Prey Proteins account for measures of protein identifiability as well as protein reproducibility, effectively allowing removal of outlier experiments that contribute noise and affect downstream inferences. The filtered set of experiments is then used in the Protein-Protein Interaction (PPI scoring step. Prey protein scoring is done by computing a Confidence Score, which accounts for the probability of occurrence of prey proteins in the bait experiments relative to the control experiment, where the significance cutoff parameter is estimated by simultaneously controlling false positives and false negatives against metrics of false discovery rate and biological coherence respectively. In summary, the ROCS method relies on automatic objective criterions for parameter estimation and error-controlled procedures. Results We illustrate the performance of our method by applying

  1. Status and Confidence, in the Lab

    OpenAIRE

    Jeffrey V. Butler

    2009-01-01

    It is widely recognized that confidence can have important economic consequences. While most of the focus has been on overconfidence, systematic variation in confidence can imply systematic variation in economic outcomes. Intriguingly, sociological and social psychological research suggests that being on the wrong side of inequality undermines confidence. This paper examines the link between inequality and confidence in a controlled, incentive-compatible laboratory setting. Inequality was int...

  2. Contrasting Diversity Values: Statistical Inferences Based on Overlapping Confidence Intervals

    Science.gov (United States)

    MacGregor-Fors, Ian; Payton, Mark E.

    2013-01-01

    Ecologists often contrast diversity (species richness and abundances) using tests for comparing means or indices. However, many popular software applications do not support performing standard inferential statistics for estimates of species richness and/or density. In this study we simulated the behavior of asymmetric log-normal confidence intervals and determined an interval level that mimics statistical tests with P(α) = 0.05 when confidence intervals from two distributions do not overlap. Our results show that 84% confidence intervals robustly mimic 0.05 statistical tests for asymmetric confidence intervals, as has been demonstrated for symmetric ones in the past. Finally, we provide detailed user-guides for calculating 84% confidence intervals in two of the most robust and highly-used freeware related to diversity measurements for wildlife (i.e., EstimateS, Distance). PMID:23437239

  3. Plasma Levels of Fatty Acid-Binding Protein 4, Retinol-Binding Protein 4, High-Molecular-Weight Adiponectin, and Cardiovascular Mortality Among Men With Type 2 Diabetes: A 22-Year Prospective Study.

    Science.gov (United States)

    Liu, Gang; Ding, Ming; Chiuve, Stephanie E; Rimm, Eric B; Franks, Paul W; Meigs, James B; Hu, Frank B; Sun, Qi

    2016-11-01

    To examine select adipokines, including fatty acid-binding protein 4, retinol-binding protein 4, and high-molecular-weight (HMW) adiponectin in relation to cardiovascular disease (CVD) mortality among patients with type 2 diabetes mellitus. Plasma levels of fatty acid-binding protein 4, retinol-binding protein 4, and HMW adiponectin were measured in 950 men with type 2 diabetes mellitus in the Health Professionals Follow-up Study. After an average of 22 years of follow-up (1993-2015), 580 deaths occurred, of whom 220 died of CVD. After multivariate adjustment for covariates, higher levels of fatty acid-binding protein 4 were significantly associated with a higher CVD mortality: comparing extreme tertiles, the hazard ratio and 95% confidence interval of CVD mortality was 1.78 (1.22-2.59; P trend=0.001). A positive association was also observed for HMW adiponectin: the hazard ratio (95% confidence interval) was 2.07 (1.42-3.06; P trend=0.0002), comparing extreme tertiles, whereas higher retinol-binding protein 4 levels were nonsignificantly associated with a decreased CVD mortality with an hazard ratio (95% confidence interval) of 0.73 (0.50-1.07; P trend=0.09). A Mendelian randomization analysis suggested that the causal relationships of HMW adiponectin and retinol-binding protein 4 would be directionally opposite to those observed based on the biomarkers, although none of the Mendelian randomization associations achieved statistical significance. These data suggest that higher levels of fatty acid-binding protein 4 and HMW adiponectin are associated with elevated CVD mortality among men with type 2 diabetes mellitus. Biological mechanisms underlying these observations deserve elucidation, but the associations of HMW adiponectin may partially reflect altered adipose tissue functionality among patients with type 2 diabetes mellitus. © 2016 American Heart Association, Inc.

  4. A Confidence Paradigm for Classification Systems

    Science.gov (United States)

    2008-09-01

    M.U. Thomas Date Dean, Graduate School of Engineering and Management Table of Contents Page List of Figures...Plato, Aristotle, Plotinus, St Augustine, St Aquinas , Machi- avelli, Descartes, Hobbes, Locke, Rousseau, Kant, Marx, Mill, Confucius) discuss having...independence, and aggregation of confidence is a linear summation of individual confidence values. Thomas and Allcock [61] develop a statistical confidence

  5. Engine Test Confidence Evaluation System

    Science.gov (United States)

    2007-09-13

    Tech nolog y Ele ment s Demonstrator: Silicon Nitride Blade Example Date of Rating: Now Feb 07 High Turbine Compressor Combustor Low Turbine Fan...TFI*STE 6 5.8*6*6*6*9*9 6 6.8 Demonstrator: Silicon Nitride Blade Example Date of Rating: Now Feb 07 High Turbine Compressor Combustor Low Turbine Fan

  6. High-Sensitivity C-Reactive Protein as a Predictor of Cardiovascular Events after ST-Elevation Myocardial Infarction

    Science.gov (United States)

    Ribeiro, Daniel Rios Pinto; Ramos, Adriane Monserrat; Vieira, Pedro Lima; Menti, Eduardo; Bordin, Odemir Luiz; de Souza, Priscilla Azambuja Lopes; de Quadros, Alexandre Schaan; Portal, Vera Lúcia

    2014-01-01

    Background The association between high-sensitivity C-reactive protein and recurrent major adverse cardiovascular events (MACE) in patients with ST-elevation myocardial infarction who undergo primary percutaneous coronary intervention remains controversial. Objective To investigate the potential association between high-sensitivity C-reactive protein and an increased risk of MACE such as death, heart failure, reinfarction, and new revascularization in patients with ST-elevation myocardial infarction treated with primary percutaneous coronary intervention. Methods This prospective cohort study included 300 individuals aged >18 years who were diagnosed with ST-elevation myocardial infarction and underwent primary percutaneous coronary intervention at a tertiary health center. An instrument evaluating clinical variables and the Thrombolysis in Myocardial Infarction (TIMI) and Global Registry of Acute Coronary Events (GRACE) risk scores was used. High-sensitivity C-reactive protein was determined by nephelometry. The patients were followed-up during hospitalization and up to 30 days after infarction for the occurrence of MACE. Student's t, Mann-Whitney, chi-square, and logistic regression tests were used for statistical analyses. P values of ≤0.05 were considered statistically significant. Results The mean age was 59.76 years, and 69.3% of patients were male. No statistically significant association was observed between high-sensitivity C-reactive protein and recurrent MACE (p = 0.11). However, high-sensitivity C-reactive protein was independently associated with 30-day mortality when adjusted for TIMI [odds ratio (OR), 1.27; 95% confidence interval (CI), 1.07-1.51; p = 0.005] and GRACE (OR, 1.26; 95% CI, 1.06-1.49; p = 0.007) risk scores. Conclusion Although high-sensitivity C-reactive protein was not predictive of combined major cardiovascular events within 30 days after ST-elevation myocardial infarction in patients who underwent primary angioplasty and stent

  7. High-Sensitivity C-Reactive Protein as a Predictor of Cardiovascular Events after ST-Elevation Myocardial Infarction

    Energy Technology Data Exchange (ETDEWEB)

    Ribeiro, Daniel Rios Pinto; Ramos, Adriane Monserrat; Vieira, Pedro Lima; Menti, Eduardo; Bordin, Odemir Luiz Jr.; Souza, Priscilla Azambuja Lopes de; Quadros, Alexandre Schaan de; Portal, Vera Lúcia, E-mail: veraportal.pesquisa@gmail.com [Programa de Pós-Graduação em Ciências da Saúde: Cardiologia - Instituto de Cardiologia/Fundação Universitária de Cardiologia, Porto Alegre, RS (Brazil)

    2014-07-15

    The association between high-sensitivity C-reactive protein and recurrent major adverse cardiovascular events (MACE) in patients with ST-elevation myocardial infarction who undergo primary percutaneous coronary intervention remains controversial. To investigate the potential association between high-sensitivity C-reactive protein and an increased risk of MACE such as death, heart failure, reinfarction, and new revascularization in patients with ST-elevation myocardial infarction treated with primary percutaneous coronary intervention. This prospective cohort study included 300 individuals aged >18 years who were diagnosed with ST-elevation myocardial infarction and underwent primary percutaneous coronary intervention at a tertiary health center. An instrument evaluating clinical variables and the Thrombolysis in Myocardial Infarction (TIMI) and Global Registry of Acute Coronary Events (GRACE) risk scores was used. High-sensitivity C-reactive protein was determined by nephelometry. The patients were followed-up during hospitalization and up to 30 days after infarction for the occurrence of MACE. Student's t, Mann-Whitney, chi-square, and logistic regression tests were used for statistical analyses. P values of ≤0.05 were considered statistically significant. The mean age was 59.76 years, and 69.3% of patients were male. No statistically significant association was observed between high-sensitivity C-reactive protein and recurrent MACE (p = 0.11). However, high-sensitivity C-reactive protein was independently associated with 30-day mortality when adjusted for TIMI [odds ratio (OR), 1.27; 95% confidence interval (CI), 1.07-1.51; p = 0.005] and GRACE (OR, 1.26; 95% CI, 1.06-1.49; p = 0.007) risk scores. Although high-sensitivity C-reactive protein was not predictive of combined major cardiovascular events within 30 days after ST-elevation myocardial infarction in patients who underwent primary angioplasty and stent implantation, it was an independent predictor

  8. Towards Measurement of Confidence in Safety Cases

    Science.gov (United States)

    Denney, Ewen; Paim Ganesh J.; Habli, Ibrahim

    2011-01-01

    Arguments in safety cases are predominantly qualitative. This is partly attributed to the lack of sufficient design and operational data necessary to measure the achievement of high-dependability targets, particularly for safety-critical functions implemented in software. The subjective nature of many forms of evidence, such as expert judgment and process maturity, also contributes to the overwhelming dependence on qualitative arguments. However, where data for quantitative measurements is systematically collected, quantitative arguments provide far more benefits over qualitative arguments, in assessing confidence in the safety case. In this paper, we propose a basis for developing and evaluating integrated qualitative and quantitative safety arguments based on the Goal Structuring Notation (GSN) and Bayesian Networks (BN). The approach we propose identifies structures within GSN-based arguments where uncertainties can be quantified. BN are then used to provide a means to reason about confidence in a probabilistic way. We illustrate our approach using a fragment of a safety case for an unmanned aerial system and conclude with some preliminary observations

  9. High CJD infectivity remains after prion protein is destroyed.

    Science.gov (United States)

    Miyazawa, Kohtaro; Emmerling, Kaitlin; Manuelidis, Laura

    2011-12-01

    The hypothesis that host prion protein (PrP) converts into an infectious prion form rests on the observation that infectivity progressively decreases in direct proportion to the decrease of PrP with proteinase K (PK) treatment. PrP that resists limited PK digestion (PrP-res, PrP(sc)) has been assumed to be the infectious form, with speculative types of misfolding encoding the many unique transmissible spongiform encephalopathy (TSE) agent strains. Recently, a PK sensitive form of PrP has been proposed as the prion. Thus we re-evaluated total PrP (sensitive and resistant) and used a cell-based assay for titration of infectious particles. A keratinase (NAP) known to effectively digest PrP was compared to PK. Total PrP in FU-CJD infected brain was reduced to ≤0.3% in a 2 h PK digest, yet there was no reduction in titer. Remaining non-PrP proteins were easily visualized with colloidal gold in this highly infectious homogenate. In contrast to PK, NAP digestion left 0.8% residual PrP after 2 h, yet decreased titer by >2.5 log; few residual protein bands remained. FU-CJD infected cells with 10× the infectivity of brain by both animal and cell culture assays were also evaluated. NAP again significantly reduced cell infectivity (>3.5 log). Extreme PK digestions were needed to reduce cell PrP to report on maximal PrP destruction and titer. It is likely that one or more residual non-PrP proteins may protect agent nucleic acids in infectious particles.

  10. Linguistic Weighted Aggregation under Confidence Levels

    Directory of Open Access Journals (Sweden)

    Chonghui Zhang

    2015-01-01

    Full Text Available We develop some new linguistic aggregation operators based on confidence levels. Firstly, we introduce the confidence linguistic weighted averaging (CLWA operator and the confidence linguistic ordered weighted averaging (CLOWA operator. These two new linguistic aggregation operators are able to consider the confidence level of the aggregated arguments provided by the information providers. We also study some of their properties. Then, based on the generalized means, we introduce the confidence generalized linguistic ordered weighted averaging (CGLOWA operator. The main advantage of the CGLOWA operator is that it includes a wide range of special cases such as the CLOWA operator, the confidence linguistic ordered weighted quadratic averaging (CLOWQA operator, and the confidence linguistic ordered weighted geometric (CLOWG operator. Finally, we develop an application of the new approach in a multicriteria decision-making under linguistic environment and illustrate it with a numerical example.

  11. High content screening for G protein-coupled receptors using cell-based protein translocation assays

    DEFF Research Database (Denmark)

    Grånäs, Charlotta; Lundholt, Betina Kerstin; Heydorn, Arne

    2005-01-01

    G protein-coupled receptors (GPCRs) have been one of the most productive classes of drug targets for several decades, and new technologies for GPCR-based discovery promise to keep this field active for years to come. While molecular screens for GPCR receptor agonist- and antagonist-based drugs...... as valuable discovery tools for several years. The application of high content cell-based screening to GPCR discovery has opened up additional possibilities, such as direct tracking of GPCRs, G proteins and other signaling pathway components using intracellular translocation assays. These assays provide...... the capability to probe GPCR function at the cellular level with better resolution than has previously been possible, and offer practical strategies for more definitive selectivity evaluation and counter-screening in the early stages of drug discovery. The potential of cell-based translocation assays for GPCR...

  12. Homologous high-throughput expression and purification of highly conserved E coli proteins

    Directory of Open Access Journals (Sweden)

    Duchmann Rainer

    2007-06-01

    Full Text Available Abstract Background Genetic factors and a dysregulated immune response towards commensal bacteria contribute to the pathogenesis of Inflammatory Bowel Disease (IBD. Animal models demonstrated that the normal intestinal flora is crucial for the development of intestinal inflammation. However, due to the complexity of the intestinal flora, it has been difficult to design experiments for detection of proinflammatory bacterial antigen(s involved in the pathogenesis of the disease. Several studies indicated a potential association of E. coli with IBD. In addition, T cell clones of IBD patients were shown to cross react towards antigens from different enteric bacterial species and thus likely responded to conserved bacterial antigens. We therefore chose highly conserved E. coli proteins as candidate antigens for abnormal T cell responses in IBD and used high-throughput techniques for cloning, expression and purification under native conditions of a set of 271 conserved E. coli proteins for downstream immunologic studies. Results As a standardized procedure, genes were PCR amplified and cloned into the expression vector pQTEV2 in order to express proteins N-terminally fused to a seven-histidine-tag. Initial small-scale expression and purification under native conditions by metal chelate affinity chromatography indicated that the vast majority of target proteins were purified in high yields. Targets that revealed low yields after purification probably due to weak solubility were shuttled into Gateway (Invitrogen destination vectors in order to enhance solubility by N-terminal fusion of maltose binding protein (MBP, N-utilizing substance A (NusA, or glutathione S-transferase (GST to the target protein. In addition, recombinant proteins were treated with polymyxin B coated magnetic beads in order to remove lipopolysaccharide (LPS. Thus, 73% of the targeted proteins could be expressed and purified in large-scale to give soluble proteins in the range of 500

  13. Interplay between human high mobility group protein 1 and replication protein A on psoralen-cross-linked DNA

    DEFF Research Database (Denmark)

    Reddy, Madhava C; Christensen, Jesper; Vasquez, Karen M

    2005-01-01

    Human high mobility group box (HMGB) 1 and -2 proteins are highly conserved and abundant chromosomal proteins that regulate chromatin structure and DNA metabolism. HMGB proteins bind preferentially to DNA that is bent or underwound and to DNA damaged by agents such as cisplatin, UVC radiation......, and benzo[a]pyrenediol epoxide (BPDE). Binding of HMGB1 to DNA adducts is thought to inhibit nucleotide excision repair (NER), leading to cell death, but the biological roles of these proteins remain obscure. We have used psoralen-modified triplex-forming oligonucleotides (TFOs) to direct a psoralen-DNA...... interstrand cross-link (ICL) to a specific site to determine the effect of HMGB proteins on recognition of these lesions. Our results reveal that human HMGB1 (but not HMGB2) binds with high affinity and specificity to psoralen ICLs, and interacts with the essential NER protein, replication protein A (RPA...

  14. Embracing the World With Confidence

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    President Hu Jintao’s Asian tour thrusts post-Olympic China into global spotlight As Chinese President Hu Jintao embarked on his first overseas trip after the Beijing Olympics, hopes were high that this tour would set the tone for post-Olympic Chinese diplomacy.

  15. Association of serum uric acid with high-sensitivity C-reactive protein in postmenopausal women.

    Science.gov (United States)

    Raeisi, A; Ostovar, A; Vahdat, K; Rezaei, P; Darabi, H; Moshtaghi, D; Nabipour, I

    2017-02-01

    To explore the independent correlation between serum uric acid and low-grade inflammation (measured by high-sensitivity C-reactive protein, hs-CRP) in postmenopausal women. A total of 378 healthy Iranian postmenopausal women were randomly selected in a population-based study. Circulating hs-CRP levels were measured by highly specific enzyme-linked immunosorbent assay method and an enzymatic calorimetric method was used to measure serum levels of uric acid. Pearson correlation coefficient, multiple linear regression and logistic regression models were used to analyze the association between uric acid and hs-CRP levels. A statistically significant correlation was seen between serum levels of uric acid and log-transformed circulating hs-CRP (r = 0.25, p uric acid levels (β = 0.20, p uric acid levels (odds ratio =1.52, 95% confidence interval 1.18-1.96). Higher serum uric acid levels were positively and independently associated with circulating hs-CRP in healthy postmenopausal women.

  16. Comparison of the Folding Mechanism of Highly Homologous Proteins in the Lipid-binding Protein Family

    Science.gov (United States)

    The folding mechanism of two closely related proteins in the intracellular lipid binding protein family, human bile acid binding protein (hBABP) and rat bile acid binding protein (rBABP) were examined. These proteins are 77% identical (93% similar) in sequence Both of these singl...

  17. Comparison of the Folding Mechanism of Highly Homologous Proteins in the Lipid-binding Protein Family

    Science.gov (United States)

    The folding mechanism of two closely related proteins in the intracellular lipid binding protein family, human bile acid binding protein (hBABP) and rat bile acid binding protein (rBABP) were examined. These proteins are 77% identical (93% similar) in sequence Both of these singl...

  18. Confidence-based somatic mutation evaluation and prioritization.

    Directory of Open Access Journals (Sweden)

    Martin Löwer

    Full Text Available Next generation sequencing (NGS has enabled high throughput discovery of somatic mutations. Detection depends on experimental design, lab platforms, parameters and analysis algorithms. However, NGS-based somatic mutation detection is prone to erroneous calls, with reported validation rates near 54% and congruence between algorithms less than 50%. Here, we developed an algorithm to assign a single statistic, a false discovery rate (FDR, to each somatic mutation identified by NGS. This FDR confidence value accurately discriminates true mutations from erroneous calls. Using sequencing data generated from triplicate exome profiling of C57BL/6 mice and B16-F10 melanoma cells, we used the existing algorithms GATK, SAMtools and SomaticSNiPer to identify somatic mutations. For each identified mutation, our algorithm assigned an FDR. We selected 139 mutations for validation, including 50 somatic mutations assigned a low FDR (high confidence and 44 mutations assigned a high FDR (low confidence. All of the high confidence somatic mutations validated (50 of 50, none of the 44 low confidence somatic mutations validated, and 15 of 45 mutations with an intermediate FDR validated. Furthermore, the assignment of a single FDR to individual mutations enables statistical comparisons of lab and computation methodologies, including ROC curves and AUC metrics. Using the HiSeq 2000, single end 50 nt reads from replicates generate the highest confidence somatic mutation call set.

  19. Market entry decisions: effects of absolute and relative confidence.

    Science.gov (United States)

    Bolger, Fergus; Pulford, Briony D; Colman, Andrew M

    2008-01-01

    In a market entry game, the number of entrants usually approaches game-theoretic equilibrium quickly, but in real-world markets business start-ups typically exceed market capacity, resulting in chronically high failure rates and suboptimal industry profits. Excessive entry has been attributed to overconfidence arising when expected payoffs depend partly on skill. In an experimental test of this hypothesis, 96 participants played 24 rounds of a market entry game, with expected payoffs dependent partly on skill on half the rounds, after their confidence was manipulated and measured. The results provide direct support for the hypothesis that high levels of confidence are largely responsible for excessive entry, and they suggest that absolute confidence, independent of interpersonal comparison, rather than confidence about one's abilities relative to others, drives excessive entry decisions when skill is involved.

  20. Food skills confidence and household gatekeepers' dietary practices.

    Science.gov (United States)

    Burton, Melissa; Reid, Mike; Worsley, Anthony; Mavondo, Felix

    2017-01-01

    Household food gatekeepers have the potential to influence the food attitudes and behaviours of family members, as they are mainly responsible for food-related tasks in the home. The aim of this study was to determine the role of gatekeepers' confidence in food-related skills and nutrition knowledge on food practices in the home. An online survey was completed by 1059 Australian dietary gatekeepers selected from the Global Market Insite (GMI) research database. Participants responded to questions about food acquisition and preparation behaviours, the home eating environment, perceptions and attitudes towards food, and demographics. Two-step cluster analysis was used to identify groups based on confidence regarding food skills and nutrition knowledge. Chi-square tests and one-way ANOVAs were used to compare the groups on the dependent variables. Three groups were identified: low confidence, moderate confidence and high confidence. Gatekeepers in the highest confidence group were significantly more likely to report lower body mass index (BMI), and indicate higher importance of fresh food products, vegetable prominence in meals, product information use, meal planning, perceived behavioural control and overall diet satisfaction. Gatekeepers in the lowest confidence group were significantly more likely to indicate more perceived barriers to healthy eating, report more time constraints and more impulse purchasing practices, and higher convenience ingredient use. Other smaller associations were also found. Household food gatekeepers with high food skills confidence were more likely to engage in several healthy food practices, while those with low food skills confidence were more likely to engage in unhealthy food practices. Food education strategies aimed at building food-skills and nutrition knowledge will enable current and future gatekeepers to make healthier food decisions for themselves and for their families. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Protein denaturation of whey protein isolates (WPIs) induced by high intensity ultrasound during heat gelation.

    Science.gov (United States)

    Frydenberg, Rikke P; Hammershøj, Marianne; Andersen, Ulf; Greve, Marie T; Wiking, Lars

    2016-02-01

    In this study, the impact of high intensity ultrasound (HIU) on proteins in whey protein isolates was examined. Effects on thermal behavior, secondary structure and nature of intra- and intermolecular bonds during heat-induced gelling were investigated. Ultrasonication (24 kHz, 300 W/cm(2), 2078 J/mL) significantly reduced denaturation enthalpies, whereas no change in secondary structure was detected by circular dichroism. The thiol-blocking agent N-ethylmaleimide was applied in order to inhibit formation of disulfide bonds during gel formation. Results showed that increased contents of α-lactalbumin (α-La) were associated with increased sensitivity to ultrasonication. The α-La:β-lactoglobulin (β-Lg) ratio greatly affected the nature of the interactions formed during gelation, where higher amounts of α-La lead to a gel more dependent on disulfide bonds. These results contribute to clarifying the mechanisms mediating the effects of HIU on whey proteins on the molecular level, thus moving further toward implementing HIU in the processing chain in the food industry. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Drying and hydration of proteins at high concentration

    NARCIS (Netherlands)

    Bouman, J.

    2015-01-01

    Proteins are the building blocks of life and serve a wide range of essential functions in organisms. Many metabolic reactions in organisms are catalysed by enzymes, DNA is replicated by proteins and in cells proteins often facilitate active transport of e.g. glucose or ions. Proteins also serve an e

  3. High-performance cation-exchange chromatofocusing of proteins.

    Science.gov (United States)

    Kang, Xuezhen; Frey, Douglas D

    2003-03-28

    Chromatofocusing using high-performance cation-exchange column packings, as opposed to the more commonly used anion-exchange column packings, is investigated with regard to the performance achieved and the range of applications possible. Linear or convex gradients in the range from pH 2.6 to 9 were formed using a variety of commercially available column packings that provide a buffering capacity in different pH ranges, and either polyampholytes or simple mixtures having a small number (three or fewer) of buffering species as the elution buffer. The resolutions achieved using cation-exchange or anion-exchange chromatofocusing were in general comparable, although for certain pairs of proteins better resolution could be achieved using one type of packing as compared to the other, evidently due to the way electrostatic charges are distributed on the protein surface. Several chromatofocusing methods were investigated that take advantage of the acid-base properties of commercially available cation-exchange column packings. These include the use of gradients with a composite shape, the use of very low pH ranges, and the use of elution buffers containing a single buffering species. The advantages of chromatofocusing over ion-exchange chromatography using a salt gradient at constant pH were illustrated by employing the former method and a cation-exchange column packing to separate beta-lactoglobulins A and B, which is a separation reported to be impossible using the latter method and a cation-exchange column packing. Trends in the apparent isoelectric points determined using cation- and anion-exchange chromatofocusing were interpreted using applicable theories. Results of this study indicate that cation-exchange chromatofocusing is a useful technique which is complementary to anion-exchange chromatofocusing and isoelectric focusing for separating proteins at both the analytical and preparative scales.

  4. Intelligence, Self-confidence and Entrepreneurship

    OpenAIRE

    Asoni, Andrea

    2011-01-01

    I investigate the effect of human capital on entrepreneurship using the National Longitudinal Survey of Youth - 1979. I find that individuals with higher measured intelligence and self-confidence are more likely to be entrepreneurs. Furthermore I present evidence suggesting that intelligence and self-confidence affect business ownership through two different channels: intelligence increases business survival while self-confidence increases business creation. Finally, once we control for intel...

  5. A microfluidic, high throughput protein crystal growth method for microgravity.

    Directory of Open Access Journals (Sweden)

    Carl W Carruthers

    Full Text Available The attenuation of sedimentation and convection in microgravity can sometimes decrease irregularities formed during macromolecular crystal growth. Current terrestrial protein crystal growth (PCG capabilities are very different than those used during the Shuttle era and that are currently on the International Space Station (ISS. The focus of this experiment was to demonstrate the use of a commercial off-the-shelf, high throughput, PCG method in microgravity. Using Protein BioSolutions' microfluidic Plug Maker™/CrystalCard™ system, we tested the ability to grow crystals of the regulator of glucose metabolism and adipogenesis: peroxisome proliferator-activated receptor gamma (apo-hPPAR-γ LBD, as well as several PCG standards. Overall, we sent 25 CrystalCards™ to the ISS, containing ~10,000 individual microgravity PCG experiments in a 3U NanoRacks NanoLab (1U = 10(3 cm.. After 70 days on the ISS, our samples were returned with 16 of 25 (64% microgravity cards having crystals, compared to 12 of 25 (48% of the ground controls. Encouragingly, there were more apo-hPPAR-γ LBD crystals in the microgravity PCG cards than the 1g controls. These positive results hope to introduce the use of the PCG standard of low sample volume and large experimental density to the microgravity environment and provide new opportunities for macromolecular samples that may crystallize poorly in standard laboratories.

  6. Confidence Intervals from One One Observation

    CERN Document Server

    Rodriguez, Carlos C

    2008-01-01

    Robert Machol's surprising result, that from a single observation it is possible to have finite length confidence intervals for the parameters of location-scale models, is re-produced and extended. Two previously unpublished modifications are included. First, Herbert Robbins nonparametric confidence interval is obtained. Second, I introduce a technique for obtaining confidence intervals for the scale parameter of finite length in the logarithmic metric. Keywords: Theory/Foundations , Estimation, Prior Distributions, Non-parametrics & Semi-parametrics Geometry of Inference, Confidence Intervals, Location-Scale models

  7. A model for developing disability confidence.

    Science.gov (United States)

    Lindsay, Sally; Cancelliere, Sara

    2017-05-15

    Many clinicians, educators, and employers lack disability confidence which can affect their interactions with, and inclusion of people with disabilities. Our objective was to explore how disability confidence developed among youth who volunteered with children who have a disability. We conducted 30 in-depth interviews (16 without a disability, 14 with disabilities), with youth aged 15-25. We analyzed our data using an interpretive, qualitative, thematic approach. We identified four main themes that led to the progression of disability confidence including: (1) "disability discomfort," referring to lacking knowledge about disability and experiencing unease around people with disabilities; (2) "reaching beyond comfort zone" where participants increased their understanding of disability and became sensitized to difference; (3) "broadened perspectives" where youth gained exposure to people with disabilities and challenged common misperceptions and stereotypes; and (4) "disability confidence" which includes having knowledge of people with disabilities, inclusive, and positive attitudes towards them. Volunteering is one way that can help to develop disability confidence. Youth with and without disabilities both reported a similar process of developing disability confidence; however, there were nuances between the two groups. Implications for Rehabilitation The development of disability confidence is important for enhancing the social inclusion of people with disabilities. Volunteering with people who have a disability, or a disability different from their own, can help to develop disability confidence which involves positive attitudes, empathy, and appropriate communication skills. Clinicians, educators, and employers should consider promoting working with disabled people through such avenues as volunteering or service learning to gain disability confidence.

  8. Mapping of Chikungunya virus interactions with host proteins identified nsP2 as a highly connected viral component.

    Science.gov (United States)

    Bouraï, Mehdi; Lucas-Hourani, Marianne; Gad, Hans Henrik; Drosten, Christian; Jacob, Yves; Tafforeau, Lionel; Cassonnet, Patricia; Jones, Louis M; Judith, Delphine; Couderc, Thérèse; Lecuit, Marc; André, Patrice; Kümmerer, Beate Mareike; Lotteau, Vincent; Desprès, Philippe; Tangy, Frédéric; Vidalain, Pierre-Olivier

    2012-03-01

    Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that has been responsible for an epidemic outbreak of unprecedented magnitude in recent years. Since then, significant efforts have been made to better understand the biology of this virus, but we still have poor knowledge of CHIKV interactions with host cell components at the molecular level. Here we describe the extensive use of high-throughput yeast two-hybrid (HT-Y2H) assays to characterize interactions between CHIKV and human proteins. A total of 22 high-confidence interactions, which essentially involved the viral nonstructural protein nsP2, were identified and further validated in protein complementation assay (PCA). These results were integrated to a larger network obtained by extensive mining of the literature for reports on alphavirus-host interactions. To investigate the role of cellular proteins interacting with nsP2, gene silencing experiments were performed in cells infected by a recombinant CHIKV expressing Renilla luciferase as a reporter. Collected data showed that heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and ubiquilin 4 (UBQLN4) participate in CHIKV replication in vitro. In addition, we showed that CHIKV nsP2 induces a cellular shutoff, as previously reported for other Old World alphaviruses, and determined that among binding partners identified by yeast two-hybrid methods, the tetratricopeptide repeat protein 7B (TTC7B) plays a significant role in this activity. Altogether, this report provides the first interaction map between CHIKV and human proteins and describes new host cell proteins involved in the replication cycle of this virus.

  9. Ultrananocrystalline Diamond Membranes for Detection of High-Mass Proteins

    Science.gov (United States)

    Kim, H.; Park, J.; Aksamija, Z.; Arbulu, M.; Blick, R. H.

    2016-12-01

    Mechanical resonators realized on the nanoscale by now offer applications in mass sensing of biomolecules with extraordinary sensitivity. The general idea is that perfect mechanical mass sensors should be of extremely small size to achieve zepto- or yoctogram sensitivity in weighing single molecules similar to a classical scale. However, the small effective size and long response time for weighing biomolecules with a cantilever restricts their usefulness as a high-throughput method. Commercial mass spectrometry (MS), on the other hand, such as electrospray ionization and matrix-assisted laser desorption and ionization (MALDI) time of flight (TOF) and their charge-amplifying detectors are the gold standards to which nanomechanical resonators have to live up to. These two methods rely on the ionization and acceleration of biomolecules and the following ion detection after a mass selection step, such as TOF. The principle we describe here for ion detection is based on the conversion of kinetic energy of the biomolecules into thermal excitation of chemical vapor deposition diamond nanomembranes via phonons followed by phonon-mediated detection via field emission of thermally emitted electrons. We fabricate ultrathin diamond membranes with large lateral dimensions for MALDI TOF MS of high-mass proteins. These diamond membranes are realized by straightforward etching methods based on semiconductor processing. With a minimal thickness of 100 nm and cross sections of up to 400 ×400 μ m2 , the membranes offer extreme aspect ratios. Ion detection is demonstrated in MALDI TOF analysis over a broad range from insulin to albumin. The resulting data in detection show much enhanced resolution as compared to existing detectors, which can offer better sensitivity and overall performance in resolving protein masses.

  10. Self-confidence, gender and academic achievement of undergraduate nursing students.

    Science.gov (United States)

    Kukulu, K; Korukcu, O; Ozdemir, Y; Bezci, A; Calik, C

    2013-04-01

    The aim of this study was to determine the self-confidence levels of nursing students and the factors related to such self-confidence. Data were obtained via a questionnaire for socio-demographic characteristics and a 'Self-Confidence Scale' prepared by the researchers. High self-confidence levels were noted in 78.6% of female students and 92.3% of male students. While 84.5% of second-year students had high self-confidence levels, this rate was 76% in fourth-year students. Female nursing students were significantly less self-confident than male students. Self-confidence should be nurtured in a caring nursing curriculum; however, there is a lack of clarity as to what confidence means, how it is perceived by students and what educators can do to instil self-confidence in nursing students.

  11. Measurement of tag confidence in user generated contents retrieval

    Science.gov (United States)

    Lee, Sihyoung; Min, Hyun-Seok; Lee, Young Bok; Ro, Yong Man

    2009-01-01

    As online image sharing services are becoming popular, the importance of correctly annotated tags is being emphasized for precise search and retrieval. Tags created by user along with user-generated contents (UGC) are often ambiguous due to the fact that some tags are highly subjective and visually unrelated to the image. They cause unwanted results to users when image search engines rely on tags. In this paper, we propose a method of measuring tag confidence so that one can differentiate confidence tags from noisy tags. The proposed tag confidence is measured from visual semantics of the image. To verify the usefulness of the proposed method, experiments were performed with UGC database from social network sites. Experimental results showed that the image retrieval performance with confidence tags was increased.

  12. Haematopoietic stem cells require a highly regulated protein synthesis rate.

    Science.gov (United States)

    Signer, Robert A J; Magee, Jeffrey A; Salic, Adrian; Morrison, Sean J

    2014-05-01

    Many aspects of cellular physiology remain unstudied in somatic stem cells, for example, there are almost no data on protein synthesis in any somatic stem cell. Here we set out to compare protein synthesis in haematopoietic stem cells (HSCs) and restricted haematopoietic progenitors. We found that the amount of protein synthesized per hour in HSCs in vivo was lower than in most other haematopoietic cells, even if we controlled for differences in cell cycle status or forced HSCs to undergo self-renewing divisions. Reduced ribosome function in Rpl24(Bst/+) mice further reduced protein synthesis in HSCs and impaired HSC function. Pten deletion increased protein synthesis in HSCs but also reduced HSC function. Rpl24(Bst/+) cell-autonomously rescued the effects of Pten deletion in HSCs; blocking the increase in protein synthesis, restoring HSC function, and delaying leukaemogenesis. Pten deficiency thus depletes HSCs and promotes leukaemia partly by increasing protein synthesis. Either increased or decreased protein synthesis impairs HSC function.

  13. A functional protein retention and release multilayer with high stability

    Science.gov (United States)

    Nie, Kun; An, Qi; Zhang, Yihe

    2016-04-01

    Effective and robust interfacial protein retention lies at the heart of the fabrication of protein-based functional interfaces, which is potentially applicable in catalysis, medical therapy, antifouling, and smart devices, but remains challenging due to the sensitive nature of proteins. This study reports a general protein retention strategy to spatial-temporally confine various types of proteins at interfacial regions. The proteins were preserved in mesoporous silica nanoparticles embedded in covalently woven multilayers. It is worth noting that the protein retention strategy effectively preserves the catalytic capabilities of the proteins, and the multilayer structure is robust enough to withstand the bubbling catalytic reactions and could be repeatedly used due to conservation of proteins. The spatiotemporal retention of proteins could be adjusted by varying the number of capping layers. Furthermore, we demonstrate that the protein-loaded interfacial layers could not only be used to construct catalytic-active interfaces, but also be integrated as the power-generating unit to propel a macroscopic floating device.Effective and robust interfacial protein retention lies at the heart of the fabrication of protein-based functional interfaces, which is potentially applicable in catalysis, medical therapy, antifouling, and smart devices, but remains challenging due to the sensitive nature of proteins. This study reports a general protein retention strategy to spatial-temporally confine various types of proteins at interfacial regions. The proteins were preserved in mesoporous silica nanoparticles embedded in covalently woven multilayers. It is worth noting that the protein retention strategy effectively preserves the catalytic capabilities of the proteins, and the multilayer structure is robust enough to withstand the bubbling catalytic reactions and could be repeatedly used due to conservation of proteins. The spatiotemporal retention of proteins could be adjusted by

  14. High-throughput production of prokaryotic membrane proteins.

    Science.gov (United States)

    Dobrovetsky, Elena; Lu, Ming Liang; Andorn-Broza, Ronit; Khutoreskaya, Galina; Bray, James E; Savchenko, Alexei; Arrowsmith, Cheryl H; Edwards, Aled M; Koth, Christopher M

    2005-01-01

    Membrane proteins constitute ~30% of prokaryotic and eukaryotic genomes but comprise a small fraction of the entries in protein structural databases. A number of features of membrane proteins render them challenging targets for the structural biologist, among which the most important is the difficulty in obtaining sufficient quantities of purified protein. We are exploring procedures to express and purify large numbers of prokaryotic membrane proteins. A set of 280 membrane proteins from Escherichia coli and Thermotoga maritima, a thermophile, was cloned and tested for expression in Escherichia coli. Under a set of standard conditions, expression could be detected in the membrane fraction for approximately 30% of the cloned targets. About 22 of the highest expressing membrane proteins were purified, typically in just two chromatographic steps. There was a clear correlation between the number of predicted transmembrane domains in a given target and its propensity to express and purify. Accordingly, the vast majority of successfully expressed and purified proteins had six or fewer transmembrane domains. We did not observe any clear advantage to the use of thermophilic targets. Two of the purified membrane proteins formed crystals. By comparison with protein production efforts for soluble proteins, where approximately 70% of cloned targets express and approximately 25% can be readily purified for structural studies [Christendat et al. (2000) Nat. Struct. Biol., 7, 903], our results demonstrate that a similar approach will succeed for membrane proteins, albeit with an expected higher attrition rate.

  15. High-Pressure-High-Temperature Processing Reduces Maillard Reaction and Viscosity in Whey Protein-Sugar Solutions.

    Science.gov (United States)

    Avila Ruiz, Geraldine; Xi, Bingyan; Minor, Marcel; Sala, Guido; van Boekel, Martinus; Fogliano, Vincenzo; Stieger, Markus

    2016-09-28

    The aim of the study was to determine the influence of pressure in high-pressure-high-temperature (HPHT) processing on Maillard reactions and protein aggregation of whey protein-sugar solutions. Solutions of whey protein isolate containing either glucose or trehalose at pH 6, 7, and 9 were treated by HPHT processing or conventional high-temperature (HT) treatments. Browning was reduced, and early and advanced Maillard reactions were retarded under HPHT processing at all pH values compared to HT treatment. HPHT induced a larger pH drop than HT treatments, especially at pH 9, which was not associated with Maillard reactions. After HPHT processing at pH 7, protein aggregation and viscosity of whey protein isolate-glucose/trehalose solutions remained unchanged. It was concluded that HPHT processing can potentially improve the quality of protein-sugar-containing foods, for which browning and high viscosities are undesired, such as high-protein beverages.

  16. 75 FR 81037 - Waste Confidence Decision Update

    Science.gov (United States)

    2010-12-23

    ... COMMISSION 10 CFR Part 51 Waste Confidence Decision Update AGENCY: Nuclear Regulatory Commission. ACTION: Update and final revision of Waste Confidence Decision. SUMMARY: The U.S. Nuclear Regulatory Commission... update to the Decision were products of rulemaking proceedings designed to assess the degree of...

  17. Self-Confidence in the Hospitality Industry

    OpenAIRE

    Michael Oshins

    2014-01-01

    Few industries rely on self-confidence to the extent that the hospitality industry does because guests must feel welcome and that they are in capable hands. This article examines the results of hundreds of student interviews with industry professionals at all levels to determine where the majority of the hospitality industry gets their self-confidence.

  18. Self-Confidence in the Hospitality Industry

    Directory of Open Access Journals (Sweden)

    Michael Oshins

    2014-02-01

    Full Text Available Few industries rely on self-confidence to the extent that the hospitality industry does because guests must feel welcome and that they are in capable hands. This article examines the results of hundreds of student interviews with industry professionals at all levels to determine where the majority of the hospitality industry gets their self-confidence.

  19. Nonparametric confidence intervals for monotone functions

    NARCIS (Netherlands)

    Groeneboom, P.; Jongbloed, G.

    2015-01-01

    We study nonparametric isotonic confidence intervals for monotone functions. In [Ann. Statist. 29 (2001) 1699–1731], pointwise confidence intervals, based on likelihood ratio tests using the restricted and unrestricted MLE in the current status model, are introduced. We extend the method to the trea

  20. Building Scientific Confidence in the Development and ...

    Science.gov (United States)

    Building Scientific Confidence in the Development and Evaluation of Read-Across Using Tox21 Approaches Slide presentation at GlobalChem conference and workshop in Washington, DC on Case Study on Building Scientific Confidence in the Development and Evaluation of Read-Across Using Tox21 Approaches

  1. Nonparametric confidence intervals for monotone functions

    NARCIS (Netherlands)

    Groeneboom, P.; Jongbloed, G.

    2015-01-01

    We study nonparametric isotonic confidence intervals for monotone functions. In [Ann. Statist. 29 (2001) 1699–1731], pointwise confidence intervals, based on likelihood ratio tests using the restricted and unrestricted MLE in the current status model, are introduced. We extend the method to the

  2. Examining Response Confidence in Multiple Text Tasks

    Science.gov (United States)

    List, Alexandra; Alexander, Patricia A.

    2015-01-01

    Students' confidence in their responses to a multiple text-processing task and their justifications for those confidence ratings were investigated. Specifically, 215 undergraduates responded to two academic questions, differing by type (i.e., discrete and open-ended) and by domain (i.e., developmental psychology and astrophysics), using a digital…

  3. Confidence and Competence with Mathematical Procedures

    Science.gov (United States)

    Foster, Colin

    2016-01-01

    Confidence assessment (CA), in which students state alongside each of their answers a confidence level expressing how certain they are, has been employed successfully within higher education. However, it has not been widely explored with school pupils. This study examined how school mathematics pupils (N?=?345) in five different secondary schools…

  4. Confidence and Competence with Mathematical Procedures

    Science.gov (United States)

    Foster, Colin

    2016-01-01

    Confidence assessment (CA), in which students state alongside each of their answers a confidence level expressing how certain they are, has been employed successfully within higher education. However, it has not been widely explored with school pupils. This study examined how school mathematics pupils (N?=?345) in five different secondary schools…

  5. Examining Response Confidence in Multiple Text Tasks

    Science.gov (United States)

    List, Alexandra; Alexander, Patricia A.

    2015-01-01

    Students' confidence in their responses to a multiple text-processing task and their justifications for those confidence ratings were investigated. Specifically, 215 undergraduates responded to two academic questions, differing by type (i.e., discrete and open-ended) and by domain (i.e., developmental psychology and astrophysics), using a digital…

  6. Lower confidence limits for structure reliability

    Institute of Scientific and Technical Information of China (English)

    CHEN Jiading; LI Ji

    2006-01-01

    For a class of data often arising in engineering,we have developed an approach to compute the lower confidence limit for structure reliability with a given confidence level.Especially,in a case with no failure and a case with only one failure,the concrete computational methods are presented.

  7. Financial Literacy, Confidence and Financial Advice Seeking

    NARCIS (Netherlands)

    Kramer, Marc M.

    2016-01-01

    We find that people with higher confidence in their own financial literacy are less likely to seek financial advice, but no relation between objective measures of literacy and advice seeking. The negative association between confidence and advice seeking is more pronounced among wealthy households.

  8. Confidence assessment. Site-descriptive modelling SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    2008-12-15

    The objective of this report is to assess the confidence that can be placed in the Laxemar site descriptive model, based on the information available at the conclusion of the surface-based investigations (SDM-Site Laxemar). In this exploration, an overriding question is whether remaining uncertainties are significant for repository engineering design or long-term safety assessment and could successfully be further reduced by more surface-based investigations or more usefully by explorations underground made during construction of the repository. Procedures for this assessment have been progressively refined during the course of the site descriptive modelling, and applied to all previous versions of the Forsmark and Laxemar site descriptive models. They include assessment of whether all relevant data have been considered and understood, identification of the main uncertainties and their causes, possible alternative models and their handling, and consistency between disciplines. The assessment then forms the basis for an overall confidence statement. The confidence in the Laxemar site descriptive model, based on the data available at the conclusion of the surface based site investigations, has been assessed by exploring: - Confidence in the site characterization data base, - remaining issues and their handling, - handling of alternatives, - consistency between disciplines and - main reasons for confidence and lack of confidence in the model. Generally, the site investigation database is of high quality, as assured by the quality procedures applied. It is judged that the Laxemar site descriptive model has an overall high level of confidence. Because of the relatively robust geological model that describes the site, the overall confidence in the Laxemar Site Descriptive model is judged to be high, even though details of the spatial variability remain unknown. The overall reason for this confidence is the wide spatial distribution of the data and the consistency between

  9. pFPL Vectors for High-Throughput Protein Localization in Fungi: Detecting Cytoplasmic Accumulation of Putative Effector Proteins.

    Science.gov (United States)

    Gong, Xiaoyan; Hurtado, Oscar; Wang, Baohua; Wu, Congqing; Yi, Mihwa; Giraldo, Martha; Valent, Barbara; Goodin, Michael; Farman, Mark

    2015-02-01

    As part of a large-scale project whose goal was to identify candidate effector proteins in Magnaporthe oryzae, we developed a suite of vectors that facilitate high-throughput protein localization experiments in fungi. These vectors utilize Gateway recombinational cloning to place a gene's promoter and coding sequences upstream and in frame with enhanced cyan fluorescent protein, green fluorescent protein (GFP), monomeric red fluorescence protein (mRFP), and yellow fluorescent protein or a nucleus-targeted mCHERRY variant. The respective Gateway cassettes were incorporated into Agrobacterium-based plasmids to allow efficient fungal transformation using hygromycin or geneticin resistance selection. mRFP proved to be more sensitive than the GFP spectral variants for monitoring proteins secreted in planta; and extensive testing showed that Gateway-derived fusion proteins produced localization patterns identical to their "directly fused" counterparts. Use of plasmid for fungal protein localization (pFPL) vectors with two different selectable markers provided a convenient way to label fungal cells with different fluorescent proteins. We demonstrate the utility of the pFPL vectors for identifying candidate effector proteins and we highlight a number of important factors that must be taken into consideration when screening for proteins that are translocated across the host plasma membrane.

  10. Self-confidence and metacognitive processes

    Directory of Open Access Journals (Sweden)

    Kleitman Sabina

    2005-01-01

    Full Text Available This paper examines the status of Self-confidence trait. Two studies strongly suggest that Self-confidence is a component of metacognition. In the first study, participants (N=132 were administered measures of Self-concept, a newly devised Memory and Reasoning Competence Inventory (MARCI, and a Verbal Reasoning Test (VRT. The results indicate a significant relationship between confidence ratings on the VRT and the Reasoning component of MARCI. The second study (N=296 employed an extensive battery of cognitive tests and several metacognitive measures. Results indicate the presence of robust Self-confidence and Metacognitive Awareness factors, and a significant correlation between them. Self-confidence taps not only processes linked to performance on items that have correct answers, but also beliefs about events that may never occur.

  11. Approaches in breeding for high quality protein maize

    Directory of Open Access Journals (Sweden)

    Denić Miloje

    2008-01-01

    Full Text Available Maize is the principal crop and major staple food in the most African and South American countries. The main problem in human nutrition in developing countries, and in livestock feed in developed countries, is insufficient production and poor quality of cereal proteins. In the case of maize, due to the very low content of essential amino acids lysine and tryptophan in grain endosperm, biological value is very low, which is main limiting factor of common maize in human nutrition and feeding of monogastric animals. Quality protein maize (QPM can help in solving of this problem. Maize production also faces serious constraints caused by agro-ecological conditions and poor socio-economic situation. To alleviate the effect of the constraints, selected genotypes with more desirable traits and appropriate field-plot techniques to create multiple-stress conditions, were used. It was found that, in downy mildew nursery distance up to 35 m from spreader plot is providing sufficient down load of spores for plant infection, provided that the testing breeding materials are planted towards to down-stream direction of the dominant wind. Using these breeding approaches large number of early, white and flint synthetics, composites and inbred lines were created with resistance or tolerance to downy mildew (DMR, maize streak virus (SR and drought (DT. Created genotypes exhibited very good kernel modification and yield potential under low and normal inputs. In the case of synthetics and composites, besides tolerance to multiple stress factors, they were competing in yield with local QPM and normal maize checks. In the case of created inbred lines high combining ability was exhibited both in non-conventional and conventional maize hybrids. Trial data revealed that in the most cases the best entries were over-yielding the best checks.

  12. Retinal proteins associated with redox regulation and protein folding play central roles in response to high glucose conditions.

    Science.gov (United States)

    Wang, Ssu-Han; Lee, Wen-Chi; Chou, Hsiu-Chuan

    2015-03-01

    Diabetic retinopathy typically causes poor vision and blindness. A previous study revealed that a high blood glucose concentration induces glycoxidation and weakens the retinal capillaries. Nevertheless, the molecular mechanisms underlying the effects of high blood glucose induced diabetic retinopathy remain to be elucidated. In the present study, we cultured the retinal pigmented epithelial cell line ARPE-19 in mannitol-balanced 5.5, 25, and 100 mM glucose media and investigated protein level alterations. Proteomic analysis revealed significant changes in 137 protein features, of which 124 demonstrated changes in a glucose concentration dependent manner. Several proteins functionally associated with redox regulation, protein folding, or the cytoskeleton are affected by increased glucose concentrations. Additional analyses also revealed that cellular oxidative stress, including endoplasmic reticulum stress, was significantly increased after treatment with high glucose concentrations. However, the mitochondrial membrane potential and cell survival remained unchanged during treatment with high glucose concentrations. To summarize, in this study, we used a comprehensive retinal pigmented epithelial cell based proteomic approach for identifying changes in protein expression associated retinal markers induced by high glucose concentrations. Our results revealed that a high glucose condition can induce cellular oxidative stress and modulate the levels of proteins with functions in redox regulation, protein folding, and cytoskeleton regulation; however, cell viability and mitochondrial integrity are not significantly disturbed under these high glucose conditions.

  13. Test Anxiety Reduction and Confidence Training: A Replication

    Science.gov (United States)

    Bowman, Noah; Driscoll, Richard

    2013-01-01

    This study was undertaken to replicate prior research in which a brief counter-conditioning and confidence training program was found to reduce anxiety and raise test scores. First-semester college students were screened with the Westside Test Anxiety Scale, and the 25 identified as having high or moderately-high anxiety were randomly divided…

  14. Tsetse salivary gland proteins 1 and 2 are high affinity nucleic acid binding proteins with residual nuclease activity.

    Directory of Open Access Journals (Sweden)

    Guy Caljon

    Full Text Available Analysis of the tsetse fly salivary gland EST database revealed the presence of a highly enriched cluster of putative endonuclease genes, including tsal1 and tsal2. Tsal proteins are the major components of tsetse fly (G. morsitans morsitans saliva where they are present as monomers as well as high molecular weight complexes with other saliva proteins. We demonstrate that the recombinant tsetse salivary gland proteins 1&2 (Tsal1&2 display DNA/RNA non-specific, high affinity nucleic acid binding with K(D values in the low nanomolar range and a non-exclusive preference for duplex. These Tsal proteins exert only a residual nuclease activity with a preference for dsDNA in a broad pH range. Knockdown of Tsal expression by in vivo RNA interference in the tsetse fly revealed a partially impaired blood digestion phenotype as evidenced by higher gut nucleic acid, hematin and protein contents.

  15. High-throughput characterization of intrinsic disorder in proteins from the Protein Structure Initiative.

    Science.gov (United States)

    Johnson, Derrick E; Xue, Bin; Sickmeier, Megan D; Meng, Jingwei; Cortese, Marc S; Oldfield, Christopher J; Le Gall, Tanguy; Dunker, A Keith; Uversky, Vladimir N

    2012-10-01

    The identification of intrinsically disordered proteins (IDPs) among the targets that fail to form satisfactory crystal structures in the Protein Structure Initiative represents a key to reducing the costs and time for determining three-dimensional structures of proteins. To help in this endeavor, several Protein Structure Initiative Centers were asked to send samples of both crystallizable proteins and proteins that failed to crystallize. The abundance of intrinsic disorder in these proteins was evaluated via computational analysis using predictors of natural disordered regions (PONDR®) and the potential cleavage sites and corresponding fragments were determined. Then, the target proteins were analyzed for intrinsic disorder by their resistance to limited proteolysis. The rates of tryptic digestion of sample target proteins were compared to those of lysozyme/myoglobin, apomyoglobin, and α-casein as standards of ordered, partially disordered and completely disordered proteins, respectively. At the next stage, the protein samples were subjected to both far-UV and near-UV circular dichroism (CD) analysis. For most of the samples, a good agreement between CD data, predictions of disorder and the rates of limited tryptic digestion was established. Further experimentation is being performed on a smaller subset of these samples in order to obtain more detailed information on the ordered/disordered nature of the proteins.

  16. Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR

    Energy Technology Data Exchange (ETDEWEB)

    Takeuchi, Koh [National Institute for Advanced Industrial Science and Technology, Molecular Profiling Research Center for Drug Discovery (Japan); Arthanari, Haribabu [Harvard Medical School, Department of Biochemistry and Molecular Pharmacology (United States); Shimada, Ichio, E-mail: shimada@iw-nmr.f.u-tokyo.ac.jp [National Institute for Advanced Industrial Science and Technology, Molecular Profiling Research Center for Drug Discovery (Japan); Wagner, Gerhard, E-mail: gerhard-wagner@hms.harvard.edu [Harvard Medical School, Department of Biochemistry and Molecular Pharmacology (United States)

    2015-12-15

    Detection of {sup 15}N in multidimensional NMR experiments of proteins has sparsely been utilized because of the low gyromagnetic ratio (γ) of nitrogen and the presumed low sensitivity of such experiments. Here we show that selecting the TROSY components of proton-attached {sup 15}N nuclei (TROSY {sup 15}N{sub H}) yields high quality spectra in high field magnets (>600 MHz) by taking advantage of the slow {sup 15}N transverse relaxation and compensating for the inherently low {sup 15}N sensitivity. The {sup 15}N TROSY transverse relaxation rates increase modestly with molecular weight but the TROSY gain in peak heights depends strongly on the magnetic field strength. Theoretical simulations predict that the narrowest line width for the TROSY {sup 15}N{sub H} component can be obtained at 900 MHz, but sensitivity reaches its maximum around 1.2 GHz. Based on these considerations, a {sup 15}N-detected 2D {sup 1}H–{sup 15}N TROSY-HSQC ({sup 15}N-detected TROSY-HSQC) experiment was developed and high-quality 2D spectra were recorded at 800 MHz in 2 h for 1 mM maltose-binding protein at 278 K (τ{sub c} ∼ 40 ns). Unlike for {sup 1}H detected TROSY, deuteration is not mandatory to benefit {sup 15}N detected TROSY due to reduced dipolar broadening, which facilitates studies of proteins that cannot be deuterated, especially in cases where production requires eukaryotic expression systems. The option of recording {sup 15}N TROSY of proteins expressed in H{sub 2}O media also alleviates the problem of incomplete amide proton back exchange, which often hampers the detection of amide groups in the core of large molecular weight proteins that are expressed in D{sub 2}O culture media and cannot be refolded for amide back exchange. These results illustrate the potential of {sup 15}N{sub H}-detected TROSY experiments as a means to exploit the high resolution offered by high field magnets near and above 1 GHz.

  17. The powerful high pressure tool for protein conformational studies

    Directory of Open Access Journals (Sweden)

    S. Marchal

    2005-08-01

    Full Text Available The pressure behavior of proteins may be summarized as a the pressure-induced disordering of their structures. This thermodynamic parameter has effects on proteins that are similar but not identical to those induced by temperature, the other thermodynamic parameter. Of particular importance are the intermolecular interactions that follow partial protein unfolding and that give rise to the formation of fibrils. Because some proteins do not form fibrils under pressure, these observations can be related to the shape of the stability diagram. Weak interactions which are differently affected by hydrostatic pressure or temperature play a determinant role in protein stability. Pressure acts on the 2º, 3º and 4º structures of proteins which are maintained by electrostatic and hydrophobic interactions and by hydrogen bonds. We present some typical examples of how pressure affects the tertiary structure of proteins (the case of prion proteins, induces unfolding (ataxin, is a convenient tool to study enzyme dissociation (enolase, and provides arguments to understand the role of the partial volume of an enzyme (butyrylcholinesterase. This approach may have important implications for the understanding of the basic mechanism of protein diseases and for the development of preventive and therapeutic measures.

  18. Confidence rating of marine eutrophication assessments

    DEFF Research Database (Denmark)

    Murray, Ciarán; Andersen, Jesper Harbo; Kaartokallio, Hermanni

    2011-01-01

    This report presents the development of a methodology for assessing confidence in eutrophication status classifications. The method can be considered as a secondary assessment, supporting the primary assessment of eutrophication status. The confidence assessment is based on a transparent scoring...... of the 'value' of the indicators on which the primary assessment is made. Such secondary assessment of confidence represents a first step towards linking status classification with information regarding their accuracy and precision and ultimately a tool for improving or targeting actions to improve the health...

  19. Studying host cell protein interactions with monoclonal antibodies using high throughput protein A chromatography.

    Science.gov (United States)

    Sisodiya, Vikram N; Lequieu, Joshua; Rodriguez, Maricel; McDonald, Paul; Lazzareschi, Kathlyn P

    2012-10-01

    Protein A chromatography is typically used as the initial capture step in the purification of monoclonal antibodies produced in Chinese hamster ovary (CHO) cells. Although exploiting an affinity interaction for purification, the level of host cell proteins in the protein A eluent varies significantly with different feedstocks. Using a batch binding chromatography method, we performed a controlled study to assess host cell protein clearance across both MabSelect Sure and Prosep vA resins. We individually spiked 21 purified antibodies into null cell culture fluid generated with a non-producing cell line, creating mock cell culture fluids for each antibody with an identical composition of host cell proteins and antibody concentration. We demonstrated that antibody-host cell protein interactions are primarily responsible for the variable levels of host cell proteins in the protein A eluent for both resins when antibody is present. Using the additives guanidine HCl and sodium chloride, we demonstrated that antibody-host cell protein interactions may be disrupted, reducing the level of host cell proteins present after purification on both resins. The reduction in the level of host cell proteins differed between antibodies suggesting that the interaction likely varies between individual antibodies but encompasses both an electrostatic and hydrophobic component.

  20. Building Scientific Confidence in Read-Across: Progress in ...

    Science.gov (United States)

    Presentation at the 41st Annual Winter Meeting of The Toxicology Forum - From Assay to Assessment: Incorporating High Throughput Strategies into Health and Safety Evaluations on Building Scientific Confidence in Read-Across: Progress in using HT Data to inform Read-Across Performance Presentation at the 41st Annual Winter Meeting of The Toxicology Forum - From Assay to Assessment: Incorporating High Throughput Strategies into Health and Safety Evaluations on Building Scientific Confidence in Read-Across: Progress in using HT Data to inform Read-Across Performance

  1. Effect of a high-protein breakfast on the postprandial ghrelin response

    NARCIS (Netherlands)

    Blom, W.A.M.; Lluch, A.; Stafleu, A.; Vinoy, S.; Holst, J.J.; Schaafsma, G.; Hendriks, H.F.J.

    2006-01-01

    Background: The most satiating macronutrient appears to be dietary protein. Few studies have investigated the effects of dietary protein on ghrelin secretion in humans. Objective: This study was designed to investigate whether a high-protein (HP) breakfast is more satiating than a high-carbohydrate

  2. Protein profiling reveals inter-individual protein homogeneity of arachnoid cyst fluid and high qualitative similarity to cerebrospinal fluid

    Directory of Open Access Journals (Sweden)

    Berle Magnus

    2011-05-01

    the majority of abundant proteins in AC fluid also can be found in CSF. Compared to plasma, as many as 104 proteins in AC were not found in the list of 3017 plasma proteins. Conclusions Based on the protein content of AC fluid, our data indicate that temporal AC is a homogenous condition, pointing towards a similar AC filling mechanism for the 14 patients examined. Most of the proteins identified in AC fluid have been identified in CSF, indicating high similarity in the qualitative protein content of AC to CSF, whereas this was not the case between AC and plasma. This indicates that AC is filled with a liquid similar to CSF. As far as we know, this is the first proteomics study that explores the AC fluid proteome.

  3. High-Effect Priority Bounded Confidence Model for Network Opinion Evolution%网络舆论演化的高影响力优先有限信任模型

    Institute of Scientific and Technical Information of China (English)

    陈桂茸; 蔡皖东; 徐会杰; 晏沛湘; 王剑平

    2013-01-01

    针对经典有限信任模型在观点更新时需考虑其他全部个体的观点,以及虚拟社会网络规模巨大、用户时间和精力有限等问题,提出了基于影响力和信任阈值、含有双重选择机制的网络舆论演化模型,并对参与网络舆论演化个体的观点坚持策略进行建模,在多个参数集下对该模型与经典有限信任模型进行仿真.结果表明,所获得结果与实际网络舆论演化的情况相符.%Artificial social networks which include thousands of members have become an important platform for network opinion evolution. People will not try their best to get and consider all other people's opinions when they give their opinions in Internet, because they do not have enough time and energy to do this, and they don't think it is- necessary. But in bounded confidence model, it needs to take into account all the other people's opinions when any people update his opinion, which is in conflict with the real networks. To solve this problem, a novelty network opinion evolution model with dual-choices based on effect and confidence was proposed, according to human behavioral patterns in real networks, and a model of people's opinion insistence strategy was made. The new model and the bounded confidence model with different sets of parameters were simulated for many times, and the results are in good agreement with what happened in real networks.

  4. Plants as a production platform for high-value proteins

    NARCIS (Netherlands)

    Westerhof, L.B.

    2014-01-01

    Summary Current treatments of inflammatory disorders are often based on therapeutic proteins. These proteins, so-called biopharmaceuticals, are isolated from a natural resource or, more often, made using cell based fermentation systems. The most common production platforms are based

  5. Plants as a production platform for high-value proteins

    NARCIS (Netherlands)

    Westerhof, L.B.

    2014-01-01

    Summary Current treatments of inflammatory disorders are often based on therapeutic proteins. These proteins, so-called biopharmaceuticals, are isolated from a natural resource or, more often, made using cell based fermentation systems. The most common production platforms are based

  6. Habituation to low or high protein intake does not modulate basal or postprandial muscle protein synthesis rates: a randomized trial.

    Science.gov (United States)

    Gorissen, Stefan Hm; Horstman, Astrid Mh; Franssen, Rinske; Kouw, Imre Wk; Wall, Benjamin T; Burd, Nicholas A; de Groot, Lisette Cpgm; van Loon, Luc Jc

    2017-02-01

    Muscle mass maintenance is largely regulated by basal muscle protein synthesis rates and the ability to increase muscle protein synthesis after protein ingestion. To our knowledge, no previous studies have evaluated the impact of habituation to either low protein intake (LOW PRO) or high protein intake (HIGH PRO) on the postprandial muscle protein synthetic response. We assessed the impact of LOW PRO compared with HIGH PRO on basal and postprandial muscle protein synthesis rates after the ingestion of 25 g whey protein. Twenty-four healthy, older men [age: 62 ± 1 y; body mass index (in kg/m(2)): 25.9 ± 0.4 (mean ± SEM)] participated in a parallel-group randomized trial in which they adapted to either a LOW PRO diet (0.7 g · kg(-1) · d(-1); n = 12) or a HIGH PRO diet (1.5 g · kg(-1) · d(-1); n = 12) for 14 d. On day 15, participants received primed continuous l-[ring-(2)H5]-phenylalanine and l-[1-(13)C]-leucine infusions and ingested 25 g intrinsically l-[1-(13)C]-phenylalanine- and l-[1-(13)C]-leucine-labeled whey protein. Muscle biopsies and blood samples were collected to assess muscle protein synthesis rates as well as dietary protein digestion and absorption kinetics. Plasma leucine concentrations and exogenous phenylalanine appearance rates increased after protein ingestion (P 0.05). Plasma exogenous phenylalanine availability over the 5-h postprandial period was greater after LOW PRO than after HIGH PRO (61% ± 1% compared with 56% ± 2%, respectively; P synthesis rates increased from 0.031% ± 0.004% compared with 0.039% ± 0.007%/h in the fasted state to 0.062% ± 0.005% compared with 0.057% ± 0.005%/h in the postprandial state after LOW PRO compared with HIGH PRO, respectively (P synthesis rates or increase postprandial muscle protein synthesis rates after ingestion of 25 g protein in older men. This trial was registered at clinicaltrials.gov as NCT01986842. © 2017 American Society for Nutrition.

  7. Accelerated growth rate induced by neonatal high-protein milk formula is not supported by increased tissue protein synthesis in low-birth-weight piglets

    OpenAIRE

    Agnès Jamin; Bernard Sève; Jean-Noël Thibault; Nathalie Floc’h

    2012-01-01

    Low-birth-weight neonates are routinely fed a high-protein formula to promote catch-up growth and antibiotics are usually associated to prevent infection. Yet the effects of such practices on tissue protein metabolism are unknown. Baby pigs were fed from age 2 to 7 or 28 d with high protein formula with or without amoxicillin supplementation, in parallel with normal protein formula, to determine tissue protein metabolism modifications. Feeding high protein formula increased growth rate betwee...

  8. European Businesses Remain Confident about China

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    @@ On June 30th, 2009, the European Union Chamber of Commerce in China launches its sixth annual European Chamber Business Confidence Survey, which is published in partnership with Roland Berger Strategy Consultants.

  9. Confidence intervals with a priori parameter bounds

    CERN Document Server

    Lokhov, A V

    2014-01-01

    We review the methods of constructing confidence intervals that account for a priori information about one-sided constraints on the parameter being estimated. We show that the so-called method of sensitivity limit yields a correct solution of the problem. Derived are the solutions for the cases of a continuous distribution with non-negative estimated parameter and a discrete distribution, specifically a Poisson process with background. For both cases, the best upper limit is constructed that accounts for the a priori information. A table is provided with the confidence intervals for the parameter of Poisson distribution that correctly accounts for the information on the known value of the background along with the software for calculating the confidence intervals for any confidence levels and magnitudes of the background (the software is freely available for download via Internet).

  10. When business is a confidence game.

    Science.gov (United States)

    Hutchinson, J W; Alba, J W

    2001-06-01

    When it comes to making business decisions, being overconfident about your choices can actually be more harmful than just guessing. Here's how managers can calibrate their confidence levels-and avoid being too sure in the wrong situations.

  11. High mobility group A-interacting proteins in cancer: focus on chromobox protein homolog 7, homeodomain interacting protein kinase 2 and PATZ

    Directory of Open Access Journals (Sweden)

    Monica Fedele

    2012-03-01

    Full Text Available The High Mobility Group A (HMGA proteins, a family of DNA architectural factors, by interacting with different proteins play crucial roles in neoplastic transformation of a wide range of tissues. Therefore, the search for HMGA-interacting partners was carried out by several laboratories in order to investigate the mechanisms underlying HMGA-dependent tumorigenesis. Three of the several HMGA-binding proteins are discussed in this review. These are the Chromobox family protein (chromobox protein homolog 7, CBX7, the homeodomain interacting protein kinase 2 (HIPK2 and the POZ/domain and Kruppel zinc finger family member, PATZ. All of them play a critical role in tumorigenesis, and may also be independent markers of cancer. Their activities are linked to cell cycle, apoptosis and senescence. In this review, we discuss the properties of each protein, including their effect on HMGA1 functions, and propose a model accounting for how their activities might be coordinated.

  12. Microintaglio Printing of In situ Synthesized Proteins Enables Rapid Printing of High-Density Protein Microarrays Directly from DNA Microarrays

    Science.gov (United States)

    Biyani, Manish; Moriyasu, Junpei; Tanaka, Yoko; Sato, Shusuke; Ueno, Shingo; Ichiki, Takanori

    2013-08-01

    A simple and versatile approach to the simultaneous on-chip synthesis and printing of proteins has been studied for high-density protein microarray applications. The method used is based on the principle of intaglio printing using microengraved plates. Unlike conventional approaches that require multistep reactions for synthesizing proteins off the chip followed by printing using a robotic spotter, our approach demonstrates the following: (i) parallel and spotter-free printing of high-density protein microarrays directly from a type of DNA microarray and (ii) microcompartmentalization of cell-free coupled transcription/translation reaction and direct transferring of picoliter protein solution per spot to pattern microarrays of 25-100 µm features.

  13. Toward a Theory of Assurance Case Confidence

    Science.gov (United States)

    2012-09-01

    assurance case claim. The framework is based on the notion of eliminative induction—the princi- ple (first put forward by Francis Bacon ) that confidence in...eliminative induction. As first proposed by Francis Bacon [Schum 2001] and extended by L. Jonathan Cohen [Cohen 1970, 1977, 1989], eliminative induction is...eliminative in- duction—the principle (first put forward by Francis Bacon ) that confidence in the truth of a hypothesis (or claim) increases as reasons for

  14. Confidence in leadership among the newly qualified.

    Science.gov (United States)

    Bayliss-Pratt, Lisa; Morley, Mary; Bagley, Liz; Alderson, Steven

    2013-10-23

    The Francis report highlighted the importance of strong leadership from health professionals but it is unclear how prepared those who are newly qualified feel to take on a leadership role. We aimed to assess the confidence of newly qualified health professionals working in the West Midlands in the different competencies of the NHS Leadership Framework. Most respondents felt confident in their abilities to demonstrate personal qualities and work with others, but less so at managing or improving services or setting direction.

  15. Confidence in value-based choice

    Science.gov (United States)

    De Martino, Benedetto; Fleming, Stephen M.; Garrett, Neil; Dolan, Raymond

    2013-01-01

    Summary Decisions are never perfect with confidence in one’s choices fluctuating over time. How subjective confidence and valuation of choice options interact at the level of brain and behavior is unknown. Using a dynamic model of the decision process we show that confidence reflects the evolution of a decision variable over time, explaining the observed relation between confidence, value, accuracy and reaction time. As predicted by our dynamic model, we show that an fMRI signal in human ventromedial prefrontal cortex (vmPFC) reflects both value comparison and confidence in the value comparison process. Crucially, individuals varied in how they related confidence to accuracy, allowing us to show that this introspective ability is predicted by a measure of functional connectivity between vmPFC and rostrolateral prefrontal cortex (rlPFC). Our findings provide a mechanistic link between noise in value comparison and metacognitive awareness of choice, enabling us both to want and to express knowledge of what we want. PMID:23222911

  16. High-throughput method for optimum solubility screening for homogeneity and crystallization of proteins

    Science.gov (United States)

    Kim, Sung-Hou [Moraga, CA; Kim, Rosalind [Moraga, CA; Jancarik, Jamila [Walnut Creek, CA

    2012-01-31

    An optimum solubility screen in which a panel of buffers and many additives are provided in order to obtain the most homogeneous and monodisperse protein condition for protein crystallization. The present methods are useful for proteins that aggregate and cannot be concentrated prior to setting up crystallization screens. A high-throughput method using the hanging-drop method and vapor diffusion equilibrium and a panel of twenty-four buffers is further provided. Using the present methods, 14 poorly behaving proteins have been screened, resulting in 11 of the proteins having highly improved dynamic light scattering results allowing concentration of the proteins, and 9 were crystallized.

  17. Plant protein kinase genes induced by drought, high salt and cold stresses

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Drought, high salt and cold are three different kinds of environment stresses that severely influence the growth, development and productivity of crops. They all decrease the water state of plant cells, and consequently result in the harm of plant from water deficit. Several genes encoding protein kinases and induced by drought, high salt and low temperature have been isolated from Arabidopsis. These protein kinases include receptor protein kinase (RPK), MAP kinases, ribosomal-protein kinases and transcription-regulation protein kinase. The expression features of these genes and the regulatory roles of these protein kinases in stress response and signal transduction are discussed.

  18. Generation of high-performance binding proteins for peptide motifs by affinity clamping

    OpenAIRE

    Koide, Shohei; Huang, Jin

    2013-01-01

    We describe concepts and methodologies for generating “Affinity Clamps”, a new class of recombinant binding proteins that achieve high affinity and high specificity toward short peptide motifs of biological importance, which is a major challenge in protein engineering. The Affinity Clamping concept exploits the potential of nonhomologous recombination of protein domains in generating large changes in protein function and the inherent binding affinity and specificity of the so-called modular i...

  19. High-performance computational solutions in protein bioinformatics

    CERN Document Server

    Mrozek, Dariusz

    2014-01-01

    Recent developments in computer science enable algorithms previously perceived as too time-consuming to now be efficiently used for applications in bioinformatics and life sciences. This work focuses on proteins and their structures, protein structure similarity searching at main representation levels and various techniques that can be used to accelerate similarity searches. Divided into four parts, the first part provides a formal model of 3D protein structures for functional genomics, comparative bioinformatics and molecular modeling. The second part focuses on the use of multithreading for

  20. Toward high sequence coverage of proteins in human breast cancer cells using on-line monolith-based HPLC-ESI-TOF MS compared to CE MS.

    Science.gov (United States)

    Yoo, Chul; Pal, Manoj; Miller, Fred R; Barder, Timothy J; Huber, Christian; Lubman, David M

    2006-06-01

    A method is developed toward high sequence coverage of proteins isolated from human breast cancer MCF10 cell lines using a 2-D liquid separations. Monolithic-capillary columns prepared by copolymerizing styrene with divinylbenzene are used to achieve high-resolution separation of peptides from protein digests. This separation is performed with minimal sample preparation directly from the 2-D liquid fractionation of the cell lysate. The monolithic column separation is directly interfaced to ESI-TOF MS to obtain a peptide map. The protein digests were also analyzed by MALDI-TOF MS and an accurate M(r) of the intact protein was obtained using an HPLC-ESI-TOF MS. The result is that these techniques provide complementary information where nearly complete sequence coverage of the protein is obtained and can be compared to the experimental M(r) value. The high sequence coverage provides information on isoforms and other post-translational modifications that would not be available from methods that result in low sequence coverage. The results from the use of monolithic columns are compared to that obtained by CE-MS. The monolithic column separations provide a rugged and highly reproducible method for separating protein digests prior to MS analysis and is suited to confidently identify biomarkers associated with cancer progression.

  1. Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

    Science.gov (United States)

    Handfield, Louis-François; Chong, Yolanda T.; Simmons, Jibril; Andrews, Brenda J.; Moses, Alan M.

    2013-01-01

    Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images. PMID:23785265

  2. Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins.

    Directory of Open Access Journals (Sweden)

    Louis-François Handfield

    Full Text Available Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images.

  3. Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins.

    Directory of Open Access Journals (Sweden)

    Louis-François Handfield

    Full Text Available Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images.

  4. Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins.

    Science.gov (United States)

    Handfield, Louis-François; Chong, Yolanda T; Simmons, Jibril; Andrews, Brenda J; Moses, Alan M

    2013-01-01

    Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images.

  5. High-Pressure-High-Temperature Processing Reduces Maillard Reaction and Viscosity in Whey Protein-Sugar Solutions

    NARCIS (Netherlands)

    Avila Ruiz, Geraldine; Xi, Bingyan; Minor, Marcel; Sala, Guido; Boekel, van Tiny; Fogliano, Vincenzo; Stieger, Markus

    2016-01-01

    The aim of the study was to determine the influence of pressure in high-pressure–high-temperature (HPHT) processing on Maillard reactions and protein aggregation of whey protein–sugar solutions. Solutions of whey protein isolate containing either glucose or trehalose at pH 6, 7, and 9 were treated

  6. Control of lipopolysaccharide-high density lipoprotein binding by acute phase protein(s).

    Science.gov (United States)

    Tobias, P S; Ulevitch, R J

    1983-10-01

    When Salmonella minnesota R595 lipopolysaccharide (LPS) is mixed with serum, the LPS eventually forms a complex with high density lipoprotein (HDL). Complex formation is conveniently followed by CsCl equilibrium density gradient centrifugation. When mixing 10 micrograms LPS with normal rabbit serum (NRS) at 37 degrees C in the presence of 20 mM EDTA, the half-life for LPS binding to HDL is typically 2 to 3 min. When the same experiment is performed with the use of acute phase rabbit serum (APRS; collected 24 hr post-induction with silver nitrate), the half-life for LPS binding to HDL is typically 40 to 100 min. Thus LPS binding to HDL occurs some 20- to 40-fold slower in APRS than in NRS. Two other phenomena have been found, the time dependencies of which correlate well with the time dependency of LPS binding to HDL in APRS. If LPS-APRS reaction mixtures are cooled to 4 degrees C shortly after mixing and are dialyzed against 2.5 mM HEPES, 15 mM NaCl, pH 7.4 buffer, LPS is recovered in the washed precipitates ("euglobulin precipitate") if, and only if, the LPS-HDL binding reaction is not complete. The amount of LPS in the precipitate correlates well with the amount of LPS that has not bound to HDL. The second phenomenon we observe is that the LPS-containing euglobulin precipitate prepared from LPS-acute phase serum reaction mixtures shortly after mixing also contains a protein, gp60, the concentration of which in the euglobulin precipitate correlates well with the amount of LPS in the precipitate. Thus three phenomena are kinetically well correlated in APRS: the degree of binding of LPS to HDL, the degree of appearance of LPS in a euglobulin fraction, and the concentration of protein gp60 in the euglobulin fraction. We were unable to precipitate gp60 from APRS in the absence of LPS, from APRS after the LPS has fully bound to HDL, or from normal serum in the presence or absence of LPS. The known properties of gp60 are not reminiscent of any other known acute phase

  7. Application of high hydrostatic pressure to dissociate aggregates and refold proteins.

    Science.gov (United States)

    Seefeldt, Matthew B; Rosendahl, Mary S; Cleland, Jeffrey L; Hesterberg, Lyndal K

    2009-06-01

    Non-denaturing pressures of around 2000 bar are effective for eliminating and refolding protein aggregates and may be applicable in various phases of protein manufacturing to decrease aggregate levels in products and improve process yields. Lower aggregate levels can result in reduced immunogenicity of proteins and enable the correct refolding of proteins that might not be recovered with traditional techniques. High pressure treatment can also be used to conduct selective PEGylation and protease cleavage reactions while minimizing protein aggregation. High pressure processes have been used in the food industry for over 50 years and large scale (300 L) systems are commercially available, enabling production of proteins on the kilogram scale. This review summarizes the utility of high pressure refolding to remove and refold protein aggregates, enhance therapeutic proteins, and facilitate manufacturing improvements at industrial scales.

  8. High-protein diet induces oxidative stress in rat brain: protective action of high-intensity exercise against lipid peroxidation

    OpenAIRE

    Camiletti-Moir??n, Daniel; Aparicio Garc??a-Molina, Virginia A.; Nebot Valenzuela, Elena; Medina, Gerardo; Mart??nez, Rosario; Kapravelou, Garyfallia; Andrade, Ana; Porres-Foulquie, Jes??s; L??pez-Jurado, Mar??a; Aranda Ram??rez, Pilar

    2015-01-01

    diets as well as aerobic exercise could promote antioxidant capacity and consequently reduce free radicals overproduction on brain. However, little is know regarding to the high-protein diets and high intensity exercise on oxidative stress production. The aim of this study was to analyse the effects of high-protein diets and high-intensity exercise (HIE) on brain oxidative stress markers. Materials and Methods: A total of 40 male Wistar rats were randomly distributed i...

  9. Single-Molecule Protein Folding Experiments Using High-Precision Optical Tweezers.

    Science.gov (United States)

    Jiao, Junyi; Rebane, Aleksander A; Ma, Lu; Zhang, Yongli

    2017-01-01

    How proteins fold from linear chains of amino acids to delicate three-dimensional structures remains a fundamental biological problem. Single-molecule manipulation based on high-resolution optical tweezers (OT) provides a powerful approach to study protein folding with unprecedented spatiotemporal resolution. In this method, a single protein or protein complex is tethered between two beads confined in optical traps and pulled. Protein unfolding induced by the mechanical force is counteracted by the spontaneous folding of the protein, reaching a dynamic equilibrium at a characteristic force and rate. The transition is monitored by the accompanying extension change of the protein and used to derive conformations and energies of folding intermediates and their associated transition kinetics. Here, we provide general strategies and detailed protocols to study folding of proteins and protein complexes using optical tweezers, including sample preparation, DNA-protein conjugation and methods of data analysis to extract folding energies and rates from the single-molecule measurements.

  10. Structures of the Ultra-High-Affinity Protein-Protein Complexes of Pyocins S2 and AP41 and Their Cognate Immunity Proteins from Pseudomonas aeruginosa.

    Science.gov (United States)

    Joshi, Amar; Grinter, Rhys; Josts, Inokentijs; Chen, Sabrina; Wojdyla, Justyna A; Lowe, Edward D; Kaminska, Renata; Sharp, Connor; McCaughey, Laura; Roszak, Aleksander W; Cogdell, Richard J; Byron, Olwyn; Walker, Daniel; Kleanthous, Colin

    2015-08-28

    How ultra-high-affinity protein-protein interactions retain high specificity is still poorly understood. The interaction between colicin DNase domains and their inhibitory immunity (Im) proteins is an ultra-high-affinity interaction that is essential for the neutralisation of endogenous DNase catalytic activity and for protection against exogenous DNase bacteriocins. The colicin DNase-Im interaction is a model system for the study of high-affinity protein-protein interactions. However, despite the fact that closely related colicin-like bacteriocins are widely produced by Gram-negative bacteria, this interaction has only been studied using colicins from Escherichia coli. In this work, we present the first crystal structures of two pyocin DNase-Im complexes from Pseudomonas aeruginosa, pyocin S2 DNase-ImS2 and pyocin AP41 DNase-ImAP41. These structures represent divergent DNase-Im subfamilies and are important in extending our understanding of protein-protein interactions for this important class of high-affinity protein complex. A key finding of this work is that mutations within the immunity protein binding energy hotspot, helix III, are tolerated by complementary substitutions at the DNase-Immunity protein binding interface. Im helix III is strictly conserved in colicins where an Asp forms polar interactions with the DNase backbone. ImAP41 contains an Asp-to-Gly substitution in helix III and our structures show the role of a co-evolved substitution where Pro in DNase loop 4 occupies the volume vacated and removes the unfulfilled hydrogen bond. We observe the co-evolved mutations in other DNase-Immunity pairs that appear to underpin the split of this family into two distinct groups.

  11. Increasing Product Confidence-Shifting Paradigms.

    Science.gov (United States)

    Phillips, Marla; Kashyap, Vishal; Cheung, Mee-Shew

    2015-01-01

    Leaders in the pharmaceutical, medical device, and food industries expressed a unilateral concern over product confidence throughout the total product lifecycle, an unsettling fact for these leaders to manage given that their products affect the lives of millions of people each year. Fueled by the heparin incident of intentional adulteration in 2008, initial efforts for increasing product confidence were focused on improving the confidence of incoming materials, with a belief that supplier performance must be the root cause. As in the heparin case, concern over supplier performance extended deep into the supply chain to include suppliers of the suppliers-which is often a blind spot for pharmaceutical, device, and food manufacturers. Resolved to address the perceived lack of supplier performance, these U.S. Food and Drug Administration (FDA)-regulated industries began to adopt the supplier relationship management strategy, developed by the automotive industry, that emphasizes "management" of suppliers for the betterment of the manufacturers. Current product and supplier management strategies, however, have not led to a significant improvement in product confidence. As a result of the enduring concern by industry leaders over the lack of product confidence, Xavier University launched the Integrity of Supply Initiative in 2012 with a team of industry leaders and FDA officials. Through a methodical research approach, data generated by the pharmaceutical, medical device, and food manufacturers surprisingly pointed to themselves as a source of the lack of product confidence, and revealed that manufacturers either unknowingly increase the potential for error or can control/prevent many aspects of product confidence failure. It is only through this paradigm shift that manufacturers can work collaboratively with their suppliers as equal partners, instead of viewing their suppliers as "lesser" entities needing to be controlled. The basis of this shift provides manufacturers

  12. Characteristics of successful opinion leaders in a bounded confidence model

    Science.gov (United States)

    Chen, Shuwei; Glass, David H.; McCartney, Mark

    2016-05-01

    This paper analyses the impact of competing opinion leaders on attracting followers in a social group based on a bounded confidence model in terms of four characteristics: reputation, stubbornness, appeal and extremeness. In the model, reputation differs among leaders and normal agents based on the weights assigned to them, stubbornness of leaders is reflected by their confidence towards normal agents, appeal of the leaders is represented by the confidence of followers towards them, and extremeness is captured by the opinion values of leaders. Simulations show that increasing reputation, stubbornness or extremeness makes it more difficult for the group to achieve consensus, but increasing the appeal will make it easier. The results demonstrate that successful opinion leaders should generally be less stubborn, have greater appeal and be less extreme in order to attract more followers in a competing environment. Furthermore, the number of followers can be very sensitive to small changes in these characteristics. On the other hand, reputation has a more complicated impact: higher reputation helps the leader to attract more followers when the group bound of confidence is high, but can hinder the leader from attracting followers when the group bound of confidence is low.

  13. ADAM SMITH: THE INVISIBLE HAND OR CONFIDENCE

    Directory of Open Access Journals (Sweden)

    Fernando Luis, Gache

    2010-01-01

    Full Text Available In 1776 Adam Smith raised the matter that an invisible hand was the one which moved the markets to obtain its efficiency. Despite in the present paper we are going to raise the hypothesis, that this invisible hand is in fact the confidence that each person feels when he is going to do business. That in addition it is unique, because it is different from the confidence of the others and that is a variable nonlinear that essentially is ligatured to respective personal histories. For that we are going to take as its bases the paper by Leopoldo Abadía (2009, with respect to the financial economy crisis that happened in 2007-2008, to evidence the form in which confidence operates. Therefore the contribution that we hope to do with this paper is to emphasize that, the level of confidence of the different actors, is the one which really moves the markets, (therefore the economy and that the crisis of the subprime mortgages is a confidence crisis at world-wide level.

  14. A high-throughput method to examine protein-nucleotide interactions identifies targets of the bacterial transcriptional regulatory protein fur.

    Science.gov (United States)

    Yu, Chunxiao; Lopez, Carlos A; Hu, Han; Xia, Yu; Freedman, David S; Reddington, Alexander P; Daaboul, George G; Unlü, M Selim; Genco, Caroline Attardo

    2014-01-01

    The Ferric uptake regulatory protein (Fur) is a transcriptional regulatory protein that functions to control gene transcription in response to iron in a number of pathogenic bacteria. In this study, we applied a label-free, quantitative and high-throughput analysis method, Interferometric Reflectance Imaging Sensor (IRIS), to rapidly characterize Fur-DNA interactions in vitro with predicted Fur binding sequences in the genome of Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhea. IRIS can easily be applied to examine multiple protein-protein, protein-nucleotide and nucleotide-nucleotide complexes simultaneously and demonstrated here that seventy percent of the predicted Fur boxes in promoter regions of iron-induced genes bound to Fur in vitro with a range of affinities as observed using this microarray screening technology. Combining binding data with mRNA expression levels in a gonococcal fur mutant strain allowed us to identify five new gonococcal genes under Fur-mediated direct regulation.

  15. Separation/enrichment of the low-content high molecular weight natural protein using protein-imprinted polymers with ARPCs

    Institute of Scientific and Technical Information of China (English)

    XIA JianJun; LONG Yi; GUO MinJie; WANG Ying; MI HuaiFeng

    2009-01-01

    We introduce a new method for separation/enrichment of the low-content cellular protein in high molecular weight on the basis of molecular imprinting.The template protein,bacterial cloned immunoglobulin binding protein (BiP),was selectively assembled with assistant recognition polymer chains (ARPCs) from their library,which consists of numerous limited length polymer chains with randomly distributed recognition and immobilizing sites.The assemblies of proteins and ARPCs were adsorbed by porous polymeric beads and immobilized by cross-linking polymerization.After the template was removed,the synthesized imprinted polymer was used to adsorb authentic BiP from endoplasmic reticulum (ER) extract,and its proportional content was enriched 45 times.It is the first time that the low-content cellular natural protein,whose molecular weight reaches 78 kDa,is enrichd by molecular imprinting.

  16. Separation/enrichment of the low-content high molecular weight natural protein using protein-imprinted polymers with ARPCs

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    We introduce a new method for separation/enrichment of the low-content cellular protein in high mo-lecular weight on the basis of molecular imprinting. The template protein, bacterial cloned immu-noglobulin binding protein (BiP), was selectively assembled with assistant recognition polymer chains (ARPCs) from their library, which consists of numerous limited length polymer chains with randomly distributed recognition and immobilizing sites. The assemblies of proteins and ARPCs were adsorbed by porous polymeric beads and immobilized by cross-linking polymerization. After the template was removed, the synthesized imprinted polymer was used to adsorb authentic BiP from endoplasmic re-ticulum (ER) extract, and its proportional content was enriched 45 times. It is the first time that the low-content cellular natural protein, whose molecular weight reaches 78 kDa, is enriched by molecular imprinting.

  17. Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta.

    Directory of Open Access Journals (Sweden)

    Zhe Zhang

    Full Text Available The high-resolution refinement of docked protein-protein complexes can provide valuable structural and mechanistic insight into protein complex formation complementing experiment. Monte Carlo (MC based approaches are frequently applied to sample putative interaction geometries of proteins including also possible conformational changes of the binding partners. In order to explore efficiency improvements of the MC sampling, several enhanced sampling techniques, including temperature or Hamiltonian replica exchange and well-tempered ensemble approaches, have been combined with the MC method and were evaluated on 20 protein complexes using unbound partner structures. The well-tempered ensemble method combined with a 2-dimensional temperature and Hamiltonian replica exchange scheme (WTE-H-REMC was identified as the most efficient search strategy. Comparison with prolonged MC searches indicates that the WTE-H-REMC approach requires approximately 5 times fewer MC steps to identify near native docking geometries compared to conventional MC searches.

  18. A monomeric G protein-coupled receptor isolated in a high-density lipoprotein particle efficiently activates its G protein

    DEFF Research Database (Denmark)

    Whorton, Matthew R; Bokoch, Michael P; Rasmussen, Søren Gøgsig Faarup;

    2007-01-01

    G protein-coupled receptors (GPCRs) respond to a diverse array of ligands, mediating cellular responses to hormones and neurotransmitters, as well as the senses of smell and taste. The structures of the GPCR rhodopsin and several G proteins have been determined by x-ray crystallography, yet...... the organization of the signaling complex between GPCRs and G proteins is poorly understood. The observations that some GPCRs are obligate heterodimers, and that many GPCRs form both homo- and heterodimers, has led to speculation that GPCR dimers may be required for efficient activation of G proteins. However......, technical limitations have precluded a definitive analysis of G protein coupling to monomeric GPCRs in a biochemically defined and membrane-bound system. Here we demonstrate that a prototypical GPCR, the beta2-adrenergic receptor (beta2AR), can be incorporated into a reconstituted high-density lipoprotein...

  19. HIPPI: highly accurate protein family classification with ensembles of HMMs

    Directory of Open Access Journals (Sweden)

    Nam-phuong Nguyen

    2016-11-01

    Full Text Available Abstract Background Given a new biological sequence, detecting membership in a known family is a basic step in many bioinformatics analyses, with applications to protein structure and function prediction and metagenomic taxon identification and abundance profiling, among others. Yet family identification of sequences that are distantly related to sequences in public databases or that are fragmentary remains one of the more difficult analytical problems in bioinformatics. Results We present a new technique for family identification called HIPPI (Hierarchical Profile Hidden Markov Models for Protein family Identification. HIPPI uses a novel technique to represent a multiple sequence alignment for a given protein family or superfamily by an ensemble of profile hidden Markov models computed using HMMER. An evaluation of HIPPI on the Pfam database shows that HIPPI has better overall precision and recall than blastp, HMMER, and pipelines based on HHsearch, and maintains good accuracy even for fragmentary query sequences and for protein families with low average pairwise sequence identity, both conditions where other methods degrade in accuracy. Conclusion HIPPI provides accurate protein family identification and is robust to difficult model conditions. Our results, combined with observations from previous studies, show that ensembles of profile Hidden Markov models can better represent multiple sequence alignments than a single profile Hidden Markov model, and thus can improve downstream analyses for various bioinformatic tasks. Further research is needed to determine the best practices for building the ensemble of profile Hidden Markov models. HIPPI is available on GitHub at https://github.com/smirarab/sepp .

  20. A peptide-retrieval strategy enables significant improvement of quantitative performance without compromising confidence of identification.

    Science.gov (United States)

    Tu, Chengjian; Shen, Shichen; Sheng, Quanhu; Shyr, Yu; Qu, Jun

    2017-01-30

    Reliable quantification of low-abundance proteins in complex proteomes is challenging largely owing to the limited number of spectra/peptides identified. In this study we developed a straightforward method to improve the quantitative accuracy and precision of proteins by strategically retrieving the less confident peptides that were previously filtered out using the standard target-decoy search strategy. The filtered-out MS/MS spectra matched to confidently-identified proteins were recovered, and the peptide-spectrum-match FDR were re-calculated and controlled at a confident level of FDR≤1%, while protein FDR maintained at ~1%. We evaluated the performance of this strategy in both spectral count- and ion current-based methods. >60% increase of total quantified spectra/peptides was respectively achieved for analyzing a spike-in sample set and a public dataset from CPTAC. Incorporating the peptide retrieval strategy significantly improved the quantitative accuracy and precision, especially for low-abundance proteins (e.g. one-hit proteins). Moreover, the capacity of confidently discovering significantly-altered proteins was also enhanced substantially, as demonstrated with two spike-in datasets. In summary, improved quantitative performance was achieved by this peptide recovery strategy without compromising confidence of protein identification, which can be readily implemented in a broad range of quantitative proteomics techniques including label-free or labeling approaches. We hypothesize that more quantifiable spectra and peptides in a protein, even including less confident peptides, could help reduce variations and improve protein quantification. Hence the peptide retrieval strategy was developed and evaluated in two spike-in sample sets with different LC-MS/MS variations using both MS1- and MS2-based quantitative approach. The list of confidently identified proteins using the standard target-decoy search strategy was fixed and more spectra/peptides with less

  1. New GATEWAY vectors for High Throughput Analyses of Protein-Protein Interactions by Bimolecular Fluorescence Complementation

    Institute of Scientific and Technical Information of China (English)

    Christian Gehl; Rainer Waadt; J(o)rg Kudla; Ralf-R. Mendel; Robert Hansch

    2009-01-01

    Complex protein interaction networks constitute plant metabolic and signaling systems. Bimolecular fluores-cence complementation (BiFC) is a suitable technique to investigate the formation of protein complexes and the locali-zation of protein-protein interactions in planta. However, the generation of large plasmid collections to facilitate the exploration of complex interaction networks is often limited by the need for conventional cloning techniques. Here, we report the implementation of a GATEWAY vector system enabling large-scale combination and investigation of can-didate proteins in BiFC studies. We describe a set of 12 GATEWAY-compatible BiFC vectors that efficiently permit the com-bination of candidate protein pairs with every possible N-or C-terminal sub-fragment of S(CFP)3A or Venus, respectively, and enable the performance of multicolor BiFC (mcBiFC). We used proteins of the plant molybdenum metabolism, in that more than 20 potentially interacting proteins are assumed to form the cellular molybdenum network, as a case study to establish the functionality of the new vectors. Using these vectors, we report the formation of the molybdopterin synthase complex by interaction of Arabidopsis proteins Cnx6 and Cnx7 detected by BiFC as well as the simultaneous formation of Cn×6/Cn×6 and Cn×6/Cn×7 complexes revealed by mcBiFC. Consequently, these GATEWAY-based BiFC vector systems should significantly facilitate the large-scale investigation of complex regulatory networks in plant cells.

  2. Shot Range and High Order Correlations in Proteins

    CERN Document Server

    Long, Shiyang

    2016-01-01

    The main chain dihedral angles play an important role to decide the protein conformation. The native states of a protein can be regard as an ensemble of a lot of similar conformations, in different conformations the main chain dihedral angles vary in a certain range. Each dihedral angle value can be described as a distribution, but only using the distribution can't describe the real conformation space. The reason is that the dihedral angle has correlation with others, especially the neighbor dihedral angles in primary sequence. In our study we analysis extensive molecular dynamics (MD) simulation trajectories of eleven proteins with different sizes and folds, we found that in stable second structure the correlations only exist between the dihedrals near to each other in primary sequence, long range correlations are rare. But in unstable structures (loop) long range correlations exist. Further we observed some characteristics of the short range correlations in different second structures ({\\alpha}-helix, {\\bet...

  3. Controversies surrounding high-protein diet intake: satiating effect and kidney and bone health.

    Science.gov (United States)

    Cuenca-Sánchez, Marta; Navas-Carrillo, Diana; Orenes-Piñero, Esteban

    2015-05-01

    Long-term consumption of a high-protein diet could be linked with metabolic and clinical problems, such as loss of bone mass and renal dysfunction. However, although it is well accepted that a high-protein diet may be detrimental to individuals with existing kidney dysfunction, there is little evidence that high protein intake is dangerous for healthy individuals. High-protein meals and foods are thought to have a greater satiating effect than high-carbohydrate or high-fat meals. The effect of high-protein diets on the modulation of satiety involves multiple metabolic pathways. Protein intake induces complex signals, with peptide hormones being released from the gastrointestinal tract and blood amino acids and derived metabolites being released in the blood. Protein intake also stimulates metabolic hormones that communicate information about energy status to the brain. Long-term ingestion of high amounts of protein seems to decrease food intake, body weight, and body adiposity in many well-documented studies. The aim of this article is to provide an extensive overview of the efficacy of high protein consumption in weight loss and maintenance, as well as the potential consequences in human health of long-term intake.

  4. Lysine-Rich Proteins in High-Lysine Hordeum Vulgare Grain

    DEFF Research Database (Denmark)

    Ingversen, J.; Køie, B.

    1973-01-01

    The salt-soluble proteins in barley grain selected for high-lysine content (Hiproly, CI 7115 and the mutants 29 and 86) and of a control (Carlsberg II) with normal lysine content, contain identical major proteins as determined by MW and electrophoretic mobility. The concentration of a protein group...

  5. Relating the Content and Confidence of Recognition Judgments

    Science.gov (United States)

    Selmeczy, Diana; Dobbins, Ian G.

    2014-01-01

    The Remember/Know procedure, developed by Tulving (1985) to capture the distinction between the conscious correlates of episodic and semantic retrieval, has spurned considerable research and debate. However, only a handful of reports have examined the recognition content beyond this dichotomous simplification. To address this, we collected participants’ written justifications in support of ordinary old/new recognition decisions accompanied by confidence ratings using a 3-point scale (high/medium/low). Unlike prior research, we did not provide the participants with any descriptions of Remembering or Knowing and thus, if the justifications mapped well onto theory, they would do so spontaneously. Word frequency analysis (unigrams, bigrams, and trigrams), independent ratings, and machine learning techniques (Support Vector Machine - SVM) converged in demonstrating that the linguistic content of high and medium confidence recognition differs in a manner consistent with dual process theories of recognition. For example, the use of ‘I remember’, particularly when combined with temporal or perceptual information (e.g., ‘when’, ‘saw’, ‘distinctly’), was heavily associated with high confidence recognition. Conversely, participants also used the absence of remembering for personally distinctive materials as support for high confidence new reports (‘would have remembered’). Thus, participants afford a special status to the presence or absence of remembering and use this actively as a basis for high confidence during recognition judgments. Additionally, the pattern of classification successes and failures of a SVM was well anticipated by the Dual Process Signal Detection model of recognition and inconsistent with a single process, strictly unidimensional approach. “One might think that memory should have something to do with remembering, and remembering is a conscious experience.”(Tulving, 1985, p. 1) PMID:23957366

  6. Illuminating plant biology: using fluorescent proteins for high-throughput analysis of protein localization and function in plants.

    Science.gov (United States)

    DeBlasio, Stacy L; Sylvester, Anne W; Jackson, David

    2010-03-01

    First discovered in jellyfish, fluorescent proteins (FPs) have been successfully optimized for use as effective biomarkers within living plant cells. When exposed to light, FPs fused to a protein or regulatory element will fluoresce, and non-invasively mark expression and protein localization, which allows for the in vivo monitoring of diverse cellular processes. In this review, we discuss how FP technology has evolved from small-scale analysis of individual genes to more high-throughput techniques for global expression and functional profiling in plants.

  7. Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein

    DEFF Research Database (Denmark)

    Vestergaard, Mike; Chan, Siu Hung Joshua; Jensen, Peter Ruhdal

    2016-01-01

    between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used...... to explore the feasibility of recombinant Bovine Alpha Lactalbumin production coupled with market prices of utilized materials. We found that recombinant protein production could be a feasible food source and an alternative to traditional sources....

  8. Maximum confidence measurements via probabilistic quantum cloning

    Institute of Scientific and Technical Information of China (English)

    Zhang Wen-Hai; Yu Long-Bao; Cao Zhuo-Liang; Ye Liu

    2013-01-01

    Probabilistic quantum cloning (PQC) cannot copy a set of linearly dependent quantum states.In this paper,we show that if incorrect copies are allowed to be produced,linearly dependent quantum states may also be cloned by the PQC.By exploiting this kind of PQC to clone a special set of three linearly dependent quantum states,we derive the upper bound of the maximum confidence measure of a set.An explicit transformation of the maximum confidence measure is presented.

  9. Surprisingly high stability of barley lipid transfer protein, LTP1, towards denaturant, heat and proteases

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Winther, J R

    2001-01-01

    Barley LTP1 belongs to a large family of plant proteins termed non-specific lipid transfer proteins. The in vivo function of these proteins is unknown, but it has been suggested that they are involved in responses towards stresses such as pathogens, drought, heat, cold and salt. Also, the proteins...... have been suggested as transporters of monomers for cutin synthesis. We have analysed the stability of LTP1 towards denaturant, heat and proteases and found it to be a highly stable protein, which apparently does not denature at temperatures up to 100 degrees C. This high stability may be important...

  10. Decomposition of high protein aquaculture feed under variable oxic conditions

    NARCIS (Netherlands)

    Torres Beristain, B.; Verdegem, M.C.J.; Kerepeczki, E.; Verreth, J.A.J.

    2006-01-01

    The microbial decomposition of nitrogen-rich organic matter in aquaculture ponds is affected by the oxic-anoxic conditions gradient at the soil¿water interface as well as by resuspension practices. To investigate these interactions, the decomposition of a 49% protein fish feed was analyzed in 10

  11. Protein Profiling Gastric Cancer and Neighboring Control Tissues Using High-Content Antibody Microarrays

    OpenAIRE

    2016-01-01

    In this study, protein profiling was performed on gastric cancer tissue samples in order to identify proteins that could be utilized for an effective diagnosis of this highly heterogeneous disease and as targets for therapeutic approaches. To this end, 16 pairs of postoperative gastric adenocarcinomas and adjacent non-cancerous control tissues were analyzed on microarrays that contain 813 antibodies targeting 724 proteins. Only 17 proteins were found to be differentially regulated, with much ...

  12. High-efficiency screening of monoclonal antibodies for membrane protein crystallography.

    Directory of Open Access Journals (Sweden)

    Hyun-Ho Lim

    Full Text Available Determination of crystal structures of membrane proteins is often limited by difficulties obtaining crystals diffracting to high resolution. Co-crystallization with Fab fragments of monoclonal antibodies has been reported to improve diffraction of membrane proteins crystals. However, it is not simple to generate useful monoclonal antibodies for membrane protein crystallography. In this report, we present an optimized process for efficient screening from immunization to final validation of monoclonal antibody for membrane protein crystallography.

  13. Protein

    Science.gov (United States)

    ... Food Service Resources Additional Resources About FAQ Contact Protein Protein is found throughout the body—in muscle, ... the heart and respiratory system, and death. All Protein Isn’t Alike Protein is built from building ...

  14. An extremely simple method for fabricating 3D protein microarrays with an anti-fouling background and high protein capacity.

    Science.gov (United States)

    Lin, Zhifeng; Ma, Yuhong; Zhao, Changwen; Chen, Ruichao; Zhu, Xing; Zhang, Lihua; Yan, Xu; Yang, Wantai

    2014-07-21

    Protein microarrays have become vital tools for various applications in biomedicine and bio-analysis during the past decade. The intense requirements for a lower detection limit and industrialization in this area have resulted in a persistent pursuit to fabricate protein microarrays with a low background and high signal intensity via simple methods. Here, we report on an extremely simple strategy to create three-dimensional (3D) protein microarrays with an anti-fouling background and a high protein capacity by photo-induced surface sequential controlled/living graft polymerization developed in our lab. According to this strategy, "dormant" groups of isopropyl thioxanthone semipinacol (ITXSP) were first introduced to a polymeric substrate through ultraviolet (UV)-induced surface abstraction of hydrogen, followed by a coupling reaction. Under visible light irradiation, the ITXSP groups were photolyzed to initiate surface living graft polymerization of poly(ethylene glycol) methyl methacrylate (PEGMMA), thus introducing PEG brushes to the substrate to generate a full anti-fouling background. Due to the living nature of this graft polymerization, there were still ITXSP groups on the chain ends of the PEG brushes. Therefore, by in situ secondary living graft cross-linking copolymerization of glycidyl methacrylate (GMA) and polyethylene glycol diacrylate (PEGDA), we could finally plant height-controllable cylinder microarrays of a 3D PEG network containing reactive epoxy groups onto the PEG brushes. Through a commonly used reaction of amine and epoxy groups, the proteins could readily be covalently immobilized onto the microarrays. This delicate design aims to overcome two universal limitations in protein microarrays: a full anti-fouling background can effectively eliminate noise caused by non-specific absorption and a 3D reactive network provides a larger protein-loading capacity to improve signal intensity. The results of non-specific protein absorption tests

  15. High expression level of soluble SARS spike protein mediated by adenovirus in HEK293 cells

    Institute of Scientific and Technical Information of China (English)

    Fei Zhong; Zhen-Yu Zhong; Shuang Liang; Xiu-Jin Li

    2006-01-01

    AIM: To develop a highly efficacious method for preparation of soluble SARS S-protein using adenovirus vector to meet the requirement for S-protein investigation.METHODS: The human adenovirus vector was used to express the soluble S-protein (corresponding to 1~1190 amino acids) fused with Myc/His tag using codon-optimized gene construct in HEK239 cells. The recombinant adenovirus bearing S-protein gene was generated by ligation method. The expressed S-protein with Myc/His tag was purified from culture medium with Ni-NTA agarose beads followed by dialysis. The S-protein was detected by Western blot and its biologic activity was analyzed by binding to Vero cells.RESULTS: Under the conditions of infection dose (MOI of 50) and expression time (48 h), the high-level expression of S-protein was obtained. The expression level was determined to be approximately 75 μg/106cells after purification. Purified soluble S-protein was readily detected by Western blot with anti-Myc antibody and showed the ability to bind to surface of Vero cells,demonstrating that the soluble S-protein could remain the biologic activity in the native molecule.CONCLUSION: The high-level expression of S-protein in HEK293 cells mediated by adenovirus can be achieved under the optimized expression conditions. The proteins possess the biologic activity, which lays a foundation for further investigation of S-protein biological function.

  16. The effects of high protein diets on thermogenesis, satiety and weight loss: a critical review.

    Science.gov (United States)

    Halton, Thomas L; Hu, Frank B

    2004-10-01

    For years, proponents of some fad diets have claimed that higher amounts of protein facilitate weight loss. Only in recent years have studies begun to examine the effects of high protein diets on energy expenditure, subsequent energy intake and weight loss as compared to lower protein diets. In this study, we conducted a systematic review of randomized investigations on the effects of high protein diets on dietary thermogenesis, satiety, body weight and fat loss. There is convincing evidence that a higher protein intake increases thermogenesis and satiety compared to diets of lower protein content. The weight of evidence also suggests that high protein meals lead to a reduced subsequent energy intake. Some evidence suggests that diets higher in protein result in an increased weight loss and fat loss as compared to diets lower in protein, but findings have not been consistent. In dietary practice, it may be beneficial to partially replace refined carbohydrate with protein sources that are low in saturated fat. Although recent evidence supports potential benefit, rigorous longer-term studies are needed to investigate the effects of high protein diets on weight loss and weight maintenance.

  17. Coefficient Omega Bootstrap Confidence Intervals: Nonnormal Distributions

    Science.gov (United States)

    Padilla, Miguel A.; Divers, Jasmin

    2013-01-01

    The performance of the normal theory bootstrap (NTB), the percentile bootstrap (PB), and the bias-corrected and accelerated (BCa) bootstrap confidence intervals (CIs) for coefficient omega was assessed through a Monte Carlo simulation under conditions not previously investigated. Of particular interests were nonnormal Likert-type and binary items.…

  18. Detecting Disease in Radiographs with Intuitive Confidence

    Directory of Open Access Journals (Sweden)

    Stefan Jaeger

    2015-01-01

    Full Text Available This paper argues in favor of a specific type of confidence for use in computer-aided diagnosis and disease classification, namely, sine/cosine values of angles represented by points on the unit circle. The paper shows how this confidence is motivated by Chinese medicine and how sine/cosine values are directly related with the two forces Yin and Yang. The angle for which sine and cosine are equal (45° represents the state of equilibrium between Yin and Yang, which is a state of nonduality that indicates neither normality nor abnormality in terms of disease classification. The paper claims that the proposed confidence is intuitive and can be readily understood by physicians. The paper underpins this thesis with theoretical results in neural signal processing, stating that a sine/cosine relationship between the actual input signal and the perceived (learned input is key to neural learning processes. As a practical example, the paper shows how to use the proposed confidence values to highlight manifestations of tuberculosis in frontal chest X-rays.

  19. Diagnosing dementia with confidence by GPs.

    NARCIS (Netherlands)

    Hout, H.P.J. van; Vernooij-Dassen, M.J.F.J.; Stalman, W.A.B.

    2007-01-01

    BACKGROUND: Earlier reports suggest limited clinical reasoning and substantial uncertainty of GPs in assessing patients suspected of dementia. OBJECTIVE: To explore the predictors of GPs to decide on the presence and absence of dementia as well as the predictors of diagnostic confidence of GPs.

  20. The confidence effects of fiscal consolidations

    NARCIS (Netherlands)

    R.M.W.J. Beetsma; J. Cimadomo; O. Furtuna; M. Giuliodori

    2014-01-01

    We explore how fiscal consolidations affect private sector confidence, a possible channel for the fiscal transmission that has received particular attention recently as a result of governments embarking on austerity trajectories in the aftermath of the crisis. Panel regressions based on the action-b

  1. The confidence effects of fiscal consolidations

    NARCIS (Netherlands)

    R. Beetsma; J. Cimadomo; O. Furtuna; M. Giuliodori

    2015-01-01

    We explore how fiscal consolidations affect private sector confidence, a possible channel for the transmission of fiscal policy that has received particular attention recently as a result of governments embarking on austerity trajectories in the aftermath of the crisis. Panel regressions based on th

  2. Confident Communication: Speaking Tips for Educators.

    Science.gov (United States)

    Parker, Douglas A.

    This resource book seeks to provide the building blocks needed for public speaking while eliminating the fear factor. The book explains how educators can perfect their oratorical capabilities as well as enjoy the security, confidence, and support needed to create and deliver dynamic speeches. Following an Introduction: A Message for Teachers,…

  3. Diagnosing dementia with confidence by GPs.

    NARCIS (Netherlands)

    Hout, H.P.J. van; Vernooij-Dassen, M.J.F.J.; Stalman, W.A.B.

    2007-01-01

    BACKGROUND: Earlier reports suggest limited clinical reasoning and substantial uncertainty of GPs in assessing patients suspected of dementia. OBJECTIVE: To explore the predictors of GPs to decide on the presence and absence of dementia as well as the predictors of diagnostic confidence of GPs. DESI

  4. Computation of confidence intervals for Poisson processes

    Science.gov (United States)

    Aguilar-Saavedra, J. A.

    2000-07-01

    We present an algorithm which allows a fast numerical computation of Feldman-Cousins confidence intervals for Poisson processes, even when the number of background events is relatively large. This algorithm incorporates an appropriate treatment of the singularities that arise as a consequence of the discreteness of the variable.

  5. Computation of confidence intervals for Poisson processes

    CERN Document Server

    Aguilar-Saavedra, J A

    2000-01-01

    We present an algorithm which allows a fast numerical computation of Feldman-Cousins confidence intervals for Poisson processes, even when the number of background events is relatively large. This algorithm incorporates an appropriate treatment of the singularities that arise as a consequence of the discreteness of the variable.

  6. Confidence building in emerging stock markets

    NARCIS (Netherlands)

    Laeven, L.; Perotti, E.C.

    2001-01-01

    Investor confidence in reliable property rights and stable, market-oriented policies are a necessary condition for financial integration and the development of emerging stock markets. Announced market-oriented policies may be reversed, however, and are initially not fully credible. We argue that sus

  7. Confidence building in emerging stock markets

    NARCIS (Netherlands)

    Perotti, E.C.; Laeven, L.; van Oijen, P.

    2000-01-01

    Investor confidence in reliable property rights and stable, market-oriented policies are a necessary condition for financial integration and the development of emerging stock markets. Announced market-oriented policies may be reversed, however, and are initially not fully credible. We argue that sus

  8. Confidence building in emerging stock markets

    NARCIS (Netherlands)

    Laeven, L.; Perotti, E.C.

    2001-01-01

    Investor confidence is a necessary condition for the development of emerging markets. Investors recognize that since market-oriented reform policies may be reversed or hindered, they face the risk of ex post policy changes with redistributive impact on investment returns. We argue that a sustained p

  9. The confidence effects of fiscal consolidations

    NARCIS (Netherlands)

    Beetsma, R.; Cimadomo, J.; Furtuna, O.; Giuliodori, M.

    2015-01-01

    We explore how fiscal consolidations affect private sector confidence, a possible channel for the transmission of fiscal policy that has received particular attention recently as a result of governments embarking on austerity trajectories in the aftermath of the crisis. Panel regressions based on

  10. Observed Consultation: Confidence and Accuracy of Assessors

    Science.gov (United States)

    Tweed, Mike; Ingham, Christopher

    2010-01-01

    Judgments made by the assessors observing consultations are widely used in the assessment of medical students. The aim of this research was to study judgment accuracy and confidence and the relationship between these. Assessors watched recordings of consultations, scoring the students on: a checklist of items; attributes of consultation; a…

  11. The confidence effects of fiscal consolidations

    NARCIS (Netherlands)

    Beetsma, R.M.W.J.; Cimadomo, J.; Furtuna, O.; Giuliodori, M.

    2014-01-01

    We explore how fiscal consolidations affect private sector confidence, a possible channel for the fiscal transmission that has received particular attention recently as a result of governments embarking on austerity trajectories in the aftermath of the crisis. Panel regressions based on the

  12. Observed Consultation: Confidence and Accuracy of Assessors

    Science.gov (United States)

    Tweed, Mike; Ingham, Christopher

    2010-01-01

    Judgments made by the assessors observing consultations are widely used in the assessment of medical students. The aim of this research was to study judgment accuracy and confidence and the relationship between these. Assessors watched recordings of consultations, scoring the students on: a checklist of items; attributes of consultation; a…

  13. Evaluating Measures of Optimism and Sport Confidence

    Science.gov (United States)

    Fogarty, Gerard J.; Perera, Harsha N.; Furst, Andrea J.; Thomas, Patrick R.

    2016-01-01

    The psychometric properties of the Life Orientation Test-Revised (LOT-R), the Sport Confidence Inventory (SCI), and the Carolina SCI (CSCI) were examined in a study involving 260 athletes. The study aimed to test the dimensional structure, convergent and divergent validity, and invariance over competition level of scores generated by these…

  14. Confidence building in emerging stock markets

    NARCIS (Netherlands)

    Perotti, E.C.; Laeven, L.; van Oijen, P.

    2000-01-01

    Investor confidence in reliable property rights and stable, market-oriented policies are a necessary condition for financial integration and the development of emerging stock markets. Announced market-oriented policies may be reversed, however, and are initially not fully credible. We argue that

  15. Nutrition Knowledge, Attitudes, and Confidence of Australian General Practice Registrars

    Directory of Open Access Journals (Sweden)

    Caryl A. Nowson

    2015-01-01

    Full Text Available Nutrition knowledge, attitudes, and confidence were assessed in General Practice Registrars (GPRs throughout Australia. Of approximately 6,000 GPRs invited to complete a nutrition survey, 93 respondents (2% completed the online survey, with 89 (20 males, 69 females providing demographic and educational information. Fifty-one percent had graduated from medical school within the last two years. From a list of 11 dietary strategies to reduce cardiovascular risk, respondents selected weight loss (84%, reducing saturated fats (90%, a maximum of two alcoholic drinks/day (82%, and increasing vegetables (83% as “highly appropriate” strategies, with only 51% indicating that salt reduction was “highly appropriate.” Two-thirds of registrars felt “moderately” (51% or “very” confident (16% providing nutrition advice. Most of them (84% recalled receiving information during training, but only 34% recalled having to demonstrate nutritional knowledge. The results indicate that this group of Australian GPRs understood most of the key dietary recommendations for reducing cardiovascular risk but lacked consensus regarding the recommendation to reduce salt intake and expressed mixed levels of confidence in providing nutritional advice. Appropriate nutrition education before and after graduation is recommended for GPRs to ensure the development of skills and confidence to support patients to make healthy dietary choices and help prevent chronic diseases.

  16. High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method

    Energy Technology Data Exchange (ETDEWEB)

    Higashiura, Akifumi, E-mail: hgsur-a@protein.osaka-u.ac.jp [Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Ohta, Kazunori; Masaki, Mika; Sato, Masaru [Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505 (Japan); Inaka, Koji [Maruwa Foods and Biosciences Inc., Nara 639-1123 (Japan); Tanaka, Hiroaki [Confocal Science Inc., Tokyo 101-0032 (Japan); Nakagawa, Atsushi [Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan)

    2013-11-01

    Using the high-pressure cryocooling method, the high-resolution X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. This is the first ultra-high-resolution structure obtained from a high-pressure cryocooled crystal. Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005 ▶) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method.

  17. Diets with high or low protein content and glycemic index for weight-loss maintenance

    DEFF Research Database (Denmark)

    Larsen, Thomas Meinert; Dalskov, Stine-Mathilde; Baak, Marleen van;

    2010-01-01

    Studies of weight-control diets that are high in protein or low in glycemic index have reached varied conclusions, probably owing to the fact that the studies had insufficient power.......Studies of weight-control diets that are high in protein or low in glycemic index have reached varied conclusions, probably owing to the fact that the studies had insufficient power....

  18. Parents' confidence in recommended childhood vaccinations: Extending the assessment, expanding the context.

    Science.gov (United States)

    Nowak, Glen J; Cacciatore, Michael A

    2017-03-04

    There has been significant and growing interest in vaccine hesitancy and confidence in the United States as well as across the globe. While studies have used confidence measures, few studies have provided in-depth assessments and no studies have assessed parents' confidence in vaccines in relationship to other frequently recommended health-related products for young children. This study used a nationally representative sample of 1000 US parents to identify confidence levels for recommended vaccinations, antibiotics, over-the-counter (OTC) medicines, and vitamins for children. The analyses examined associations between confidence ratings, vaccination behaviors and intentions, and trust in healthcare provider, along with associations between confidence ratings and use of the other health-related products. Parents' confidence in vaccines was relatively high and high relative to antibiotics, OTC medicines and vitamins. For all 4 health-related products examined, past product experience and knowledge of bad or adverse outcomes negatively impacted parents' confidence levels. Confidence levels were associated with both trust in advice from their child's healthcare provider and acceptance of healthcare provider recommendations. Parents in some groups, such as those with lower income and education levels, were more likely to have less confidence not just in vaccines, but also in antibiotics and OTC medicines for children. Overall, the findings extend understanding of vaccine confidence, including by placing it into a broader context.

  19. The Effect of Adaptive Confidence Strategies in Computer-Assisted Instruction on Learning and Learner Confidence

    Science.gov (United States)

    Warren, Richard Daniel

    2012-01-01

    The purpose of this research was to investigate the effects of including adaptive confidence strategies in instructionally sound computer-assisted instruction (CAI) on learning and learner confidence. Seventy-one general educational development (GED) learners recruited from various GED learning centers at community colleges in the southeast United…

  20. The Effect of Adaptive Confidence Strategies in Computer-Assisted Instruction on Learning and Learner Confidence

    Science.gov (United States)

    Warren, Richard Daniel

    2012-01-01

    The purpose of this research was to investigate the effects of including adaptive confidence strategies in instructionally sound computer-assisted instruction (CAI) on learning and learner confidence. Seventy-one general educational development (GED) learners recruited from various GED learning centers at community colleges in the southeast United…

  1. Novel condensation products having high activity to insolubilize proteins and protein-insolubilized products

    Energy Technology Data Exchange (ETDEWEB)

    Krasnobajew, V.; Boeniger, R.

    1980-01-01

    According to the invention a substantially more active product with respect to the fixing or insolubilization pf proteins, including enzymes, is obtained when 1,3 phenylenediamine is condensed with glutardialdehyde. One application of the process is the enzymatic hydrolysis of lactose in milk products by lactase.

  2. Regulation of Autophagy-Related Protein and Cell Differentiation by High Mobility Group Box 1 Protein in Adipocytes

    Directory of Open Access Journals (Sweden)

    Huanhuan Feng

    2016-01-01

    Full Text Available High mobility group box 1 protein (HMGB1 is a molecule related to the development of inflammation. Autophagy is vital to maintain cellular homeostasis and protect against inflammation of adipocyte injury. Our recent work focused on the relationship of HMGB1 and autophagy in 3T3-L1 cells. In vivo experimental results showed that, compared with the normal-diet group, the high-fat diet mice displayed an increase in adipocyte size in the epididymal adipose tissues. The expression levels of HMGB1 and LC3II also increased in epididymal adipose tissues in high-fat diet group compared to the normal-diet mice. The in vitro results indicated that HMGB1 protein treatment increased LC3II formation in 3T3-L1 preadipocytes in contrast to that in the control group. Furthermore, LC3II formation was inhibited through HMGB1 knockdown by siRNA. Treatment with the HMGB1 protein enhanced LC3II expression after 2 and 4 days but decreased the expression after 8 and 10 days among various differentiation stages of adipocytes. By contrast, FABP4 expression decreased on the fourth day and increased on the eighth day. Hence, the HMGB1 protein modulated autophagy-related proteins and lipid-metabolism-related genes in adipocytes and could be a new target for treatment of obesity and related metabolic diseases.

  3. Effects of high-protein vs. high- fat snacks on appetite control, satiety, and eating initiation in healthy women.

    Science.gov (United States)

    Ortinau, Laura C; Hoertel, Heather A; Douglas, Steve M; Leidy, Heather J

    2014-09-29

    The purpose of this study was to determine whether a high-protein afternoon yogurt snack improves appetite control, satiety, and reduces subsequent food intake compared to other commonly-consumed, energy dense, high-fat snacks. Twenty, healthy women (age: 27 ± 2 y; BMI: 23.4 ± 0.7 kg/m2) completed the randomized crossover design study which included 3, 8-h testing days comparing the following 160 kcal afternoon snacks: high-protein yogurt (14 g protein/25 g CHO/0 g fat); high-fat crackers (0 g protein/19 g CHO/9 g fat); and high-fat chocolate (2 g protein/19 g CHO/9 g fat). Participants were acclimated to each snack for 3 consecutive days. On day 4, the participants consumed a standardized breakfast and lunch; the respective snack was consumed 3-h post-lunch. Perceived hunger and fullness were assessed throughout the afternoon until dinner was voluntarily requested. An ad libitum dinner was then provided. The consumption of the yogurt snack led to greater reductions in afternoon hunger vs. chocolate (p chocolate snack (p chocolate (p < 0.05). No other differences were detected. These data suggest that, when compared to high-fat snacks, eating less energy dense, high-protein snacks like yogurt improves appetite control, satiety, and reduces subsequent food intake in healthy women.

  4. Bioinformatic analysis of CaBP/calneuron proteins reveals a family of highly conserved vertebrate Ca2+-binding proteins

    Directory of Open Access Journals (Sweden)

    Burgoyne Robert D

    2010-04-01

    Full Text Available Abstract Background Ca2+-binding proteins are important for the transduction of Ca2+ signals into physiological outcomes. As in calmodulin many of the Ca2+-binding proteins bind Ca2+ through EF-hand motifs. Amongst the large number of EF-hand containing Ca2+-binding proteins are a subfamily expressed in neurons and retinal photoreceptors known as the CaBPs and the related calneuron proteins. These were suggested to be vertebrate specific but exactly which family members are expressed outside of mammalian species had not been examined. Findings We have carried out a bioinformatic analysis to determine when members of this family arose and the conserved aspects of the protein family. Sequences of human members of the family obtained from GenBank were used in Blast searches to identify corresponding proteins encoded in other species using searches of non-redundant proteins, genome sequences and mRNA sequences. Sequences were aligned and compared using ClustalW. Some families of Ca2+-binding proteins are known to show a progressive expansion in gene number as organisms increase in complexity. In contrast, the results for CaBPs and calneurons showed that a full complement of CaBPs and calneurons are present in the teleost fish Danio rerio and possibly in cartilaginous fish. These findings suggest that the entire family of genes may have arisen at the same time during vertebrate evolution. Certain members of the family (for example the short form of CaBP1 and calneuron 1 are highly conserved suggesting essential functional roles. Conclusions The findings support the designation of the calneurons as a distinct sub-family. While the gene number for CaBPs/calneurons does not increase, a distinctive evolutionary change in these proteins in vertebrates has been an increase in the number of splice variants present in mammals.

  5. High-Fidelity DNA Sensing by Protein Binding Fluctuations

    CERN Document Server

    Tlusty, Tsvi; Libchaber, Albert; 10.1103/PhysRevLett.93.258103

    2010-01-01

    One of the major functions of RecA protein in the cell is to bind single-stranded DNA exposed upon damage, thereby triggering the SOS repair response.We present fluorescence anisotropy measurements at the binding onset, showing enhanced DNA length discrimination induced by adenosine triphosphate consumption. Our model explains the observed DNA length sensing as an outcome of out-of equilibrium binding fluctuations, reminiscent of microtubule dynamic instability. The cascade architecture of the binding fluctuations is a generalization of the kinetic proofreading mechanism. Enhancement of precision by an irreversible multistage pathway is a possible design principle in the noisy biological environment.

  6. Hydrolyzed collagen (gelatin decreases food efficiency and the bioavailability of high-quality protein in rats

    Directory of Open Access Journals (Sweden)

    Cláudia Cantelli Daud BORDIN

    2015-08-01

    Full Text Available Objective Although deficient in all indispensable amino acids, gelatin is used in protein-restricted diets. Food efficiency and protein quality of casein and gelatin mixtures in low protein diets in Wistar rats were investigated. Methods The rats were treated with protein-restricted diets (10.0 and 12.5% containing casein (control diets, casein with gelatin mixtures (4:1 of protein content, and gelatin as sources of protein. The food conversion ratio, protein efficiency ratio, relative and corrected protein efficiency ratio, true protein digestibility, and hepatic parameters were estimated. Results After 28 days of the experiment, food efficiency of 10.0% casein/gelatin diet decreased when compared to that of 10.0% casein diet, and the protein efficiency ratio of the casein/gelatin mixtures (10.0%=2.41 and 12.5%=2.03 were lower than those of the casein (10.0%=2.90 and 12.5%=2.32. After 42 days of the experiment, the weight of the liver of the animals treated with 10.0 and 12.5% casein/gelatin diets, and the liver protein retention of the 12.5% casein/gelatin diet group of animals were lower than those of the control group. Conclusion Gelatin decreases food efficiency and high-quality protein bioavailability in protein-restricted diets.

  7. Impact of an Advanced Cardiac Life Support Simulation Laboratory Experience on Pharmacy Student Confidence and Knowledge.

    Science.gov (United States)

    Maxwell, Whitney D; Mohorn, Phillip L; Haney, Jason S; Phillips, Cynthia M; Lu, Z Kevin; Clark, Kimberly; Corboy, Alex; Ragucci, Kelly R

    2016-10-25

    Objective. To assess the impact of an advanced cardiac life support (ACLS) simulation on pharmacy student confidence and knowledge. Design. Third-year pharmacy students participated in a simulation experience that consisted of team roles training, high-fidelity ACLS simulations, and debriefing. Students completed a pre/postsimulation confidence and knowledge assessment. Assessment. Overall, student knowledge assessment scores and student confidence scores improved significantly. Student confidence and knowledge changes from baseline were not significantly correlated. Conversely, a significant, weak positive correlation between presimulation studying and both presimulation confidence and presimulation knowledge was discovered. Conclusions. Overall, student confidence and knowledge assessment scores in ACLS significantly improved from baseline; however, student confidence and knowledge were not significantly correlated.

  8. Acidic ribosomal proteins and histone H3 from Leishmania present a high rate of divergence

    Directory of Open Access Journals (Sweden)

    Ysabel Montoya

    2000-08-01

    Full Text Available Another additional peculiarity in Leishmania will be discussed about of the amino acid divergence rate of three structural proteins: acidic ribosomal P1 and P2b proteins, and histone H3 by using multiple sequence alignment and dendrograms. These structural proteins present a high rate of divergence regarding to their homologous protein in Trypanosoma cruzi. At this regard, L. (V. peruviana P1 and T. cruzi P1 showed 57.4% of divergence rate. Likewise, L. (V. braziliensis histone H3 and acidic ribosomal P2 protein exhibited 31.8% and 41.7% respectively of rate of divergence in comparison with their homologous in T. cruzi.

  9. Low copper and high manganese levels in prion protein plaques

    Science.gov (United States)

    Johnson, Christopher J.; Gilbert, P.U.P.A.; Abrecth, Mike; Baldwin, Katherine L.; Russell, Robin E.; Pedersen, Joel A.; McKenzie, Debbie

    2013-01-01

    Accumulation of aggregates rich in an abnormally folded form of the prion protein characterize the neurodegeneration caused by transmissible spongiform encephalopathies (TSEs). The molecular triggers of plaque formation and neurodegeneration remain unknown, but analyses of TSE-infected brain homogenates and preparations enriched for abnormal prion protein suggest that reduced levels of copper and increased levels of manganese are associated with disease. The objectives of this study were to: (1) assess copper and manganese levels in healthy and TSE-infected Syrian hamster brain homogenates; (2) determine if the distribution of these metals can be mapped in TSE-infected brain tissue using X-ray photoelectron emission microscopy (X-PEEM) with synchrotron radiation; and (3) use X-PEEM to assess the relative amounts of copper and manganese in prion plaques in situ. In agreement with studies of other TSEs and species, we found reduced brain levels of copper and increased levels of manganese associated with disease in our hamster model. We also found that the in situ levels of these metals in brainstem were sufficient to image by X-PEEM. Using immunolabeled prion plaques in directly adjacent tissue sections to identify regions to image by X-PEEM, we found a statistically significant relationship of copper-manganese dysregulation in prion plaques: copper was depleted whereas manganese was enriched. These data provide evidence for prion plaques altering local transition metal distribution in the TSE-infected central nervous system.

  10. SOCIAL MEDIA – VITAL INSTRUMENT IN GAINING CONSUMERS CONFIDENCE

    Directory of Open Access Journals (Sweden)

    Mirela-Cristina VOICU

    2016-06-01

    Full Text Available Given that, currently, the consumer has become more demanding and organizations face some of the greatest challenges due to the economic climate of recent years, the need to build and cultivate strong relationships has become vital not only for the company's success but also for its survival. And solid relationships are built over time through confidence. Trust is one of the most important elements in the process of purchasing and consumer loyalty; it is difficult to obtain but easy to lose. Companies that are enjoying a high degree of confidence benefit from best quotations for their shares, higher profits and a better retention of the best employees. The effects of the lack of confidence are obvious (unsatisfied consumers, lost sales and very expensive for the company. In this context, through the following paper we seek to bring more understanding on how a company can gain the confidence of consumers given that the forms of communication that consumers prefer and that are gaining momentum currently, are taking place online, especially in the social media.

  11. Nurturing Confidence in Preservice Elementary Science Teachers

    Science.gov (United States)

    Bleicher, Robert E.

    2007-12-01

    This study examined changes in personal science teaching self-efficacy (PSTE), outcome expectancy (STOE), and science conceptual understanding and relationships among these in preservice teachers. Seventy preservice teachers enrolled in science teaching methods courses participated in this study. PSTE, STOE, and science conceptual understanding increased significantly during participation in the course. The study established that novice learners with minimal prior knowledge could not be expected to understand and employ core concepts in their learning schema without extensive guidance. The relationship between science learning confidence and science teaching confidence has not been theoretically delineated in the area of science teacher education. Findings suggest there may be important connections between the 2 for preservice teachers that would be fruitful areas for future research.

  12. Confidence leak in perceptual decision-making

    Science.gov (United States)

    Rahnev, Dobromir; Koizumi, Ai; McCurdy, Li Yan; D’Esposito, Mark; Lau, Hakwan

    2015-01-01

    We live in a continuous environment in which the visual scene changes on a slow timescale. It has been shown that, to exploit such environmental stability, the brain creates a “continuity field” such that objects seen seconds ago influence the perception of current objects. What is unknown is whether a similar mechanism exists at the level of our metacognitive representations. In three experiments we demonstrate a robust inter-task “confidence leak” that cannot be explained by response priming or attentional fluctuations. Observers’ ability to modulate this confidence leak predicted higher capacity for metacognition as well as greater gray matter volume in the prefrontal cortex. A model based on normative principles from Bayesian inference explained the results by postulating that observers subjectively estimate the perceptual signal strength in a stable environment. These results point to the existence of a novel metacognitive mechanism mediated by regions in prefrontal cortex. PMID:26408037

  13. ;Agreement; in the IPCC Confidence measure

    Science.gov (United States)

    Rehg, William; Staley, Kent

    2017-02-01

    The Intergovernmental Panel on Climate Change (IPCC) has, in its most recent Assessment Report (AR5), articulated guidelines for evaluating and communicating uncertainty that include a qualitative scale of confidence. We examine one factor included in that scale: the ;degree of agreement.; Some discussions of the degree of agreement in AR5 suggest that the IPCC is employing a consensus-oriented social epistemology. We consider the application of the degree of agreement factor in practice in AR5. Our findings, though based on a limited examination, suggest that agreement attributions do not so much track the overall consensus among investigators as the degree to which relevant research findings substantively converge in offering support for IPCC claims. We articulate a principle guiding confidence attributions in AR5 that centers not on consensus but on the notion of support. In concluding, we tentatively suggest a pluralist approach to the notion of support.

  14. Learning about confidence intervals with software R

    OpenAIRE

    Gariela Gonçalves; Luís Afonso; Marta Ferreira; Teresa Ferro; Nascimento, Maria M.

    2013-01-01

    This work was to study the feasibility of implementing a teaching method that employs software, in a Computational Mathematics course, involving students and teachers through the use of the statistical software R in carrying out practical work, such as strengthening the traditional teaching. The statistical inference, namely the determination of confidence intervals, was the content selected for this experience. It was intended show, first of all, that it is possible to promote, through t...

  15. Understanding Confidence Intervals With Visual Representations

    OpenAIRE

    Navruz, Bilgin; DELEN, Erhan

    2014-01-01

    In the present paper, we showed how confidence intervals (CIs) are valuable and useful in research studies when they are used in the correct form with correct interpretations. The sixth edition of the APA (2010) Publication Manual strongly recommended reporting CIs in research studies, and it was described as “the best reporting strategy” (p. 34). Misconceptions and correct interpretations of CIs were presented from several textbooks. In addition, limitations of the null hypothesis statistica...

  16. Self-Confidence and Social Interactions

    OpenAIRE

    Roland Benabou; Jean Tirole

    2000-01-01

    This paper studies the interactions between an individual's self esteem and his social environment in the workplace, at school, and in personal relationships. Because a person generally has only imperfect knowledge of his own abilities, people who derive benefits from his performance (parent, spouse, friend, teacher, manager, etc.) have incentives to manipulate his self confidence. We first study situations where an informed principal chooses an incentive structure, such as offering payments ...

  17. Confidence Sets for a Change-Point.

    Science.gov (United States)

    1986-10-01

    probability credible set for j. In fact, even without the explicit evaluation in (1), one knows from a general theorem of Stein (1965) and Hora and...confidence sets with smallest expected measure, Ann. Statist. , 10, 1283-94. Hora , R. B. and Buehler, R. J. (1966), Fiducial theory and invariant...simple cumulative sum type statistic for the change-point problem -’-"C with zero -one observations, Biometrika 67, 79-84. Raferty, A. E. and Akman, V

  18. Machine learning in computational biology to accelerate high-throughput protein expression

    DEFF Research Database (Denmark)

    Sastry, Anand; Monk, Jonathan M.; Tegel, Hanna

    2017-01-01

    and machine learning identifies protein properties that hinder the HPA high-throughput antibody production pipeline. We predict protein expression and solubility with accuracies of 70% and 80%, respectively, based on a subset of key properties (aromaticity, hydropathy and isoelectric point). We guide...... the selection of protein fragments based on these characteristics to optimize high-throughput experimentation. Availability and implementation: We present the machine learning workflow as a series of IPython notebooks hosted on GitHub (https://github.com/SBRG/Protein_ML). The workflow can be used as a template...

  19. The role of high-protein diets in body weight management and health.

    Science.gov (United States)

    Te Morenga, Lisa; Mann, Jim

    2012-08-01

    Studies examining the health benefits of high-protein diets typical of most affluent and many developing countries are not consistent. Prospective epidemiological studies relating dietary protein to clinical and metabolic endpoints suggest increased weight gain and increased risk of diabetes amongst those with a high protein intake and an increased risk of cancer with high intakes of red meat, but lower blood pressure and possibly a reduced risk of heart disease with higher protein intakes. The potential for high-protein diets to confer greater benefit than other diets has been examined using ad libitum and energy restricted diets. Of greatest interest have been the comparisons between high-protein and high-carbohydrate diets. Many trials have reported greater weight loss especially in the context of ad libitum diets over the short-to medium-term, sparing of lean body mass, lowering of triglyceride levels, improved HDL: total cholesterol ratio and improved glycaemic control. Limited data regarding insulin sensitivity are less consistent. A major difficulty in interpreting the results of these studies is that carbohydrate quality has not been taken into account. Furthermore, longer term comparisons of weight reducing diets differing in macronutrient composition have reported similar outcomes, suggesting that compliance is a more important consideration. Nevertheless dietary patterns with high-protein intakes are appropriate for weight reduction and weight maintenance and may be useful for those who have high triglyceride levels and other features of the metabolic syndrome.

  20. Influence of Acute High Glucose on Protein Abundance Changes in Murine Glomerular Mesangial Cells

    Directory of Open Access Journals (Sweden)

    Michelle T. Barati

    2016-01-01

    Full Text Available The effects of acute exposure to high glucose levels as experienced by glomerular mesangial cells in postprandial conditions and states such as in prediabetes were investigated using proteomic methods. Two-dimensional gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry methods were used to identify protein expression patterns in immortalized rat mesangial cells altered by 2 h high glucose (HG growth conditions as compared to isoosmotic/normal glucose control (NG⁎ conditions. Unique protein expression changes at 2 h HG treatment were measured for 51 protein spots. These proteins could be broadly grouped into two categories: (1 proteins involved in cell survival/cell signaling and (2 proteins involved in stress response. Immunoblot experiments for a protein belonging to both categories, prohibitin (PHB, supported a trend for increased total expression as well as significant increases in an acidic PHB isoform. Additional studies confirmed the regulation of proteasomal subunit alpha-type 2 and the endoplasmic reticulum chaperone and oxidoreductase PDI (protein disulfide isomerase, suggesting altered ER protein folding capacity and proteasomal function in response to acute HG. We conclude that short term high glucose induces subtle changes in protein abundances suggesting posttranslational modifications and regulation of pathways involved in proteostasis.

  1. Confidence and coverage for Bland-Altman limits of agreement and their approximate confidence intervals.

    Science.gov (United States)

    Carkeet, Andrew; Goh, Yee Teng

    2016-09-01

    Bland and Altman described approximate methods in 1986 and 1999 for calculating confidence limits for their 95% limits of agreement, approximations which assume large subject numbers. In this paper, these approximations are compared with exact confidence intervals calculated using two-sided tolerance intervals for a normal distribution. The approximations are compared in terms of the tolerance factors themselves but also in terms of the exact confidence limits and the exact limits of agreement coverage corresponding to the approximate confidence interval methods. Using similar methods the 50th percentile of the tolerance interval are compared with the k values of 1.96 and 2, which Bland and Altman used to define limits of agreements (i.e. [Formula: see text]+/- 1.96Sd and [Formula: see text]+/- 2Sd). For limits of agreement outer confidence intervals, Bland and Altman's approximations are too permissive for sample sizes confidence limits the approximations are poorer, being permissive for sample sizes of confidence intervals for 95% limits of agreements, based on two-sided tolerance factors, can be calculated easily based on tables and should be used in preference to the approximate methods, especially for small sample sizes. © The Author(s) 2016.

  2. Neural network definitions of highly predictable protein secondary structure classes

    Energy Technology Data Exchange (ETDEWEB)

    Lapedes, A. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States); Steeg, E. [Toronto Univ., ON (Canada). Dept. of Computer Science; Farber, R. [Los Alamos National Lab., NM (United States)

    1994-02-01

    We use two co-evolving neural networks to determine new classes of protein secondary structure which are significantly more predictable from local amino sequence than the conventional secondary structure classification. Accurate prediction of the conventional secondary structure classes: alpha helix, beta strand, and coil, from primary sequence has long been an important problem in computational molecular biology. Neural networks have been a popular method to attempt to predict these conventional secondary structure classes. Accuracy has been disappointingly low. The algorithm presented here uses neural networks to similtaneously examine both sequence and structure data, and to evolve new classes of secondary structure that can be predicted from sequence with significantly higher accuracy than the conventional classes. These new classes have both similarities to, and differences with the conventional alpha helix, beta strand and coil.

  3. High pressure NMR study of a small protein, gurmarin

    Energy Technology Data Exchange (ETDEWEB)

    Inoue, Kyoko; Yamada, Hiroaki [Kobe University, Division of Molecular Science, Graduate School of Science and Technology, and Department of Chemistry, Faculty of Science (Japan); Imoto, Toshiaki [Tottori University, Faculty of Medicine (Japan); Akasaka, Kazuyuki [Kobe University, Division of Molecular Science, Graduate School of Science and Technology, and Department of Chemistry, Faculty of Science (Japan)

    1998-11-15

    The effect of pressure on the structure of gurmarin, a globular, 35-residue protein from Gymnema sylvestre, was studied in aqueous environment (95% 1H2O/5% 2H2O, pH 2.0) with an on-line variable pressure NMR system operating at 750 MHz. Two-dimensional TOCSY and NOESY spectra were measured as functions of pressure between 1 and 2000 bar at 40 deg. C . Practically all the proton signals of gurmarin underwent some shifts with pressure, showing that the entire protein structure responds to, and is altered by, pressure. Most amide protons showed different degrees of low field shifts with pressure, namely 0-0.2 ppm with an average of 0.051 ppm at 2000 bar, showing that they are involved in hydrogen bonding and that these hydrogen bonds are shortened by pressure by different degrees. The tendency was also confirmed that the chemical shifts of the amide protons exposed to the solvent (water) are more sensitive to pressure than those internally hydrogen bonded with carbonyls. The pressure-induced shifts of the H{alpha} signals of the residues in the {beta}-sheet showed a negative correlation with the 'folding' shifts (difference between the shift at 1 bar and that of a random coil), suggesting that the main-chain torsion angles of the {beta}-sheet are slightly altered by pressure. Significant pressure-induced shifts were also observed for the side-chain protons (but no larger than 10% of the 'folding' shifts), demonstrating that the tertiary structure of gurmarin is also affected by pressure. Finally, the linearity of the pressure-induced shifts suggests that the compressibility of gurmarin is invariant in the pressure range between 1 and 2000 bar.

  4. Lower weight gain and hepatic lipid content in hamsters fed high fat diets supplemented with white rice protein, brown rice protein, soy protein, and their hydrolysates.

    Science.gov (United States)

    Zhang, Huijuan; Bartley, Glenn E; Mitchell, Cheryl R; Zhang, Hui; Yokoyama, Wallace

    2011-10-26

    The physiological effects of the hydrolysates of white rice protein (WRP), brown rice protein (BRP), and soy protein (SP) hydrolyzed by the food grade enzyme, alcalase2.4 L, were compared to the original protein source. Male Syrian Golden hamsters were fed high-fat diets containing either 20% casein (control) or 20% extracted proteins or their hydrolysates as the protein source for 3 weeks. The brown rice protein hydrolysate (BRPH) diet group reduced weight gain 76% compared with the control. Animals fed the BRPH supplemented diet also had lower final body weight, liver weight, very low density lipoprotein cholesterol (VLDL-C), and liver cholesterol, and higher fecal fat and bile acid excretion than the control. Expression levels of hepatic genes for lipid oxidation, PPARα, ACOX1, and CPT1, were highest for hamsters fed the BRPH supplemented diet. Expression of CYP7A1, the gene regulating bile acid synthesis, was higher in all test groups. Expression of CYP51, a gene coding for an enzyme involved in cholesterol synthesis, was highest in the BRPH diet group. The results suggest that BRPH includes unique peptides that reduce weight gain and hepatic cholesterol synthesis.

  5. Phenylketonuria : High plasma phenylalanine decreases cerebral protein synthesis

    NARCIS (Netherlands)

    Hoeksma, Marieke; Reijngoud, Dirk-Jan; Pruim, Jan; de Valk, Harold W.; Paans, Anne M. J.; van Spronsen, Francjan J.

    2009-01-01

    Left untreated, phenylketonuria biochemically results in high phenylalanine concentrations in blood and tissues, and clinically especially in severe mental retardation. Treatment consists of severe dietary restriction of phenylalanine with more or less normal intellectual outcome as result when star

  6. High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder.

    Science.gov (United States)

    Peng, Zhenling; Kurgan, Lukasz

    2015-10-15

    Intrinsically disordered proteins and regions (IDPs and IDRs) lack stable 3D structure under physiological conditions in-vitro, are common in eukaryotes, and facilitate interactions with RNA, DNA and proteins. Current methods for prediction of IDPs and IDRs do not provide insights into their functions, except for a handful of methods that address predictions of protein-binding regions. We report first-of-its-kind computational method DisoRDPbind for high-throughput prediction of RNA, DNA and protein binding residues located in IDRs from protein sequences. DisoRDPbind is implemented using a runtime-efficient multi-layered design that utilizes information extracted from physiochemical properties of amino acids, sequence complexity, putative secondary structure and disorder and sequence alignment. Empirical tests demonstrate that it provides accurate predictions that are competitive with other predictors of disorder-mediated protein binding regions and complementary to the methods that predict RNA- and DNA-binding residues annotated based on crystal structures. Application in Homo sapiens, Mus musculus, Caenorhabditis elegans and Drosophila melanogaster proteomes reveals that RNA- and DNA-binding proteins predicted by DisoRDPbind complement and overlap with the corresponding known binding proteins collected from several sources. Also, the number of the putative protein-binding regions predicted with DisoRDPbind correlates with the promiscuity of proteins in the corresponding protein-protein interaction networks. Webserver: http://biomine.ece.ualberta.ca/DisoRDPbind/.

  7. Assessment of the Protein-Protein Interactions in a Highly Concentrated Antibody Solution by Using Raman Spectroscopy.

    Science.gov (United States)

    Ota, Chikashi; Noguchi, Shintaro; Nagatoishi, Satoru; Tsumoto, Kouhei

    2016-04-01

    To investigate the protein-protein interactions of a highly concentrated antibody solution that could cause oligomerization or aggregation and to develop a better understanding of the optimization of drug formulations. In this study, we used Raman spectroscopy to investigate the structure and interactions of a highly concentrated antibody solution over a wide range of concentrations (10-200 mg/mL) with the aid of a multivariate analysis. Our analysis of the amide I band, I 856 /I 830 of Tyr, and the relative intensity at 1004 cm(-1) of the Phe and OH stretching region at around 3000 cm(-1) showed that across this wide range of concentrations, the secondary structure of the IgG molecules did not change; however, short-range attractive interactions around the Tyr and Phe residues occurred as the distance between the IgG molecules decreased with increasing concentration. Analysis of the OH stretching region at around 3000 cm(-1) showed that these short-range attractive interactions correlated with the amount of hydrated water around the IgG molecules. Our data show that Raman spectroscopy can provide valuable information of the protein-protein interactions based on conformational approaches to support conventional colloidal approaches, especially for analyses of highly concentrated solutions.

  8. Highly hydrophilic proteins in prokaryotes and eukaryotes are common during conditions of water deficit.

    Science.gov (United States)

    Garay-Arroyo, A; Colmenero-Flores, J M; Garciarrubio, A; Covarrubias, A A

    2000-02-25

    The late embryogenesis abundant (LEA) proteins are plant proteins that are synthesized at the onset of desiccation in maturing seeds and in vegetative organs exposed to water deficit. Here, we show that most LEA proteins are comprised in a more widespread group, which we call "hydrophilins." The defining characteristics of hydrophilins are high glycine content (>6%) and a high hydrophilicity index (>1.0). By data base searching, we show that this criterion selectively differentiates most known LEA proteins as well as additional proteins from different taxons. We found that within the genomes of Escherichia coli and Saccharomyces cerevisiae, only 5 and 12 proteins, respectively, meet our criterion. Despite their deceivingly loose definition, hydrophilins usually represent stress. Evidence for the participation of one of the E. coli hydrophilins in the adaptive response to hyperosmotic conditions is presented. Apparently, hydrophilins represent analogous adaptations to a common problem in such diverse taxons as prokaryotes and eukaryotes.

  9. Simulators help improve student confidence to acquire skills in urology.

    Science.gov (United States)

    Rodríguez-Díez, M C; Díez, N; Merino, I; Velis, J M; Tienza, A; Robles-García, J E

    2014-01-01

    To know the level of confidence of fifth year medical students in order to perform maneuvers in bladder catheterization and rectal examination before and after training with simulators. To be able to assess student satisfaction regarding the use of the simulation as a learning method. The study was conducted in the Simulation Center of the Faculty of Medicine. A total of 173 students who completed a practical workshop on the subject of Urology participated. The students were asked to answer anonymous questionnaires on their level of confidence in performing a bladder catheterization and rectal examination before and after the workshop as well as their satisfaction in using the simulation as a training tool. The workshops were organized using groups of 10 students. A teacher or a resident in that area of expertise supervised each student individually, resolving their doubts and teaching them the proper technique. All the evaluations made on the different abilities were significantly higher after training (P<.001). Significant differences were found in the confidence level between men and women before the training regarding male urethral catheterization maneuvers and recognition of normal or pathological prostate, The confidence level was lower in women (P<.05). These differences disappeared after training. The level of overall satisfaction with the workshop was high, going from 4.47 ± 0.9 to a maximum score of 5. Simulation is a training method that helps improve the confidence of the medical student in performing a bladder catheterization and digital rectal examination. Copyright © 2013 AEU. Published by Elsevier Espana. All rights reserved.

  10. The relationship between confidence in charitable organizations and volunteering revisited

    NARCIS (Netherlands)

    Bekkers, René H.F.P.; Bowman, Woods

    2009-01-01

    Confidence in charitable organizations (charitable confidence) would seem to be an important prerequisite for philanthropic behavior. Previous research relying on cross-sectional data has suggested that volunteering promotes charitable confidence and vice versa. This research note, using new longitu

  11. The relationship between confidence in charitable organizations and volunteering revisited

    NARCIS (Netherlands)

    Bekkers, René H.F.P.; Bowman, Woods

    2009-01-01

    Confidence in charitable organizations (charitable confidence) would seem to be an important prerequisite for philanthropic behavior. Previous research relying on cross-sectional data has suggested that volunteering promotes charitable confidence and vice versa. This research note, using new

  12. High hydrostatic pressure processing: a method having high success potential in pollen protein extraction

    Science.gov (United States)

    Murat Altuner, Ergin; Çeter, Talip; Alpas, Hami

    2012-06-01

    Even a single peptide that is present in the pollen wall and cytoplasm could cause pollen allergy. To produce skin-prick test kits, the first step is the extraction of these molecules. In this study, Cedrus atlantica pollens were subjected to 220 and 330 MPa for 10 and 30 min in order to extract these molecules. After high hydrostatic pressure processing (HHPP), the total amounts of proteins (TAPs) are measured and compared with the results of the conventional extraction method (CEM). As a result, the TAPs extracted by HHPP is 18.0210 μ g/mL at 220 MPa for 10 min, 22.5770 μ g/mL at 220 MPa for 30 min, 23.3810 μ g/mL at 330 MPa for 10 min and 25.9270 μ g/mL at 330 MPa for 30 min, while this is 1.9460 μ g/mL in 24 h by the CEM. In addition to these results, visual pollen deformation and eruption, pollen wall and surface damage have also been observed.

  13. Locus heterogeneity disease genes encode proteins with high interconnectivity in the human protein interaction network.

    Science.gov (United States)

    Keith, Benjamin P; Robertson, David L; Hentges, Kathryn E

    2014-01-01

    Mutations in genes potentially lead to a number of genetic diseases with differing severity. These disease genes have been the focus of research in recent years showing that the disease gene population as a whole is not homogeneous, and can be categorized according to their interactions. Locus heterogeneity describes a single disorder caused by mutations in different genes each acting individually to cause the same disease. Using datasets of experimentally derived human disease genes and protein interactions, we created a protein interaction network to investigate the relationships between the products of genes associated with a disease displaying locus heterogeneity, and use network parameters to suggest properties that distinguish these disease genes from the overall disease gene population. Through the manual curation of known causative genes of 100 diseases displaying locus heterogeneity and 397 single-gene Mendelian disorders, we use network parameters to show that our locus heterogeneity network displays distinct properties from the global disease network and a Mendelian network. Using the global human proteome, through random simulation of the network we show that heterogeneous genes display significant interconnectivity. Further topological analysis of this network revealed clustering of locus heterogeneity genes that cause identical disorders, indicating that these disease genes are involved in similar biological processes. We then use this information to suggest additional genes that may contribute to diseases with locus heterogeneity.

  14. The role of cholesteryl ester transfer protein and phospholipid transfer protein in the remodeling of plasma high-density lipoproteins.

    Science.gov (United States)

    Lagrost, L

    1997-08-01

    Recent studies demonstrated that alterations in the size distribution of high-density lipoproteins (HDLs) constitute reliable markers for the risk of coronary artery disease. These observations suggested that the determination of the size distribution of HDL subpopulations by using polyacrylamide gradient gel electrophoresis might constitute an effective tool in clinical practice for the detection of patients with elevated risk. During the last decade, concordant observations revealed that all the HDL subpopulations are metabolically interrelated, and their relative abundances are dependent on the activity of several plasma factors, among them the cholesteryl ester transfer protein (CETP) and the phospholipid transfer protein (PLTP). As reviewed in the present article, although both CETP and PLTP can promote the size redistribution or conversion of HDL, the two plasma lipid transfer proteins can alter differently the plasma HDL distribution profile through distinct mechanisms. (Trends Cardiovasc Med 1997;7:218-224). © 1997, Elsevier Science Inc.

  15. A combinatorial histidine scanning library approach to engineer highly pH-dependent protein switches.

    Science.gov (United States)

    Murtaugh, Megan L; Fanning, Sean W; Sharma, Tressa M; Terry, Alexandra M; Horn, James R

    2011-09-01

    There is growing interest in the development of protein switches, which are proteins whose function, such as binding a target molecule, can be modulated through environmental triggers. Efforts to engineer highly pH sensitive protein-protein interactions typically rely on the rational introduction of ionizable groups in the protein interface. Such experiments are typically time intensive and often sacrifice the protein's affinity at the permissive pH. The underlying thermodynamics of proton-linkage dictate that the presence of multiple ionizable groups, which undergo a pK(a) change on protein binding, are necessary to result in highly pH-dependent binding. To test this hypothesis, a novel combinatorial histidine library was developed where every possible combination of histidine and wild-type residue is sampled throughout the interface of a model anti-RNase A single domain VHH antibody. Antibodies were coselected for high-affinity binding and pH-sensitivity using an in vitro, dual-function selection strategy. The resulting antibodies retained near wild-type affinity yet became highly sensitive to small decreases in pH, drastically decreasing their binding affinity, due to the incorporation of multiple histidine groups. Several trends were observed, such as histidine "hot-spots," which will help enhance the development of pH switch proteins as well as increase our understanding of the role of ionizable residues in protein interfaces. Overall, the combinatorial approach is rapid, general, and robust and should be capable of producing highly pH-sensitive protein affinity reagents for a number of different applications. Copyright © 2011 The Protein Society.

  16. High-Affinity, Small-Molecule Peptidomimetic Inhibitors of MLL1/WDR5 Protein-Protein Interaction

    Energy Technology Data Exchange (ETDEWEB)

    Karatas, Hacer; Townsend, Elizabeth C; Cao, Fang; Chen, Yong; Bernard, Denzil; Liu, Liu; Lei, Ming; Dou, Yali; Wang, Shaomeng [Michigan; (HHMI)

    2013-02-12

    Mixed lineage leukemia 1 (MLL1) is a histone H3 lysine 4 (H3K4) methyltransferase, and targeting the MLL1 enzymatic activity has been proposed as a novel therapeutic strategy for the treatment of acute leukemia harboring MLL1 fusion proteins. The MLL1/WDR5 protein–protein interaction is essential for MLL1 enzymatic activity. In the present study, we designed a large number of peptidomimetics to target the MLL1/WDR5 interaction based upon -CO-ARA-NH–, the minimum binding motif derived from MLL1. Our study led to the design of high-affinity peptidomimetics, which bind to WDR5 with Ki < 1 nM and function as potent antagonists of MLL1 activity in a fully reconstituted in vitro H3K4 methyltransferase assay. Determination of co-crystal structures of two potent peptidomimetics in complex with WDR5 establishes their structural basis for high-affinity binding to WDR5. Evaluation of one such peptidomimetic, MM-102, in bone marrow cells transduced with MLL1-AF9 fusion construct shows that the compound effectively decreases the expression of HoxA9 and Meis-1, two critical MLL1 target genes in MLL1 fusion protein mediated leukemogenesis. MM-102 also specifically inhibits cell growth and induces apoptosis in leukemia cells harboring MLL1 fusion proteins. Our study provides the first proof-of-concept for the design of small-molecule inhibitors of the WDR5/MLL1 protein–protein interaction as a novel therapeutic approach for acute leukemia harboring MLL1 fusion proteins.

  17. High concentrations of protein test substances may have non-toxic effects on Daphnia magna: implications for regulatory study designs and ecological risk assessments for GM crops.

    Science.gov (United States)

    Raybould, Alan; Burns, Andrea; Hamer, Mick

    2014-01-01

    Laboratory testing for possible adverse effects of insecticidal proteins on non-target organisms (NTOs) is an important part of many ecological risk assessments for regulatory decision-making about the cultivation of insect-resistant genetically modified (IRGM) crops. To increase confidence in the risk assessments, regulatory guidelines for effects testing specify that representative surrogate species for NTOs are exposed to concentrations of insecticidal proteins that are in excess of worst-case predicted exposures in the field. High concentrations in effects tests are achieved by using protein test substances produced in microbes, such as Escherichia coli. In a study that exposed Daphnia magna to a single high concentration of a microbial test substance containing Vip3Aa20, the insecticidal protein in MIR162 maize, small reductions in growth were observed. These effects were surprising as many other studies strongly suggest that the activity of Vip3Aa20 is limited to Lepidoptera. A plausible explanation for the effect on growth is that high concentrations of test substance have a non-toxic effect on Daphnia, perhaps by reducing its feeding rate. A follow-up study tested that hypothesis by exposing D. magna to several concentrations of Vip3Aa20, and a high concentration of a non-toxic protein, bovine serum albumin (BSA). Vip3Aa20 and BSA had sporadic effects on the reproduction and growth of D. magna. The pattern of the effects suggests that they result from non-toxic effects of high concentrations of protein, and not from toxicity. The implications of these results for regulatory NTO effects testing and ERA of IRGM crops are discussed.

  18. High concentrations of protein test substances may have non-toxic effects on Daphnia magna: Implications for regulatory study designs and ecological risk assessments for GM crops

    Science.gov (United States)

    Raybould, Alan; Burns, Andrea; Hamer, Mick

    2014-01-01

    Laboratory testing for possible adverse effects of insecticidal proteins on non-target organisms (NTOs) is an important part of many ecological risk assessments for regulatory decision-making about the cultivation of insect-resistant genetically modified (IRGM) crops. To increase confidence in the risk assessments, regulatory guidelines for effects testing specify that representative surrogate species for NTOs are exposed to concentrations of insecticidal proteins that are in excess of worst-case predicted exposures in the field. High concentrations in effects tests are achieved by using protein test substances produced in microbes, such as Escherichia coli. In a study that exposed Daphnia magna to a single high concentration of a microbial test substance containing Vip3Aa20, the insecticidal protein in MIR162 maize, small reductions in growth were observed. These effects were surprising as many other studies strongly suggest that the activity of Vip3Aa20 is limited to Lepidoptera. A plausible explanation for the effect on growth is that high concentrations of test substance have a non-toxic effect on Daphnia, perhaps by reducing its feeding rate. A follow-up study tested that hypothesis by exposing D. magna to several concentrations of Vip3Aa20, and a high concentration of a non-toxic protein, bovine serum albumin (BSA). Vip3Aa20 and BSA had sporadic effects on the reproduction and growth of D. magna. The pattern of the effects suggests that they result from non-toxic effects of high concentrations of protein, and not from toxicity. The implications of these results for regulatory NTO effects testing and ERA of IRGM crops are discussed. PMID:25523175

  19. A high-throughput method to examine protein-nucleotide interactions identifies targets of the bacterial transcriptional regulatory protein fur.

    Directory of Open Access Journals (Sweden)

    Chunxiao Yu

    Full Text Available The Ferric uptake regulatory protein (Fur is a transcriptional regulatory protein that functions to control gene transcription in response to iron in a number of pathogenic bacteria. In this study, we applied a label-free, quantitative and high-throughput analysis method, Interferometric Reflectance Imaging Sensor (IRIS, to rapidly characterize Fur-DNA interactions in vitro with predicted Fur binding sequences in the genome of Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhea. IRIS can easily be applied to examine multiple protein-protein, protein-nucleotide and nucleotide-nucleotide complexes simultaneously and demonstrated here that seventy percent of the predicted Fur boxes in promoter regions of iron-induced genes bound to Fur in vitro with a range of affinities as observed using this microarray screening technology. Combining binding data with mRNA expression levels in a gonococcal fur mutant strain allowed us to identify five new gonococcal genes under Fur-mediated direct regulation.

  20. Optimisation of ultrafiltration of a highly viscous protein solution using spiral-wound modules

    DEFF Research Database (Denmark)

    Lipnizki, Jens; Casani, S.; Jonsson, Gunnar Eigil

    2005-01-01

    The ultrafiltration process of highly viscous protein process water with spiral-wound modules was optimised by analysing the fouling and developing a strategy to reduce it. It was shown that the flux reduction during filtration is mainly caused by the adsorption of proteins on the membrane and no...

  1. Effect of high hydrostatic pressure processing on in vitro digestion of milk proteins and fats

    Science.gov (United States)

    The use of high hydrostatic pressure processing (HPP) is increasing in popularity in the food industry. Its ability to modify milk proteins and fats suggests that it may be useful in creating foods that suppress appetite; however, its effect on the digestibility of proteins and fats is unclear. The...

  2. Critical parameters in cost-effective alkaline extraction for high protein yield from leaves

    NARCIS (Netherlands)

    Zhang, C.; Sanders, J.P.M.; Bruins, M.E.

    2014-01-01

    Leaves are potential resources for feed or food, but their applications are limited due to a high proportion of insoluble protein and inefficient processing. To overcome these problems, parameters of alkaline extraction were evaluated using green tea residue (GTR). Protein extraction could be maximi

  3. Expression and Characterisation of Recombinant Rhodocyclus tenuis High Potential Iron-Sulphur Protein

    DEFF Research Database (Denmark)

    Caspersen, Michael Bjerg; Bennet, K.; Christensen, Hans Erik Mølager

    2000-01-01

    The high potential iron-sulfur protein (HiPIP) from Rhodocyclus tenuis strain 2761 has been overproduced in Escherichia coli from its structural gene, purified to apparent homogeneity, and then characterized by an array of methods. UV-visible spectra of the reduced and oxidized recombinant protein...

  4. Highly Elastic and Conductive Human-Based Protein Hybrid Hydrogels.

    Science.gov (United States)

    Annabi, Nasim; Shin, Su Ryon; Tamayol, Ali; Miscuglio, Mario; Bakooshli, Mohsen Afshar; Assmann, Alexander; Mostafalu, Pooria; Sun, Jeong-Yun; Mithieux, Suzanne; Cheung, Louis; Tang, Xiaowu Shirley; Weiss, Anthony S; Khademhosseini, Ali

    2016-01-01

    A highly elastic hybrid hydrogel of methacryloyl-substituted recombinant human tropoelastin (MeTro) and graphene oxide (GO) nanoparticles are developed. The synergistic effect of these two materials significantly enhances both ultimate strain (250%), reversible rotation (9700°), and the fracture energy (38.8 ± 0.8 J m(-2) ) in the hybrid network. Furthermore, improved electrical signal propagation and subsequent contraction of the muscles connected by hybrid hydrogels are observed in ex vivo tests.

  5. Textural performance of crosslinked or reduced-calcium milk protein ingredients in model high-protein nutrition bars.

    Science.gov (United States)

    Banach, J C; Clark, S; Metzger, L E; Lamsal, B P

    2016-08-01

    Transglutaminase (Tgase) crosslinking and calcium reduction were investigated as ways to improve the texture and storage stability of high-protein nutrition (HPN) bars formulated with milk protein concentrate (MPC) and micellar casein concentrate (MCC). The MPC and MCC crosslinked at none, low, and high levels, and a reduced-calcium MPC (RCMPC) were each formulated into model HPN bars. Hardness, crumbliness, moisture content, pH, color, and water activity of the HPN bars were measured during accelerated storage. The HPN bars prepared with MPC were harder and more cohesive than those prepared with MCC. Higher levels of Tgase crosslinking improved HPN bar cohesiveness and decreased hardening during storage. The RCMPC produced softer, yet crumblier HPN bars. Small textural differences were observed for the HPN bars formulated with the transglutaminase crosslinked proteins or RCMPC when compared with their respective controls. However, modification only slightly improved protein ingredient ability to slow hardening while balancing cohesion and likely requires further improvement for increased applicability in soft-texture HPN bars.

  6. Farmers' confidence in vaccinating badgers against bovine tuberculosis.

    Science.gov (United States)

    Enticott, G; Maye, D; Ilbery, B; Fisher, R; Kirwan, J

    2012-02-25

    This paper examines UK farmers' levels of confidence in vaccinating badgers against bovine tuberculosis (bTB) and their trust in the Government's ability to deal with bTB. In 2010, a badger vaccine based on the BCG vaccine was licensed following field trials and used as part of the UK Government's Badger Vaccination Deployment Project. A stratified random sample of cattle farmers in five different locations of England was surveyed using a telephone survey to elicit their views of badger vaccination. The survey provided a total of 341 responses with a response rate of 80 per cent. Results suggest that the farmers are cautious about badger vaccination, appearing to be neither overly confident nor unconfident in it. However, the farmers did not reveal high levels of trust in the Government to manage bTB policy or badger vaccination. There were no differences in the levels of confidence or trust between farms that were under bTB restrictions at the time of the survey and those that were not or between farms with historically high levels of bTB. Analysis of principal components suggests that 33 per cent of the farmers accepted badger vaccination, but that acceptance is dependent on the wider social and political environment.

  7. False memories and memory confidence in borderline patients.

    Science.gov (United States)

    Schilling, Lisa; Wingenfeld, Katja; Spitzer, Carsten; Nagel, Matthias; Moritz, Steffen

    2013-12-01

    Mixed results have been obtained regarding memory in patients with borderline personality disorder (BPD). Prior reports and anecdotal evidence suggests that patients with BPD are prone to false memories but this assumption has to been put to firm empirical test, yet. Memory accuracy and confidence was assessed in 20 BPD patients and 22 healthy controls using a visual variant of the false memory (Deese-Roediger-McDermott) paradigm which involved a negative and a positive-valenced picture. Groups did not differ regarding veridical item recognition. Importantly, patients did not display more false memories than controls. At trend level, borderline patients rated more items as new with high confidence compared to healthy controls. The results tentatively suggest that borderline patients show uncompromised visual memory functions and display no increased susceptibility for distorted memories. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Structures of the ultra-high-affinity protein–protein complexes of pyocins S2 and AP41 and their cognate immunity proteins from pseudomonas aeruginosa

    OpenAIRE

    Joshi, Amar; Grinter, Rhys; Josts, Inokentijs; Chen, Sabrina; Wojdyla, Justyna; Lowe, Edward; Kaminska, Renata; Sharp, Connor; McCaughey, Laura; Roszak, Aleksander; Cogdell, Richard; Byron, Olwyn; Walker, Daniel; Kleanthous, Colin

    2015-01-01

    How ultra-high-affinity protein–protein interactions retain high specificity is still poorly understood. The interaction between colicin DNase domains and their inhibitory immunity (Im) proteins is an ultra-high-affinity interaction that is essential for the neutralisation of endogenous DNase catalytic activity and for protection against exogenous DNase bacteriocins. The colicin DNase–Im interaction is a model system for the study of high-affinity protein–protein interactions. However, despit...

  9. High Protein Intake Improves Insulin Sensitivity but Exacerbates Bone Resorption in Immobility (WISE Study)

    Science.gov (United States)

    Heer, Martina; Smith, Scott M.; Frings-Meuthen, Petra; Zwart, Sara R.; Baecker, Natalie

    2012-01-01

    Inactivity, like bed rest (BR), causes insulin resistance (IR) and bone loss even in healthy subjects. High protein intake seems to mitigate this IR but might exacerbate bone loss. We hypothesized that high protein intake (animal:vegetable protein ratio: 60:40), isocaloric, compared to the control group plus high potassium intake would prevent IR without affecting bone turnover. After a 20-day ambulatory adaptation to controlled confinement and diet, 16 women participated in a 60-day, 6 deg head-down-tilt BR and were assigned randomly to one of the two groups. Control subjects (CON, n=8) received 1g/kg body mass/d dietary protein. Nutrition subjects (NUT, n=8) received 1.45g/kg body mass/d dietary protein plus 7.2g branched chain amino acids per day during BR. All subjects received 1670 kcal/d. Bed rest decreased glucose disposal by 35% (pprotein intake prevented insulin resistance, but exacerbated bed rest induced increase in bone resorption markers C-telopeptide (> 30%) and Ntelopeptide (>20%) (both: pprotein intake. We conclude from these results that high protein intake might positively affect glucose tolerance, but might also foster bone loss. Further long-duration studies are mandatory before high protein intake for diabetic patients, who have an increased fracture risk, might be recommended.

  10. Protein dynamics governed by interfaces of high polarity and low packing density.

    Directory of Open Access Journals (Sweden)

    Vladimir Espinosa Angarica

    Full Text Available The folding pathway, three-dimensional structure and intrinsic dynamics of proteins are governed by their amino acid sequences. Internal protein surfaces with physicochemical properties appropriate to modulate conformational fluctuations could play important roles in folding and dynamics. We show here that proteins contain buried interfaces of high polarity and low packing density, coined as LIPs: Light Interfaces of high Polarity, whose physicochemical properties make them unstable. The structures of well-characterized equilibrium and kinetic folding intermediates indicate that the LIPs of the corresponding native proteins fold late and are involved in local unfolding events. Importantly, LIPs can be identified using very fast and uncomplicated computational analysis of protein three-dimensional structures, which provides an easy way to delineate the protein segments involved in dynamics. Since LIPs can be retained while the sequences of the interacting segments diverge significantly, proteins could in principle evolve new functional features reusing pre-existing encoded dynamics. Large-scale identification of LIPS may contribute to understanding evolutionary constraints of proteins and the way protein intrinsic dynamics are encoded.

  11. On the Potential Origins of the High Stability of Reconstructed Ancestral Proteins.

    Science.gov (United States)

    Trudeau, Devin L; Kaltenbach, Miriam; Tawfik, Dan S

    2016-10-01

    Ancestral reconstruction provides instrumental insights regarding the biochemical and biophysical characteristics of past proteins. A striking observation relates to the remarkably high thermostability of reconstructed ancestors. The latter has been linked to high environmental temperatures in the Precambrian era, the era relating to most reconstructed proteins. We found that inferred ancestors of the serum paraoxonase (PON) enzyme family, including the mammalian ancestor, exhibit dramatically increased thermostabilities compared with the extant, human enzyme (up to 30 °C higher melting temperature). However, the environmental temperature at the time of emergence of mammals is presumed to be similar to the present one. Additionally, the mammalian PON ancestor has superior folding properties (kinetic stability)-unlike the extant mammalian PONs, it expresses in E. coli in a soluble and functional form, and at a high yield. We discuss two potential origins of this unexpectedly high stability. First, ancestral stability may be overestimated by a "consensus effect," whereby replacing amino acids that are rare in contemporary sequences with the amino acid most common in the family increases protein stability. Comparison to other reconstructed ancestors indicates that the consensus effect may bias some but not all reconstructions. Second, we note that high stability may relate to factors other than high environmental temperature such as oxidative stress or high radiation levels. Foremost, intrinsic factors such as high rates of genetic mutations and/or of transcriptional and translational errors, and less efficient protein quality control systems, may underlie the high kinetic and thermodynamic stability of past proteins.

  12. MALDI-TOF MS for quality control of high protein content sport supplements.

    Science.gov (United States)

    De Ceglie, Cristina; Calvano, Cosima D; Zambonin, Carlo G

    2015-06-01

    High protein content sport nutritional supplements are found as powder products containing, as ingredients, amino acids and proteins with important nutritional values as milk, soy and egg proteins. An EU Food Supplements Directive (2002) requires that supplements should be safe, both in dosages and in purity. It is important, then, to develop rapid and sensitive methods to be employed for the quality control of these substances. In this work, we apply, for the first time, matrix-assisted laser desorption ionization-mass spectrometry as a fast, reproducible and sensitive method for the quality control of sport nutritional supplements based on proteins. To this aim, several commercial egg- and/or milk-based powder products have been processed by in gel or in solution digestion and analyzed in comparison to pure standard products. This strategy allowed to assess the reliability of the indications on proteins (as caseins, whey proteins and ovalbumin) declared in the label of several sport nutritional supplements.

  13. Confidence assessment. Site descriptive modelling SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    2008-09-15

    The objective of this report is to assess the confidence that can be placed in the Forsmark site descriptive model, based on the information available at the conclusion of the surface-based investigations (SDM-Site Forsmark). In this exploration, an overriding question is whether remaining uncertainties are significant for repository engineering design or long-term safety assessment and could successfully be further reduced by more surface based investigations or more usefully by explorations underground made during construction of the repository. The confidence in the Forsmark site descriptive model, based on the data available at the conclusion of the surface-based site investigations, have been assessed by exploring: Confidence in the site characterisation data base; Key remaining issues and their handling; Handling of alternative models; Consistency between disciplines; and, Main reasons for confidence and lack of confidence in the model. It is generally found that the key aspects of importance for safety assessment and repository engineering of the Forsmark site descriptive model are associated with a high degree of confidence. Because of the robust geological model that describes the site, the overall confidence in Forsmark site descriptive model is judged to be high. While some aspects have lower confidence this lack of confidence is handled by providing wider uncertainty ranges, bounding estimates and/or alternative models. Most, but not all, of the low confidence aspects have little impact on repository engineering design or for long-term safety. Poor precision in the measured data are judged to have limited impact on uncertainties on the site descriptive model, with the exceptions of inaccuracy in determining the position of some boreholes at depth in 3-D space, as well as the poor precision of the orientation of BIPS images in some boreholes, and the poor precision of stress data determined by overcoring at the locations where the pre

  14. High mobility group box 1 protein as a late-acting mediator of acute lung inflammation.

    Science.gov (United States)

    Lutz, Waldemar; Stetkiewicz, Jan

    2004-01-01

    Acute inflammatory lung injury is often a delayed complication of critical illness and is associated with increased mortality. High mobility group box 1 (HMGB1) protein, in addition to its role as a transcriptional regulator factor, has been identified as a late mediator of endotoxin lethality and might be also involved in the development and progression of acute lung injury. HMGB1 protein itself can cause an acute inflammatory response manifested by increased production of proinflammatory cytokines and neutrophil accumulation. The delayed kinetics of HMGB1 protein release indicate that this protein is a distal mediator of acute inflamatory lung injury. Anti-HMGB1 protein antibodies attenuated endotoxin-induced lung injury, but not the early release of TNF-alpha and IL-1beta, indicating that HMGB1 protein is a late mediator of endotoxin-induced acute lung injury. HMGB1 protein is not released by apoptotic cells but is passively released by necrotic or damaged somatic and immune cells and it functions as a major stimulus of necrosis-induced inflammation. HMGB1 protein is also released by activated monocytes/macrophages and induces delayed and biphasic release of proinflammatory mediators from these cells. HMGB1 protein failed to stimulate cytokines release in lymphocytes, indicating that cellular stimulation is specific. We would like to suggest that HMGB1 protein may be also a primary mediator of the inflammatory responses to lung cells injury caused by toxic environmental chemicals.

  15. Serum Protein Profile Study of Clinical Samples Using High Performance Liquid Chromatography-Laser Induced Fluorescence

    DEFF Research Database (Denmark)

    Karemore, Gopal Raghunath; Ukendt, Sujatha; Rai, Lavanya

    2009-01-01

    The serum protein profiles of normal subjects, patients diagnosed with cervical cancer, and oral cancer were recorded using High Performance Liquid Chromatography combined with Laser Induced Fluorescence detection (HPLC-LIF). Serum protein profiles of the above three classes were tested for estab......The serum protein profiles of normal subjects, patients diagnosed with cervical cancer, and oral cancer were recorded using High Performance Liquid Chromatography combined with Laser Induced Fluorescence detection (HPLC-LIF). Serum protein profiles of the above three classes were tested...... for establishing the ability of HPLC-LIF protein profiling technique for discrimination, using hard clustering and Fuzzy clustering methods. The clustering algorithms have quite successfully classified the profiles as belonging to normal, cancer of cervix, and oral cancer conditions....

  16. Effects of a high protein diet on cognition and brain metabolism in cirrhotic rats.

    Science.gov (United States)

    Méndez-López, M; Méndez, M; Arias, J; Arias, J L

    2015-10-01

    Hepatic encephalopathy (HE) is a neurological complication observed in patients with liver disease. Patients who suffer from HE present neuropsychiatric, neuromuscular and behavioral symptoms. Animal models proposed to study HE resulting from cirrhosis mimic the clinical characteristics of cirrhosis and portal hypertension, and require the administration of hepatotoxins such as thioacetamide (TAA). The aim of this study was to assess the effects of a high protein diet on motor function, anxiety and memory processes in a model of cirrhosis induced by TAA administration. In addition, we used cytochrome c-oxidase (COx) histochemistry to assess the metabolic activity of the limbic system regions. Male rats were distributed into groups: control, animals with cirrhosis, Control rats receiving a high protein diet, and animals with cirrhosis receiving a high protein diet. Results showed preserved motor function and normal anxiety levels in all the groups. The animals with cirrhosis showed an impairment in active avoidance behavior and spatial memory, regardless of the diet they received. However, the animals with cirrhosis and a high protein diet showed longer escape latencies on the spatial memory task. The model of cirrhosis presented an under-activation of the dentate gyrus and CA3 hippocampal subfields and the medial part of the medial mammillary nucleus. The results suggest that a high protein intake worsens spatial memory deficits shown by the TAA-induced model of cirrhosis. However, high protein ingestion has no influence on the COx hypoactivity associated with the model.

  17. Effect of a high-protein breakfast on the postprandial ghrelin response

    DEFF Research Database (Denmark)

    Blom, Wendy A M; Lluch, Anne; Stafleu, Annette

    2006-01-01

    -carbohydrate breakfast (HC) through suppression of postprandial ghrelin concentrations or through other physiologic processes. DESIGN: Fifteen healthy men were studied in a single-blind, crossover design. Blood samples and subjective measures of satiety were assessed frequently for 3 h after the consumption of 2......BACKGROUND: The most satiating macronutrient appears to be dietary protein. Few studies have investigated the effects of dietary protein on ghrelin secretion in humans. OBJECTIVE: This study was designed to investigate whether a high-protein (HP) breakfast is more satiating than a high...

  18. High throughput atmospheric pressure plasma-induced graft polymerization for identifying protein-resistant surfaces.

    Science.gov (United States)

    Gu, Minghao; Kilduff, James E; Belfort, Georges

    2012-02-01

    Three critical aspects of searching for and understanding how to find highly resistant surfaces to protein adhesion are addressed here with specific application to synthetic membrane filtration. They include the (i) discovery of a series of previously unreported monomers from a large library of monomers with high protein resistance and subsequent low fouling characteristics for membrane ultrafiltration of protein-containing fluids, (ii) development of a new approach to investigate protein-resistant mechanisms from structure-property relationships, and (iii) adaptation of a new surface modification method, called atmospheric pressure plasma-induced graft polymerization (APP), together with a high throughput platform (HTP), for low cost vacuum-free synthesis of anti-fouling membranes. Several new high-performing chemistries comprising two polyethylene glycol (PEG), two amines and one zwitterionic monomers were identified from a library (44 commercial monomers) of five different classes of monomers as strong protein-resistant monomers. Combining our analysis here, using the Hansen solubility parameters (HSP) approach, and data from the literature, we conclude that strong interactions with water (hydrogen bonding) and surface flexibility are necessary for producing the highest protein resistance. Superior protein-resistant surfaces and subsequent anti-fouling performance was obtained with the HTP-APP as compared with our earlier HTP-photo graft-induced polymerization (PGP).

  19. Measurement of confidence: the development and psychometric evaluation of a stroke-specific, measure of confidence.

    Science.gov (United States)

    Horne, Jane C; Lincoln, Nadina B; Logan, Pip A

    2017-04-01

    To design, develop and psychometrically evaluate a stroke-specific measure of confidence, the Confidence after Stroke Measure (CaSM). Cross-sectional. Adults in the community. Stroke survivors and healthy elderly participants. Questionnaire items were generated based on the literature and qualitative interviews and piloted with expert groups to establish face validity. A 53-item CaSM was administered to stroke survivors and healthy elderly participants in the community. A second copy was posted four weeks later. Completed questionnaires were analysed for extreme responses, missing values, construct validity (factor analysis), convergent validity, divergent validity, reliability (internal consistency and temporal stability) and comparing responses according to age and gender. Stroke ( n = 101) and healthy elderly participants ( n = 101) returned questionnaires. Eight items were removed that had extreme responses and large numbers of missing values. Six items had item total correlations Confidence, Positive Attitude and Social Confidence, which explained 52% of variance. Cronbach's alpha coefficient demonstrated good internal consistency ( α = 0.94). A test re-test on the 27 items indicated good temporal stability ( r = 0.85, P = 0.001). The 27-item CaSM was a valid and reliable measure for assessing confidence in stroke survivors.

  20. Confidence and rejection in automatic speech recognition

    Science.gov (United States)

    Colton, Larry Don

    Automatic speech recognition (ASR) is performed imperfectly by computers. For some designated part (e.g., word or phrase) of the ASR output, rejection is deciding (yes or no) whether it is correct, and confidence is the probability (0.0 to 1.0) of it being correct. This thesis presents new methods of rejecting errors and estimating confidence for telephone speech. These are also called word or utterance verification and can be used in wordspotting or voice-response systems. Open-set or out-of-vocabulary situations are a primary focus. Language models are not considered. In vocabulary-dependent rejection all words in the target vocabulary are known in advance and a strategy can be developed for confirming each word. A word-specific artificial neural network (ANN) is shown to discriminate well, and scores from such ANNs are shown on a closed-set recognition task to reorder the N-best hypothesis list (N=3) for improved recognition performance. Segment-based duration and perceptual linear prediction (PLP) features are shown to perform well for such ANNs. The majority of the thesis concerns vocabulary- and task-independent confidence and rejection based on phonetic word models. These can be computed for words even when no training examples of those words have been seen. New techniques are developed using phoneme ranks instead of probabilities in each frame. These are shown to perform as well as the best other methods examined despite the data reduction involved. Certain new weighted averaging schemes are studied but found to give no performance benefit. Hierarchical averaging is shown to improve performance significantly: frame scores combine to make segment (phoneme state) scores, which combine to make phoneme scores, which combine to make word scores. Use of intermediate syllable scores is shown to not affect performance. Normalizing frame scores by an average of the top probabilities in each frame is shown to improve performance significantly. Perplexity of the wrong

  1. Effect of pressure on secondary structure of proteins under ultra high pressure liquid chromatographic conditions.

    Science.gov (United States)

    Makarov, Alexey; LoBrutto, Rosario; Karpinski, Paul

    2013-11-29

    There are several spectroscopic techniques such as IR and CD, that allow for analyzing protein secondary structure in solution. However, a majority of these techniques require using purified protein, concentrated enough in the solution, to produce a relevant spectrum. Fundamental principles for the usage of reversed-phase ultra high pressure liquid chromatography (UHPLC) as an alternative technique to study protein secondary structures in solution were investigated. Several "model" proteins, as well as several small ionizable and neutral molecules, were used for these studies. The studies were conducted with UHPLC in isocratic mode, using premixed mobile phases at constant flow rate and temperature. The pressure was modified by a backpressure regulator from about 6000psi to about 12,000psi. It was found that when using a mobile phase composition at which proteins were fully denatured (loss of alpha-helix secondary structure), the retention factors of the proteins increased upon pressure increase in the same manner as non-proteins. When using a mobile phase composition in which proteins were not fully denatured, it was observed that the retention factors of the proteins displayed a much steeper (by one order of magnitude) increase in retention upon pressure increase. It was concluded that in a mobile phase in which the protein is not initially fully denatured, the increase of pressure may facilitate the folding back of the protein to its native state (alpha-helix secondary structure). The impact of different mobile phase compositions on the denaturation of the proteins was studied using CD (Circular Dichroism). Moreover, the effect of flow rate on retention of proteins and small molecules was studied at constant pressure on the different pore size silicas and the impact of internal frictional heating was evaluated.

  2. Engineering Student Self-Assessment through Confidence-Based Scoring

    Science.gov (United States)

    Yuen-Reed, Gigi; Reed, Kyle B.

    2015-01-01

    A vital aspect of an answer is the confidence that goes along with it. Misstating the level of confidence one has in the answer can have devastating outcomes. However, confidence assessment is rarely emphasized during typical engineering education. The confidence-based scoring method described in this study encourages students to both think about…

  3. Mediated Sources of Public Confidence: Lazarsfeld and Merton Revisited.

    Science.gov (United States)

    Simonson, Peter

    1999-01-01

    Contributes to scholarship on mass media's role in generating public confidence. Discusses the current crisis of confidence, confidence as "faith-together," varied routes by which media confer status, and ways both journalistic expose and public debate can generate cynicism and undercut public confidence. Sketches three types of civil…

  4. Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein

    Energy Technology Data Exchange (ETDEWEB)

    Shaikh, Afshan; Shaikh, Afshan S.; Tang, Yinjie; Mukhopadhyay, Aindrila; Keasling, Jay D.

    2008-06-27

    {sup 13}C-based metabolic flux analysis provides valuable information about bacterial physiology. Though many biological processes rely on the synergistic functions of microbial communities, study of individual organisms in a mixed culture using existing flux analysis methods is difficult. Isotopomer-based flux analysis typically relies on hydrolyzed amino acids from a homogeneous biomass. Thus metabolic flux analysis of a given organism in a mixed culture requires its separation from the mixed culture. Swift and efficient cell separation is difficult and a major hurdle for isotopomer-based flux analysis of mixed cultures. Here we demonstrate the use of a single highly-expressed protein to analyze the isotopomer distribution of amino acids from one organism. Using the model organism E. coli expressing a plasmid-borne, his-tagged Green Fluorescent Protein (GFP), we show that induction of GFP does not affect E. coli growth kinetics or the isotopomer distribution in nine key metabolites. Further, the isotopomer labeling patterns of amino acids derived from purified GFP and total cell protein are indistinguishable, indicating that amino acids from a purified protein can be used to infer metabolic fluxes of targeted organisms in a mixed culture. This study provides the foundation to extend isotopomer-based flux analysis to study metabolism of individual strains in microbial communities.

  5. Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning

    Directory of Open Access Journals (Sweden)

    Tanel Pärnamaa

    2017-05-01

    Full Text Available High-throughput microscopy of many single cells generates high-dimensional data that are far from straightforward to analyze. One important problem is automatically detecting the cellular compartment where a fluorescently-tagged protein resides, a task relatively simple for an experienced human, but difficult to automate on a computer. Here, we train an 11-layer neural network on data from mapping thousands of yeast proteins, achieving per cell localization classification accuracy of 91%, and per protein accuracy of 99% on held-out images. We confirm that low-level network features correspond to basic image characteristics, while deeper layers separate localization classes. Using this network as a feature calculator, we train standard classifiers that assign proteins to previously unseen compartments after observing only a small number of training examples. Our results are the most accurate subcellular localization classifications to date, and demonstrate the usefulness of deep learning for high-throughput microscopy.

  6. Confidence intervals for annual wind power production******

    Directory of Open Access Journals (Sweden)

    Bensoussan Alain

    2014-01-01

    Full Text Available Wind power is an intermittent resource due to wind speed intermittency. However wind speed can be described as a stochastic process with short memory. This allows us to derive a central limit theorem for the annual or pluri-annual wind power production and then get quantiles of the wind power production for one, ten or twenty years future periods. On the one hand, the interquantile spread offers a measurement of the intrinsic uncertainties of wind power production. On the other hand, different quantiles with different periods of time are used by financial institutions to quantify the financial risk of the wind turbine. Our method is then applied to real datasets corresponding to a French wind turbine. Since confidence intervals can be enhanced by taking into account seasonality, we present some tools for change point analysis on wind series.

  7. Confidence crisis of results in biomechanics research.

    Science.gov (United States)

    Knudson, Duane

    2017-11-01

    Many biomechanics studies have small sample sizes and incorrect statistical analyses, so reporting of inaccurate inferences and inflated magnitude of effects are common in the field. This review examines these issues in biomechanics research and summarises potential solutions from research in other fields to increase the confidence in the experimental effects reported in biomechanics. Authors, reviewers and editors of biomechanics research reports are encouraged to improve sample sizes and the resulting statistical power, improve reporting transparency, improve the rigour of statistical analyses used, and increase the acceptance of replication studies to improve the validity of inferences from data in biomechanics research. The application of sports biomechanics research results would also improve if a larger percentage of unbiased effects and their uncertainty were reported in the literature.

  8. Setting confidence intervals in coincidence search analysis

    CERN Document Server

    Baggio, L; Baggio, Lucio; Prodi, Giovanni A.

    2003-01-01

    The main technique that has been used to estimate the rate of gravitational wave (gw) bursts is to search for coincidence among times of arrival of candidate events in different detectors. Coincidences are modeled as a (possibly non-stationary) random time series background with gw events embedded in it, at random times but constant average rate. It is critical to test whether the statistics of the coincidence counts is Poisson, because the counts in a single detector often are not. At some point a number of parameters are tuned to increase the chance of detection by reducing the expected background: source direction, epoch vetoes based on sensitivity, goodness-of-fit thresholds, etc. Therefore, the significance of the confidence intervals itself has to be renormalized. This review is an insight of the state-of-the-art methods employed in the recent search performed by the International Gravitational Event Collaboration for the worldwide network of resonant bar detectors.

  9. Disparities in Confidence to Manage Chronic Diseases in Men

    Directory of Open Access Journals (Sweden)

    Keith Elder

    2014-08-01

    Full Text Available Background: Chronic diseases are highly prevalent among men in the United States and chronic disease management is problematic for men, particularly for racial and ethnic minority men. Objectives: This study examined the association between health information seeking and confidence to manage chronic diseases among men. Methods: Study data were drawn from the 2007 Health Tracking Household Survey and analyzed using multiple binary logistic regressions. The analytical sample included 2,653 men, 18 years and older with a chronic illness. Results: Health information seeking was not associated with confidence to manage chronic illnesses. African-American men had lower odds than White men to agree to take actions to prevent symptoms with their health. Hispanic men had lower odds than White men to agree to tell a doctor concerns they have, even when not asked. Conclusions: Racial and ethnic minority men with a chronic condition appear to be less confident to manage their health compared to white men. Chronic disease management needs greater exploration to understand the best ways to help racial and ethnic minority men successfully manage their chronic condition.

  10. Confidence sets for optimal factor levels of a response surface.

    Science.gov (United States)

    Wan, Fang; Liu, Wei; Bretz, Frank; Han, Yang

    2016-12-01

    Construction of confidence sets for the optimal factor levels is an important topic in response surfaces methodology. In Wan et al. (2015), an exact (1-α) confidence set has been provided for a maximum or minimum point (i.e., an optimal factor level) of a univariate polynomial function in a given interval. In this article, the method has been extended to construct an exact (1-α) confidence set for the optimal factor levels of response surfaces. The construction method is readily applied to many parametric and semiparametric regression models involving a quadratic function. A conservative confidence set has been provided as an intermediate step in the construction of the exact confidence set. Two examples are given to illustrate the application of the confidence sets. The comparison between confidence sets indicates that our exact confidence set is better than the only other confidence set available in the statistical literature that guarantees the (1-α) confidence level. © 2016, The International Biometric Society.

  11. Fusing photovoltaic data for improved confidence intervals

    Directory of Open Access Journals (Sweden)

    Ansgar Steland

    2017-01-01

    Full Text Available Characterizing and testing photovoltaic modules requires carefully made measurements on important variables such as the power output under standard conditions. When additional data is available, which has been collected using a different measurement system and therefore may be of different accuracy, the question arises how one can combine the information present in both data sets. In some cases one even has prior knowledge about the ordering of the variances of the measurement errors, which is not fully taken into account by commonly known estimators. We discuss several statistical estimators to combine the sample means of independent series of measurements, both under the assumption of heterogeneous variances and ordered variances. The critical issue is then to assess the estimator’s variance and to construct confidence intervals. We propose and discuss the application of a new jackknife variance estimator devised by [1] to such photovoltaic data, in order to assess the variability of common mean estimation under heterogeneous and ordered variances in a reliable and nonparametric way. When serial correlations are present, which usually a ect the marginal variances, it is proposed to construct a thinned data set by downsampling the series in such a way that autocorrelations are removed or dampened. We propose a data adaptive procedure which downsamples a series at irregularly spaced time points in such a way that the autocorrelations are minimized. The procedures are illustrated by applying them to real photovoltaic power output measurements from two different sun light flashers. In addition, focusing on simulations governed by real photovoltaic data, we investigate the accuracy of the jackknife approach and compare it with other approaches. Among those is a variance estimator based on Nair’s formula for Gaussian data and, as a parametric alternative, two Bayesian models. We investigate the statistical accuracy of the resulting confidence

  12. The 2010 Retirement Confidence Survey: confidence stabilizing, but preparations continue to erode.

    Science.gov (United States)

    Helman, Ruth; Copeland, Craig; VanDerhei, Jack

    2010-03-01

    20TH ANNUAL RCS: The 2010 Retirement Confidence Survey-the 20th annual wave of this survey-finds that the record-low confidence levels measured during the past two years of economic decline appear to have bottomed out. The percentage of workers veryconfident about having enough money for a comfortable retirement has stabilized at 16 percent, which is statistically equivalent to the 20-year low of 13 percent measured in 2009 (Fig. 1, pg. 7). Retiree confidence about having a financially secure retirement has also stabilized, with 19 percent saying now they are very confident (statistically equivalent to the 20 percent measured in 2009) (Fig. 2, pg. 8). Worker confidence about paying for basic expenses in retirement has rebounded slightly, with 29 percent now saying they are very confident about having enough money to pay for basic expenses during retirement (up from 25 percent in 2009, but still down from 34 percent in 2008) (Fig. 3, pg. 9). PREPARATIONS STILL ERODING: Fewer workers report that they and/or their spouse have saved for retirement (69 percent, down from 75 percent in 2009 but statistically equivalent to 72 percent in 2008) (Fig. 11, page 14). Moreover, fewer workers say that they and/or their spouse are currently saving for retirement (60 percent, down from 65 percent in 2009 but statistically equivalent to percentages measured in other years) (Fig. 13, pg. 15). MORE PEOPLE HAVE NO SAVINGS AT ALL: An increased percentage of workers report they have virtually no savings and investments. Among RCS workers providing this type of information, 27 percent say they have less than $1,000 in savings (up from 20 percent in 2009). In total, more than half of workers (54 percent) report that the total value of their household's savings and investments, excluding the value of their primary home and any defined benefit plans, is less than $25,000 (Fig. 14, pg. 16). CLUELESS ABOUT SAVINGS GOALS: Many workers continue to be unaware of how much they need to save for

  13. HPTLC-aptastaining – Innovative protein detection system for high-performance thin-layer chromatography

    Science.gov (United States)

    Morschheuser, Lena; Wessels, Hauke; Pille, Christina; Fischer, Judith; Hünniger, Tim; Fischer, Markus; Paschke-Kratzin, Angelika; Rohn, Sascha

    2016-01-01

    Protein analysis using high-performance thin-layer chromatography (HPTLC) is not commonly used but can complement traditional electrophoretic and mass spectrometric approaches in a unique way. Due to various detection protocols and possibilities for hyphenation, HPTLC protein analysis is a promising alternative for e.g., investigating posttranslational modifications. This study exemplarily focused on the investigation of lysozyme, an enzyme which is occurring in eggs and technologically added to foods and beverages such as wine. The detection of lysozyme is mandatory, as it might trigger allergenic reactions in sensitive individuals. To underline the advantages of HPTLC in protein analysis, the development of innovative, highly specific staining protocols leads to improved sensitivity for protein detection on HPTLC plates in comparison to universal protein derivatization reagents. This study aimed at developing a detection methodology for HPTLC separated proteins using aptamers. Due to their affinity and specificity towards a wide range of targets, an aptamer based staining procedure on HPTLC (HPTLC-aptastaining) will enable manifold analytical possibilities. Besides the proof of its applicability for the very first time, (i) aptamer-based staining of proteins is applicable on different stationary phase materials and (ii) furthermore, it can be used as an approach for a semi-quantitative estimation of protein concentrations. PMID:27220270

  14. HPTLC-aptastaining - Innovative protein detection system for high-performance thin-layer chromatography

    Science.gov (United States)

    Morschheuser, Lena; Wessels, Hauke; Pille, Christina; Fischer, Judith; Hünniger, Tim; Fischer, Markus; Paschke-Kratzin, Angelika; Rohn, Sascha

    2016-05-01

    Protein analysis using high-performance thin-layer chromatography (HPTLC) is not commonly used but can complement traditional electrophoretic and mass spectrometric approaches in a unique way. Due to various detection protocols and possibilities for hyphenation, HPTLC protein analysis is a promising alternative for e.g., investigating posttranslational modifications. This study exemplarily focused on the investigation of lysozyme, an enzyme which is occurring in eggs and technologically added to foods and beverages such as wine. The detection of lysozyme is mandatory, as it might trigger allergenic reactions in sensitive individuals. To underline the advantages of HPTLC in protein analysis, the development of innovative, highly specific staining protocols leads to improved sensitivity for protein detection on HPTLC plates in comparison to universal protein derivatization reagents. This study aimed at developing a detection methodology for HPTLC separated proteins using aptamers. Due to their affinity and specificity towards a wide range of targets, an aptamer based staining procedure on HPTLC (HPTLC-aptastaining) will enable manifold analytical possibilities. Besides the proof of its applicability for the very first time, (i) aptamer-based staining of proteins is applicable on different stationary phase materials and (ii) furthermore, it can be used as an approach for a semi-quantitative estimation of protein concentrations.

  15. Evaluation of three high abundance protein depletion kits for umbilical cord serum proteomics

    Directory of Open Access Journals (Sweden)

    Nie Jing

    2011-05-01

    Full Text Available Abstract Background High abundance protein depletion is a major challenge in the study of serum/plasma proteomics. Prior to this study, most commercially available kits for depletion of highly abundant proteins had only been tested and evaluated in adult serum/plasma, while the depletion efficiency on umbilical cord serum/plasma had not been clarified. Structural differences between some adult and fetal proteins (such as albumin make it likely that depletion approaches for adult and umbilical cord serum/plasma will be variable. Therefore, the primary purposes of the present study are to investigate the efficiencies of several commonly-used commercial kits during high abundance protein depletion from umbilical cord serum and to determine which kit yields the most effective and reproducible results for further proteomics research on umbilical cord serum. Results The immunoaffinity based kits (PROTIA-Sigma and 5185-Agilent displayed higher depletion efficiency than the immobilized dye based kit (PROTBA-Sigma in umbilical cord serum samples. Both the PROTIA-Sigma and 5185-Agilent kit maintained high depletion efficiency when used three consecutive times. Depletion by the PROTIA-Sigma Kit improved 2DE gel quality by reducing smeared bands produced by the presence of high abundance proteins and increasing the intensity of other protein spots. During image analysis using the identical detection parameters, 411 ± 18 spots were detected in crude serum gels, while 757 ± 43 spots were detected in depleted serum gels. Eight spots unique to depleted serum gels were identified by MALDI- TOF/TOF MS, seven of which were low abundance proteins. Conclusions The immunoaffinity based kits exceeded the immobilized dye based kit in high abundance protein depletion of umbilical cord serum samples and dramatically improved 2DE gel quality for detection of trace biomarkers.

  16. Assessment of protein synthesis in highly aerobic canine species at the onset and during exercise training.

    Science.gov (United States)

    Miller, Benjamin F; Ehrlicher, Sarah E; Drake, Joshua C; Peelor, Frederick F; Biela, Laurie M; Pratt-Phillips, Shannon; Davis, Michael; Hamilton, Karyn L

    2015-04-01

    Canis lupus familiaris, the domesticated dog, is capable of extreme endurance performance. The ability to perform sustained aerobic exercise is dependent on a well-developed mitochondrial reticulum. In this study we examined the cumulative muscle protein and DNA synthesis in groups of athletic dogs at the onset of an exercise training program and following a strenuous exercise training program. We hypothesized that both at the onset and during an exercise training program there would be greater mitochondrial protein synthesis rates compared with sedentary control with no difference in mixed or cytoplasmic protein synthesis rates. Protein synthetic rates of three protein fractions and DNA synthesis were determined over 1 wk using (2)H2O in competitive Alaskan Huskies and Labrador Retrievers trained for explosive device detection. Both groups of dogs had very high rates of skeletal muscle protein synthesis in the sedentary state [Alaskan Huskies: Mixed = 2.28 ± 0.12, cytoplasmic (Cyto) = 2.91 ± 0.10, and mitochondrial (Mito) = 2.62 ± 0.07; Labrador Retrievers: Mixed = 3.88 ± 0.37, Cyto = 3.85 ± 0.06, and Mito = 2.92 ± 0.20%/day]. Mitochondrial (Mito) protein synthesis rates did not increase at the onset of an exercise training program. Exercise-trained dogs maintained Mito protein synthesis during exercise training when mixed (Mixed) and cytosolic (Cyto) fractions decreased, and this coincided with a decrease in p-RpS6 but also a decrease in p-ACC signaling. Contrary to our hypothesis, canines did not have large increases in mitochondrial protein synthesis at the onset or during an exercise training program. However, dogs have a high rate of protein synthesis compared with humans that perhaps does not necessitate an extra increase in protein synthesis at the onset of aerobic exercise training.

  17. Multidimensional confidence regions for pareto, exponential, and normal distributions

    OpenAIRE

    Lennartz, Jens

    2017-01-01

    The two classical approaches in estimation theory are point estimation and confidence interval estimation. A confidence interval contains the unknown parameter of interest of a parametric family of distributions with a probability greater than or equal to a certain value, called confidence coefficient or confidence level. If we deal with multiparametric families of distributions, we are interested in simultaneously estimating the parameter vector by determining a multidimensional confidence r...

  18. Identification and monitoring of host cell proteins by mass spectrometry combined with high performance immunochemistry testing.

    Directory of Open Access Journals (Sweden)

    Katrin Bomans

    Full Text Available Biotherapeutics are often produced in non-human host cells like Escherichia coli, yeast, and various mammalian cell lines. A major focus of any therapeutic protein purification process is to reduce host cell proteins to an acceptable low level. In this study, various E. coli host cell proteins were identified at different purifications steps by HPLC fractionation, SDS-PAGE analysis, and tryptic peptide mapping combined with online liquid chromatography mass spectrometry (LC-MS. However, no host cell proteins could be verified by direct LC-MS analysis of final drug substance material. In contrast, the application of affinity enrichment chromatography prior to comprehensive LC-MS was adequate to identify several low abundant host cell proteins at the final drug substance level. Bacterial alkaline phosphatase (BAP was identified as being the most abundant host cell protein at several purification steps. Thus, we firstly established two different assays for enzymatic and immunological BAP monitoring using the cobas® technology. By using this strategy we were able to demonstrate an almost complete removal of BAP enzymatic activity by the established therapeutic protein purification process. In summary, the impact of fermentation, purification, and formulation conditions on host cell protein removal and biological activity can be conducted by monitoring process-specific host cell proteins in a GMP-compatible and high-throughput (> 1000 samples/day manner.

  19. A universal, high recovery assay for protein quantitation through temperature programmed liquid chromatography (TPLC).

    Science.gov (United States)

    Orton, Dennis J; Doucette, Alan A

    2013-03-15

    As an alternative to direct UV absorbance measurements, estimation of total protein concentration is typically conducted through colorimetric reagent assays. However, for protein-limited applications, the proportion of the sample sacrificed to the assay becomes increasingly significant. This work demonstrates a method for quantitation of protein samples with high recovery. Temperature programmed liquid chromatography (TPLC) with absorbance detection at 214nm permits accurate estimation of total protein concentration from samples containing as little as 0.75μg. The method incorporates a temperature gradient from 25 to 80°C to facilitate elution of total protein into a single fraction. Analyte recovery, as measured from 1 and 10μg protein extracts of Escherichia coli, is shown to exceed 93%. Extinction coefficients at 214nm were calculated across the human proteome, providing a relative standard deviation of 21% (versus 42% at 280nm), suggesting absorbance values at 214nm provide a more consistent measure of protein concentration. These results translate to a universal protein detection strategy exhibiting a coefficient of variation below 10%. Together with the sensitivity and tolerance to contaminants, TPLC with UV detection is a favorable alternative to colorimetric assay for total protein quantitation, particularly in sample-limited applications.

  20. Protein profile of exhaled breath condensate determined by high resolution mass spectrometry.

    Science.gov (United States)

    Muccilli, Vera; Saletti, Rosaria; Cunsolo, Vincenzo; Ho, Jenny; Gili, Elisa; Conte, Enrico; Sichili, Stefania; Vancheri, Carlo; Foti, Salvatore

    2015-02-01

    A method based on liquid chromatography/high resolution tandem mass spectrometry coupled with electrophoretic separation, for determination and relative quantification of the protein composition of exhaled breath condensate (EBC), was developed. Application of the procedure to a sample of EBC, pooled from nine healthy subjects, resulted in the identification of 167 unique gene products, 113 of which not previously reported in EBC samples. The abundance of the protein identified was estimated by means of the exponentially modified protein abundance index protocol (emPAI). Cytokeratins were by far the most abundant proteins in EBC samples. Many of the identified proteins were associated with multiple cellular location with cytoplasm constituting the largest group. Cytosol, nucleus, membrane, cytoskeleton and extracellular were other abundantly represented locations. No amylase was detected, suggesting the absence of saliva protein contamination. The profile obtained represents the most comprehensive protein characterization of EBC so far reported and demonstrates that this approach provides a powerful tool for investigating the protein profile of EBC samples. Compared with analogous investigations, this study also shows that the protein profile of EBC is strongly affected by the sampling method adopted.

  1. Profiling of integral membrane proteins and their post translational modifications using high-resolution mass spectrometry

    Science.gov (United States)

    Souda, Puneet; Ryan, Christopher M.; Cramer, William A.; Whitelegge, Julian

    2011-01-01

    Integral membrane proteins pose challenges to traditional proteomics approaches due to unique physicochemical properties including hydrophobic transmembrane domains that limit solubility in aqueous solvents. A well resolved intact protein molecular mass profile defines a protein’s native covalent state including post-translational modifications, and is thus a vital measurement toward full structure determination. Both soluble loop regions and transmembrane regions potentially contain post-translational modifications that must be characterized if the covalent primary structure of a membrane protein is to be defined. This goal has been achieved using electrospray-ionization mass spectrometry (ESI-MS) with low-resolution mass analyzers for intact protein profiling, and high-resolution instruments for top-down experiments, toward complete covalent primary structure information. In top-down, the intact protein profile is supplemented by gas-phase fragmentation of the intact protein, including its transmembrane regions, using collisionally activated and/or electroncapture dissociation (CAD/ECD) to yield sequence-dependent high-resolution MS information. Dedicated liquid chromatography systems with aqueous/organic solvent mixtures were developed allowing us to demonstrate that polytopic integral membrane proteins are amenable to ESI-MS analysis, including top-down measurements. Covalent post-translational modifications are localized regardless of their position in transmembrane domains. Top-down measurements provide a more detail oriented high-resolution description of post-transcriptional and post-translational diversity for enhanced understanding beyond genomic translation. PMID:21982782

  2. Plasma PCSK9 concentrations during an oral fat load and after short term high-fat, high-fat high-protein and high-fructose diets

    Directory of Open Access Journals (Sweden)

    Cariou Bertrand

    2013-01-01

    Full Text Available Abstract Background PCSK9 (Proprotein Convertase Subtilisin Kexin type 9 is a circulating protein that promotes hypercholesterolemia by decreasing hepatic LDL receptor protein. Under non interventional conditions, its expression is driven by sterol response element binding protein 2 (SREBP2 and follows a diurnal rhythm synchronous with cholesterol synthesis. Plasma PCSK9 is associated to LDL-C and to a lesser extent plasma triglycerides and insulin resistance. We aimed to verify the effect on plasma PCSK9 concentrations of dietary interventions that affect these parameters. Methods We performed nutritional interventions in young healthy male volunteers and offspring of type 2 diabetic (OffT2D patients that are more prone to develop insulin resistance, including: i acute post-prandial hyperlipidemic challenge (n=10, ii 4 days of high-fat (HF or high-fat/high-protein (HFHP (n=10, iii 7 (HFruc1, n=16 or 6 (HFruc2, n=9 days of hypercaloric high-fructose diets. An acute oral fat load was also performed in two patients bearing the R104C-V114A loss-of-function (LOF PCSK9 mutation. Plasma PCSK9 concentrations were measured by ELISA. For the HFruc1 study, intrahepatocellular (IHCL and intramyocellular lipids were measured by 1H magnetic resonance spectroscopy. Hepatic and whole-body insulin sensitivity was assessed with a two-step hyperinsulinemic-euglycemic clamp (0.3 and 1.0 mU.kg-1.min-1. Findings HF and HFHP short-term diets, as well as an acute hyperlipidemic oral load, did not significantly change PCSK9 concentrations. In addition, post-prandial plasma triglyceride excursion was not altered in two carriers of PCSK9 LOF mutation compared with non carriers. In contrast, hypercaloric 7-day HFruc1 diet increased plasma PCSK9 concentrations by 28% (p=0.05 in healthy volunteers and by 34% (p=0.001 in OffT2D patients. In another independent study, 6-day HFruc2 diet increased plasma PCSK9 levels by 93% (p Conclusions Plasma PCSK9 concentrations vary

  3. Iron-Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein-Protein Interaction.

    Science.gov (United States)

    Delewski, Wojciech; Paterkiewicz, Bogumiła; Manicki, Mateusz; Schilke, Brenda; Tomiczek, Bartłomiej; Ciesielski, Szymon J; Nierzwicki, Lukasz; Czub, Jacek; Dutkiewicz, Rafal; Craig, Elizabeth A; Marszalek, Jaroslaw

    2016-03-01

    Biogenesis of iron-sulfur clusters (FeS) is a highly conserved process involving Hsp70 and J-protein chaperones. However, Hsp70 specialization differs among species. In most eukaryotes, including Schizosaccharomyces pombe, FeS biogenesis involves interaction between the J-protein Jac1 and the multifunctional Hsp70 Ssc1. But, in Saccharomyces cerevisiae and closely related species, Jac1 interacts with the specialized Hsp70 Ssq1, which emerged through duplication of SSC1. As little is known about how gene duplicates affect the robustness of their protein interaction partners, we analyzed the functional and evolutionary consequences of Ssq1 specialization on the ubiquitous J-protein cochaperone Jac1, by comparing S. cerevisiae and S. pombe. Although deletion of JAC1 is lethal in both species, alanine substitutions within the conserved His-Pro-Asp (HPD) motif, which is critical for Jac1:Hsp70 interaction, have species-specific effects. They are lethal in S. pombe, but not in S. cerevisiae. These in vivo differences correlated with in vitro biochemical measurements. Charged residues present in the J-domain of S. cerevisiae Jac1, but absent in S. pombe Jac1, are important for tolerance of S. cerevisiae Jac1 to HPD alterations. Moreover, Jac1 orthologs from species that encode Ssq1 have a higher sequence divergence. The simplest interpretation of our results is that Ssq1's coevolution with Jac1 resulted in expansion of their binding interface, thus increasing the efficiency of their interaction. Such an expansion could in turn compensate for negative effects of HPD substitutions. Thus, our results support the idea that the robustness of Jac1 emerged as consequence of its highly efficient and specific interaction with Ssq1. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Identification of seroreactive proteins of Leptospira interrogans serovar copenhageni using a high-density protein microarray approach.

    Science.gov (United States)

    Lessa-Aquino, Carolina; Borges Rodrigues, Camila; Pablo, Jozelyn; Sasaki, Rie; Jasinskas, Algis; Liang, Li; Wunder, Elsio A; Ribeiro, Guilherme S; Vigil, Adam; Galler, Ricardo; Molina, Douglas; Liang, Xiaowu; Reis, Mitermayer G; Ko, Albert I; Medeiros, Marco Alberto; Felgner, Philip L

    2013-01-01

    Leptospirosis is a widespread zoonotic disease worldwide. The lack of an adequate laboratory test is a major barrier for diagnosis, especially during the early stages of illness, when antibiotic therapy is most effective. Therefore, there is a critical need for an efficient diagnostic test for this life threatening disease. In order to identify new targets that could be used as diagnostic makers for leptopirosis, we constructed a protein microarray chip comprising 61% of Leptospira interrogans proteome and investigated the IgG response from 274 individuals, including 80 acute-phase, 80 convalescent-phase patients and 114 healthy control subjects from regions with endemic, high endemic, and no endemic transmission of leptospirosis. A nitrocellulose line blot assay was performed to validate the accuracy of the protein microarray results. We found 16 antigens that can discriminate between acute cases and healthy individuals from a region with high endemic transmission of leptospirosis, and 18 antigens that distinguish convalescent cases. Some of the antigens identified in this study, such as LipL32, the non-identical domains of the Lig proteins, GroEL, and Loa22 are already known to be recognized by sera from human patients, thus serving as proof-of-concept for the serodiagnostic antigen discovery approach. Several novel antigens were identified, including the hypothetical protein LIC10215 which showed good sensitivity and specificity rates for both acute- and convalescent-phase patients. Our study is the first large-scale evaluation of immunodominant antigens associated with naturally acquired leptospiral infection, and novel as well as known serodiagnostic leptospiral antigens that are recognized by antibodies in the sera of leptospirosis cases were identified. The novel antigens identified here may have potential use in both the development of new tests and the improvement of currently available assays for diagnosing this neglected tropical disease. Further

  5. Identification of seroreactive proteins of Leptospira interrogans serovar copenhageni using a high-density protein microarray approach.

    Directory of Open Access Journals (Sweden)

    Carolina Lessa-Aquino

    Full Text Available Leptospirosis is a widespread zoonotic disease worldwide. The lack of an adequate laboratory test is a major barrier for diagnosis, especially during the early stages of illness, when antibiotic therapy is most effective. Therefore, there is a critical need for an efficient diagnostic test for this life threatening disease.In order to identify new targets that could be used as diagnostic makers for leptopirosis, we constructed a protein microarray chip comprising 61% of Leptospira interrogans proteome and investigated the IgG response from 274 individuals, including 80 acute-phase, 80 convalescent-phase patients and 114 healthy control subjects from regions with endemic, high endemic, and no endemic transmission of leptospirosis. A nitrocellulose line blot assay was performed to validate the accuracy of the protein microarray results.We found 16 antigens that can discriminate between acute cases and healthy individuals from a region with high endemic transmission of leptospirosis, and 18 antigens that distinguish convalescent cases. Some of the antigens identified in this study, such as LipL32, the non-identical domains of the Lig proteins, GroEL, and Loa22 are already known to be recognized by sera from human patients, thus serving as proof-of-concept for the serodiagnostic antigen discovery approach. Several novel antigens were identified, including the hypothetical protein LIC10215 which showed good sensitivity and specificity rates for both acute- and convalescent-phase patients.Our study is the first large-scale evaluation of immunodominant antigens associated with naturally acquired leptospiral infection, and novel as well as known serodiagnostic leptospiral antigens that are recognized by antibodies in the sera of leptospirosis cases were identified. The novel antigens identified here may have potential use in both the development of new tests and the improvement of currently available assays for diagnosing this neglected tropical disease

  6. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... for the vegetarian proteins, whether they have carbohydrate. Protein Choices Plant-Based Proteins Plant-based protein foods ...

  7. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

    Directory of Open Access Journals (Sweden)

    Courdy Samir J

    2008-12-01

    Full Text Available Abstract Background High throughput signature sequencing holds many promises, one of which is the ready identification of in vivo transcription factor binding sites, histone modifications, changes in chromatin structure and patterns of DNA methylation across entire genomes. In these experiments, chromatin immunoprecipitation is used to enrich for particular DNA sequences of interest and signature sequencing is used to map the regions to the genome (ChIP-Seq. Elucidation of these sites of DNA-protein binding/modification are proving instrumental in reconstructing networks of gene regulation and chromatin remodelling that direct development, response to cellular perturbation, and neoplastic transformation. Results Here we present a package of algorithms and software that makes use of control input data to reduce false positives and estimate confidence in ChIP-Seq peaks. Several different methods were compared using two simulated spike-in datasets. Use of control input data and a normalized difference score were found to more than double the recovery of ChIP-Seq peaks at a 5% false discovery rate (FDR. Moreover, both a binomial p-value/q-value and an empirical FDR were found to predict the true FDR within 2–3 fold and are more reliable estimators of confidence than a global Poisson p-value. These methods were then used to reanalyze Johnson et al.'s neuron-restrictive silencer factor (NRSF ChIP-Seq data without relying on extensive qPCR validated NRSF sites and the presence of NRSF binding motifs for setting thresholds. Conclusion The methods developed and tested here show considerable promise for reducing false positives and estimating confidence in ChIP-Seq data without any prior knowledge of the chIP target. They are part of a larger open source package freely available from http://useq.sourceforge.net/.

  8. Robotic high-throughput purification of affinity-tagged recombinant proteins.

    Science.gov (United States)

    Wiesler, Simone C; Weinzierl, Robert O J

    2015-01-01

    Affinity purification of recombinant proteins has become the method of choice to obtain good quantities and qualities of proteins for a variety of downstream biochemical applications. While manual or FPLC-assisted purification techniques are generally time-consuming and labor-intensive, the advent of high-throughput technologies and liquid handling robotics has simplified and accelerated this process significantly. Additionally, without the human factor as a potential source of error, automated purification protocols allow for the generation of large numbers of proteins simultaneously and under directly comparable conditions. The delivered material is ideal for activity comparisons of different variants of the same protein. Here, we present our strategy for the simultaneous purification of up to 24 affinity-tagged proteins for activity measurements in biochemical assays. The protocol described is suitable for the scale typically required in individual research laboratories.

  9. Eyewitness confidence : the relation between accuracy and confidence in episodic memory

    NARCIS (Netherlands)

    Odinot, Geralda

    2008-01-01

    Many decisions in the legal system are based on eyewitness evidence. It seems to be a matter of common sense that the level of confidence expressed by a witness can be used as a diagnostic tool to discriminate between accurate and inaccurate memories. Contrary to this general belief, the bulk of

  10. Eyewitness confidence : the relation between accuracy and confidence in episodic memory

    NARCIS (Netherlands)

    Odinot, Geralda

    2008-01-01

    Many decisions in the legal system are based on eyewitness evidence. It seems to be a matter of common sense that the level of confidence expressed by a witness can be used as a diagnostic tool to discriminate between accurate and inaccurate memories. Contrary to this general belief, the bulk of emp

  11. Confidence intervals make a difference : Effects of showing confidence intervals on inferential reasoning

    NARCIS (Netherlands)

    Hoekstra, Rink; Johnson, Addie; Kiers, Henk A. L.

    2012-01-01

    The use of confidence intervals (CIs) as an addition or as an alternative to null hypothesis significance testing (NHST) has been promoted as a means to make researchers more aware of the uncertainty that is inherent in statistical inference. Little is known, however, about whether presenting result

  12. Effect of high contents of dietary animal-derived protein or carbohydrates on canine fecal microbiota

    NARCIS (Netherlands)

    Hang, I.; Rinttila, T.; Zentek, J.; Kettunen, A.; Alaja, S.; Apajalahti, J.A.; Harmoinen, J.; Vos, de W.M.; Spillmann, T.

    2012-01-01

    BACKGROUND: Considerable evidence suggests that food impacts both the gastro-intestinal (GI) function and the microbial ecology of the canine GI tract. The aim of this study was to evaluate the influence of high-carbohydrate (HC), high-protein (HP) and dry commercial (DC) diets on the canine colonic

  13. Perceived thickness and creaminess modulates the short-term satiating effects of high-protein drinks.

    Science.gov (United States)

    Bertenshaw, Emma J; Lluch, Anne; Yeomans, Martin R

    2013-08-28

    Previous research suggests that increasing beverage protein content enhances subsequent satiety, but whether this effect is entirely attributable to post-ingestive effects of protein or is partly caused by the distinct sensory characteristics imparted by the presence of protein remains unclear. To try and discriminate nutritive from sensory effects of added protein, we contrasted effects of three higher-energy (about 1·2 MJ) and one lower-energy (LE: 0·35 MJ) drink preloads on subsequent appetite and lunch intake. Two higher-energy drinks had 44% of energy from protein, one with the sensory characteristics of a juice drink (HP2, low-sensory protein) and the second a thicker and creamier (HPþ, high-sensory protein) drink. The high-carbohydrate preload (HCþ, high-sensory carbohydrate) was matched for thickness and creaminess to the HPþ drink. Participants (healthy male volunteers, n 26) consumed significantly less at lunch after the HPþ(566 g) and HCþ(572 g) than after HP2 (623 g) and LE (668 g) drinks, although the compensation for drink energy accounted for only 50% of extra energy at best. Appetite ratings indicated that participants felt significantly less hungry and more full immediately before lunch in HPþ and HCþ groups compared with LE, with HP2 being intermediate. The finding that protein generated stronger satiety in the context of a thicker creamier drink (HPþ but not HP2) and that an isoenergetic carbohydrate drink (HCþ), matched in thickness and creaminess to the HPþ drink, generated the same pattern of satiety as HPþ, both suggest an important role for these sensory cues in the development of protein-based satiety.

  14. Silkworm pupae (Bombyx mori) are new sources of high quality protein and lipid.

    Science.gov (United States)

    Tomotake, Hiroyuki; Katagiri, Mitsuaki; Yamato, Masayuki

    2010-01-01

    This study was performed to evaluate the nutritional value of silkworm pupae (Bombyx mori) and the content of α-glucosidase inhibitor. The percentages of total protein and lipid contents by dry weight were 55.6 and 32.2%, respectively. Silkworm pupae protein had high levels of essential amino acids such as valine, methionine and phenylalanine. The contents of essential amino acids in silkworm pupae protein satisfied the FAO/WHO/UNU suggested requirements (2007). In addition, they also possessed n-3 fatty acids, especially α-linolenic acid (36.3%), as a major component. The 50% ethanol extract of silkworm pupae contained 1-deoxynojirimycin (DNJ), which is a potent α-glucosidase inhibitor. These results suggest that silkworm pupae are a new source of high quality protein, lipid, and α-glucosidase inhibitor.

  15. Nanoparticle self-assembly by a highly stable recombinant spider wrapping silk protein subunit.

    Science.gov (United States)

    Xu, Lingling; Tremblay, Marie-Laurence; Orrell, Kathleen E; Leclerc, Jérémie; Meng, Qing; Liu, Xiang-Qin; Rainey, Jan K

    2013-10-01

    Artificial spider silk proteins may form fibers with exceptional strength and elasticity. Wrapping silk, or aciniform silk, is the toughest of the spider silks, and has a very different protein composition than other spider silks. Here, we present the characterization of an aciniform protein (AcSp1) subunit named W1, consisting of one AcSp1 199 residue repeat unit from Argiope trifasciata. The structural integrity of recombinant W1 is demonstrated in a variety of buffer conditions and time points. Furthermore, we show that W1 has a high thermal stability with reversible denaturation at ∼71°C and forms self-assembled nanoparticle in near-physiological conditions. W1 therefore represents a highly stable and structurally robust module for protein-based nanoparticle formation. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  16. [Research progress in roles of high-risk human papillomavirus E2 protein].

    Science.gov (United States)

    Wu, En-Qi; Tang, Yuan-Yu

    2014-03-01

    High-risk human papillomavirus (HPV) is the principal cause of various cancers including cervical cancer, anal cancer, vulvar cancer, and some head and neck cancers. In the viral life cycle, by interacting with both viral and host DNA and proteins, the HPV E2 protein plays a pivotal role in viral transcriptional regulation and DNA replication, and it is also associated with modification of various cellular processes, including host gene transcription, RNA processing, apoptosis, ubiquitination, and intracellular trafficking, to create a convenient environment for a replicative cycle of the virus and contribute to the HPV pathogenesis. Elucidating the roles of E2 protein throughout the viral life cycle will improve our understanding of the viral life cycle and pathogenesis and help us identify novel antiviral agents with therapeutic potential. This article reviews the research progress in the structure, roles, and activity of high-risk HPV E2 protein, particularly that of HPV-16.

  17. Likelihood based observability analysis and confidence intervals for predictions of dynamic models

    CERN Document Server

    Kreutz, Clemens; Timmer, Jens

    2011-01-01

    Mechanistic dynamic models of biochemical networks such as Ordinary Differential Equations (ODEs) contain unknown parameters like the reaction rate constants and the initial concentrations of the compounds. The large number of parameters as well as their nonlinear impact on the model responses hamper the determination of confidence regions for parameter estimates. At the same time, classical approaches translating the uncertainty of the parameters into confidence intervals for model predictions are hardly feasible. In this article it is shown that a so-called prediction profile likelihood yields reliable confidence intervals for model predictions, despite arbitrarily complex and high-dimensional shapes of the confidence regions for the estimated parameters. Prediction confidence intervals of the dynamic states allow a data-based observability analysis. The approach renders the issue of sampling a high-dimensional parameter space into evaluating one-dimensional prediction spaces. The method is also applicable ...

  18. High-throughput kinase assays with protein substrates using fluorescent polymer superquenching

    Directory of Open Access Journals (Sweden)

    Weatherford Wendy

    2005-05-01

    Full Text Available Abstract Background High-throughput screening is used by the pharmaceutical industry for identifying lead compounds that interact with targets of pharmacological interest. Because of the key role that aberrant regulation of protein phosphorylation plays in diseases such as cancer, diabetes and hypertension, kinases have become one of the main drug targets. With the exception of antibody-based assays, methods to screen for specific kinase activity are generally restricted to the use of small synthetic peptides as substrates. However, the use of natural protein substrates has the advantage that potential inhibitors can be detected that affect enzyme activity by binding to a site other than the catalytic site. We have previously reported a non-radioactive and non-antibody-based fluorescence quench assay for detection of phosphorylation or dephosphorylation using synthetic peptide substrates. The aim of this work is to develop an assay for detection of phosphorylation of chemically unmodified proteins based on this polymer superquenching platform. Results Using a modified QTL Lightspeed™ assay, phosphorylation of native protein was quantified by the interaction of the phosphorylated proteins with metal-ion coordinating groups co-located with fluorescent polymer deposited onto microspheres. The binding of phospho-protein inhibits a dye-labeled "tracer" peptide from associating to the phosphate-binding sites present on the fluorescent microspheres. The resulting inhibition of quench generates a "turn on" assay, in which the signal correlates with the phosphorylation of the substrate. The assay was tested on three different proteins: Myelin Basic Protein (MBP, Histone H1 and Phosphorylated heat- and acid-stable protein (PHAS-1. Phosphorylation of the proteins was detected by Protein Kinase Cα (PKCα and by the Interleukin -1 Receptor-associated Kinase 4 (IRAK4. Enzyme inhibition yielded IC50 values that were comparable to those obtained using

  19. The effects of high temperature level on square Bt protein concentration of Bt cotton

    Institute of Scientific and Technical Information of China (English)

    WANG Jun; CHEN Yuan; YAO Meng-hao; LI Yuan; WEN Yu-jin; ZHANG Xiang; CHEN De-hua

    2015-01-01

    Higher bol worm survival rates were detected after high temperature presented during square period in Bt cotton. The objective of this study was to investigate the effects of high temperature level on the Bt efifcacy of two different types of Bt cotton cultivars at squaring stage. During the 2011 to 2013 cotton growth seasons, high temperature treatments ranged from 34 to 44°C in climate chambers, and ifeld experiments under high temperature weather with various temperature levels were conducted to investigate the effects of the high temperature level on square Bt protein concentration and nitrogen metabolism. The climate chamber experiments showed that the square insecticidal protein contents reduced after 24 h elevated temperature treatments for both cultivars, whereas signiifcant declines of the square insecticidal protein contents were detected at temperature >38°C, and only slightly numerical reductions were observed when temperature below 38°C. Similar high temperature responses were also observed at the two ifeld experimental sites in 2013. Correspondingly, high temperature below 38°C seems have little effect on the square amino acid concentrations, soluble protein contents, glutam-ic-pyruvic transaminase (GPT) and glutamic-oxalacetic transaminase (GOT) activities as wel as protease and peptidase activities; however, when the temperature was above 38°C, reduced soluble protein contents, enhanced amino acid con-centrations, decreased GPT and GOT activities, bolstered protease and peptidase activities in square were detected. In general, the higher the temperature is (>38°C), the larger the changes for the above compound contents and key enzymes activities of the square protein cycle. The ifndings indicated that the unstable insect resistance of the square was related to high temperature level during square stage.

  20. Fall 2014 SEI Research Review High Confidence Cyber Physical Systems

    Science.gov (United States)

    2014-10-28

    FY11,FY12 LENS Collaborators • Prof. Marsha Chechik, Univ. of Toronto • Prof. Ed Clarke, CMU /CS • Prof. Lui Sha, UIUC • Prof. John Lehoczky... CMU /Stat • Prof. Raj Rajkumar, CMU /ECE • Prof. Anthony Rowe, CMU /ECE • Prof. Paul Scerri, CMU /RI • Prof. Natasha Sharygina, Univ. of Lugano • Prof

  1. Highly selective isolation and purification of heme proteins in biological samples using multifunctional magnetic nanospheres.

    Science.gov (United States)

    Liu, Yating; Li, Yan; Wei, Yun

    2014-12-01

    Magnetic particles with suitable surface modification are capable of binding proteins selectively, and magnetic separations have advantages of rapidity, convenience, and high selectivity. In this paper, new magnetic nanoparticles modified with imidazolium ionic liquid (Fe3O4 @SiO2 @ILs) were successfully fabricated. N-Methylimidazolium was immobilized onto silica-coated magnetic nanoparticles via γ-chloropropyl modification as a magnetic nanoadsorbent for heme protein separation. The particle size was about 90 nm without significant aggregation during the preparation process. Hemoglobin as one of heme proteins used in this experiment was compared with other nonheme proteins. It has been found that the magnetic nanoparticles can be used for more rapid, efficient, and specific adsorption of hemoglobin with a binding capacity as high as 5.78 mg/mg. In comparison with other adsorption materials of proteins in the previous reports, Fe3 O4 @SiO2 @ILs magnetic nanoparticles exhibit the excellent performance in isolation of heme proteins with higher binding capacity and selectivity. In addition, a short separation time makes the functionalized nanoparticles suitable for purifying unstable proteins, as well as having other potential applications in a variety of biomedical fields.

  2. Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling.

    Science.gov (United States)

    Ozer, Abdullah; Tome, Jacob M; Friedman, Robin C; Gheba, Dan; Schroth, Gary P; Lis, John T

    2015-08-01

    Because RNA-protein interactions have a central role in a wide array of biological processes, methods that enable a quantitative assessment of these interactions in a high-throughput manner are in great demand. Recently, we developed the high-throughput sequencing-RNA affinity profiling (HiTS-RAP) assay that couples sequencing on an Illumina GAIIx genome analyzer with the quantitative assessment of protein-RNA interactions. This assay is able to analyze interactions between one or possibly several proteins with millions of different RNAs in a single experiment. We have successfully used HiTS-RAP to analyze interactions of the EGFP and negative elongation factor subunit E (NELF-E) proteins with their corresponding canonical and mutant RNA aptamers. Here we provide a detailed protocol for HiTS-RAP that can be completed in about a month (8 d hands-on time). This includes the preparation and testing of recombinant proteins and DNA templates, clustering DNA templates on a flowcell, HiTS and protein binding with a GAIIx instrument, and finally data analysis. We also highlight aspects of HiTS-RAP that can be further improved and points of comparison between HiTS-RAP and two other recently developed methods, quantitative analysis of RNA on a massively parallel array (RNA-MaP) and RNA Bind-n-Seq (RBNS), for quantitative analysis of RNA-protein interactions.

  3. On the formation of highly charged gaseous ions from unfolded proteins by electrospray ionization.

    Science.gov (United States)

    Konermann, Lars; Rodriguez, Antony D; Liu, Jiangjiang

    2012-08-07

    Electrospray ionization (ESI) of native proteins results in a narrow distribution of low protonation states. ESI for these folded species proceeds via the charged residue mechanism. In contrast, ESI of unfolded proteins yields a wide distribution of much higher charge states. The current work develops a model that can account for this effect. Recent molecular dynamics simulations revealed that ESI for unfolded polypeptide chains involves protein ejection from nanodroplets, representing a type of ion evaporation mechanism (IEM). We point out the analogies between this IEM, and the dissociation of gaseous protein complexes after collisional activation. The latter process commences with unraveling of a single subunit, in concert with Coulombically driven proton transfer. The subunit then separates from the residual complex as a highly charged ion. We propose that similar charge equilibration events accompany the IEM of unfolded proteins, thereby causing the formation of high ESI charge states. A bead chain model is used for examining how charge is partitioned as protein and droplet separate. It is shown that protein ejection from differently sized ESI droplets generates a range of protonation states. The predicted behavior agrees well with experimental data.

  4. Theoretical analysis of a high performance protein imprint on a nanosensor

    Directory of Open Access Journals (Sweden)

    Jianfa Chen

    2016-03-01

    Full Text Available The structural details and flexibilities of protein impose significant challenges to develop protein imprint, especially for the selection of functional monomer. Using NAMD, AutoDock 4 and AutoDock Vina, we investigated the formation of a high performance protein imprint on a nanosensor that detected human papillomavirus (HPV biomarker protein E7 with high sensitivity. According to molecular dynamics, the phenolic oligomers were shown to assemble with the E7 protein and form a complex at specific targeting areas on the protein. Docking analysis efficiently screened chemical compounds by evaluating the binding affinity. A new parameter, i.e., average binding energy (ΔG/contact, was used together with binding energy (ΔG to screen compounds. The screening went through 189 compounds and identified a subpopulation of 22 compounds showing unique characteristics of binding, and could potentially be used to develop the specific and robust imprint. Accordingly, the study implicated a novel approach to screen functional compounds for rational design of the protein imprint.

  5. Automatic classification and pattern discovery in high-throughput protein crystallization trials.

    Science.gov (United States)

    Cumbaa, Christian; Jurisica, Igor

    2005-01-01

    Conceptually, protein crystallization can be divided into two phases search and optimization. Robotic protein crystallization screening can speed up the search phase, and has a potential to increase process quality. Automated image classification helps to increase throughput and consistently generate objective results. Although the classification accuracy can always be improved, our image analysis system can classify images from 1,536-well plates with high classification accuracy (85%) and ROC score (0.87), as evaluated on 127 human-classified protein screens containing 5,600 crystal images and 189,472 non-crystal images. Data mining can integrate results from high-throughput screens with information about crystallizing conditions, intrinsic protein properties, and results from crystallization optimization. We apply association mining, a data mining approach that identifies frequently occurring patterns among variables and their values. This approach segregates proteins into groups based on how they react in a broad range of conditions, and clusters cocktails to reflect their potential to achieve crystallization. These results may lead to crystallization screen optimization, and reveal associations between protein properties and crystallization conditions. We also postulate that past experience may lead us to the identification of initial conditions favorable to crystallization for novel proteins.

  6. How surface composition of high milk proteins powders is influenced by spray-drying temperature.

    Science.gov (United States)

    Gaiani, C; Morand, M; Sanchez, C; Tehrany, E Arab; Jacquot, M; Schuck, P; Jeantet, R; Scher, J

    2010-01-01

    High milk proteins powders are common ingredients in many food products. The surface composition of these powders is expected to play an essential role during their storage, handling and/or final application. Therefore, an eventual control of the surface composition by modifying the spray-drying temperature could be very useful in the improvement of powder quality and the development of new applications. For this purpose, the influence of five spray-drying temperatures upon the surface composition of the powders was investigated by X-ray photoelectron spectroscopy. The major milk proteins were studied: native micellar casein and native whey, both more or less enriched in lactose. The results show a surface enrichment in lipids for all the powders and in proteins for many powders. Whatever the drying temperature, lipids and proteins are preferentially located near the surface whereas lactose is found in the core. This surface enrichment is also highly affected by the spray-drying temperature. More lipids, more proteins and less lactose are systematically observed at the surface of powders spray-dried at lower outlet air temperatures. The nature of proteins is also found essential; surface enrichment in lipids being much stronger for whey proteins containing powders than for casein containing powders. Additionally, we found a direct correlation between the lipids surface concentration and the wetting ability for the 25 powders studied.

  7. Soy protein isolate inhibits hepatic tumor promotion in mice fed a high-fat liquid diet.

    Science.gov (United States)

    Mercer, Kelly E; Pulliam, Casey F; Pedersen, Kim B; Hennings, Leah; Ronis, Martin Jj

    2017-03-01

    Alcoholic and nonalcoholic fatty liver diseases are risk factors for development of hepatocellular carcinoma, but the underlying mechanisms are poorly understood. On the other hand, ingestion of soy-containing diets may oppose the development of certain cancers. We previously reported that replacing casein with a soy protein isolate reduced tumor promotion in the livers of mice with alcoholic liver disease after feeding a high fat ethanol liquid diet following initiation with diethylnitrosamine. Feeding soy protein isolate inhibited processes that may contribute to tumor promotion including inflammation, sphingolipid signaling, and Wnt/β-catenin signaling. We have extended these studies to characterize liver tumor promotion in a model of nonalcoholic fatty liver disease produced by chronic feeding of high-fat liquid diets in the absence of ethanol. Mice treated with diethylnitrosamine on postnatal day 14 were fed a high-fat liquid diet made with casein or SPI as the sole protein source for 16 weeks in adulthood. Relative to mice fed normal chow, a high fat/casein diet led to increased tumor promotion, hepatocyte proliferation, steatosis, and inflammation. Replacing casein with soy protein isolate counteracted these effects. The high fat diets also resulted in a general increase in transcripts for Wnt/β-catenin pathway components, which may be an important mechanism, whereby hepatic tumorigenesis is promoted. However, soy protein isolate did not block Wnt signaling in this nonalcoholic fatty liver disease model. We conclude that replacing casein with soy protein isolate blocks development of steatosis, inflammation, and tumor promotion in diethylnitrosamine-treated mice fed high fat diets. Impact statement The impact of dietary components on cancer is a topic of great interest for both the general public and the scientific community. Liver cancer is currently the second leading form of cancer deaths worldwide. Our study has addressed the effect of the protein

  8. Retention of nativelike conformation by proteins embedded in high external electric fields

    Science.gov (United States)

    Pompa, P. P.; Bramanti, A.; Maruccio, G.; Cingolani, R.; De Rienzo, F.; Corni, S.; Di Felice, R.; Rinaldi, R.

    2005-05-01

    In this Communication, we show that proteins embedded in high external electric fields are capable of retaining a nativelike fold pattern. We have tested the metalloprotein azurin, immobilized onto SiO2 substrates in air with proper electrode configuration, by applying static fields up to 106-107V/m. The effects on the conformational properties of protein molecules have been determined by means of intrinsic fluorescence measurements. Experimental results indicate that no significant field-induced conformational alteration occurs. Such results are also discussed and supported by theoretical predictions of the inner protein fields.

  9. Protein-bound toxins: added value in their removal with high convective volumes.

    Science.gov (United States)

    Abad, Soraya; Vega, Almudena; Quiroga, Borja; Arroyo, David; Panizo, Nayara; Reque, Javier Eduardo; López-Gómez, Juan Manuel

    Chronic kidney disease is associated with an increased risk of cardiovascular events. In recent years, protein-bound toxins have become more important due to their association with increased morbidity and mortality, characterised by inadequate clearance during dialysis. The purpose of this study is to assess the influence of high convective volumes on postdilution online haemodiafiltration (OL-HDF) on the removal of medium-sized molecules, small molecules and protein-bound molecules.

  10. Electrical protein detection in cell lysates using high-density peptide-aptamer microarrays

    Directory of Open Access Journals (Sweden)

    Evans David

    2008-01-01

    Full Text Available Abstract Background The dissection of biological pathways and of the molecular basis of disease requires devices to analyze simultaneously a staggering number of protein isoforms in a given cell under given conditions. Such devices face significant challenges, including the identification of probe molecules specific for each protein isoform, protein immobilization techniques with micrometer or submicrometer resolution, and the development of a sensing mechanism capable of very high-density, highly multiplexed detection. Results We present a novel strategy that offers practical solutions to these challenges, featuring peptide aptamers as artificial protein detectors arrayed on gold electrodes with feature sizes one order of magnitude smaller than existing formats. We describe a method to immobilize specific peptide aptamers on individual electrodes at the micrometer scale, together with a robust and label-free electronic sensing system. As a proving proof of principle experiment, we demonstrate the specific recognition of cyclin-dependent protein kinases in whole-cell lysates using arrays of ten electrodes functionalized with individual peptide aptamers, with no measurable cross-talk between electrodes. The sensitivity is within the clinically relevant range and can detect proteins against the high, whole-cell lysate background. Conclusion The use of peptide aptamers selected in vivo to recognize specific protein isoforms, the ability to functionalize each microelectrode individually, the electronic nature and scalability of the label-free detection and the scalability of the array fabrication combine to yield the potential for highly multiplexed devices with increasingly small detection areas and higher sensitivities that may ultimately allow the simultaneous monitoring of tens or hundreds of thousands of protein isoforms.

  11. High-Level Production of Heterologous Protein by Engineered Yeasts Grown in Cottage Cheese Whey

    OpenAIRE

    Maullu, Carlo; Lampis, Giorgio; Desogus, Alessandra; Ingianni, Angela; Rossolini, Gian Maria; Pompei, Raffaello

    1999-01-01

    Cottage cheese whey is a cheese industry by-product still rich in proteins and lactose. Its recycling is seldom cost-effective. In this work we show that the lactose-utilizing yeast Kluyveromyces lactis, engineered for production of recombinant human lysozyme, can be grown in cottage cheese whey, resulting in high-level production of the heterologous protein (125 μg/ml).

  12. A high throughput screen for RGS proteins using steady state monitoring of free phosphate formation.

    Directory of Open Access Journals (Sweden)

    C Aaron Monroy

    Full Text Available G-protein coupled receptors are a diverse group that are the target of over 50% of marketed drugs. Activation of these receptors results in the exchange of bound GDP for GTP in the Gα subunit of the heterotrimeric G-protein. The Gα subunit dissociates from the β/γ subunits and both proceed to affect downstream signaling targets. The signal terminates by the hydrolysis of GTP to GDP and is temporally regulated by Regulators of G-protein Signaling (RGS proteins that act as GTPase Activating Proteins (GAPs. This makes RGS proteins potentially desirable targets for "tuning" the effects of current therapies as well as developing novel pharmacotherapies. Current methods for evaluating RGS activity depend on laborious and/or expensive techniques. In this study we developed a simple and inexpensive assay for the steady state analysis of RGS protein GAP activity, using RGS4, RGS8 and RGS17 as models. Additionally, we report the use of RGS4 as a model for high throughput assay development. After initial setup, this assay can be conducted in a highly parallel fashion with a read time of less than 8 minutes for a 1536-well plate. The assay exhibited a robust Z-factor of 0.6 in a 1536-well plate. We conducted a pilot screen for inhibitors using a small, 2320 compound library. From this screen, 13 compounds were identified as compounds for further analysis. The successful development of this assay for high-throughput screening provides a low cost, high speed, simple method for assessing RGS protein activity.

  13. High Mobility Group Box Protein-1 Correlates with Renal Function in Chronic Kidney Disease (CKD)

    OpenAIRE

    Bruchfeld, Annette; Qureshi, Abdul Rashid; Lindholm, Bengt; Barany, Peter; Yang, Lihong; Stenvinkel, Peter; Tracey, Kevin J.

    2007-01-01

    Chronic kidney disease (CKD) is associated with inflammation and malnutrition and carries a markedly increased risk of cardiovascular disease (CVD). High Mobility Group Box Protein-1 (HMGB-1) is a 30-kDa nuclear and cytosolic protein known as a transcription and growth factor, recently identified as a proinflammatory mediator of tissue injury. Recent data implicates HMGB-1 in endotoxin lethality, rheumatoid arthritis, and atherosclerosis. The aim of this post-hoc, cross-sectional study was to...

  14. Effects of high hydrostatic pressure on emulsifying properties of sweet potato protein in model protein-hydrocolloids system.

    Science.gov (United States)

    Khan, Nasir Mehmood; Mu, Tai-Hua; Ali, Farman; Arogundade, Lawrence A; Khan, Zia Ullah; Zhang, Maio; Ahmad, Shujaat; Sun, Hong-Nan

    2015-02-15

    The effects of high hydrostatic pressure (HHP) on emulsifying properties of sweet potato protein (SPP) in presence of 0.1%, 0.3% and 0.5% (w/v) of guar gum (GG) and glycerol monostearate (GMS) were investigated. Emulsifying stability index (ESI) of the SPP with GG revealed significant increase (Pmodel while such case was not observed for SPP-GMS model. The flow index for SPP-GG emulsion model was found to decrease with increase in HHP treatment and had non-Newtonian behaviour. The SPP-GMS emulsion models with HHP treatments showed comparatively lower viscosities but had more Newtonian flow character.

  15. Exhibitors: Full of Confidence Adequate Preparation

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    From March 26th,three most important trade fairs for Chinese textile industry opened successively inBeijing.Several exhibitors showed their confidence and preparation to TA Weekly. Bosideng:CHIC is an everlasting marketing chance"We’ll definitely participate in CHIC 2009,with even moreinvestment."Gao Dekang,the President of Bosideng Co.,Ltd said,"Bosideng is going to make full use of this trade fair for furtherdevelopment."According to the organizer of CHIC 2009,Bosidengreserved 1000 square meters for its show."CHIC witnessed the blooming development of Chinese clothingindustry for the last ten years.CHIC has made a progress to catch upwith the world trend as well as in the social influence.It has becomethe pioneer of fashion and is regarded as the releasing center,innovation center and brand center."As a long-term participant,Bosideng has the right to say these words.It is in this fair,Bosideng

  16. Prenatal high protein exposure decreases energy expenditure and increases adiposity in young rats.

    Science.gov (United States)

    Daenzer, Maren; Ortmann, Sylvia; Klaus, Susanne; Metges, Cornelia C

    2002-02-01

    Epidemiologic results suggest that protein intake in infancy and later adiposity might be related. We examined whether high dietary protein exposure in utero and/or during postnatal life affects body fatness. Two groups of female rats were mated and pair-fed isocaloric high (40% protein; HP) or adequate protein (20% protein; AP) diets throughout pregnancy. The male offspring were suckled (3 wk) by foster mothers pair-fed HP or AP diets, resulting in 4 pre-/postnatal groups (AP-AP, AP-HP, HP-AP, HP-HP). Subsequently, they were pair-fed the same diets their nurses received during lactation until wk 9. Offspring of HP dams had a lower body weight on d 2 of life than their AP counterparts (7.6 +/- 0.7 vs. 8.3 +/- 0.8 g; P total energy expenditure at wk 9 (P < 0.05). Postnatal HP alone had no significant effect on body composition or metabolic rate. These results indicate that in utero exposure to a high protein level reprograms body weight and energy homeostasis.

  17. Limitations of yeast surface display in engineering proteins of high thermostability.

    Science.gov (United States)

    Park, Sheldon; Xu, Yao; Stowell, Xiaoran Fu; Gai, Feng; Saven, Jeffery G; Boder, Eric T

    2006-05-01

    Engineering proteins that can fold to unique structures remains a challenge. Protein stability has previously been engineered via the observed correlation between thermal stability and eukaryotic secretion level. To explore the limits of an expression-based approach, variants of the highly thermostable three-helix bundle protein alpha3D were studied using yeast surface display. A library of alpha3D mutants was created to explore the possible correlation of protein stability and fold with expression level. Five efficiently expressed mutants were then purified and further studied biochemically. Despite their differences in stability, most mutants expressed at levels comparable with that of wild-type alpha3D. Two other related sequences (alpha3A and alpha3B) that form collapsed, stable molten globules but lack a uniquely folded structure were similarly expressed at high levels by yeast display. Together these observations suggest that the quality control system in yeast is unable to discriminate between well-folded proteins of high stability and molten globules. The present study, therefore, suggests that an optimization of the surface display efficiency on yeast may yield proteins that are thermally and chemically stable yet are poorly folded.

  18. The Relationship Between Eyewitness Confidence and Identification Accuracy: A New Synthesis.

    Science.gov (United States)

    Wixted, John T; Wells, Gary L

    2017-05-01

    The U.S. legal system increasingly accepts the idea that the confidence expressed by an eyewitness who identified a suspect from a lineup provides little information as to the accuracy of that identification. There was a time when this pessimistic assessment was entirely reasonable because of the questionable eyewitness-identification procedures that police commonly employed. However, after more than 30 years of eyewitness-identification research, our understanding of how to properly conduct a lineup has evolved considerably, and the time seems ripe to ask how eyewitness confidence informs accuracy under more pristine testing conditions (e.g., initial, uncontaminated memory tests using fair lineups, with no lineup administrator influence, and with an immediate confidence statement). Under those conditions, mock-crime studies and police department field studies have consistently shown that, for adults, (a) confidence and accuracy are strongly related and (b) high-confidence suspect identifications are remarkably accurate. However, when certain non-pristine testing conditions prevail (e.g., when unfair lineups are used), the accuracy of even a high-confidence suspect ID is seriously compromised. Unfortunately, some jurisdictions have not yet made reforms that would create pristine testing conditions and, hence, our conclusions about the reliability of high-confidence identifications cannot yet be applied to those jurisdictions. However, understanding the information value of eyewitness confidence under pristine testing conditions can help the criminal justice system to simultaneously achieve both of its main objectives: to exonerate the innocent (by better appreciating that initial, low-confidence suspect identifications are error prone) and to convict the guilty (by better appreciating that initial, high-confidence suspect identifications are surprisingly accurate under proper testing conditions).

  19. Confidence Intervals from Normalized Data: A correction to Cousineau (2005

    Directory of Open Access Journals (Sweden)

    Richard D. Morey

    2008-09-01

    Full Text Available Presenting confidence intervals around means is a common method of expressing uncertainty in data. Loftus and Masson (1994 describe confidence intervals for means in within-subjects designs. These confidence intervals are based on the ANOVA mean squared error. Cousineau (2005 presents an alternative to the Loftus and Masson method, but his method produces confidence intervals that are smaller than those of Loftus and Masson. I show why this is the case and offer a simple correction that makes the expected size of Cousineau confidence intervals the same as that of Loftus and Masson confidence intervals.

  20. Mixed compared with single-source proteins in high-protein diets affect kidney structure and function differentially in obese fa/fa Zucker rats.

    Science.gov (United States)

    Devassy, Jessay G; Wojcik, Jennifer L; Ibrahim, Naser H M; Zahradka, Peter; Taylor, Carla G; Aukema, Harold M

    2017-02-01

    Questions remain regarding the potential negative effects of dietary high protein (HP) on kidney health, particularly in the context of obesity in which the risk for renal disease is already increased. To examine whether some of the variability in HP effects on kidney health may be due to source of protein, obese fa/fa Zucker rats were given HP (35% of energy from protein) diets containing either casein, soy protein, or a mixed source of animal and plant proteins for 12 weeks. Control lean and obese rats were given diets containing casein at normal protein (15% of energy from protein) levels. Body weight and blood pressure were measured, and markers of renal structural changes, damage, and function were assessed. Obesity alone resulted in mild renal changes, as evidenced by higher kidney weights, proteinuria, and glomerular volumes. In obese rats, increasing the protein level using the single, but not mixed, protein sources resulted in higher renal fibrosis compared with the lean rats. The mixed-protein HP group also had lower levels of serum monocyte chemoattractant protein-1, even though this diet further increased kidney and glomerular size. Soy and mixed-protein HP diets also resulted in a small number of damaged glomeruli, while soy compared with mixed-protein HP diet delayed the increase in blood pressure over time. Since obesity itself confers added risk of renal disease, an HP diet from mixed-protein sources that enables weight loss but has fewer risks to renal health may be advantageous.

  1. Whey protein reduces early life weight gain in mice fed a high-fat diet

    DEFF Research Database (Denmark)

    Tranberg, Britt; Hellgren, Lars; Lykkesfeldt, Jens;

    2013-01-01

    An increasing number of studies indicate that dairy products, including whey protein, alleviate several disorders of the metabolic syndrome. Here, we investigated the effects of whey protein isolate (whey) in mice fed a high-fat diet hypothesising that the metabolic effects of whey would...... be associated with changes in the gut microbiota composition. Five-week-old male C57BL/6 mice were fed a high-fat diet ad libitum for 14 weeks with the protein source being either whey or casein. Faeces were collected at week 0, 7, and 13 and the fecal microbiota was analysed by denaturing gradient gel...... reduced weight gain in young C57BL/6 mice fed a high-fat diet compared to casein. Although the effect on weight gain ceased, whey alleviated glucose intolerance, improved insulin sensitivity and reduced plasma cholesterol. These findings could not be explained by changes in food intake or gut microbiota...

  2. Practical strategies for the evaluation of high-affinity protein/nucleic acid interactions.

    Science.gov (United States)

    Altschuler, Sarah E; Lewis, Karen A; Wuttke, Deborah S

    2013-01-01

    The quantitative evaluation of binding interactions between proteins and nucleic acids is highly sensitive to a variety of experimental conditions. Optimization of these conditions is critical for obtaining high quality, reproducible data, particularly in the context of very high affinity interactions. Here, we discuss the practical considerations involved in optimizing the apparent binding constant of an interaction as measured by two common quantitative assays, electrophoretic mobility shift assay and double-filter binding when measuring extremely tight protein/nucleic acid interactions with sub-nanomolar binding affinities. We include specific examples from two telomere end-binding protein systems, Schizo -saccharomyces pombe Pot1 and Saccharomyces cerevisiae Cdc13, to demonstrate potential experimental pitfalls and some useful strategies for optimization.

  3. Endocytic proteins drive vesicle growth via instability in high membrane tension environment

    CERN Document Server

    Walani, Nikhil; Agrawal, Ashutosh

    2015-01-01

    Clathrin-mediated endocytosis (CME) is a key pathway for transporting cargo into cells via membrane vesicles. It plays an integral role in nutrient import, signal transduction, neurotransmission and cellular entry of pathogens and drug-carrying nanoparticles. As CME entails substantial local remodeling of the plasma membrane, the presence of membrane tension offers resistance to bending and hence, vesicle formation. Experiments show that in such high tension conditions, actin dynamics is required to carry out CME successfully. In this study, we build upon these pioneering experimental studies to provide fundamental mechanistic insights into the roles of two key endocytic proteins, namely, actin and BAR proteins in driving vesicle formation in high membrane tension environment. Our study reveals a new actin force induced `snap-through instability' that triggers a rapid shape transition from a shallow invagination to a highly invaginated tubular structure. We show that the association of BAR proteins stabilizes...

  4. Practical strategies for the evaluation of high-affinity protein/nucleic acid interactions

    Directory of Open Access Journals (Sweden)

    Sarah E. Altschuler

    2013-09-01

    Full Text Available The quantitative evaluation of binding interactions between proteins and nucleic acids is highly sensitive to a variety of experimental conditions. Optimization of these conditions is critical for obtaining high quality, reproducible data, particularly in the context of very high affinity interactions. Here, we discuss the practical considerations involved in optimizing the apparent binding constant of an interaction as measured by two common quantitative assays, electrophoretic mobility shift assay and double-filter binding when measuring extremely tight protein/nucleic acid interactions with sub-nanomolar binding affinities. We include specific examples from two telomere end-binding protein systems, Schizosaccharomyces pombe Pot1 and Saccharomyces cerevisiae Cdc13, to demonstrate potential experimental pitfalls and some useful strategies for optimization.

  5. A novel optical technique to characterize fiberization of textured vegetable proteins under high-moisture extrusion

    Science.gov (United States)

    Yao, Gang; Liu, Keshun; Hsieh, Fu-Hung

    2004-11-01

    There have been great interests in using twin-screw extruders under high moisture conditions to produce textured vegetable proteins. Unlike the low moisture extrusion counterpart, a product extruded under high moisture can have well-defined fiber orientation and bears a strong resemblance to muscle meat. The textural properties of such extruded products are important for consumer acceptance. In this study, we developed a novel fluorescence polarization based technique that measures the fiber formation of extruded protein products. The experimental results using our new technique showed good agreements with results obtained from visual inspection and digital imaging of the dissected samples. The new technique provides an in vivo and noninvasive approach to characterize the fiber formation of textured vegetable proteins under high moisture extrusion. It has a potential to be used as a real time monitoring tool in food extrusion studies.

  6. Sources of sport confidence, imagery type and performance among competitive athletes: the mediating role of sports confidence.

    Science.gov (United States)

    Levy, A R; Perry, J; Nicholls, A R; Larkin, D; Davies, J

    2015-01-01

    This study explored the mediating role of sport confidence upon (1) sources of sport confidence-performance relationship and (2) imagery-performance relationship. Participants were 157 competitive athletes who completed state measures of confidence level/sources, imagery type and performance within one hour after competition. Among the current sample, confirmatory factor analysis revealed appropriate support for the nine-factor SSCQ and the five-factor SIQ. Mediational analysis revealed that sport confidence had a mediating influence upon the achievement source of confidence-performance relationship. In addition, both cognitive and motivational imagery types were found to be important sources of confidence, as sport confidence mediated imagery type- performance relationship. Findings indicated that athletes who construed confidence from their own achievements and report multiple images on a more frequent basis are likely to benefit from enhanced levels of state sport confidence and subsequent performance.

  7. Low thermodynamic but high kinetic stability of an antifreeze protein from Rhagium mordax.

    Science.gov (United States)

    Friis, Dennis S; Johnsen, Johannes L; Kristiansen, Erlend; Westh, Peter; Ramløv, Hans

    2014-06-01

    The equilibrium heat stability and the kinetic heat tolerance of a recombinant antifreeze protein (AFP) from the beetle Rhagium mordax (RmAFP1) are studied through differential scanning calorimetry and circular dichroism spectroscopy. In contrast to other insect AFPs studied with this respect, the RmAFP1 has only one disulfide bridge. The melting temperature, Tm , of the protein is determined to be 28.5°C (pH 7.4), which is much lower than most of those reported for AFPs or globular proteins in general. Despite its low melting temperature, both biophysical and activity measurements show that the protein almost completely refolds into the native state after repeated exposure of 70°C. RmAFP1 thus appears to be kinetically stable even far above its melting temperature. Thermodynamically, the insect AFPs seem to be dividable in three groups, relating to their content of disulfide bridges and widths of the ice binding motifs; high melting temperature AFPs (high disulfide content, TxT motifs), low melting temperature but high refolding capability AFPs (one disulfide bridge, TxTxTxT motifs) and irreversibly unfolded AFPs at low temperatures (no disulfide bridges, TxTxTxTxT motifs). The property of being able to cope with high temperature exposures may appear peculiar for proteins which strictly have their effect at subzero temperatures. Different aspects of this are discussed.

  8. Devclopment of the Forage Riees WithHigh Protein Gontent in Hunan

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@The meaning of the high protein forage rices Rices may be classified by itsuses as human'sfood.animal's on poultry's feed,or the raw materials of various industries.For ricesused as people's food.its breeding objectives are focused on the varietal characters such as medium amylose content .high rale of head rice.hyaline smoothmilled grains and delicious taste:for those used in making rice meal.beer,gourmet powder,etc.specially on high amylose content:while in wine making,it should be focused on big white belly and white beart,but low protein content in particular.As for the rices used as feed,the most important is its high rate of pre -protein in the brown rice ,leaving its grain appearance out of consideration.Thcrefore,the so called forage rice (FR)sgiykd be a kind of paddy rice with high pre-protein content of brown rice(≥8.25%)and high grain yicld (≥8.25t/ha),to be used as the composition of the animal feed by applying cultivation management oplimized under the suitable growth duration and strong pest resistance.

  9. Site-specific conjugation of an antibody-binding protein catalyzed by horseradish peroxidase creates a multivalent protein conjugate with high affinity to IgG.

    Science.gov (United States)

    Minamihata, Kosuke; Goto, Masahiro; Kamiya, Noriho

    2015-01-01

    Cross-linking proteins offers an approach to enhance the distinct function of proteins due to the multivalent effect. In this study, we demonstrated the preparation of a multivalent antibody-binding protein possessing high affinity to IgG by conjugating a number of antibody-binding proteins using the horseradish peroxidase (HRP)-mediated protein conjugation method. By introducing a peptide tag containing a tyrosine (Y-tag) to the C-terminus of the model protein, a chimera protein of protein G and protein A (pG2 pA), the Tyr residue in the Y-tag was efficiently recognized by HRP and cross-linked with each other to yield a pG2 pA conjugate, composed of mainly two to three units of pG2 pA. The cross-linking occurred site specifically at the Tyr residue in the Y-tag and introduction of the Y-tag showed no effect on the function of pG2 pA. The affinity of the Y-tagged pG2 pA conjugate against IgG clearly increased because of the multivalent effect, demonstrating the benefit of this protein cross-linking reaction, which yields functional protein oligomers. Such multivalent protein conjugates created by this reaction should have potential to be used in ELISA and Western blotting applications in which highly sensitive detection of target molecules is desired.

  10. Determining Frequentist Confidence Limits Using a Directed Parameter Space Search

    Science.gov (United States)

    Daniel, Scott F.; Connolly, Andrew J.; Schneider, Jeff

    2014-10-01

    We consider the problem of inferring constraints on a high-dimensional parameter space with a computationally expensive likelihood function. We propose a machine learning algorithm that maps out the Frequentist confidence limit on parameter space by intelligently targeting likelihood evaluations so as to quickly and accurately characterize the likelihood surface in both low- and high-likelihood regions. We compare our algorithm to Bayesian credible limits derived by the well-tested Markov Chain Monte Carlo (MCMC) algorithm using both multi-modal toy likelihood functions and the seven yr Wilkinson Microwave Anisotropy Probe cosmic microwave background likelihood function. We find that our algorithm correctly identifies the location, general size, and general shape of high-likelihood regions in parameter space while being more robust against multi-modality than MCMC.

  11. High-protein diets in hyperlipidemia : effect of wheat gluten on serum lipids, uric acid, and renal function

    NARCIS (Netherlands)

    Jenkins, D.J.A.; Kendall, C.W.C.; Vidgen, E.; Augustin, L.S.A.; Erk, van M.; Geelen, A.; Parker, T.; Faulkner, D.; Vuksan, V.; Josse, R.G.; Leiter, L.A.; Connelly, P.W.

    2001-01-01

    BACKGROUND: The metabolic effects of diets high in vegetable protein have not been assessed despite much recent interest in the effect of soy proteins in reducing serum cholesterol. OBJECTIVE: We assessed the metabolic effects of diets high in vegetable protein (specifically, wheat gluten) on serum

  12. GPRC6a is not required for the effects of a high-protein diet on body weight in mice.

    Science.gov (United States)

    Kinsey-Jones, James S; Alamshah, Amin; McGavigan, Anne K; Spreckley, Eleanor; Banks, Katherine; Cereceda Monteoliva, Nicholas; Norton, Mariana; Bewick, Gavin A; Murphy, Kevin G

    2015-06-01

    The G-protein coupled receptor family C group 6 member A (GPRC6A) is activated by proteinogenic amino acids and may sense amino acids in the gastrointestinal tract and the brain. The study investigated whether GPRC6A was necessary for the effects of low- and high-protein diets on body weight and food intake in mice. The role of GPRC6A in mediating the effects of a low-protein diet on body weight was investigated in GPRC6a knockout (GPRC6a-KO) and wild-type (WT) mice fed a control diet (18% protein) or a low-protein diet (6% protein) for 9 days. The role of GPRC6A in mediating the effects of a high-protein diet on body weight was investigated in GPRC6a-KO and WT mice fed a control diet (18% protein) or a high-protein diet (50% protein) for 5 weeks. A high-protein diet reduced body weight gain and food intake compared with a control diet in both WT and GPRC6a-KO mice. A low-protein diet decreased body weight gain in GPRC6a-KO mice. GPRC6A was not necessary for the effects of a low- or high-protein diet on body weight and likely does not play a role in protein-induced satiety. © 2015 The Obesity Society.

  13. Co-Immobilization of Proteins and DNA Origami Nanoplates to Produce High-Contrast Biomolecular Nanoarrays.

    Science.gov (United States)

    Hager, Roland; Burns, Jonathan R; Grydlik, Martyna J; Halilovic, Alma; Haselgrübler, Thomas; Schäffler, Friedrich; Howorka, Stefan

    2016-06-01

    The biofunctionalization of nanopatterned surfaces with DNA origami nanostructures is an important topic in nanobiotechnology. An unexplored challenge is, however, to co-immobilize proteins with DNA origami at pre-determined substrate sites in high contrast relative to the nontarget areas. The immobilization should, in addition, preferably be achieved on a transparent substrate to allow ultrasensitive optical detection. If successful, specific co-binding would be a step towards stoichiometrically defined arrays with few to individual protein molecules per site. Here, we successfully immobilize with high specificity positively charged avidin proteins and negatively charged DNA origami nanoplates on 100 nm-wide carbon nanoislands while suppressing undesired adsorption to surrounding nontarget areas. The arrays on glass slides achieve unprecedented selectivity factors of up to 4000 and allow ultrasensitive fluorescence read-out. The co-immobilization onto the nanoislands leads to layered biomolecular architectures, which are functional because bound DNA origami influences the number of capturing sites on the nanopatches for other proteins. The novel hybrid DNA origami-protein nanoarrays allow the fabrication of versatile research platforms for applications in biosensing, biophysics, and cell biology, and, in addition, represent an important step towards single-molecule protein arrays.

  14. High protein pre-term infant formula: effect on nutrient balance, metabolic status and growth.

    Science.gov (United States)

    Cooke, Richard; Embleton, Nick; Rigo, Jacques; Carrie, Annelise; Haschke, Ferdinand; Ziegler, Ekhard

    2006-02-01

    Several lines of evidence suggest that formula with protein content of 3.0 g/100 kcal does not fully meet the protein needs of very-low-birth weight infants. Our purpose was to compare nitrogen balance, metabolic status and growth in infants fed a standard (3.0 g/100 kcal; RegPro) and high (3.6 g/100 kcal; HiPro) protein infant formula. Infants were fed both formulas, each formula for one week in balanced cross-over design. Metabolic status was monitored throughout. Nutrient balance and plasma amino acids were determined at the end of each week. Data were analysed using a linear mixed model. Eighteen infants were studied. Nine infants received the RegPro and nine received HiPro formula first. Nitrogen intake, absorption and retention were greater with the HiPro formula. None of the infants developed uremia or metabolic acidosis but retinol-binding-protein and weight gain were greater with the HiPro formula. Increased protein accretion paralleled by better weight gain without evidence of metabolic stress indicates that a formula with a protein content of 3.6 g/100 kcal better meets protein needs in these rapidly-growing infants. Further studies are needed to determine whether these short-term outcomes will be translated into long-term benefits.

  15. An improved quantitative mass spectrometry analysis of tumor specific mutant proteins at high sensitivity.

    Science.gov (United States)

    Ruppen-Cañás, Isabel; López-Casas, Pedro P; García, Fernando; Ximénez-Embún, Pilar; Muñoz, Manuel; Morelli, M Pia; Real, Francisco X; Serna, Antonio; Hidalgo, Manuel; Ashman, Keith

    2012-05-01

    New disease specific biomarkers, especially for cancer, are urgently needed to improve individual diagnosis, prognosis, and treatment selection, that is, for personalized medicine. Genetic mutations that affect protein function drive cancer. Therefore, the detection of such mutations represents a source of cancer specific biomarkers. Here we confirm the implementation of the mutant protein specific immuno-SRM (where SRM is selective reaction monitoring) mass spectrometry method of RAS proteins reported by Wang et al. [Proc. Natl. Acad. Sci. USA 2011, 108, 2444-2449], which exploits an antibody to simultaneously capture the different forms of the target protein and the resolving power and sensitivity of LC-MS/MS and improve the technique by using a more sensitive mass spectrometer. The mutant form G12D was quantified by SRM on a QTRAP 5500 mass spectrometer and the MIDAS workflow was used to confirm the sequence of the targeted peptides. This assay has been applied to quantify wild type and mutant RAS proteins in patient tumors, xenografted human tissue, and benign human epidermal tumors at high sensitivity. The limit of detection for the target proteins was as low as 12 amol (0.25 pg). It requires low starting amounts of tissue (ca.15 mg) that could be obtained from a needle aspiration biopsy. The described strategy could find application in the clinical arena and be applied to the study of expression of protein variants in disease.

  16. Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites.

    Science.gov (United States)

    Weill, Nathanaël; Rognan, Didier

    2010-01-01

    Inferring the biological function of a protein from its three-dimensional structure as well as explaining why a drug may bind to various targets is of crucial importance to modern drug discovery. Here we present a generic 4833-integer vector describing druggable protein-ligand binding sites that can be applied to any protein and any binding cavity. The fingerprint registers counts of pharmacophoric triplets from the Calpha atomic coordinates of binding-site-lining residues. Starting from a customized data set of diverse protein-ligand binding site pairs, the most appropriate metric and a similarity threshold could be defined for similar binding sites. The method (FuzCav) has been used in various scenarios: (i) screening a collection of 6000 binding sites for similarity to different queries; (ii) classifying protein families (serine endopeptidases, protein kinases) by binding site diversity; (iii) discriminating adenine-binding cavities from decoys. The fingerprint generation and comparison supports ultra-high throughput (ca. 1000 measures/s), does not require prior alignment of protein binding sites, and is able to detect local similarity among subpockets. It is thus particularly well suited to the functional annotation of novel genomic structures with low sequence identity to known X-ray templates.

  17. Concentration-Induced Association in a Protein System Caused by a Highly Directional Patch Attraction.

    Science.gov (United States)

    Li, Weimin; Persson, Björn A; Lund, Mikael; Bergenholtz, Johan; Zackrisson Oskolkova, Malin

    2016-09-01

    Self-association of the protein lactoferrin is studied in solution using small-angle X-ray scattering techniques. Effective static structure factors have been shown to exhibit either a monotonic or a nonmonotonic dependence on protein concentration in the small wavevector limit, depending on salt concentration. The behavior correlates with a nonmonotonic dependence of the second virial coefficient on salt concentration, such that a maximum appears in the structure factor at a low protein concentration when the second virial coefficient is negative and close to a minimum. The results are interpreted in terms of an integral equation theory with explicit dimers, formulated by Wertheim, which provides a consistent framework able to explain the behavior in terms of a monomer-dimer equilibrium that appears because of a highly directional patch attraction. Short attraction ranges preclude trimer formation, which explains why the protein system behaves as if it were subject to a concentration-dependent isotropic protein-protein attraction. Superimposing an isotropic interaction, comprising screened Coulomb repulsion and van der Waals attraction, on the patch attraction allows for a semiquantitative modeling of the complete transition pathway from monomers in the dilute limit to monomer-dimer systems at somewhat higher protein concentrations.

  18. Fc-Binding Ligands of Immunoglobulin G: An Overview of High Affinity Proteins and Peptides

    Directory of Open Access Journals (Sweden)

    Weonu Choe

    2016-12-01

    Full Text Available The rapidly increasing application of antibodies has inspired the development of several novel methods to isolate and target antibodies using smart biomaterials that mimic the binding of Fc-receptors to antibodies. The Fc-binding domain of antibodies is the primary binding site for e.g., effector proteins and secondary antibodies, whereas antigens bind to the Fab region. Protein A, G, and L, surface proteins expressed by pathogenic bacteria, are well known to bind immunoglobulin and have been widely exploited in antibody purification strategies. Several difficulties are encountered when bacterial proteins are used in antibody research and application. One of the major obstacles hampering the use of bacterial proteins is sample contamination with trace amounts of these proteins, which can invoke an immune response in the host. Many research groups actively develop synthetic ligands that are able to selectively and strongly bind to antibodies. Among the reported ligands, peptides that bind to the Fc-domain of antibodies are attractive tools in antibody research. Besides their use as high affinity ligands in antibody purification chromatography, Fc-binding peptides are applied e.g., to localize antibodies on nanomaterials and to increase the half-life of proteins in serum. In this review, recent developments of Fc-binding peptides are presented and their binding characteristics and diverse applications are discussed.

  19. Alternative confidence measure for local matching stereo algorithms

    CSIR Research Space (South Africa)

    Ndhlovu, T

    2009-11-01

    Full Text Available The authors present a confidence measure applied to individual disparity estimates in local matching stereo correspondence algorithms. It aims at identifying textureless areas, where most local matching algorithms fail. The confidence measure works...

  20. Mathematical Foundations for a Theory of Confidence Structures.

    Science.gov (United States)

    Balch, Michael Scott

    2012-10-01

    This paper introduces a new mathematical object: the confidence structure. A confidence structure represents inferential uncertainty in an unknown parameter by defining a belief function whose output is commensurate with Neyman-Pearson confidence. Confidence structures on a group of input variables can be propagated through a function to obtain a valid confidence structure on the output of that function. The theory of confidence structures is created by enhancing the extant theory of confidence distributions with the mathematical generality of Dempster-Shafer evidence theory. Mathematical proofs grounded in random set theory demonstrate the operative properties of confidence structures. The result is a new theory which achieves the holistic goals of Bayesian inference while maintaining the empirical rigor of frequentist inference.

  1. Assessing Residents' Confidence in the Context of Pharmacotherapy Competence.

    Science.gov (United States)

    Rakofsky, Jeffrey J; Garlow, Steven J; Haroon, Ebrahim; Hermida, Adriana P; Young, John Q; Dunlop, Boadie W

    2017-06-01

    We aimed to determine whether residents' confidence initiating medications increased with the number of times they prescribed individual medications and to quantify the relationship between prescription frequency and gains in confidence. From July 2011 to June 2014, PGY-3 residents completed a survey of confidence levels at their psychopharmacology clinic orientation and then again 12 months later. The Emory Healthcare electronic medical record was used to identify all medications prescribed by each resident during their 12-month rotation and the frequency of these prescriptions. Confidence in initiating treatment with all medicines/medication classes increased over the 12-month period. For three of the medication classes for which residents indicated they were least confident at orientation, the number of prescriptions written during the year was significantly associated with an increase in confidence. Measuring resident confidence is a relevant and achievable outcome and provides data for educators regarding the amount of experience needed to increase confidence.

  2. Mathematical Foundations for a Theory of Confidence Structures

    Science.gov (United States)

    Balch, Michael Scott

    2012-01-01

    This paper introduces a new mathematical object: the confidence structure. A confidence structure represents inferential uncertainty in an unknown parameter by defining a belief function whose output is commensurate with Neyman-Pearson confidence. Confidence structures on a group of input variables can be propagated through a function to obtain a valid confidence structure on the output of that function. The theory of confidence structures is created by enhancing the extant theory of confidence distributions with the mathematical generality of Dempster-Shafer evidence theory. Mathematical proofs grounded in random set theory demonstrate the operative properties of confidence structures. The result is a new theory which achieves the holistic goals of Bayesian inference while maintaining the empirical rigor of frequentist inference. PMID:25190904

  3. On the Confidence Interval for the parameter of Poisson Distribution

    CERN Document Server

    Bityukov, S I; Taperechkina, V A

    2000-01-01

    In present paper the possibility of construction of continuous analogue of Poisson distribution with the search of bounds of confidence intervals for parameter of Poisson distribution is discussed and the results of numerical construction of confidence intervals are presented.

  4. Sustaining Vaccine Confidence in the 21st Century

    Directory of Open Access Journals (Sweden)

    Karin Hardt

    2013-06-01

    Full Text Available Vaccination provides many health and economic benefits to individuals and society, and public support for immunization programs is generally high. However, the benefits of vaccines are often not fully valued when public discussions on vaccine safety, quality or efficacy arise, and the spread of misinformation via the internet and other media has the potential to undermine immunization programs. Factors associated with improved public confidence in vaccines include evidence-based decision-making procedures and recommendations, controlled processes for licensing and monitoring vaccine safety and effectiveness and disease surveillance. Community engagement with appropriate communication approaches for each audience is a key factor in building trust in vaccines. Vaccine safety/quality issues should be handled rapidly and transparently by informing and involving those most affected and those concerned with public health in effective ways. Openness and transparency in the exchange of information between industry and other stakeholders is also important. To maximize the safety of vaccines, and thus sustain trust in vaccines, partnerships are needed between public health sector stakeholders. Vaccine confidence can be improved through collaborations that ensure high vaccine uptake rates and that inform the public and other stakeholders of the benefits of vaccines and how vaccine safety is constantly assessed, assured and communicated.

  5. Fractionation of whey proteins with high-capacity superparamagnetic ion-exchangers

    DEFF Research Database (Denmark)

    Heebøll-Nielsen, Anders; Justesen, Sune; Thomas, Owen R. T.

    2004-01-01

    In this study we describe the design, preparation and testing of superparamagnetic anion-exchangers, and their use together with cation-exchangers in the fractionation of bovine whey proteins as a model study for high-gradient magnetic fishing. Adsorbents prepared by attachment of trimethyl amine...... to 337 mg g-1 with a dissociation constant of 0.042 µM. The latter anion-exchanger was selected for studies of whey protein fractionation. In these, crude bovine whey was treated with a superparamagnetic cation-exchanger to adsorb basic protein species, and the supernatant arising from this treatment......) was achieved with some simultaneous binding of immunoglobulins (Ig). The immunoglobulins were separated from the other two proteins by desorbing with a low concentration of NaCl (=0.4 M), whereas lactoferrin and lactoperoxidase were co-eluted in significantly purer form, e.g. lactoperoxidase was purified 28...

  6. High resolution TOF MS coupled to CE for the analysis of isotopically resolved intact proteins.

    Science.gov (United States)

    Taichrib, Angelina; Pelzing, Matthias; Pellegrino, Cristoforo; Rossi, Mara; Neusüss, Christian

    2011-06-10

    Intact protein analysis by mass spectrometry is of great interest for the characterisation of biotechnological products. Exact mass measurement in combination with isotopic resolution allows the detection of modifications leading to small mass changes like deamidation or reduction of disulfide bonds directly on the level of the intact protein. Here, a concept is presented based on time-of-flight mass spectrometry. A bench top TOF MS and a high resolution TOF MS were used to resolve the isotopes of intact recombinant human growth hormone and intact human erythropoietin, respectively. Thus, these 22 and around 30kDa large proteins can be characterised sensitively in great detail and along with capillary electrophoretic separation unambiguous identification of minor protein modifications like deamidation is possible. Copyright © 2011 Elsevier B.V. All rights reserved.

  7. Fractionation of whey proteins with high-capacity superparamagnetic ion-exchangers

    DEFF Research Database (Denmark)

    Heebøll-Nielsen, Anders; Justesen, S.F.L.; Thomas, Owen R. T.

    2004-01-01

    In this study we describe the design, preparation and testing of superparamagnetic anion-exchangers, and their use together with cation-exchangers in the fractionation of bovine whey proteins as a model study for high-gradient magnetic fishing. Adsorbents prepared by attachment of trimethyl amine...... to 337 mg g(-1) with a dissociation constant of 0.042 muM. The latter anion-exchanger was selected for studies of whey protein fractionation. In these, crude bovine whey was treated with a superparamagnetic cation-exchanger to adsorb basic protein species, and the supernatant arising from this treatment......) was achieved with some simultaneous binding of immunoglobulins (1g). The immunoglobulins were separated from the other two proteins by desorbing with a low concentration of NaCl (less than or equal to0.4 M), whereas lactoferrin and lactoperoxidase were co-eluted in significantly purer form, e...

  8. Generalized confidence interval plots using commands or dialogs

    OpenAIRE

    Roger Newson

    2005-01-01

    Confidence intervals may be presented as publication-ready tables or as presentation-ready plots. -eclplot- produces plots of estimates and confidence intervals. It inputs a dataset (or resultsset) with one observation per parameter and variables containing estimates, lower and upper confidence limits, and a fourth variable, against which the confidence intervals are plotted. This resultsset can be used for producing both plots and tables, and may be generated using a spreadsheet or using -st...

  9. Two-Sided Tests and One-Sided Confidence Bounds

    OpenAIRE

    1994-01-01

    Based on the duality between tests and confidence sets we introduce a new method to derive one-sided confidence bounds following the rejection of a null hypothesis with two-sided alternatives. This method imputes that the experimenter is only interested in confidence bounds if the null hypothesis is rejected. Furthermore, we suppose that he is only interested in the direction and a lower confidence bound concerning the distance of the true parameter value to the parameter values in the null h...

  10. Improving Quality Using Architecture Fault Analysis with Confidence Arguments

    Science.gov (United States)

    2015-03-01

    Improving Quality Using Architecture Fault Analysis with Confidence Arguments Peter H. Feiler Charles B. Weinstock John B. Goodenough...Design 8 2.3 Architecture Fault Modeling and Analysis with EMV2 8 2.4 Confidence Map Concepts and Notation 11 Overview of the Stepper-Motor System...Comparison of the SMS Designs 43 Establishing Confidence in the SMS 45 6.1 Confidence Maps for SMS 45 CMU/SEI-2015-TR-006 | SOFTWARE ENGINEERING

  11. How to Strengthen Child Learners’Self-confidence

    Institute of Scientific and Technical Information of China (English)

    李文敬

    2013-01-01

    Self-confidence is closely related to L2 learning. In order to make their learners enjoy English learning, English teach-ers need to strengthen the learners’English learning confidence. This article is to find out English teachers’role to strengthening learners’self-confidence in ELL by means of class observation. The writer concludes improving speaking ability; giving praise and offering gentle error correcting can help to strengthen the learners’confidence.

  12. Increasing Self-Confidence of Indonesian Low Ability Student with Green’s Motivational Strategies

    Science.gov (United States)

    Siregar, I.; Darhim; Asih, E. C. M.

    2017-02-01

    Self-confidence is the important factor of mathematical learning, But in the reality, many 8th grade students do not have good self-confidence. To increasing the self-confidence is used Green’s motivational strategies. So the purpose of the research is to know whether the Green’s motivational strategies can increase the self-confidence of 8th grade students. The research focus on Indonesian junior high school student with lower ability. The research used qualitative research method, with basic qualitative research approach design. The activity included teaching material development and interview with student. From all conversation on the interview with students, students have satisfied feel. Students’s self-confidence has changed better. All students show up that they can handle all matematical problems.

  13. A family of E. coli expression vectors for laboratory scale and high throughput soluble protein production

    Directory of Open Access Journals (Sweden)

    Bottomley Stephen P

    2006-03-01

    Full Text Available Abstract Background In the past few years, both automated and manual high-throughput protein expression and purification has become an accessible means to rapidly screen and produce soluble proteins for structural and functional studies. However, many of the commercial vectors encoding different solubility tags require different cloning and purification steps for each vector, considerably slowing down expression screening. We have developed a set of E. coli expression vectors with different solubility tags that allow for parallel cloning from a single PCR product and can be purified using the same protocol. Results The set of E. coli expression vectors, encode for either a hexa-histidine tag or the three most commonly used solubility tags (GST, MBP, NusA and all with an N-terminal hexa-histidine sequence. The result is two-fold: the His-tag facilitates purification by immobilised metal affinity chromatography, whilst the fusion domains act primarily as solubility aids during expression, in addition to providing an optional purification step. We have also incorporated a TEV recognition sequence following the solubility tag domain, which allows for highly specific cleavage (using TEV protease of the fusion protein to yield native protein. These vectors are also designed for ligation-independent cloning and they possess a high-level expressing T7 promoter, which is suitable for auto-induction. To validate our vector system, we have cloned four different genes and also one gene into all four vectors and used small-scale expression and purification techniques. We demonstrate that the vectors are capable of high levels of expression and that efficient screening of new proteins can be readily achieved at the laboratory level. Conclusion The result is a set of four rationally designed vectors, which can be used for streamlined cloning, expression and purification of target proteins in the laboratory and have the potential for being adaptable to a high

  14. Opinion formation with time-varying bounded confidence

    Science.gov (United States)

    Liu, QiPeng; Zhang, SiYing

    2017-01-01

    When individuals in social groups communicate with one another and are under the influence of neighbors’ opinions, they typically revise their own opinions to adapt to such peer opinions. The individual threshold of bounded confidence will thus be affected by both a change in individual confidence and by neighbor influence. Individuals thus update their own opinions with new bounded confidence, while their updated opinions also influence their neighbors’ opinions. Based on this reasoned factual assumption, we propose an opinion dynamics model with time-varying bounded confidence. A directed network is formed by the rule of the individual bounded confidence threshold. The threshold of individual bounded confidence involves both confidence variation and the in/out degree of the individual node. When the confidence variation is greater, an individual’s confidence in persisting in his own opinion in interactions is weaker, and the individual is more likely to adopt neighbors’ opinions. In networks, the in/out degree is determined by individual neighbors. Our main research involves the process of opinion evolution and the basic laws of opinion cluster formation. Group opinions converge exponentially to consensus with stable neighbors. An individual opinion evolution is determined by the average neighbor opinion effect strength. We also explore the conditions involved in forming a stable neighbor relationship and the influence of the confidence variation in the convergence of the threshold of bounded confidence. The results show that the influence on opinion evolution is greater with increased confidence variation. PMID:28264038

  15. 78 FR 56621 - Draft Waste Confidence Generic Environmental Impact Statement

    Science.gov (United States)

    2013-09-13

    ...; ] NUCLEAR REGULATORY COMMISSION 10 CFR Part 51 RIN 3150-AJ20 Draft Waste Confidence Generic Environmental... Confidence Generic Environmental Impact Statement,'' that forms the regulatory basis for the proposed... Confidence rule). The NRC staff plans to hold 12 public meetings during the public comment period to present...

  16. Opinion formation with time-varying bounded confidence.

    Science.gov (United States)

    Zhang, YunHong; Liu, QiPeng; Zhang, SiYing

    2017-01-01

    When individuals in social groups communicate with one another and are under the influence of neighbors' opinions, they typically revise their own opinions to adapt to such peer opinions. The individual threshold of bounded confidence will thus be affected by both a change in individual confidence and by neighbor influence. Individuals thus update their own opinions with new bounded confidence, while their updated opinions also influence their neighbors' opinions. Based on this reasoned factual assumption, we propose an opinion dynamics model with time-varying bounded confidence. A directed network is formed by the rule of the individual bounded confidence threshold. The threshold of individual bounded confidence involves both confidence variation and the in/out degree of the individual node. When the confidence variation is greater, an individual's confidence in persisting in his own opinion in interactions is weaker, and the individual is more likely to adopt neighbors' opinions. In networks, the in/out degree is determined by individual neighbors. Our main research involves the process of opinion evolution and the basic laws of opinion cluster formation. Group opinions converge exponentially to consensus with stable neighbors. An individual opinion evolution is determined by the average neighbor opinion effect strength. We also explore the conditions involved in forming a stable neighbor relationship and the influence of the confidence variation in the convergence of the threshold of bounded confidence. The results show that the influence on opinion evolution is greater with increased confidence variation.

  17. 21 CFR 26.37 - Confidence building activities.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Confidence building activities. 26.37 Section 26... COMMUNITY Specific Sector Provisions for Medical Devices § 26.37 Confidence building activities. (a) At the beginning of the transitional period, the Joint Sectoral Group will establish a joint confidence building...

  18. 7 CFR 97.18 - Applications handled in confidence.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Applications handled in confidence. 97.18 Section 97.18 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING... confidence. (a) Pending applications shall be handled in confidence. Except as provided below, no information...

  19. Coverage Accuracy of Confidence Intervals in Nonparametric Regression

    Institute of Scientific and Technical Information of China (English)

    Song-xi Chen; Yong-song Qin

    2003-01-01

    Point-wise confidence intervals for a nonparametric regression function with random design points are considered. The confidence intervals are those based on the traditional normal approximation and the empirical likelihood. Their coverage accuracy is assessed by developing the Edgeworth expansions for the coverage probabilities. It is shown that the empirical likelihood confidence intervals are Bartlett correctable.

  20. Developing Self-confidence%培养自信心

    Institute of Scientific and Technical Information of China (English)

    Robert Kokoska

    2006-01-01

    @@ Ideally,self-confidence is something you develop early and maintain throughout life. For many of us,though, that just isn't the case-either the process of developing self-confidence is stymied early on,or we lose confidence because of life events.