ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes.

PubMed

Otto, Thomas Dan; Catanho, Marcos; Tristão, Cristian; Bezerra, Márcia; Fernandes, Renan Mathias; Elias, Guilherme Steinberger; Scaglia, Alexandre Capeletto; Bovermann, Bill; Berstis, Viktors; Lifschitz, Sergio; de Miranda, Antonio Basílio; Degrave, Wim

2010-03-01

Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith-Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach. The database can be accessed through http://proteinworlddb.org

Plus Disease in Retinopathy of Prematurity: Improving Diagnosis by Ranking Disease Severity and Using Quantitative Image Analysis.

PubMed

Kalpathy-Cramer, Jayashree; Campbell, J Peter; Erdogmus, Deniz; Tian, Peng; Kedarisetti, Dharanish; Moleta, Chace; Reynolds, James D; Hutcheson, Kelly; Shapiro, Michael J; Repka, Michael X; Ferrone, Philip; Drenser, Kimberly; Horowitz, Jason; Sonmez, Kemal; Swan, Ryan; Ostmo, Susan; Jonas, Karyn E; Chan, R V Paul; Chiang, Michael F

2016-11-01

To determine expert agreement on relative retinopathy of prematurity (ROP) disease severity and whether computer-based image analysis can model relative disease severity, and to propose consideration of a more continuous severity score for ROP. We developed 2 databases of clinical images of varying disease severity (100 images and 34 images) as part of the Imaging and Informatics in ROP (i-ROP) cohort study and recruited expert physician, nonexpert physician, and nonphysician graders to classify and perform pairwise comparisons on both databases. Six participating expert ROP clinician-scientists, each with a minimum of 10 years of clinical ROP experience and 5 ROP publications, and 5 image graders (3 physicians and 2 nonphysician graders) who analyzed images that were obtained during routine ROP screening in neonatal intensive care units. Images in both databases were ranked by average disease classification (classification ranking), by pairwise comparison using the Elo rating method (comparison ranking), and by correlation with the i-ROP computer-based image analysis system. Interexpert agreement (weighted κ statistic) compared with the correlation coefficient (CC) between experts on pairwise comparisons and correlation between expert rankings and computer-based image analysis modeling. There was variable interexpert agreement on diagnostic classification of disease (plus, preplus, or normal) among the 6 experts (mean weighted κ, 0.27; range, 0.06-0.63), but good correlation between experts on comparison ranking of disease severity (mean CC, 0.84; range, 0.74-0.93) on the set of 34 images. Comparison ranking provided a severity ranking that was in good agreement with ranking obtained by classification ranking (CC, 0.92). Comparison ranking on the larger dataset by both expert and nonexpert graders demonstrated good correlation (mean CC, 0.97; range, 0.95-0.98). The i-ROP system was able to model this continuous severity with good correlation (CC, 0.86). Experts diagnose plus disease on a continuum, with poor absolute agreement on classification but good relative agreement on disease severity. These results suggest that the use of pairwise rankings and a continuous severity score, such as that provided by the i-ROP system, may improve agreement on disease severity in the future. Copyright © 2016 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

An Analytic Hierarchy Process for School Quality and Inspection: Model Development and Application

ERIC Educational Resources Information Center

Al Qubaisi, Amal; Badri, Masood; Mohaidat, Jihad; Al Dhaheri, Hamad; Yang, Guang; Al Rashedi, Asma; Greer, Kenneth

2016-01-01

Purpose: The purpose of this paper is to develop an analytic hierarchy planning-based framework to establish criteria weights and to develop a school performance system commonly called school inspections. Design/methodology/approach: The analytic hierarchy process (AHP) model uses pairwise comparisons and a measurement scale to generate the…

ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes

PubMed Central

Otto, Thomas Dan; Catanho, Marcos; Tristão, Cristian; Bezerra, Márcia; Fernandes, Renan Mathias; Elias, Guilherme Steinberger; Scaglia, Alexandre Capeletto; Bovermann, Bill; Berstis, Viktors; Lifschitz, Sergio; de Miranda, Antonio Basílio; Degrave, Wim

2010-01-01

Motivation: Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith–Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid™, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach. Availability: The database can be accessed through http://proteinworlddb.org Contact: otto@fiocruz.br PMID:20089515

Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment

PubMed Central

2014-01-01

Background Protein model quality assessment is an essential component of generating and using protein structural models. During the Tenth Critical Assessment of Techniques for Protein Structure Prediction (CASP10), we developed and tested four automated methods (MULTICOM-REFINE, MULTICOM-CLUSTER, MULTICOM-NOVEL, and MULTICOM-CONSTRUCT) that predicted both local and global quality of protein structural models. Results MULTICOM-REFINE was a clustering approach that used the average pairwise structural similarity between models to measure the global quality and the average Euclidean distance between a model and several top ranked models to measure the local quality. MULTICOM-CLUSTER and MULTICOM-NOVEL were two new support vector machine-based methods of predicting both the local and global quality of a single protein model. MULTICOM-CONSTRUCT was a new weighted pairwise model comparison (clustering) method that used the weighted average similarity between models in a pool to measure the global model quality. Our experiments showed that the pairwise model assessment methods worked better when a large portion of models in the pool were of good quality, whereas single-model quality assessment methods performed better on some hard targets when only a small portion of models in the pool were of reasonable quality. Conclusions Since digging out a few good models from a large pool of low-quality models is a major challenge in protein structure prediction, single model quality assessment methods appear to be poised to make important contributions to protein structure modeling. The other interesting finding was that single-model quality assessment scores could be used to weight the models by the consensus pairwise model comparison method to improve its accuracy. PMID:24731387

Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment.

PubMed

Cao, Renzhi; Wang, Zheng; Cheng, Jianlin

2014-04-15

Protein model quality assessment is an essential component of generating and using protein structural models. During the Tenth Critical Assessment of Techniques for Protein Structure Prediction (CASP10), we developed and tested four automated methods (MULTICOM-REFINE, MULTICOM-CLUSTER, MULTICOM-NOVEL, and MULTICOM-CONSTRUCT) that predicted both local and global quality of protein structural models. MULTICOM-REFINE was a clustering approach that used the average pairwise structural similarity between models to measure the global quality and the average Euclidean distance between a model and several top ranked models to measure the local quality. MULTICOM-CLUSTER and MULTICOM-NOVEL were two new support vector machine-based methods of predicting both the local and global quality of a single protein model. MULTICOM-CONSTRUCT was a new weighted pairwise model comparison (clustering) method that used the weighted average similarity between models in a pool to measure the global model quality. Our experiments showed that the pairwise model assessment methods worked better when a large portion of models in the pool were of good quality, whereas single-model quality assessment methods performed better on some hard targets when only a small portion of models in the pool were of reasonable quality. Since digging out a few good models from a large pool of low-quality models is a major challenge in protein structure prediction, single model quality assessment methods appear to be poised to make important contributions to protein structure modeling. The other interesting finding was that single-model quality assessment scores could be used to weight the models by the consensus pairwise model comparison method to improve its accuracy.

Comparison of type 2 diabetes mellitus incidence in different phases of hepatitis B virus infection: A meta-analysis.

PubMed

Shen, Yi; Zhang, Sheng; Wang, Xulin; Wang, Yuanyuan; Zhang, Jian; Qin, Gang; Li, Wenchao; Ding, Kun; Zhang, Lei; Liang, Feng

2017-10-01

Because whether hepatitis B virus infection increases the risk of type 2 diabetes mellitus has been a controversial topic, pair-wise and network meta-analyses of published literature were carried out to accurately evaluate the association between different phases of hepatitis B virus infection and the risk of type 2 diabetes mellitus. A comprehensive literature retrieval was conducted from the PubMed, Embase, Cochrane Library and Chinese Database to identify epidemiological studies on the association between hepatitis B virus infection and the risk of type 2 diabetes mellitus that were published from 1999 to 2015. A pair-wise meta-analysis of direct evidence was performed to estimate the pooled odds ratios and 95% confidence intervals. A network meta-analysis was conducted, including the construction of a network plot, inconsistency plot, predictive interval plot, comparison-adjusted funnel plot and rank diagram, to graphically link the direct and indirect comparisons between different hepatitis B virus infective phases. Eighteen publications (n=113 639) describing 32 studies were included in this meta-analysis. In the pair-wise meta-analysis, the pooled odds ratio for type 2 diabetes mellitus in chronic hepatitis B cirrhosis patients was 1.76 (95% confidence interval: 1.44-2.14) when compared with non-cirrhotic chronic hepatitis B patients. In the network meta-analysis, six comparisons of four hepatitis B virus infectious states indicated the following descending order for the risk of type 2 diabetes mellitus: hepatitis B cirrhosis patients, non-cirrhotic chronic hepatitis B patients, hepatitis B virus carriers and non-hepatitis B virus controls. This study suggests that hepatitis B virus infection is not an independent risk factor for type 2 diabetes mellitus, but the development of cirrhosis may increase the incidence of type 2 diabetes mellitus cirrhosis. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

A Generic multi-dimensional feature extraction method using multiobjective genetic programming.

PubMed

Zhang, Yang; Rockett, Peter I

2009-01-01

In this paper, we present a generic feature extraction method for pattern classification using multiobjective genetic programming. This not only evolves the (near-)optimal set of mappings from a pattern space to a multi-dimensional decision space, but also simultaneously optimizes the dimensionality of that decision space. The presented framework evolves vector-to-vector feature extractors that maximize class separability. We demonstrate the efficacy of our approach by making statistically-founded comparisons with a wide variety of established classifier paradigms over a range of datasets and find that for most of the pairwise comparisons, our evolutionary method delivers statistically smaller misclassification errors. At very worst, our method displays no statistical difference in a few pairwise comparisons with established classifier/dataset combinations; crucially, none of the misclassification results produced by our method is worse than any comparator classifier. Although principally focused on feature extraction, feature selection is also performed as an implicit side effect; we show that both feature extraction and selection are important to the success of our technique. The presented method has the practical consequence of obviating the need to exhaustively evaluate a large family of conventional classifiers when faced with a new pattern recognition problem in order to attain a good classification accuracy.

Non-Cooperative Group Decision Support Systems: Problems and Some Solutions.

DTIC Science & Technology

1986-09-01

appears that in these situations the 46 content of the problem and the structure of the problem is " fuzzy ." It requires an active cooperation between the...some unstructured parts will remain. This partial ’unstructurability’ is due to uncertainty, fuzziness , ignorance, and an inability to...according to the Analytic Hierarchy Process ( AHP ) technique (Gui, 1985). The AHP algorithm consists of the following steps; (i) Perform a pairwise comparison

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

PubMed Central

2007-01-01

Background Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this problem, however, are forced to employ constraints that reduce computation by restricting the alignments and/or structures (i.e. folds) that are permissible. In this paper, a new methodology is presented for the purpose of establishing alignment constraints based on nucleotide alignment and insertion posterior probabilities. Using a hidden Markov model, posterior probabilities of alignment and insertion are computed for all possible pairings of nucleotide positions from the two sequences. These alignment and insertion posterior probabilities are additively combined to obtain probabilities of co-incidence for nucleotide position pairs. A suitable alignment constraint is obtained by thresholding the co-incidence probabilities. The constraint is integrated with Dynalign, a free energy minimization algorithm for joint alignment and secondary structure prediction. The resulting method is benchmarked against the previous version of Dynalign and against other programs for pairwise RNA structure prediction. Results The proposed technique eliminates manual parameter selection in Dynalign and provides significant computational time savings in comparison to prior constraints in Dynalign while simultaneously providing a small improvement in the structural prediction accuracy. Savings are also realized in memory. In experiments over a 5S RNA dataset with average sequence length of approximately 120 nucleotides, the method reduces computation by a factor of 2. The method performs favorably in comparison to other programs for pairwise RNA structure prediction: yielding better accuracy, on average, and requiring significantly lesser computational resources. Conclusion Probabilistic analysis can be utilized in order to automate the determination of alignment constraints for pairwise RNA structure prediction methods in a principled fashion. These constraints can reduce the computational and memory requirements of these methods while maintaining or improving their accuracy of structural prediction. This extends the practical reach of these methods to longer length sequences. The revised Dynalign code is freely available for download. PMID:17445273

Neural networks distinguish between taste qualities based on receptor cell population responses.

PubMed

Varkevisser, B; Peterson, D; Ogura, T; Kinnamon, S C

2001-06-01

Response features of taste receptor cell action potentials were examined using an artificial neural network to determine whether they contain information about taste quality. Using the loose patch technique to record from hamster taste buds in vivo we recorded population responses of single fungiform papillae to NaCl (100 mM), sucrose (200 mM) and the synthetic sweetener NC-00274-01 (NC-01) (200 microM). Features of each response describing both burst and inter-burst characteristics were then presented to an artificial neural network for pairwise classification of taste stimuli. Responses to NaCl could be distinguished from those to both NC-01 and sucrose with accuracies of up to 86%. In contrast, pairwise comparisons between sucrose and NC-01 were not successful, scoring at chance (50%). Also, comparisons between two different concentrations of NaCl, 0.01 and 0.005 M, scored at chance. Pairwise comparisons using only those features that relate to the inter-burst behavior of the response (i.e. bursting rate) did not hinder the performance of the neural network as both sweeteners versus NaCl received scores of 75--85%. Comparisons using features corresponding to each individual burst scored poorly, receiving scores only slightly above chance. We then compared the sweeteners with varying concentrations of NaCl (0.1, 0.01, 0.005 and 0.001 M) using only those features corresponding to bursting rate within a 1 s time window. The neural network was capable of distinguishing between NaCl and NC-01 at all concentrations tested; while comparisons between NaCl and sucrose received high scores at all concentrations except 0.001 M. These results show that two different taste qualities can be distinguished from each other based solely on the bursting rates of action potentials in single taste buds and that this distinction is independent of stimulation intensity down to 0.001 M NaCl. These data suggest that action potentials in taste receptor cells may play a role in taste quality coding.

Smile attractiveness related to buccal corridor space in 3 different facial types: A perception of 3 ethnic groups of Malaysians.

PubMed

Nimbalkar, Smita; Oh, Yih Y; Mok, Reei Y; Tioh, Jing Y; Yew, Kai J; Patil, Pravinkumar G

2018-03-16

Buccal corridor space and its variations greatly influence smile attractiveness. Facial types are different for different ethnic populations, and so is smile attractiveness. The subjective perception of smile attractiveness of different populations may vary in regard to different buccal corridor spaces and facial patterns. The purpose of this study was to determine esthetic perceptions of the Malaysian population regarding the width of buccal corridor spaces and their effect on smile esthetics in individuals with short, normal, and long faces. The image of a smiling individual with a mesofacial face was modified to create 2 different facial types (brachyfacial and dolicofacial). Each face form was further modified into 5 different buccal corridors (2%, 10%, 15%, 22%, and 28%). The images were submitted to 3 different ethnic groups of evaluators (Chinese, Malay, Indian; 100 each), ranging between 17 and 21 years of age. A visual analog scale (50 mm in length) was used for assessment. The scores given to each image were compared with the Kruskal-Wallis test, and pairwise comparison was performed using the Mann-Whitney U test (α=.05). All 3 groups of evaluators could distinguish gradations of dark spaces in the buccal corridor at 2%, 10%, and 28%. Statistically significant differences were observed among 3 groups of evaluators in esthetic perception when pairwise comparisons were performed. A 15% buccal corridor was found to score esthetically equally within 3 face types by all 3 groups of evaluators. The Indian population was more critical in evaluation than the Chinese or Malay populations. In a pairwise comparison, more significant differences were found between long and short faces and the normal face; the normal face was compared with long and short faces separately. The width of the buccal corridor space influences smile attractiveness in different facial types. A medium buccal corridor (15%) is the esthetic characteristic preferred by all groups of evaluators in short, normal, and long face types. Copyright © 2017 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Adverse events and treatment failure leading to discontinuation of recently approved antipsychotic drugs in schizophrenia: A network meta-analysis.

PubMed

Tonin, Fernanda S; Piazza, Thais; Wiens, Astrid; Fernandez-Llimos, Fernando; Pontarolo, Roberto

2015-12-01

Objective:We aimed to gather evidence of the discontinuation rates owing to adverse events or treatment failure for four recently approved antipsychotics (asenapine, blonanserin, iloperidone, and lurasidone).Methods: A systematic review followed by pairwise meta-analysis and mixed treatment comparison meta analysis(MTC) was performed, including randomized controlled trials (RCTs) that compared the use of the above-mentioned drugs versus placebo in patients with schizophrenia. An electronic search was conducted in PubMed, Scopus, Science Direct, Scielo, the Cochrane Library, and International Pharmaceutical Abstracts(January 2015). The included trials were at least single blinded. The main outcome measures extracted were discontinuation owing to adverse events and discontinuation owing to treatment failure.Results: Fifteen RCTs were identified (n = 5400 participants) and 13 of them were amenable for use in our meta-analyses. No significant differences were observed between any of the four drugs and placebo as regards discontinuation owing to adverse events, whether in pairwise meta-analysis or in MTC. All drugs presented a better profile than placebo on discontinuation owing to treatment failure, both in pairwise meta-analysis and MTC. Asenapine was found to be the best therapy in terms of tolerability owing to failure,while lurasidone was the worst treatment in terms of adverse events. The evidence around blonanserin is weak.Conclusion: MTCs allowed the creation of two different rank orders of these four antipsychotic drugs in two outcome measures. This evidence-generating method allows direct and indirect comparisons, supporting approval and pricing decisions when lacking sufficient, direct, head-to-head trials.

Process perspective on image quality evaluation

NASA Astrophysics Data System (ADS)

Leisti, Tuomas; Halonen, Raisa; Kokkonen, Anna; Weckman, Hanna; Mettänen, Marja; Lensu, Lasse; Ritala, Risto; Oittinen, Pirkko; Nyman, Göte

2008-01-01

The psychological complexity of multivariate image quality evaluation makes it difficult to develop general image quality metrics. Quality evaluation includes several mental processes and ignoring these processes and the use of a few test images can lead to biased results. By using a qualitative/quantitative (Interpretation Based Quality, IBQ) methodology, we examined the process of pair-wise comparison in a setting, where the quality of the images printed by laser printer on different paper grades was evaluated. Test image consisted of a picture of a table covered with several objects. Three other images were also used, photographs of a woman, cityscape and countryside. In addition to the pair-wise comparisons, observers (N=10) were interviewed about the subjective quality attributes they used in making their quality decisions. An examination of the individual pair-wise comparisons revealed serious inconsistencies in observers' evaluations on the test image content, but not on other contexts. The qualitative analysis showed that this inconsistency was due to the observers' focus of attention. The lack of easily recognizable context in the test image may have contributed to this inconsistency. To obtain reliable knowledge of the effect of image context or attention on subjective image quality, a qualitative methodology is needed.

A spreadsheet template compatible with Microsoft Excel and iWork Numbers that returns the simultaneous confidence intervals for all pairwise differences between multiple sample means.

PubMed

Brown, Angus M

2010-04-01

The objective of the method described in this paper is to develop a spreadsheet template for the purpose of comparing multiple sample means. An initial analysis of variance (ANOVA) test on the data returns F--the test statistic. If F is larger than the critical F value drawn from the F distribution at the appropriate degrees of freedom, convention dictates rejection of the null hypothesis and allows subsequent multiple comparison testing to determine where the inequalities between the sample means lie. A variety of multiple comparison methods are described that return the 95% confidence intervals for differences between means using an inclusive pairwise comparison of the sample means. 2009 Elsevier Ireland Ltd. All rights reserved.

Realistic decision-making processes in a vaccination game

NASA Astrophysics Data System (ADS)

Iwamura, Yoshiro; Tanimoto, Jun

2018-03-01

Previous studies of vaccination games have nearly always assumed a pairwise comparison between a focal and neighboring player for the strategy updating rule, which comes from numerous compiled studies on spatial versions of 2-player and 2-strategy (2 × 2) games such as the spatial prisoner's dilemma (SPD). We propose, in this study, new update rules because the human decision-making process of whether to commit to a vaccination is obviously influenced by a "sense of crisis" or "fear" urging him/her toward vaccination, otherwise they will likely be infected. The rule assumes that an agent evaluates whether getting a vaccination or trying to free ride should be attempted based on observations of whether neighboring non-vaccinators were able to successfully free ride during the previous time-step. Compared to the conventional updating rule (standard pairwise comparison assuming a Fermi function), the new rules generally realize higher vaccination coverage and smaller final epidemic sizes. One rule in particular shows very good performance with significantly smaller epidemic sizes despite comparable levels of vaccination coverage. This is because the specific update rule helps vaccinators spread widely in the domain, which effectively hampers the spread of epidemics.

Evaluation of criteria for sustainability of community-based rural homestay programs via a modified pairwise comparison method

NASA Astrophysics Data System (ADS)

Ramli, Rohaini; Kasim, Maznah Mat; Ramli, Razamin; Kayat, Kalsom; Razak, Rafidah Abd

2014-12-01

Ministry of Tourism and Culture Malaysia has long introduced homestay programs across the country to enhance the quality of life of people, especially those living in rural areas. This type of program is classified as a community-based tourism (CBT) as it is expected to economically improve livelihood through cultural and community associated activities. It is the aspiration of the ministry to see that the income imbalance between people in the rural and urban areas is reduced, thus would contribute towards creating more developed states of Malaysia. Since 1970s, there are 154 homestay programs registered with the ministry. However, the performance and sustainability of the programs are still not satisfying. There are only a number of homestay programs that perform well and able to sustain. Thus, the aim of this paper is to identify relevant criteria contributing to the sustainability of a homestay program. The criteria are evaluated for their levels of importance via the use of a modified pairwise method and analyzed for other potentials. The findings will help the homestay operators to focus on the necessary criteria and thus, effectively perform as the CBT business initiative.

Reporting of analyses from randomized controlled trials with multiple arms: a systematic review.

PubMed

Baron, Gabriel; Perrodeau, Elodie; Boutron, Isabelle; Ravaud, Philippe

2013-03-27

Multiple-arm randomized trials can be more complex in their design, data analysis, and result reporting than two-arm trials. We conducted a systematic review to assess the reporting of analyses in reports of randomized controlled trials (RCTs) with multiple arms. The literature in the MEDLINE database was searched for reports of RCTs with multiple arms published in 2009 in the core clinical journals. Two reviewers extracted data using a standardized extraction form. In total, 298 reports were identified. Descriptions of the baseline characteristics and outcomes per group were missing in 45 reports (15.1%) and 48 reports (16.1%), respectively. More than half of the articles (n = 171, 57.4%) reported that a planned global test comparison was used (that is, assessment of the global differences between all groups), but 67 (39.2%) of these 171 articles did not report details of the planned analysis. Of the 116 articles reporting a global comparison test, 12 (10.3%) did not report the analysis as planned. In all, 60% of publications (n = 180) described planned pairwise test comparisons (that is, assessment of the difference between two groups), but 20 of these 180 articles (11.1%) did not report the pairwise test comparisons. Of the 204 articles reporting pairwise test comparisons, the comparisons were not planned for 44 (21.6%) of them. Less than half the reports (n = 137; 46%) provided baseline and outcome data per arm and reported the analysis as planned. Our findings highlight discrepancies between the planning and reporting of analyses in reports of multiple-arm trials.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

PubMed

Bastien, Olivier; Ortet, Philippe; Roy, Sylvaine; Maréchal, Eric

2005-03-10

Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

Neurons the decision makers, Part I: The firing function of a single neuron.

PubMed

Saaty, Thomas

2017-02-01

This paper is concerned with understanding synthesis of electric signals in the neural system based on making pairwise comparisons. Fundamentally, every person and every animal are born with the talent to compare stimuli from things that share properties in space or over time. Comparisons always need experience to distinguish among things. Pairwise comparisons are numerically reciprocal. If a value is assigned to the larger of two elements that have a given property when compared with the smaller one, then the smaller has the reciprocal of that value when compared with the larger. Because making comparisons requires the reciprocal property, we need mathematics that can cope with division. There are four division algebras that would allow us to use our reciprocals arising from comparisons: The real numbers, the complex numbers, the non-commutative quaternions and the non-associative octonions. Rather than inferring function as from electric flow in a network, in this paper we infer the flow from function. Neurons fire in response to stimuli and their firings vary relative to the intensities of the stimuli. We believe neurons use some kind of pairwise comparison mechanism to determine when to fire based on the stimuli they receive. The ideas we develop here about flows are used to deduce how a system based on this kind of firing determination works and can be described. Furthermore the firing of neurons requires continuous comparisons. To develop a formula describing the output of these pairwise comparisons requires solving Fredholm's equation of the second kind which is satisfied if and only if a simple functional equation has solutions. The Fourier transform of the real solution of this equation leads to inverse square laws like those that are common in physics. The Fourier transform applied to a complex valued solution leads to Dirac type of firings. Such firings are dense in the very general fields of functions known as Sobolev spaces and thus can be used to represent the very diverse phenomena in and around us. The non-commutative solution in quaternions can be interpreted as rotations in space. The also non-commutative and non-associative solution in octonions has yet to be adequately interpreted outside physics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of Brief Psychoeducational Program on Stigma in Malaysian Pre-clinical Medical Students: A Randomized Controlled Trial.

PubMed

Fernandez, Aaron; Tan, Kit-Aun; Knaak, Stephanie; Chew, Boon How; Ghazali, Sazlina Shariff

2016-12-01

If presented with serious mental illness (SMI), individuals' low help-seeking behaviors and poor adherence to treatment are associated with negative stereotypes and attitudes of healthcare providers. In this study, we examined the effects of a brief psychoeducational program on reducing stigma in pre-clinical medical students. One hundred and two pre-clinical medical students (20-23 years old) were randomly assigned to face-to-face contact + educational lecture (n = 51) condition or video-based contact + educational lecture (n = 51) condition. Measures of pre-clinical medical students' mental illness-related stigma using the Opening Minds Stigma Scale for Health Care Providers (OMS-HC) were administered at pre-, post-treatment, and 1-month follow-up. A 2 (condition: face-to-face contact + educational lecture, video-based contact + educational lecture) by 3 (time: pre-treatment, post-treatment, and 1-month follow-up) mixed model MANOVA was conducted on the Attitudes, Disclosure and Help-Seeking, and Social Distance OMS-HC subscales. Participants' scores on all subscales changed significantly across time, regardless of conditions. To determine how participants' scores changed significantly over time on each subscale, Bonferroni follow-up comparisons were performed to access pairwise differences for the main effect of time. Specifically, pairwise comparisons produced a significant reduction in Social Distance subscale between pre-treatment and post-treatment and between pre-treatment and 1-month follow-up, and a significant increase between post-treatment and 1-month follow-up, regardless of conditions. With respect to the Attitudes and Disclosure and Help-Seeking subscales, pairwise comparisons produced a significant reduction in scores between pre-treatment and post-treatment and a significant increase between post-treatment and 1-month follow-up. Our findings provide additional evidence that educational lecture on mental illness, coupled with either face-to-face contact or video-based contact, is predictive of positive outcomes in anti-stigma programs targeting future healthcare providers.

Quantitative Tools for Examining the Vocalizations of Juvenile Songbirds

PubMed Central

Wellock, Cameron D.; Reeke, George N.

2012-01-01

The singing of juvenile songbirds is highly variable and not well stereotyped, a feature that makes it difficult to analyze with existing computational techniques. We present here a method suitable for analyzing such vocalizations, windowed spectral pattern recognition (WSPR). Rather than performing pairwise sample comparisons, WSPR measures the typicality of a sample against a large sample set. We also illustrate how WSPR can be used to perform a variety of tasks, such as sample classification, song ontogeny measurement, and song variability measurement. Finally, we present a novel measure, based on WSPR, for quantifying the apparent complexity of a bird's singing. PMID:22701474

Pairwise comparisons and visual perceptions of equal area polygons.

PubMed

Adamic, P; Babiy, V; Janicki, R; Kakiashvili, T; Koczkodaj, W W; Tadeusiewicz, R

2009-02-01

The number of studies related to visual perception has been plentiful in recent years. Participants rated the areas of five randomly generated shapes of equal area, using a reference unit area that was displayed together with the shapes. Respondents were 179 university students from Canada and Poland. The average error estimated by respondents using the unit square was 25.75%. The error was substantially decreased to 5.51% when the shapes were compared to one another in pairs. This gain of 20.24% for this two-dimensional experiment was substantially better than the 11.78% gain reported in the previous one-dimensional experiments. This is the first statistically sound two-dimensional experiment demonstrating that pairwise comparisons improve accuracy.

PWC - PAIRWISE COMPARISON SOFTWARE: SOFTWARE PROGRAM FOR PAIRWISE COMPARISON TASK FOR PSYCHOMETRIC SCALING AND COGNITIVE RESEARCH

NASA Technical Reports Server (NTRS)

Ricks, W. R.

1994-01-01

PWC is used for pair-wise comparisons in both psychometric scaling techniques and cognitive research. The cognitive tasks and processes of a human operator of automated systems are now prominent considerations when defining system requirements. Recent developments in cognitive research have emphasized the potential utility of psychometric scaling techniques, such as multidimensional scaling, for representing human knowledge and cognitive processing structures. Such techniques involve collecting measurements of stimulus-relatedness from human observers. When data are analyzed using this scaling approach, an n-dimensional representation of the stimuli is produced. This resulting representation is said to describe the subject's cognitive or perceptual view of the stimuli. PWC applies one of the many techniques commonly used to acquire the data necessary for these types of analyses: pair-wise comparisons. PWC administers the task, collects the data from the test subject, and formats the data for analysis. It therefore addresses many of the limitations of the traditional "pen-and-paper" methods. By automating the data collection process, subjects are prevented from going back to check previous responses, the possibility of erroneous data transfer is eliminated, and the burden of the administration and taking of the test is eased. By using randomization, PWC ensures that subjects see the stimuli pairs presented in random order, and that each subject sees pairs in a different random order. PWC is written in Turbo Pascal v6.0 for IBM PC compatible computers running MS-DOS. The program has also been successfully compiled with Turbo Pascal v7.0. A sample executable is provided. PWC requires 30K of RAM for execution. The standard distribution medium for this program is a 5.25 inch 360K MS-DOS format diskette. Two electronic versions of the documentation are included on the diskette: one in ASCII format and one in MS Word for Windows format. PWC was developed in 1993.

Socioeconomic inequalities in child mortality: comparisons across nine developing countries.

PubMed Central

Wagstaff, A.

2000-01-01

This paper generates and analyses survey data on inequalities in mortality among infants and children aged under five years by consumption in Brazil, Côte d'Ivoire, Ghana, Nepal, Nicaragua, Pakistan, the Philippines, South Africa, and Viet Nam. The data were obtained from the Living Standards Measurement Study and the Cebu Longitudinal Health and Nutrition Survey. Mortality rates were estimated directly where complete fertility histories were available and indirectly otherwise. Mortality distributions were compared between countries by means of concentration curves and concentration indices: dominance checks were carried out for all pairwise intercountry comparisons; standard errors were calculated for the concentration indices; and tests of intercountry differences in inequality were performed. PMID:10686730

Systematic review with meta-analysis: comparative efficacy of immunosuppressants and biologics for reducing hospitalisation and surgery in Crohn's disease and ulcerative colitis.

PubMed

Mao, E J; Hazlewood, G S; Kaplan, G G; Peyrin-Biroulet, L; Ananthakrishnan, A N

2017-01-01

Crohn's disease (CD) and ulcerative colitis (UC) have a progressive course leading to hospitalisation and surgery. The ability of existing therapies to alter disease course is not clearly defined. To investigate the comparative efficacy of currently available inflammatory bowel disease (IBD) therapies to reduce hospitalisation and surgery. We conducted a systematic review in MEDLINE/PubMed for randomised controlled trials (RCT) published between January 1980 and May 2016 examining efficacy of biological or immunomodulator therapy in IBD. We performed direct comparisons of pooled proportions of hospitalisation and surgery. Pair-wise comparisons using a random-effects Bayesian network meta-analysis were performed to assess comparative efficacy of different treatments. We identified seven randomised controlled trials (5 CD; 2 UC) comparing three biologics and one immunomodulator with placebo. In CD, anti-TNF biologics significantly reduced hospitalisation [Odds ratio (OR) 0.46, 95% confidence interval (CI) 0.36-0.60] and surgery (OR 0.23, 95% CI 0.13-0.42) compared to placebo. No statistically significant reduction was noted with azathioprine or vedolizumab. Azathioprine was inferior to both infliximab and adalimumab in preventing CD-related hospitalisation (>97.5% probability). Anti-TNF biologics significantly reduced hospitalisation (OR 0.48, 95% CI 0.29-0.80) and surgery (OR 0.67, 95% CI 0.46-0.97) in UC. There were no statistically significant differences in the pair-wise comparisons between active treatments. In CD and UC, anti-TNF biologics are efficacious in reducing the odds of hospitalisation by half and surgery by 33-77%. Azathioprine and vedolizumab were not associated with a similar improvement, but robust conclusions may be limited due to paucity of RCTs. © 2016 John Wiley & Sons Ltd.

Experimental characterization of pairwise correlations from triple quantum correlated beams generated by cascaded four-wave mixing processes

NASA Astrophysics Data System (ADS)

Wang, Wei; Cao, Leiming; Lou, Yanbo; Du, Jinjian; Jing, Jietai

2018-01-01

We theoretically and experimentally characterize the performance of the pairwise correlations from triple quantum correlated beams based on the cascaded four-wave mixing (FWM) processes. The pairwise correlations between any two of the beams are theoretically calculated and experimentally measured. The experimental and theoretical results are in good agreement. We find that two of the three pairwise correlations can be in the quantum regime. The other pairwise correlation is always in the classical regime. In addition, we also measure the triple-beam correlation which is always in the quantum regime. Such unbalanced and controllable pairwise correlation structures may be taken as advantages in practical quantum communications, for example, hierarchical quantum secret sharing. Our results also open the way for the classification and application of quantum states generated from the cascaded FWM processes.

On the use of star-shaped genealogies in inference of coalescence times.

PubMed Central

Rosenberg, Noah A; Hirsh, Aaron E

2003-01-01

Genealogies from rapidly growing populations have approximate "star" shapes. We study the degree to which this approximation holds in the context of estimating the time to the most recent common ancestor (T(MRCA)) of a set of lineages. In an exponential growth scenario, we find that unless the product of population size (N) and growth rate (r) is at least approximately 10(5), the "pairwise comparison estimator" of T(MRCA) that derives from the star genealogy assumption has bias of 10-50%. Thus, the estimator is appropriate only for large populations that have grown very rapidly. The "tree-length estimator" of T(MRCA) is more biased than the pairwise comparison estimator, having low bias only for extremely large values of Nr. PMID:12930771

Market Competitiveness Evaluation of Mechanical Equipment with a Pairwise Comparisons Hierarchical Model.

PubMed

Hou, Fujun

2016-01-01

This paper provides a description of how market competitiveness evaluations concerning mechanical equipment can be made in the context of multi-criteria decision environments. It is assumed that, when we are evaluating the market competitiveness, there are limited number of candidates with some required qualifications, and the alternatives will be pairwise compared on a ratio scale. The qualifications are depicted as criteria in hierarchical structure. A hierarchical decision model called PCbHDM was used in this study based on an analysis of its desirable traits. Illustration and comparison shows that the PCbHDM provides a convenient and effective tool for evaluating the market competitiveness of mechanical equipment. The researchers and practitioners might use findings of this paper in application of PCbHDM.

Comparative Performance of Reagents and Platforms for Quantitation of Cytomegalovirus DNA by Digital PCR

PubMed Central

Gu, Z.; Sam, S. S.; Sun, Y.; Tang, L.; Pounds, S.; Caliendo, A. M.

2016-01-01

A potential benefit of digital PCR is a reduction in result variability across assays and platforms. Three sets of PCR reagents were tested on two digital PCR systems (Bio-Rad and RainDance), using three different sets of PCR reagents for quantitation of cytomegalovirus (CMV). Both commercial quantitative viral standards and 16 patient samples (n = 16) were tested. Quantitative accuracy (compared to nominal values) and variability were determined based on viral standard testing results. Quantitative correlation and variability were assessed with pairwise comparisons across all reagent-platform combinations for clinical plasma sample results. The three reagent sets, when used to assay quantitative standards on the Bio-Rad system, all showed a high degree of accuracy, low variability, and close agreement with one another. When used on the RainDance system, one of the three reagent sets appeared to have a much better correlation to nominal values than did the other two. Quantitative results for patient samples showed good correlation in most pairwise comparisons, with some showing poorer correlations when testing samples with low viral loads. Digital PCR is a robust method for measuring CMV viral load. Some degree of result variation may be seen, depending on platform and reagents used; this variation appears to be greater in samples with low viral load values. PMID:27535685

Prioritization based on neutral genetic diversity may fail to conserve important characteristics in cattle breeds.

PubMed

Hall, S J G; Lenstra, J A; Deeming, D C

2012-06-01

Conservation of the intraspecific genetic diversity of livestock species requires protocols that assess between-breed genetic variability and also take into account differences among individuals within breeds. Here, we focus on variation between breeds. Conservation of neutral genetic variation has been seen as promoting, through linkage processes, the retention of useful and potentially useful variation. Using public information on beef cattle breeds, with a total of 165 data sets each relating to a breed comparison of a performance variable, we have tested this paradigm by calculating the correlations between pairwise breed differences in performance and pairwise genetic distances deduced from biochemical and immunological polymorphisms, microsatellites and single-nucleotide polymorphisms. As already observed in floral and faunal biodiversity, significant positive correlations (n=54) were found, but many correlations were non-significant (n=100) or significantly negative (n=11). This implies that maximizing conserved neutral genetic variation with current techniques may conserve breed-level genetic variation in some traits but not in others and supports the view that genetic distance measurements based on neutral genetic variation are not sufficient as a determinant of conservation priority among breeds. © 2011 Blackwell Verlag GmbH.

Fast and Frugal Framing Effects?

ERIC Educational Resources Information Center

Mccloy, Rachel; Beaman, C. Philip; Frosch, Caren A.; Goddard, Kate

2010-01-01

Using 3 experiments, we examine whether simple pairwise comparison judgments, involving the "recognition heuristic" (Goldstein & Gigerenzer, 2002), are sensitive to implicit cues to the nature of the comparison required. In Experiments 1 and 2, we show that participants frequently choose the recognized option of a pair if asked to make "larger"…

Pythagorean fuzzy analytic hierarchy process to multi-criteria decision making

NASA Astrophysics Data System (ADS)

Mohd, Wan Rosanisah Wan; Abdullah, Lazim

2017-11-01

A numerous approaches have been proposed in the literature to determine the criteria of weight. The weight of criteria is very significant in the process of decision making. One of the outstanding approaches that used to determine weight of criteria is analytic hierarchy process (AHP). This method involves decision makers (DMs) to evaluate the decision to form the pair-wise comparison between criteria and alternatives. In classical AHP, the linguistic variable of pairwise comparison is presented in terms of crisp value. However, this method is not appropriate to present the real situation of the problems because it involved the uncertainty in linguistic judgment. For this reason, AHP has been extended by incorporating the Pythagorean fuzzy sets. In addition, no one has found in the literature proposed how to determine the weight of criteria using AHP under Pythagorean fuzzy sets. In order to solve the MCDM problem, the Pythagorean fuzzy analytic hierarchy process is proposed to determine the criteria weight of the evaluation criteria. Using the linguistic variables, pairwise comparison for evaluation criteria are made to the weights of criteria using Pythagorean fuzzy numbers (PFNs). The proposed method is implemented in the evaluation problem in order to demonstrate its applicability. This study shows that the proposed method provides us with a useful way and a new direction in solving MCDM problems with Pythagorean fuzzy context.

Multiple graph regularized protein domain ranking.

PubMed

Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin

2012-11-19

Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

Multiple graph regularized protein domain ranking

PubMed Central

2012-01-01

Background Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. Results To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. Conclusion The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. PMID:23157331

Social relationships as a major determinant in the valuation of health states.

PubMed

Frick, Ulrich; Irving, Hyacinth; Rehm, Jürgen

2012-03-01

To empirically determine the impact of the capacity to sustain social relationships on valuing health states. 68 clinical experts conducted a health state valuation exercise in five sites using pairwise comparison, ranking, and person trade-off as elicitation methods. 23,840 pairwise comparisons of a total of 379 health states were analyzed by conditional logistic regression. Social relationships had a clear monotonic association with perceived disability: the more limited the capacity to sustain social relationships, the more disabling the resulting health state valuations. The highest level of limitations with respect to social relationships was associated with slightly lower impact on health state valuations compared to the highest level of limitations in physical functioning. Social relationships showed an independent contribution to health state valuations and should be included in health state measures.

[Analysis of variance of repeated data measured by water maze with SPSS].

PubMed

Qiu, Hong; Jin, Guo-qin; Jin, Ru-feng; Zhao, Wei-kang

2007-01-01

To introduce the method of analyzing repeated data measured by water maze with SPSS 11.0, and offer a reference statistical method to clinical and basic medicine researchers who take the design of repeated measures. Using repeated measures and multivariate analysis of variance (ANOVA) process of the general linear model in SPSS and giving comparison among different groups and different measure time pairwise. Firstly, Mauchly's test of sphericity should be used to judge whether there were relations among the repeatedly measured data. If any (P

Non-pairwise additivity of the leading-order dispersion energy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hollett, Joshua W., E-mail: j.hollett@uwinnipeg.ca

2015-02-28

The leading-order (i.e., dipole-dipole) dispersion energy is calculated for one-dimensional (1D) and two-dimensional (2D) infinite lattices, and an infinite 1D array of infinitely long lines, of doubly occupied locally harmonic wells. The dispersion energy is decomposed into pairwise and non-pairwise additive components. By varying the force constant and separation of the wells, the non-pairwise additive contribution to the dispersion energy is shown to depend on the overlap of density between neighboring wells. As well separation is increased, the non-pairwise additivity of the dispersion energy decays. The different rates of decay for 1D and 2D lattices of wells is explained inmore » terms of a Jacobian effect that influences the number of nearest neighbors. For an array of infinitely long lines of wells spaced 5 bohrs apart, and an inter-well spacing of 3 bohrs within a line, the non-pairwise additive component of the leading-order dispersion energy is −0.11 kJ mol{sup −1} well{sup −1}, which is 7% of the total. The polarizability of the wells and the density overlap between them are small in comparison to that of the atomic densities that arise from the molecular density partitioning used in post-density-functional theory (DFT) damped dispersion corrections, or DFT-D methods. Therefore, the nonadditivity of the leading-order dispersion observed here is a conservative estimate of that in molecular clusters.« less

Network meta-analysis: a technique to gather evidence from direct and indirect comparisons

PubMed Central

2017-01-01

Systematic reviews and pairwise meta-analyses of randomized controlled trials, at the intersection of clinical medicine, epidemiology and statistics, are positioned at the top of evidence-based practice hierarchy. These are important tools to base drugs approval, clinical protocols and guidelines formulation and for decision-making. However, this traditional technique only partially yield information that clinicians, patients and policy-makers need to make informed decisions, since it usually compares only two interventions at the time. In the market, regardless the clinical condition under evaluation, usually many interventions are available and few of them have been studied in head-to-head studies. This scenario precludes conclusions to be drawn from comparisons of all interventions profile (e.g. efficacy and safety). The recent development and introduction of a new technique – usually referred as network meta-analysis, indirect meta-analysis, multiple or mixed treatment comparisons – has allowed the estimation of metrics for all possible comparisons in the same model, simultaneously gathering direct and indirect evidence. Over the last years this statistical tool has matured as technique with models available for all types of raw data, producing different pooled effect measures, using both Frequentist and Bayesian frameworks, with different software packages. However, the conduction, report and interpretation of network meta-analysis still poses multiple challenges that should be carefully considered, especially because this technique inherits all assumptions from pairwise meta-analysis but with increased complexity. Thus, we aim to provide a basic explanation of network meta-analysis conduction, highlighting its risks and benefits for evidence-based practice, including information on statistical methods evolution, assumptions and steps for performing the analysis. PMID:28503228

Microarray analysis of port wine stains before and after pulsed dye laser treatment.

PubMed

Laquer, Vivian T; Hevezi, Peter A; Albrecht, Huguette; Chen, Tina S; Zlotnik, Albert; Kelly, Kristen M

2013-02-01

Neither the pathogenesis of port wine stain (PWS) birthmarks nor tissue effects of pulsed dye laser (PDL) treatment of these lesions is fully understood. There are few published reports utilizing gene expression analysis in human PWS skin. We aim to compare gene expression in PWS before and after PDL, using DNA microarrays that represent most, if not all, human genes to obtain comprehensive molecular profiles of PWS lesions and PDL-associated tissue effects. Five human subjects had PDL treatment of their PWS. One week later, three biopsies were taken from each subject: normal skin (N); untreated PWS (PWS); PWS post-PDL (PWS + PDL). Samples included two lower extremity lesions, two facial lesions, and one facial nodule. High-quality total RNA isolated from skin biopsies was processed and applied to Affymetrix Human gene 1.0ST microarrays for gene expression analysis. We performed a 16 pair-wise comparison identifying either up- or down-regulated genes between N versus PWS and PWS versus PWS + PDL for four of the donor samples. The PWS nodule (nPWS) was analyzed separately. There was significant variation in gene expression profiles between individuals. By doing pair-wise comparisons between samples taken from the same donor, we were able to identify genes that may participate in the formation of PWS lesions and PDL tissue effects. Genes associated with immune, epidermal, and lipid metabolism were up-regulated in PWS skin. The nPWS exhibited more profound differences in gene expression than the rest of the samples, with significant differential expression of genes associated with angiogenesis, tumorigenesis, and inflammation. In summary, gene expression profiles from N, PWS, and PWS + PDL demonstrated significant variation within samples from the same donor and between donors. By doing pair-wise comparisons between samples taken from the same donor and comparing these results between donors, we were able to identify genes that may participate in formation of PWS and PDL effects. Our preliminary results indicate changes in gene expression of angiogenesis-related genes, suggesting that dysregulation of angiogenic signals and/or components may contribute to PWS pathology. Copyright © 2012 Wiley Periodicals, Inc.

Interactive collision detection for deformable models using streaming AABBs.

PubMed

Zhang, Xinyu; Kim, Young J

2007-01-01

We present an interactive and accurate collision detection algorithm for deformable, polygonal objects based on the streaming computational model. Our algorithm can detect all possible pairwise primitive-level intersections between two severely deforming models at highly interactive rates. In our streaming computational model, we consider a set of axis aligned bounding boxes (AABBs) that bound each of the given deformable objects as an input stream and perform massively-parallel pairwise, overlapping tests onto the incoming streams. As a result, we are able to prevent performance stalls in the streaming pipeline that can be caused by expensive indexing mechanism required by bounding volume hierarchy-based streaming algorithms. At runtime, as the underlying models deform over time, we employ a novel, streaming algorithm to update the geometric changes in the AABB streams. Moreover, in order to get only the computed result (i.e., collision results between AABBs) without reading back the entire output streams, we propose a streaming en/decoding strategy that can be performed in a hierarchical fashion. After determining overlapped AABBs, we perform a primitive-level (e.g., triangle) intersection checking on a serial computational model such as CPUs. We implemented the entire pipeline of our algorithm using off-the-shelf graphics processors (GPUs), such as nVIDIA GeForce 7800 GTX, for streaming computations, and Intel Dual Core 3.4G processors for serial computations. We benchmarked our algorithm with different models of varying complexities, ranging from 15K up to 50K triangles, under various deformation motions, and the timings were obtained as 30 approximately 100 FPS depending on the complexity of models and their relative configurations. Finally, we made comparisons with a well-known GPU-based collision detection algorithm, CULLIDE [4] and observed about three times performance improvement over the earlier approach. We also made comparisons with a SW-based AABB culling algorithm [2] and observed about two times improvement.

APOLLO: a quality assessment service for single and multiple protein models.

PubMed

Wang, Zheng; Eickholt, Jesse; Cheng, Jianlin

2011-06-15

We built a web server named APOLLO, which can evaluate the absolute global and local qualities of a single protein model using machine learning methods or the global and local qualities of a pool of models using a pair-wise comparison approach. Based on our evaluations on 107 CASP9 (Critical Assessment of Techniques for Protein Structure Prediction) targets, the predicted quality scores generated from our machine learning and pair-wise methods have an average per-target correlation of 0.671 and 0.917, respectively, with the true model quality scores. Based on our test on 92 CASP9 targets, our predicted absolute local qualities have an average difference of 2.60 Å with the actual distances to native structure. http://sysbio.rnet.missouri.edu/apollo/. Single and pair-wise global quality assessment software is also available at the site.

Differential Item Functioning Detection Across Two Methods of Defining Group Comparisons

PubMed Central

Sari, Halil Ibrahim

2014-01-01

This study compares two methods of defining groups for the detection of differential item functioning (DIF): (a) pairwise comparisons and (b) composite group comparisons. We aim to emphasize and empirically support the notion that the choice of pairwise versus composite group definitions in DIF is a reflection of how one defines fairness in DIF studies. In this study, a simulation was conducted based on data from a 60-item ACT Mathematics test (ACT; Hanson & Béguin). The unsigned area measure method (Raju) was used as the DIF detection method. An application to operational data was also completed in the study, as well as a comparison of observed Type I error rates and false discovery rates across the two methods of defining groups. Results indicate that the amount of flagged DIF or interpretations about DIF in all conditions were not the same across the two methods, and there may be some benefits to using composite group approaches. The results are discussed in connection to differing definitions of fairness. Recommendations for practice are made. PMID:29795837

KECSA-Movable Type Implicit Solvation Model (KMTISM)

PubMed Central

2015-01-01

Computation of the solvation free energy for chemical and biological processes has long been of significant interest. The key challenges to effective solvation modeling center on the choice of potential function and configurational sampling. Herein, an energy sampling approach termed the “Movable Type” (MT) method, and a statistical energy function for solvation modeling, “Knowledge-based and Empirical Combined Scoring Algorithm” (KECSA) are developed and utilized to create an implicit solvation model: KECSA-Movable Type Implicit Solvation Model (KMTISM) suitable for the study of chemical and biological systems. KMTISM is an implicit solvation model, but the MT method performs energy sampling at the atom pairwise level. For a specific molecular system, the MT method collects energies from prebuilt databases for the requisite atom pairs at all relevant distance ranges, which by its very construction encodes all possible molecular configurations simultaneously. Unlike traditional statistical energy functions, KECSA converts structural statistical information into categorized atom pairwise interaction energies as a function of the radial distance instead of a mean force energy function. Within the implicit solvent model approximation, aqueous solvation free energies are then obtained from the NVT ensemble partition function generated by the MT method. Validation is performed against several subsets selected from the Minnesota Solvation Database v2012. Results are compared with several solvation free energy calculation methods, including a one-to-one comparison against two commonly used classical implicit solvation models: MM-GBSA and MM-PBSA. Comparison against a quantum mechanics based polarizable continuum model is also discussed (Cramer and Truhlar’s Solvation Model 12). PMID:25691832

An Outbreak of Streptococcus pyogenes in a Mental Health Facility: Advantage of Well-Timed Whole-Genome Sequencing Over emm Typing.

PubMed

Bergin, Sarah M; Periaswamy, Balamurugan; Barkham, Timothy; Chua, Hong Choon; Mok, Yee Ming; Fung, Daniel Shuen Sheng; Su, Alex Hsin Chuan; Lee, Yen Ling; Chua, Ming Lai Ivan; Ng, Poh Yong; Soon, Wei Jia Wendy; Chu, Collins Wenhan; Tan, Siyun Lucinda; Meehan, Mary; Ang, Brenda Sze Peng; Leo, Yee Sin; Holden, Matthew T G; De, Partha; Hsu, Li Yang; Chen, Swaine L; de Sessions, Paola Florez; Marimuthu, Kalisvar

2018-05-09

OBJECTIVEWe report the utility of whole-genome sequencing (WGS) conducted in a clinically relevant time frame (ie, sufficient for guiding management decision), in managing a Streptococcus pyogenes outbreak, and present a comparison of its performance with emm typing.SETTINGA 2,000-bed tertiary-care psychiatric hospital.METHODSActive surveillance was conducted to identify new cases of S. pyogenes. WGS guided targeted epidemiological investigations, and infection control measures were implemented. Single-nucleotide polymorphism (SNP)-based genome phylogeny, emm typing, and multilocus sequence typing (MLST) were performed. We compared the ability of WGS and emm typing to correctly identify person-to-person transmission and to guide the management of the outbreak.RESULTSThe study included 204 patients and 152 staff. We identified 35 patients and 2 staff members with S. pyogenes. WGS revealed polyclonal S. pyogenes infections with 3 genetically distinct phylogenetic clusters (C1-C3). Cluster C1 isolates were all emm type 4, sequence type 915 and had pairwise SNP differences of 0-5, which suggested recent person-to-person transmissions. Epidemiological investigation revealed that cluster C1 was mediated by dermal colonization and transmission of S. pyogenes in a male residential ward. Clusters C2 and C3 were genomically diverse, with pairwise SNP differences of 21-45 and 26-58, and emm 11 and mostly emm120, respectively. Clusters C2 and C3, which may have been considered person-to-person transmissions by emm typing, were shown by WGS to be unlikely by integrating pairwise SNP differences with epidemiology.CONCLUSIONSWGS had higher resolution than emm typing in identifying clusters with recent and ongoing person-to-person transmissions, which allowed implementation of targeted intervention to control the outbreak.Infect Control Hosp Epidemiol 2018;1-9.

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

PubMed

Brown, Peter; Pullan, Wayne; Yang, Yuedong; Zhou, Yaoqi

2016-02-01

The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org yaoqi.zhou@griffith.edu.au. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Comparing methods for modelling spreading cell fronts.

PubMed

Markham, Deborah C; Simpson, Matthew J; Maini, Philip K; Gaffney, Eamonn A; Baker, Ruth E

2014-07-21

Spreading cell fronts play an essential role in many physiological processes. Classically, models of this process are based on the Fisher-Kolmogorov equation; however, such continuum representations are not always suitable as they do not explicitly represent behaviour at the level of individual cells. Additionally, many models examine only the large time asymptotic behaviour, where a travelling wave front with a constant speed has been established. Many experiments, such as a scratch assay, never display this asymptotic behaviour, and in these cases the transient behaviour must be taken into account. We examine the transient and the asymptotic behaviour of moving cell fronts using techniques that go beyond the continuum approximation via a volume-excluding birth-migration process on a regular one-dimensional lattice. We approximate the averaged discrete results using three methods: (i) mean-field, (ii) pair-wise, and (iii) one-hole approximations. We discuss the performance of these methods, in comparison to the averaged discrete results, for a range of parameter space, examining both the transient and asymptotic behaviours. The one-hole approximation, based on techniques from statistical physics, is not capable of predicting transient behaviour but provides excellent agreement with the asymptotic behaviour of the averaged discrete results, provided that cells are proliferating fast enough relative to their rate of migration. The mean-field and pair-wise approximations give indistinguishable asymptotic results, which agree with the averaged discrete results when cells are migrating much more rapidly than they are proliferating. The pair-wise approximation performs better in the transient region than does the mean-field, despite having the same asymptotic behaviour. Our results show that each approximation only works in specific situations, thus we must be careful to use a suitable approximation for a given system, otherwise inaccurate predictions could be made. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evaluation of a novel waste heat recovery system for the cement industry using multi-criteria analysis (MCA) approach

NASA Astrophysics Data System (ADS)

Han, Yue; Guo, Junshan; Zheng, Wei; Ding, Junqi; Zhu, Lingkai; Che, Yongqiang; Zhang, Yanpeng

2017-12-01

Based on a novel waste heat recovery project established in a cement plant, this paper aims to evaluate the performance of the project using multi-criteria analysis (MCA) approach. Economic, environmental, social, and technical perspectives were concerned and analyzed. Different sustainability criteria and indicators related with the project were evaluated through ranking/rating process and pairwise comparison. Results have shown similar outcomes, that ten out of eleven criteria are favorable at a high standard, which reveals the project’s success. Although the project has performed so well in economic, environmental and technical terms, social aspects have some weak points, and measures should be taken to improve social benefit.

Preliminary Assessment of Detection Efficiency for the Geostationary Lightning Mapper Using Intercomparisons with Ground-Based Systems

NASA Technical Reports Server (NTRS)

Bateman, Monte; Mach, Douglas; Blakeslee, Richard J.; Koshak, William

2018-01-01

As part of the calibration/validation (cal/val) effort for the Geostationary Lightning Mapper (GLM) on GOES-16, we need to assess instrument performance (detection efficiency and accuracy). One major effort is to calculate the detection efficiency of GLM by comparing to multiple ground-based systems. These comparisons will be done pair-wise between GLM and each other source. A complication in this process is that the ground-based systems sense different properties of the lightning signal than does GLM (e.g., RF vs. optical). Also, each system has a different time and space resolution and accuracy. Preliminary results indicate that GLM is performing at or above its specification.

Estimation of Salivary Parameters among Autoimmune Thyroiditis Patients.

PubMed

Syed, Yasmeen Amthul; Reddy, Bh Satheesh; Ramamurthy, T K; Rajendra, Kavitha; Nerella, Narendra Kumar; Krishnan, Meenakshi; Ramesh, M V; Mohammed, Rezwana Begum

2017-07-01

Saliva is a complex secretion that protects and lubricates the oral cavity. Various systemic diseases and their treatment alter the salivary gland function; one such disease is Autoimmune Thyroid Disease (AITD). AITD has been postulated to exert its hormonal influence on the salivary glands, leading to reduced salivary output. There's a paucity of literature, verifying the stated conjunction in human subjects. The aim was to investigate the salivary profile in AITD patients and its comparison with controls. Descriptive cross-sectional comparative study was conducted using convenience sampling method for screening the presence of thyroid disorders. Two groups comprising of 30 patients in each group diagnosed with autoimmune hypothyroiditis (n=30) and hyperthyroiditis (n=30) respectively and thirty healthy volunteers who were age and sex matched were included as controls. Saliva was collected and evaluated for Unstimulated Salivary Flow Rate (USSFR), pH and buffer capacity. ANOVA and Tukey post-hoc test was performed to find the statistical significance and for pairwise comparison. Statistically significant difference was observed between autoimmune hypothyroiditis, autoimmune hyperthyroiditis and control group with respect to USSFR (p<0.007), pH (p<0.001) and buffer capacity (p<0.001). On pairwise comparisons statistically significant difference was observed between autoimmune hypothyroiditis and autoimmune hyperthyroiditis with respect to controls. We conclude that significant involvement of salivary glands may occur in cases of AITD. Our study showed significant reduction of sialometric values in AITD patients when compared to controls. A strong clinical suspicion of thyroid diseases should be considered when there is chronic hyposalivation; hence thyroid profile must also be done, if the known causes have been excluded.

Comparison of the social contact patterns among school-age children in specific seasons, locations, and times.

PubMed

Luh, Dih-Ling; You, Zhi-Shin; Chen, Szu-Chieh

2016-03-01

Social contact patterns among school-age children play an important role in the epidemiology of infectious disease. This study explored how people interact in specific seasons (flu season and non-flu season), environmental settings (city and county), and times (weekend and weekday). We conducted a survey of junior high school students (grades 7-8) using an established questionnaire during May-June 2013 and December 2013. The sample size with pair-wise comparisons for the times (weekday/weekend) and stratification by location and seasons were 75, 87, 105 and 106, respectively. The sample size with pair-wise comparisons for the seasons (flu/non-flu) and stratification by location were 54 and 83, respectively. Conversation and skin-to-skin contact behaviors were surveyed through diary-based questionnaires, of which 665 valid questionnaires were returned. There was no difference in the number of contacts during the flu and non-flu seasons, with averages of 16.3 (S.D.=12.9) and 14.6 (S.D.=9.5) people, respectively. However, statistical analysis showed that the average number of contacts in Taichung City and Yilan County were significantly different (p<0.001). Weekdays were associated with 23-28% more contacts than weekend days during both the non-flu and flu seasons (p<0.001) (Wilcoxon signed-rank test). Our work has important implications for the dynamic modeling of infectious diseases and performance analysis of human contact numbers and contact characteristics for schoolchildren in specific seasons, places, and times. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

A machine learning approach for ranking clusters of docked protein‐protein complexes by pairwise cluster comparison

PubMed Central

Pfeiffenberger, Erik; Chaleil, Raphael A.G.; Moal, Iain H.

2017-01-01

ABSTRACT Reliable identification of near‐native poses of docked protein–protein complexes is still an unsolved problem. The intrinsic heterogeneity of protein–protein interactions is challenging for traditional biophysical or knowledge based potentials and the identification of many false positive binding sites is not unusual. Often, ranking protocols are based on initial clustering of docked poses followed by the application of an energy function to rank each cluster according to its lowest energy member. Here, we present an approach of cluster ranking based not only on one molecular descriptor (e.g., an energy function) but also employing a large number of descriptors that are integrated in a machine learning model, whereby, an extremely randomized tree classifier based on 109 molecular descriptors is trained. The protocol is based on first locally enriching clusters with additional poses, the clusters are then characterized using features describing the distribution of molecular descriptors within the cluster, which are combined into a pairwise cluster comparison model to discriminate near‐native from incorrect clusters. The results show that our approach is able to identify clusters containing near‐native protein–protein complexes. In addition, we present an analysis of the descriptors with respect to their power to discriminate near native from incorrect clusters and how data transformations and recursive feature elimination can improve the ranking performance. Proteins 2017; 85:528–543. © 2016 Wiley Periodicals, Inc. PMID:27935158

Classification of complex information: inference of co-occurring affective states from their expressions in speech.

PubMed

Sobol-Shikler, Tal; Robinson, Peter

2010-07-01

We present a classification algorithm for inferring affective states (emotions, mental states, attitudes, and the like) from their nonverbal expressions in speech. It is based on the observations that affective states can occur simultaneously and different sets of vocal features, such as intonation and speech rate, distinguish between nonverbal expressions of different affective states. The input to the inference system was a large set of vocal features and metrics that were extracted from each utterance. The classification algorithm conducted independent pairwise comparisons between nine affective-state groups. The classifier used various subsets of metrics of the vocal features and various classification algorithms for different pairs of affective-state groups. Average classification accuracy of the 36 pairwise machines was 75 percent, using 10-fold cross validation. The comparison results were consolidated into a single ranked list of the nine affective-state groups. This list was the output of the system and represented the inferred combination of co-occurring affective states for the analyzed utterance. The inference accuracy of the combined machine was 83 percent. The system automatically characterized over 500 affective state concepts from the Mind Reading database. The inference of co-occurring affective states was validated by comparing the inferred combinations to the lexical definitions of the labels of the analyzed sentences. The distinguishing capabilities of the system were comparable to human performance.

Evaluation of key driver categories influencing sustainable waste management development with the analytic hierarchy process (AHP): Serbia example.

PubMed

Tot, Bojana; Srđević, Bojan; Vujić, Bogdana; Russo, Mário Augusto Tavares; Vujić, Goran

2016-08-01

The problems of waste management have become increasingly complex in recent decades. The increasing amount of generated waste, adopted legislation in the field of waste management, administrative issues, economic impacts and social awareness are important drivers in achieving a sustainable waste management system. However, in practice, there are many other drivers that are often mutually in conflict. The purpose of this research is to define the precise driver and their corresponding sub-drivers, which are relevant for developing a waste management system and, on the basis of their importance, to determine which has the predominant influence on the slow development of a waste management system at the national and regional level, within the Republic of Serbia and similar countries of southeast Europe. This research presents two levels of decision making: the first is a pair-wise comparison of the drivers in relation to the goal and the second is a pair-wise comparison of the sub-drivers in relation to the driver and in relation to the goal. Results of performed analyses on the waste management drivers were integrated via the decision-making process supported by an analytic hierarchy process (AHP). The final results of this research shows that the Institutional-Administrative driver is the most important for developing a sustainable waste management system. © The Author(s) 2016.

Metabolic network prediction through pairwise rational kernels.

PubMed

Roche-Lima, Abiel; Domaratzki, Michael; Fristensky, Brian

2014-09-26

Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to another reaction. Many pathways remain incompletely characterized. One of the major challenges of computational biology is to obtain better models of metabolic pathways. Existing models are dependent on the annotation of the genes. This propagates error accumulation when the pathways are predicted by incorrectly annotated genes. Pairwise classification methods are supervised learning methods used to classify new pair of entities. Some of these classification methods, e.g., Pairwise Support Vector Machines (SVMs), use pairwise kernels. Pairwise kernels describe similarity measures between two pairs of entities. Using pairwise kernels to handle sequence data requires long processing times and large storage. Rational kernels are kernels based on weighted finite-state transducers that represent similarity measures between sequences or automata. They have been effectively used in problems that handle large amount of sequence information such as protein essentiality, natural language processing and machine translations. We create a new family of pairwise kernels using weighted finite-state transducers (called Pairwise Rational Kernel (PRK)) to predict metabolic pathways from a variety of biological data. PRKs take advantage of the simpler representations and faster algorithms of transducers. Because raw sequence data can be used, the predictor model avoids the errors introduced by incorrect gene annotations. We then developed several experiments with PRKs and Pairwise SVM to validate our methods using the metabolic network of Saccharomyces cerevisiae. As a result, when PRKs are used, our method executes faster in comparison with other pairwise kernels. Also, when we use PRKs combined with other simple kernels that include evolutionary information, the accuracy values have been improved, while maintaining lower construction and execution times. The power of using kernels is that almost any sort of data can be represented using kernels. Therefore, completely disparate types of data can be combined to add power to kernel-based machine learning methods. When we compared our proposal using PRKs with other similar kernel, the execution times were decreased, with no compromise of accuracy. We also proved that by combining PRKs with other kernels that include evolutionary information, the accuracy can also also be improved. As our proposal can use any type of sequence data, genes do not need to be properly annotated, avoiding accumulation errors because of incorrect previous annotations.

Characterization of demographic expansions from pairwise comparisons of linked microsatellite haplotypes.

PubMed

Navascués, Miguel; Hardy, Olivier J; Burgarella, Concetta

2009-03-01

This work extends the methods of demographic inference based on the distribution of pairwise genetic differences between individuals (mismatch distribution) to the case of linked microsatellite data. Population genetics theory describes the distribution of mutations among a sample of genes under different demographic scenarios. However, the actual number of mutations can rarely be deduced from DNA polymorphisms. The inclusion of mutation models in theoretical predictions can improve the performance of statistical methods. We have developed a maximum-pseudolikelihood estimator for the parameters that characterize a demographic expansion for a series of linked loci evolving under a stepwise mutation model. Those loci would correspond to DNA polymorphisms of linked microsatellites (such as those found on the Y chromosome or the chloroplast genome). The proposed method was evaluated with simulated data sets and with a data set of chloroplast microsatellites that showed signal for demographic expansion in a previous study. The results show that inclusion of a mutational model in the analysis improves the estimates of the age of expansion in the case of older expansions.

BiodMHC: an online server for the prediction of MHC class II-peptide binding affinity.

PubMed

Wang, Lian; Pan, Danling; Hu, Xihao; Xiao, Jinyu; Gao, Yangyang; Zhang, Huifang; Zhang, Yan; Liu, Juan; Zhu, Shanfeng

2009-05-01

Effective identification of major histocompatibility complex (MHC) molecules restricted peptides is a critical step in discovering immune epitopes. Although many online servers have been built to predict class II MHC-peptide binding affinity, they have been trained on different datasets, and thus fail in providing a unified comparison of various methods. In this paper, we present our implementation of seven popular predictive methods, namely SMM-align, ARB, SVR-pairwise, Gibbs sampler, ProPred, LP-top2, and MHCPred, on a single web server named BiodMHC (http://biod.whu.edu.cn/BiodMHC/index.html, the software is available upon request). Using a standard measure of AUC (Area Under the receiver operating characteristic Curves), we compare these methods by means of not only cross validation but also prediction on independent test datasets. We find that SMM-align, ProPred, SVR-pairwise, ARB, and Gibbs sampler are the five best-performing methods. For the binding affinity prediction of class II MHC-peptide, BiodMHC provides a convenient online platform for researchers to obtain binding information simultaneously using various methods.

GetReal in network meta-analysis: a review of the methodology.

PubMed

Efthimiou, Orestis; Debray, Thomas P A; van Valkenhoef, Gert; Trelle, Sven; Panayidou, Klea; Moons, Karel G M; Reitsma, Johannes B; Shang, Aijing; Salanti, Georgia

2016-09-01

Pairwise meta-analysis is an established statistical tool for synthesizing evidence from multiple trials, but it is informative only about the relative efficacy of two specific interventions. The usefulness of pairwise meta-analysis is thus limited in real-life medical practice, where many competing interventions may be available for a certain condition and studies informing some of the pairwise comparisons may be lacking. This commonly encountered scenario has led to the development of network meta-analysis (NMA). In the last decade, several applications, methodological developments, and empirical studies in NMA have been published, and the area is thriving as its relevance to public health is increasingly recognized. This article presents a review of the relevant literature on NMA methodology aiming to pinpoint the developments that have appeared in the field. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

SU-E-T-608: Performance Comparison of Four Commercial Treatment Planning Systems Applied to Intensity-Modulated Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Y; Li, R; Chi, Z

Purpose: To compare the performances of four commercial treatment planning systems (TPS) used for the intensity-modulated radiotherapy (IMRT). Methods: Ten patients of nasopharyngeal (4 cases), esophageal (3 cases) and cervical (3 cases) cancer were randomly selected from a 3-month IMRT plan pool at one radiotherapy center. For each patient, four IMRT plans were newly generated by using four commercial TPS (Corvus, Monaco, Pinnacle and Xio), and then verified with Matrixx (two-dimensional array/IBA Company) on Varian23EX accelerator. A pass rate (PR) calculated from the Gamma index by OminiPro IMRT 1.5 software was evaluated at four plan verification standards (1%/1mm, 2%/2mm, 3%/3mm,more » 4%/4mm and 5%/5mm) for each treatment plan. Overall and multiple pairwise comparisons of PRs were statistically conducted by analysis of covariance (ANOVA) F and LSD tests among four TPSs. Results: Overall significant (p>0.05) differences of PRs were found among four TPSs with F test values of 3.8 (p=0.02), 21.1(>0.01), 14.0 (>0.01), 8.3(>0.01) at standards of 1%/1mm to 4%/4mm respectively, except at 5%/5mm standard with 2.6 (p=0.06). All means (standard deviation) of PRs at 3%/3mm of 94.3 ± 3.3 (Corvus), 98.8 ± 0.8 (Monaco), 97.5± 1.7 (Pinnacle), 98.4 ± 1.0 (Xio) were above 90% and met clinical requirement. Multiple pairwise comparisons had not demonstrated a consistent low or high pattern on either TPS. Conclusion: Matrixx dose verification results show that the validation pass rates of Monaco and Xio plans are relatively higher than those of the other two; Pinnacle plan shows slight higher pass rate than Corvus plan; lowest pass rate was achieved by the Corvus plan among these four kinds of TPS.« less

Comparing Performances of Multiple Comparison Methods in Commonly Used 2 × C Contingency Tables.

PubMed

Cangur, Sengul; Ankarali, Handan; Pasin, Ozge

2016-12-01

This study aims at mentioning briefly multiple comparison methods such as Bonferroni, Holm-Bonferroni, Hochberg, Hommel, Marascuilo, Tukey, Benjamini-Hochberg and Gavrilov-Benjamini-Sarkar for contingency tables, through the data obtained from a medical research and examining their performances by simulation study which was constructed as the total 36 scenarios to 2 × 4 contingency table. As results of simulation, it was observed that when the sample size is more than 100, the methods which can preserve the nominal alpha level are Gavrilov-Benjamini-Sarkar, Holm-Bonferroni and Bonferroni. Marascuilo method was found to be a more conservative than Bonferroni. It was found that Type I error rate for Hommel method is around 2 % in all scenarios. Moreover, when the proportions of the three populations are equal and the proportion value of the fourth population is far at a level of ±3 standard deviation from the other populations, the power value for Unadjusted All-Pairwise Comparison approach is at least a bit higher than the ones obtained by Gavrilov-Benjamini-Sarkar, Holm-Bonferroni and Bonferroni. Consequently, Gavrilov-Benjamini-Sarkar and Holm-Bonferroni methods have the best performance according to simulation. Hommel and Marascuilo methods are not recommended to be used because they have medium or lower performance. In addition, we have written a Minitab macro about multiple comparisons for use in scientific research.

Factors affecting color correction of retroreflective markings.

DOT National Transportation Integrated Search

2001-09-01

A nighttime field study was conducted to assess the effects of retroreflective material area, distribution, and : color on judgments of conspicuity. Participants, seated in a stationary vehicle, took part in a pairwise comparison : of the stimuli. Th...

Ethanol modifies the effect of handling stress on gene expression: problems in the analysis of two-way gene expression studies in mouse brain.

PubMed

Rulten, Stuart L; Ripley, Tamzin L; Manerakis, Ektor; Stephens, David N; Mayne, Lynne V

2006-08-02

Studies analysing the effects of acute treatments on animal behaviour and brain biochemistry frequently use pairwise comparisons between sham-treated and -untreated animals. In this study, we analyse expression of tPA, Grik2, Smarca2 and the transcription factor, Sp1, in mouse cerebellum following acute ethanol treatment. Expression is compared to saline-injected and -untreated control animals. We demonstrate that acute i.p. injection of saline may alter gene expression in a gene-specific manner and that ethanol may modify the effects of sham treatment on gene expression, as well as inducing specific effects independent of any handling related stress. In addition to demonstrating the complexity of gene expression in response to physical and environmental stress, this work raises questions on the interpretation and validity of studies relying on pairwise comparisons.

Improving pairwise comparison of protein sequences with domain co-occurrence

PubMed Central

Gascuel, Olivier

2018-01-01

Comparing and aligning protein sequences is an essential task in bioinformatics. More specifically, local alignment tools like BLAST are widely used for identifying conserved protein sub-sequences, which likely correspond to protein domains or functional motifs. However, to limit the number of false positives, these tools are used with stringent sequence-similarity thresholds and hence can miss several hits, especially for species that are phylogenetically distant from reference organisms. A solution to this problem is then to integrate additional contextual information to the procedure. Here, we propose to use domain co-occurrence to increase the sensitivity of pairwise sequence comparisons. Domain co-occurrence is a strong feature of proteins, since most protein domains tend to appear with a limited number of other domains on the same protein. We propose a method to take this information into account in a typical BLAST analysis and to construct new domain families on the basis of these results. We used Plasmodium falciparum as a case study to evaluate our method. The experimental findings showed an increase of 14% of the number of significant BLAST hits and an increase of 25% of the proteome area that can be covered with a domain. Our method identified 2240 new domains for which, in most cases, no model of the Pfam database could be linked. Moreover, our study of the quality of the new domains in terms of alignment and physicochemical properties show that they are close to that of standard Pfam domains. Source code of the proposed approach and supplementary data are available at: https://gite.lirmm.fr/menichelli/pairwise-comparison-with-cooccurrence PMID:29293498

Cost-efficient designs for three-arm trials with treatment delivered by health professionals: Sample sizes for a combination of nested and crossed designs

PubMed Central

Moerbeek, Mirjam

2018-01-01

Background This article studies the design of trials that compare three treatment conditions that are delivered by two types of health professionals. The one type of health professional delivers one treatment, and the other type delivers two treatments, hence, this design is a combination of a nested and crossed design. As each health professional treats multiple patients, the data have a nested structure. This nested structure has thus far been ignored in the design of such trials, which may result in an underestimate of the required sample size. In the design stage, the sample sizes should be determined such that a desired power is achieved for each of the three pairwise comparisons, while keeping costs or sample size at a minimum. Methods The statistical model that relates outcome to treatment condition and explicitly takes the nested data structure into account is presented. Mathematical expressions that relate sample size to power are derived for each of the three pairwise comparisons on the basis of this model. The cost-efficient design achieves sufficient power for each pairwise comparison at lowest costs. Alternatively, one may minimize the total number of patients. The sample sizes are found numerically and an Internet application is available for this purpose. The design is also compared to a nested design in which each health professional delivers just one treatment. Results Mathematical expressions show that this design is more efficient than the nested design. For each pairwise comparison, power increases with the number of health professionals and the number of patients per health professional. The methodology of finding a cost-efficient design is illustrated using a trial that compares treatments for social phobia. The optimal sample sizes reflect the costs for training and supervising psychologists and psychiatrists, and the patient-level costs in the three treatment conditions. Conclusion This article provides the methodology for designing trials that compare three treatment conditions while taking the nesting of patients within health professionals into account. As such, it helps to avoid underpowered trials. To use the methodology, a priori estimates of the total outcome variances and intraclass correlation coefficients must be obtained from experts’ opinions or findings in the literature. PMID:29316807

Estimation of Salivary Parameters among Autoimmune Thyroiditis Patients

PubMed Central

Reddy, BH Satheesh; Ramamurthy, TK; Rajendra, Kavitha; Nerella, Narendra Kumar; Krishnan, Meenakshi; Ramesh, MV; Mohammed, Rezwana Begum

2017-01-01

Introduction Saliva is a complex secretion that protects and lubricates the oral cavity. Various systemic diseases and their treatment alter the salivary gland function; one such disease is Autoimmune Thyroid Disease (AITD). AITD has been postulated to exert its hormonal influence on the salivary glands, leading to reduced salivary output. There’s a paucity of literature, verifying the stated conjunction in human subjects. Aim The aim was to investigate the salivary profile in AITD patients and its comparison with controls. Materials and Methods Descriptive cross-sectional comparative study was conducted using convenience sampling method for screening the presence of thyroid disorders. Two groups comprising of 30 patients in each group diagnosed with autoimmune hypothyroiditis (n=30) and hyperthyroiditis (n=30) respectively and thirty healthy volunteers who were age and sex matched were included as controls. Saliva was collected and evaluated for Unstimulated Salivary Flow Rate (USSFR), pH and buffer capacity. ANOVA and Tukey post-hoc test was performed to find the statistical significance and for pairwise comparison. Results Statistically significant difference was observed between autoimmune hypothyroiditis, autoimmune hyperthyroiditis and control group with respect to USSFR (p<0.007), pH (p<0.001) and buffer capacity (p<0.001). On pairwise comparisons statistically significant difference was observed between autoimmune hypothyroiditis and autoimmune hyperthyroiditis with respect to controls. Conclusion We conclude that significant involvement of salivary glands may occur in cases of AITD. Our study showed significant reduction of sialometric values in AITD patients when compared to controls. A strong clinical suspicion of thyroid diseases should be considered when there is chronic hyposalivation; hence thyroid profile must also be done, if the known causes have been excluded. PMID:28893031

Geometric measure of pairwise quantum discord for superpositions of multipartite generalized coherent states

NASA Astrophysics Data System (ADS)

Daoud, M.; Ahl Laamara, R.

2012-07-01

We give the explicit expressions of the pairwise quantum correlations present in superpositions of multipartite coherent states. A special attention is devoted to the evaluation of the geometric quantum discord. The dynamics of quantum correlations under a dephasing channel is analyzed. A comparison of geometric measure of quantum discord with that of concurrence shows that quantum discord in multipartite coherent states is more resilient to dissipative environments than is quantum entanglement. To illustrate our results, we consider some special superpositions of Weyl-Heisenberg, SU(2) and SU(1,1) coherent states which interpolate between Werner and Greenberger-Horne-Zeilinger states.

A comparison of fitness-case sampling methods for genetic programming

NASA Astrophysics Data System (ADS)

Martínez, Yuliana; Naredo, Enrique; Trujillo, Leonardo; Legrand, Pierrick; López, Uriel

2017-11-01

Genetic programming (GP) is an evolutionary computation paradigm for automatic program induction. GP has produced impressive results but it still needs to overcome some practical limitations, particularly its high computational cost, overfitting and excessive code growth. Recently, many researchers have proposed fitness-case sampling methods to overcome some of these problems, with mixed results in several limited tests. This paper presents an extensive comparative study of four fitness-case sampling methods, namely: Interleaved Sampling, Random Interleaved Sampling, Lexicase Selection and Keep-Worst Interleaved Sampling. The algorithms are compared on 11 symbolic regression problems and 11 supervised classification problems, using 10 synthetic benchmarks and 12 real-world data-sets. They are evaluated based on test performance, overfitting and average program size, comparing them with a standard GP search. Comparisons are carried out using non-parametric multigroup tests and post hoc pairwise statistical tests. The experimental results suggest that fitness-case sampling methods are particularly useful for difficult real-world symbolic regression problems, improving performance, reducing overfitting and limiting code growth. On the other hand, it seems that fitness-case sampling cannot improve upon GP performance when considering supervised binary classification.

Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes

PubMed Central

Lin, Michael F.; Deoras, Ameya N.; Rasmussen, Matthew D.; Kellis, Manolis

2008-01-01

Comparative genomics of multiple related species is a powerful methodology for the discovery of functional genomic elements, and its power should increase with the number of species compared. Here, we use 12 Drosophila genomes to study the power of comparative genomics metrics to distinguish between protein-coding and non-coding regions. First, we study the relative power of different comparative metrics and their relationship to single-species metrics. We find that even relatively simple multi-species metrics robustly outperform advanced single-species metrics, especially for shorter exons (≤240 nt), which are common in animal genomes. Moreover, the two capture largely independent features of protein-coding genes, with different sensitivity/specificity trade-offs, such that their combinations lead to even greater discriminatory power. In addition, we study how discovery power scales with the number and phylogenetic distance of the genomes compared. We find that species at a broad range of distances are comparably effective informants for pairwise comparative gene identification, but that these are surpassed by multi-species comparisons at similar evolutionary divergence. In particular, while pairwise discovery power plateaued at larger distances and never outperformed the most advanced single-species metrics, multi-species comparisons continued to benefit even from the most distant species with no apparent saturation. Last, we find that genes in functional categories typically considered fast-evolving can nonetheless be recovered at very high rates using comparative methods. Our results have implications for comparative genomics analyses in any species, including the human. PMID:18421375

Diffusion-weighted imaging of the liver at 3 T using section-selection gradient reversal: emphasis on chemical shift artefacts and lesion conspicuity.

PubMed

Lee, J S; Kim, Y K; Jeong, W K; Choi, D; Lee, W J

2015-04-01

To assess the value of section-selection gradient reversal (SSGR) in liver diffusion-weighted imaging (DWI) by comparing it to conventional DWI with an emphasis on chemical shift artefacts and lesion conspicuity. Forty-eight patients (29 men and 19 women; age range 33-80 years) with 48 liver lesions underwent two DWI examinations using spectral presaturation with inversion recovery fat suppression with and without SSGR at 3 T. Two reviewers evaluated each DWI (b = 100 and b = 800 image) with respect to chemical shift artefacts and liver lesion conspicuity using five-point scales and performed pairwise comparisons between the two DWIs. The signal-to-noise ratio (SNR) of the liver and the lesion and the lesion-liver contrast-to-noise ratio (CNR) were also calculated. SSGR-DWI was significantly better than conventional DWI with respect to chemical shift artefacts and lesion conspicuity in both separate reviews and pairwise comparisons (p < 0.05). There were significant differences in the SNR of the liver (b = 100 and b = 800 images) and lesion (b = 800) between SSGR-DWI and conventional DWI (p < 0.05). Applying the SSGR method to DWI using SPIR fat suppression at 3 T could significantly reduce chemical shift artefacts without incurring additional acquisition time or SNR penalties, which leads to increased conspicuity of focal liver lesions. Copyright © 2014 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Dimensions of landscape preferences from pairwise comparisons

Treesearch

F. González Bernaldez; F. Parra

1979-01-01

Analysis of landscape preferences allows the detection of major dimensions as:(1) the opposition between "natural and humanized", (comprising features like vegetation cover, cultivation, pattern of landscape elements, artifacts, excavations, etc.); (2) polarity "precision/ambiguity" (involving opposition between: predominance of straight, vertical...

The effects of spatially displaced visual feedback on remote manipulator performance

NASA Technical Reports Server (NTRS)

Smith, Randy L.; Stuart, Mark A.

1989-01-01

The effects of spatially displaced visual feedback on the operation of a camera viewed remote manipulation task are analyzed. A remote manipulation task is performed by operators exposed to the following different viewing conditions: direct view of the work site; normal camera view; reversed camera view; inverted/reversed camera view; and inverted camera view. The task completion performance times are statistically analyzed with a repeated measures analysis of variance, and a Newman-Keuls pairwise comparison test is administered to the data. The reversed camera view is ranked third out of four camera viewing conditions, while the normal viewing condition is found significantly slower than the direct viewing condition. It is shown that generalization to remote manipulation applications based upon the results of direct manipulation studies are quite useful, but they should be made cautiously.

Evaluating the Quality of Evidence from a Network Meta-Analysis

PubMed Central

Salanti, Georgia; Del Giovane, Cinzia; Chaimani, Anna; Caldwell, Deborah M.; Higgins, Julian P. T.

2014-01-01

Systematic reviews that collate data about the relative effects of multiple interventions via network meta-analysis are highly informative for decision-making purposes. A network meta-analysis provides two types of findings for a specific outcome: the relative treatment effect for all pairwise comparisons, and a ranking of the treatments. It is important to consider the confidence with which these two types of results can enable clinicians, policy makers and patients to make informed decisions. We propose an approach to determining confidence in the output of a network meta-analysis. Our proposed approach is based on methodology developed by the Grading of Recommendations Assessment, Development and Evaluation (GRADE) Working Group for pairwise meta-analyses. The suggested framework for evaluating a network meta-analysis acknowledges (i) the key role of indirect comparisons (ii) the contributions of each piece of direct evidence to the network meta-analysis estimates of effect size; (iii) the importance of the transitivity assumption to the validity of network meta-analysis; and (iv) the possibility of disagreement between direct evidence and indirect evidence. We apply our proposed strategy to a systematic review comparing topical antibiotics without steroids for chronically discharging ears with underlying eardrum perforations. The proposed framework can be used to determine confidence in the results from a network meta-analysis. Judgements about evidence from a network meta-analysis can be different from those made about evidence from pairwise meta-analyses. PMID:24992266

Molecular markers for establishing distinctness in vegetatively propagated crops: a case study in grapevine.

PubMed

Ibáñez, Javier; Vélez, M Dolores; de Andrés, M Teresa; Borrego, Joaquín

2009-11-01

Distinctness, uniformity and stability (DUS) testing of varieties is usually required to apply for Plant Breeders' Rights. This exam is currently carried out using morphological traits, where the establishment of distinctness through a minimum distance is the key issue. In this study, the possibility of using microsatellite markers for establishing the minimum distance in a vegetatively propagated crop (grapevine) has been evaluated. A collection of 991 accessions have been studied with nine microsatellite markers and pair-wise compared, and the highest intra-variety distance and the lowest inter-variety distance determined. The collection included 489 different genotypes, and synonyms and sports. Average values for number of alleles per locus (19), Polymorphic Information Content (0.764) and heterozygosities observed (0.773) and expected (0.785) indicated the high level of polymorphism existing in grapevine. The maximum intra-variety variability found was one allele between two accessions of the same variety, of a total of 3,171 pair-wise comparisons. The minimum inter-variety variability found was two alleles between two pairs of varieties, of a total of 119,316 pair-wise comparisons. In base to these results, the minimum distance required to set distinctness in grapevine with the nine microsatellite markers used could be established in two alleles. General rules for the use of the system as a support for establishing distinctness in vegetatively propagated crops are discussed.

Hybrid pairwise likelihood analysis of animal behavior experiments.

PubMed

Cattelan, Manuela; Varin, Cristiano

2013-12-01

The study of the determinants of fights between animals is an important issue in understanding animal behavior. For this purpose, tournament experiments among a set of animals are often used by zoologists. The results of these tournament experiments are naturally analyzed by paired comparison models. Proper statistical analysis of these models is complicated by the presence of dependence between the outcomes of fights because the same animal is involved in different contests. This paper discusses two different model specifications to account for between-fights dependence. Models are fitted through the hybrid pairwise likelihood method that iterates between optimal estimating equations for the regression parameters and pairwise likelihood inference for the association parameters. This approach requires the specification of means and covariances only. For this reason, the method can be applied also when the computation of the joint distribution is difficult or inconvenient. The proposed methodology is investigated by simulation studies and applied to real data about adult male Cape Dwarf Chameleons. © 2013, The International Biometric Society.

Scale dependence in species turnover reflects variance in species occupancy.

PubMed

McGlinn, Daniel J; Hurlbert, Allen H

2012-02-01

Patterns of species turnover may reflect the processes driving community dynamics across scales. While the majority of studies on species turnover have examined pairwise comparison metrics (e.g., the average Jaccard dissimilarity), it has been proposed that the species-area relationship (SAR) also offers insight into patterns of species turnover because these two patterns may be analytically linked. However, these previous links only apply in a special case where turnover is scale invariant, and we demonstrate across three different plant communities that over 90% of the pairwise turnover values are larger than expected based on scale-invariant predictions from the SAR. Furthermore, the degree of scale dependence in turnover was negatively related to the degree of variance in the occupancy frequency distribution (OFD). These findings suggest that species turnover diverges from scale invariance, and as such pairwise turnover and the slope of the SAR are not redundant. Furthermore, models developed to explain the OFD should be linked with those developed to explain species turnover to achieve a more unified understanding of community structure.

Web-Beagle: a web server for the alignment of RNA secondary structures.

PubMed

Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

2015-07-01

Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Document Level Assessment of Document Retrieval Systems in a Pairwise System Evaluation

ERIC Educational Resources Information Center

Rajagopal, Prabha; Ravana, Sri Devi

2017-01-01

Introduction: The use of averaged topic-level scores can result in the loss of valuable data and can cause misinterpretation of the effectiveness of system performance. This study aims to use the scores of each document to evaluate document retrieval systems in a pairwise system evaluation. Method: The chosen evaluation metrics are document-level…

Screening synteny blocks in pairwise genome comparisons through integer programming.

PubMed

Tang, Haibao; Lyons, Eric; Pedersen, Brent; Schnable, James C; Paterson, Andrew H; Freeling, Michael

2011-04-18

It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple "subgenomes" derived from genome duplications, we need to relax the traditional requirements of "one-to-one" syntenic matchings of genomic regions in order to reflect "one-to-many" or more generally "many-to-many" matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this "quota-based" screening of synteny blocks in order to appropriately fill a quota of syntenic relationships within one genome or between two genomes having WGD events. We have formulated the synteny block screening as an optimization problem known as "Binary Integer Programming" (BIP), which is solved using existing linear programming solvers. The computer program QUOTA-ALIGN performs this task by creating a clear objective function that maximizes the compatible set of synteny blocks under given constraints on overlaps and depths (corresponding to the duplication history in respective genomes). Such a procedure is useful for any pairwise synteny alignments, but is most useful in lineages affected by multiple WGDs, like plants or fish lineages. For example, there should be a 1:2 ploidy relationship between genome A and B if genome B had an independent WGD subsequent to the divergence of the two genomes. We show through simulations and real examples using plant genomes in the rosid superorder that the quota-based screening can eliminate ambiguous synteny blocks and focus on specific genomic evolutionary events, like the divergence of lineages (in cross-species comparisons) and the most recent WGD (in self comparisons). The QUOTA-ALIGN algorithm screens a set of synteny blocks to retain only those compatible with a user specified ploidy relationship between two genomes. These blocks, in turn, may be used for additional downstream analyses such as identifying true orthologous regions in interspecific comparisons. There are two major contributions of QUOTA-ALIGN: 1) reducing the block screening task to a BIP problem, which is novel; 2) providing an efficient software pipeline starting from all-against-all BLAST to the screened synteny blocks with dot plot visualizations. Python codes and full documentations are publicly available http://github.com/tanghaibao/quota-alignment. QUOTA-ALIGN program is also integrated as a major component in SynMap http://genomevolution.com/CoGe/SynMap.pl, offering easier access to thousands of genomes for non-programmers. © 2011 Tang et al; licensee BioMed Central Ltd.

Relationship between Omnibus and Post-hoc Tests: An Investigation of performance of the F test in ANOVA.

PubMed

Chen, Tian; Xu, Manfei; Tu, Justin; Wang, Hongyue; Niu, Xiaohui

2018-02-25

Comparison of groups is a common statistical test in many biomedical and psychosocial research studies. When there are more than two groups, one first performs an omnibus test for an overall difference across the groups. If this null is rejected, one then proceeds to the next step of post-hoc pairwise group comparisons to determine sources of difference. Otherwise, one stops and declares no group difference. A common belief is that if the omnibus test is significant, there must exist at least two groups that are significantly different and vice versa. Thus, when the omnibus test is significant, but no post-hoc between-group comparison shows significant difference, one is bewildered at what is going on and wondering how to interpret the results. At the end of the spectrum, when the omnibus test is not significant, one wonders if all post-hoc tests will be non-significant as well so that stopping after a nonsignificant omnibus test will not lead to any missed opportunity of finding group difference. In this report, we investigate this perplexing phenomenon and discuss how to interpret such results.

Sensory enhancing insoles improve athletic performance during a hexagonal agility task.

PubMed

Miranda, Daniel L; Hsu, Wen-Hao; Gravelle, Denise C; Petersen, Kelsey; Ryzman, Rachael; Niemi, James; Lesniewski-Laas, Nicholas

2016-05-03

Athletes incorporate afferent signals from the mechanoreceptors of their plantar feet to provide information about posture, stability, and joint position. Sub-threshold stochastic resonance (SR) sensory enhancing insoles have been shown to improve balance and proprioception in young and elderly participant populations. Balance and proprioception are correlated with improved athletic performance, such as agility. Agility is defined as the ability to quickly change direction. An athlete's agility is commonly evaluated during athletic performance testing to assess their ability to participate in a competitive sporting event. Therefore, the purpose of this study was to examine the effects of SR insoles during a hexagonal agility task routinely used by coaches and sports scientists. Twenty recreational athletes were recruited to participate in this study. Each athlete was asked to perform a set of hexagonal agility trials while SR stimulation was either on or off. Vicon motion capture was used to measure feet position during six successful trials for each stimulation condition. Stimulation condition was randomized in a pairwise fashion. The study outcome measures were the task completion time and the positional accuracy of footfalls. Pairwise comparisons revealed a 0.12s decrease in task completion time (p=0.02) with no change in hopping accuracy (p=0.99) when SR stimulation was on. This is the first study to show athletic performance benefits while wearing proprioception and balance improving equipment on healthy participants. With further development, a self-contained sensory enhancing insole device could be used by recreational and professional athletes to improve movements that require rapid changes in direction. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures

PubMed Central

Manolakos, Elias S.

2015-01-01

Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub. PMID:26605332

Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures.

PubMed

Sharma, Anuj; Manolakos, Elias S

2015-01-01

Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub.

A Comparative Study of Pairwise Learning Methods Based on Kernel Ridge Regression.

PubMed

Stock, Michiel; Pahikkala, Tapio; Airola, Antti; De Baets, Bernard; Waegeman, Willem

2018-06-12

Many machine learning problems can be formulated as predicting labels for a pair of objects. Problems of that kind are often referred to as pairwise learning, dyadic prediction, or network inference problems. During the past decade, kernel methods have played a dominant role in pairwise learning. They still obtain a state-of-the-art predictive performance, but a theoretical analysis of their behavior has been underexplored in the machine learning literature. In this work we review and unify kernel-based algorithms that are commonly used in different pairwise learning settings, ranging from matrix filtering to zero-shot learning. To this end, we focus on closed-form efficient instantiations of Kronecker kernel ridge regression. We show that independent task kernel ridge regression, two-step kernel ridge regression, and a linear matrix filter arise naturally as a special case of Kronecker kernel ridge regression, implying that all these methods implicitly minimize a squared loss. In addition, we analyze universality, consistency, and spectral filtering properties. Our theoretical results provide valuable insights into assessing the advantages and limitations of existing pairwise learning methods.

Prioritization of highway maintenance functions using multi-attribute decision making with fuzzy pairwise comparison.

DOT National Transportation Integrated Search

2011-09-01

"As is the case for most of the Departments of Transportation in the U.S., the Texas Department of : Transportation has been experiencing fluctuations of budget for maintaining and preserving its highway : infrastructure over the recent years. If the...

Automatic Camera Calibration Using Multiple Sets of Pairwise Correspondences.

PubMed

Vasconcelos, Francisco; Barreto, Joao P; Boyer, Edmond

2018-04-01

We propose a new method to add an uncalibrated node into a network of calibrated cameras using only pairwise point correspondences. While previous methods perform this task using triple correspondences, these are often difficult to establish when there is limited overlap between different views. In such challenging cases we must rely on pairwise correspondences and our solution becomes more advantageous. Our method includes an 11-point minimal solution for the intrinsic and extrinsic calibration of a camera from pairwise correspondences with other two calibrated cameras, and a new inlier selection framework that extends the traditional RANSAC family of algorithms to sampling across multiple datasets. Our method is validated on different application scenarios where a lack of triple correspondences might occur: addition of a new node to a camera network; calibration and motion estimation of a moving camera inside a camera network; and addition of views with limited overlap to a Structure-from-Motion model.

Using Analytic Hierarchy Process in Textbook Evaluation

ERIC Educational Resources Information Center

Kato, Shigeo

2014-01-01

This study demonstrates the application of the analytic hierarchy process (AHP) in English language teaching materials evaluation, focusing in particular on its potential for systematically integrating different components of evaluation criteria in a variety of teaching contexts. AHP is a measurement procedure wherein pairwise comparisons are made…

A Comparison of Online, Video Synchronous, and Traditional Learning Modes for an Introductory Undergraduate Physics Course

NASA Astrophysics Data System (ADS)

Faulconer, E. K.; Griffith, J.; Wood, B.; Acharyya, S.; Roberts, D.

2018-05-01

While the equivalence between online and traditional classrooms has been well-researched, very little of this includes college-level introductory Physics. Only one study explored Physics at the whole-class level rather than specific course components such as a single lab or a homework platform. In this work, we compared the failure rate, grade distribution, and withdrawal rates in an introductory undergraduate Physics course across several learning modes including traditional face-to-face instruction, synchronous video instruction, and online classes. Statistically significant differences were found for student failure rates, grade distribution, and withdrawal rates but yielded small effect sizes. Post-hoc pair-wise test was run to determine differences between learning modes. Online students had a significantly lower failure rate than students who took the class via synchronous video classroom. While statistically significant differences were found for grade distributions, the pair-wise comparison yielded no statistically significance differences between learning modes when using the more conservative Bonferroni correction in post-hoc testing. Finally, in this study, student withdrawal rates were lowest for students who took the class in person (in-person classroom and synchronous video classroom) than online. Students that persist in an online introductory Physics class are more likely to achieve an A than in other modes. However, the withdrawal rate is higher from online Physics courses. Further research is warranted to better understand the reasons for higher withdrawal rates in online courses. Finding the root cause to help eliminate differences in student performance across learning modes should remain a high priority for education researchers and the education community as a whole.

Effects of caffeic acid phenethyl ester on palatal mucosal defects and tooth extraction sockets

PubMed Central

Günay, Ahmet; Arpağ, Osman Fatih; Atilgan, Serhat; Yaman, Ferhan; Atalay, Yusuf; Acikan, İzzet

2014-01-01

Aim The purpose of this study was to evaluate the effects of caffeic acid phenethyl ester (CAPE) on palatal mucosal defects and tooth extraction sockets in an experimental model. Materials and methods Forty-two male Sprague-Dawley rats with a mean age of 7 weeks and weighing 280–490 g were used in this study. The rats were randomly divided into two groups: group A (the control group, n=21) and group B (the experimental group, n=21). Under anesthesia with ketamine (8 mg/100 g, intraperitoneally), palatal mucosal defects were created and tooth extraction was performed in the rats in groups A and B. Group A received no treatment, whereas group B received CAPE. CAPE was injected daily (10 μmol/kg, intraperitoneally). The rats were killed on days 7, 14, and 30 after the procedures. Palatal mucosa healing and changes in bone tissue and fibrous tissue were evaluated histopathologically. Result Pairwise comparisons showed no statistically significant difference between days 7 and 14 in either group (P>0.05). At day 30, bone healing was significantly better in group B (CAPE) than in group A (control) (P<0.05). Fibrinogen levels at day 30 were significantly higher in group A (control) than in group B (CAPE) (P<0.05). Pairwise comparisons showed no statistically significant difference in palatal mucosa healing levels between days 7 and 14 in both groups (P>0.05). Conclusion In conclusion, the findings of this study suggest that CAPE can significantly improve tooth socket healing. PMID:25364232

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs.

PubMed

Blazewicz, Jacek; Frohmberg, Wojciech; Kierzynka, Michal; Pesch, Erwin; Wojciechowski, Pawel

2011-05-20

Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest future. To overcome this challenge several GPU (Graphics Processing Unit) computing approaches have been proposed lately. These solutions show a great potential of a GPU platform but in most cases address the problem of sequence database scanning and computing only the alignment score whereas the alignment itself is omitted. Thus, the need arose to implement the global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. In this paper we present the solution that performs the alignment of every given sequence pair, which is a required step for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Performed tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions. Moreover, multiple GPUs support with load balancing makes the application very scalable. The article shows that the backtracking procedure of the sequence alignment algorithms may be designed to fit in with the GPU architecture. Therefore, our algorithm, apart from scores, is able to compute pairwise alignments. This opens a wide range of new possibilities, allowing other methods from the area of molecular biology to take advantage of the new computational architecture. Performed tests show that the efficiency of the implementation is excellent. Moreover, the speed of our GPU-based algorithms can be almost linearly increased when using more than one graphics card.

Multilinguals' Perceptions of Feeling Different When Switching Languages

ERIC Educational Resources Information Center

Dewaele, Jean-Marc; Nakano, Seiji

2013-01-01

Research into multilingualism and personality has shown that a majority of multilinguals report feeling different when they switch from one language to another. The present study looks at perceived shifts on five scales of feelings (feeling logical, serious, emotional, fake and different) in pair-wise comparisons between languages following the…

An Extension of Dominance Analysis to Canonical Correlation Analysis

ERIC Educational Resources Information Center

Huo, Yan; Budescu, David V.

2009-01-01

Dominance analysis (Budescu, 1993) offers a general framework for determination of relative importance of predictors in univariate and multivariate multiple regression models. This approach relies on pairwise comparisons of the contribution of predictors in all relevant subset models. In this article we extend dominance analysis to canonical…

Near-road measurements for nitrogen dioxide and its association with traffic exposure zones

EPA Science Inventory

Near-road measurements for nitrogen dioxide (NO₂) using passive air samplers were collected weekly in traffic exposure zones (TEZs) in the Research Triangle area of North Carolina (USA) during Fall 2014. Land use regression (LUR) analysis and pairwise comparisons of T...

Assessment of Geographic and Host-Associated Population Variations of the Carob Moth, Ectomyelois ceratoniae, on Pomegranate, Fig, Pistachio and Walnut, Using AFLP Markers

PubMed Central

Mozaffarian, Fariba; Mardi, Mohsen; Sarafrazi, Alimorad; Nouri Ganbalani, Gadir

2008-01-01

The carob moth, Ectomyelois ceratoniae (Zeller 1839) (Lepidoptera: Pyralidae) is the most important pest of pomegranate, Punica granatum L. (Myrtales: Ponicaceae), in Iran. In this study, 6 amplified fragment length polymorphism primer combinations were used to survey the genetic structure of the geographic and putative host-associated populations of this pest in Iran. An AMOVA was performed on test populations. Pairwise differences, Mantel test, multidimensional analysis, cluster analysis and migration rate were calculated for 5 geographic populations of E. ceratoniae sharing the same host, pomegranate. In another part of the study, 3 comparisons were performed on pairwise populations that were collected on different hosts (pomegranate, fig, pistachio and walnut) in same geographic regions. The results showed high within population variation (85.51% of total variation), however geographic populations differed significantly. The Mantel test did not show correlations between genetic and geographic distances. The probable factors that affect genetic distances are discussed. Multidimensional scaling analysis, migration rate and cluster analysis on geographic populations showed that the Arsanjan population was the most different from the others while the Saveh population was more similar to the Sabzevar population. The comparisons didn't show any host fidelity in test populations. It seems that the ability of E. ceratoniae to broaden its host range with no fidelity to hosts can decrease the efficiency of common control methods that are used on pomegranate. The results of this study suggest that in spite of the effects of geographic barriers, high within-population genetic variation, migration rate and gene flow can provide the opportunity for emerging new phenotypes or behaviors in pest populations, such as broadening host range, changing egg lying places, or changing over-wintering sites to adapt to difficult conditions such as those caused by intensive control methods. PMID:20345296

A novel combined approach of diffuse reflectance UV-Vis-NIR spectroscopy and multivariate analysis for non-destructive examination of blue ballpoint pen inks in forensic application

NASA Astrophysics Data System (ADS)

Kumar, Raj; Sharma, Vishal

2017-03-01

The present research is focused on the analysis of writing inks using destructive UV-Vis spectroscopy (dissolution of ink by the solvent) and non-destructive diffuse reflectance UV-Vis-NIR spectroscopy along with Chemometrics. Fifty seven samples of blue ballpoint pen inks were analyzed under optimum conditions to determine the differences in spectral features of inks among same and different manufacturers. Normalization was performed on the spectroscopic data before chemometric analysis. Principal Component Analysis (PCA) and K-mean cluster analysis were used on the data to ascertain whether the blue ballpoint pen inks could be differentiated by their UV-Vis/UV-Vis NIR spectra. The discriminating power is calculated by qualitative analysis by the visual comparison of the spectra (absorbance peaks), produced by the destructive and non-destructive methods. In the latter two methods, the pairwise comparison is made by incorporating the clustering method. It is found that chemometric method provides better discriminating power (98.72% and 99.46%, in destructive and non-destructive, respectively) in comparison to the qualitative analysis (69.67%).

webPIPSA: a web server for the comparison of protein interaction properties

PubMed Central

Richter, Stefan; Wenzel, Anne; Stein, Matthias; Gabdoulline, Razif R.; Wade, Rebecca C.

2008-01-01

Protein molecular interaction fields are key determinants of protein functionality. PIPSA (Protein Interaction Property Similarity Analysis) is a procedure to compare and analyze protein molecular interaction fields, such as the electrostatic potential. PIPSA may assist in protein functional assignment, classification of proteins, the comparison of binding properties and the estimation of enzyme kinetic parameters. webPIPSA is a web server that enables the use of PIPSA to compare and analyze protein electrostatic potentials. While PIPSA can be run with downloadable software (see http://projects.eml.org/mcm/software/pipsa), webPIPSA extends and simplifies a PIPSA run. This allows non-expert users to perform PIPSA for their protein datasets. With input protein coordinates, the superposition of protein structures, as well as the computation and analysis of electrostatic potentials, is automated. The results are provided as electrostatic similarity matrices from an all-pairwise comparison of the proteins which can be subjected to clustering and visualized as epograms (tree-like diagrams showing electrostatic potential differences) or heat maps. webPIPSA is freely available at: http://pipsa.eml.org. PMID:18420653

Rapid encoding of relationships between spatially remote motion signals.

PubMed

Maruya, Kazushi; Holcombe, Alex O; Nishida, Shin'ya

2013-02-06

For visual processing, the temporal correlation of remote local motion signals is a strong cue to detect meaningful large-scale structures in the retinal image, because related points are likely to move together regardless of their spatial separation. While the processing of multi-element motion patterns involved in biological motion and optic flow has been studied intensively, the encoding of simpler pairwise relationships between remote motion signals remains poorly understood. We investigated this process by measuring the temporal rate limit for perceiving the relationship of two motion directions presented at the same time at different spatial locations. Compared to luminance or orientation, motion comparison was more rapid. Performance remained very high even when interstimulus separation was increased up to 100°. Motion comparison also remained rapid regardless of whether the two motion directions were similar to or different from each other. The exception was a dramatic slowing when the elements formed an orthogonal "T," in which two motions do not perceptually group together. Motion presented at task-irrelevant positions did not reduce performance, suggesting that the rapid motion comparison could not be ascribed to global optic flow processing. Our findings reveal the existence and unique nature of specialized processing that encodes long-range relationships between motion signals for quick appreciation of global dynamic scene structure.

SU-F-T-312: Identifying Distinct Radiation Therapy Plan Classes Through Multi-Dimensional Analysis of Plan Complexity Metrics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Desai, V; Labby, Z; Culberson, W

Purpose: To determine whether body site-specific treatment plans form unique “plan class” clusters in a multi-dimensional analysis of plan complexity metrics such that a single beam quality correction determined for a representative plan could be universally applied within the “plan class”, thereby increasing the dosimetric accuracy of a detector’s response within a subset of similarly modulated nonstandard deliveries. Methods: We collected 95 clinical volumetric modulated arc therapy (VMAT) plans from four body sites (brain, lung, prostate, and spine). The lung data was further subdivided into SBRT and non-SBRT data for a total of five plan classes. For each control pointmore » in each plan, a variety of aperture-based complexity metrics were calculated and stored as unique characteristics of each patient plan. A multiple comparison of means analysis was performed such that every plan class was compared to every other plan class for every complexity metric in order to determine which groups could be considered different from one another. Statistical significance was assessed after correcting for multiple hypothesis testing. Results: Six out of a possible 10 pairwise plan class comparisons were uniquely distinguished based on at least nine out of 14 of the proposed metrics (Brain/Lung, Brain/SBRT lung, Lung/Prostate, Lung/SBRT Lung, Lung/Spine, Prostate/SBRT Lung). Eight out of 14 of the complexity metrics could distinguish at least six out of the possible 10 pairwise plan class comparisons. Conclusion: Aperture-based complexity metrics could prove to be useful tools to quantitatively describe a distinct class of treatment plans. Certain plan-averaged complexity metrics could be considered unique characteristics of a particular plan. A new approach to generating plan-class specific reference (pcsr) fields could be established through a targeted preservation of select complexity metrics or a clustering algorithm that identifies plans exhibiting similar modulation characteristics. Measurements and simulations will better elucidate potential plan-class specific dosimetry correction factors.« less

Parent-Child Similarity in Environmental Attitudes: A Pairwise Comparison

ERIC Educational Resources Information Center

Leppanen, Jaana M.; Haahla, Anu E.; Lensu, Anssi M.; Kuitunen, Markku T.

2012-01-01

Are adolescents' environmental attitudes similar to their parents' attitudes? The main objective of this study is to examine what quantitative associations, if any, exist in parent-child environmental attitudes within the family. The survey data was collected assessing attitudes toward the environment and nature from 15-year-old students (n = 237)…

Comparison of English Language Rhythm and Kalhori Kurdish Language Rhythm

ERIC Educational Resources Information Center

Taghva, Nafiseh; Zadeh, Vahideh Abolhasani

2016-01-01

Interval-based method is a method of studying the rhythmic quantitative features of languages. This method use Pairwise Variability Index (PVI) to consider the variability of vocalic duration and inter-vocalic duration of sentences which leads to classification of languages rhythm into stress-timed languages and syllable-timed ones. This study…

Comparison of Human and Latent Semantic Analysis (LSA) Judgements of Pairwise Document Similarities for a News Corpus

DTIC Science & Technology

2004-09-01

University. Miro Kraetzl critically assessed the manuscript before it was sent for review. References Allan, J., Callan, J., Croft, W.B., Ballesteros, L...Conference (TREC 6). NIST Special Publication 500-240. Baayen,R.H. (2001). Word Frequency Distributions. Kluwer Academic Publishers, P.O. Box 322 , 3300

A Study of the Use of Pairwise Comparison in the Context of Social Online Moderation

ERIC Educational Resources Information Center

Tarricone, Pina; Newhouse, C. Paul

2016-01-01

Traditional moderation of student assessments is often carried out with groups of teachers working face-to-face in a specified location making judgements concerning the quality of representations of achievement. This traditional model has relied little on modern information communications technologies and has been logistically challenging. We…

CMap 1.01: a comparative mapping application for the internet

USDA-ARS?s Scientific Manuscript database

CMap is a web-based tool for displaying and comparing maps of any type and from any species. A user can compare an unlimited number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession. CMap is freely available, can ...

Defining the Molecular Actions of Dietary Fatty Acids in Breast Cancer: Selective Modulation of Peroxisome Proliferator-Activated Receptor Gamma. Addendum

DTIC Science & Technology

2008-05-01

0.05 significance threshold. Fol- owing ANOVA, Fisher’s least significant difference, LSD , air-wise comparison was implemented post-hoc. Briefly, the SD...average absolute difference etween any two groups was greater than the LSD critical alue, then the pair-wise comparison for those two groups ere...Xu, Y., Hin- shaw , J.C., Zimmerman, G.A., Hama, K., Aoki, J., Arai, H., Prestwich, G.D., 2003. Identification of an intracellular receptor for

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

PubMed

Tong, Jing; Pei, Jimin; Grishin, Nick V

2015-09-03

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

Phylogenetic rooting using minimal ancestor deviation.

PubMed

Tria, Fernando Domingues Kümmel; Landan, Giddy; Dagan, Tal

2017-06-19

Ancestor-descendent relations play a cardinal role in evolutionary theory. Those relations are determined by rooting phylogenetic trees. Existing rooting methods are hampered by evolutionary rate heterogeneity or the unavailability of auxiliary phylogenetic information. Here we present a rooting approach, the minimal ancestor deviation (MAD) method, which accommodates heterotachy by using all pairwise topological and metric information in unrooted trees. We demonstrate the performance of the method, in comparison to existing rooting methods, by the analysis of phylogenies from eukaryotes and prokaryotes. MAD correctly recovers the known root of eukaryotes and uncovers evidence for the origin of cyanobacteria in the ocean. MAD is more robust and consistent than existing methods, provides measures of the root inference quality and is applicable to any tree with branch lengths.

Feature Based Retention Time Alignment for Improved HDX MS Analysis

NASA Astrophysics Data System (ADS)

Venable, John D.; Scuba, William; Brock, Ansgar

2013-04-01

An algorithm for retention time alignment of mass shifted hydrogen-deuterium exchange (HDX) data based on an iterative distance minimization procedure is described. The algorithm performs pairwise comparisons in an iterative fashion between a list of features from a reference file and a file to be time aligned to calculate a retention time mapping function. Features are characterized by their charge, retention time and mass of the monoisotopic peak. The algorithm is able to align datasets with mass shifted features, which is a prerequisite for aligning hydrogen-deuterium exchange mass spectrometry datasets. Confidence assignments from the fully automated processing of a commercial HDX software package are shown to benefit significantly from retention time alignment prior to extraction of deuterium incorporation values.

Does technique matter; a pilot study exploring weighting techniques for a multi-criteria decision support framework.

PubMed

van Til, Janine; Groothuis-Oudshoorn, Catharina; Lieferink, Marijke; Dolan, James; Goetghebeur, Mireille

2014-01-01

There is an increased interest in the use of multi-criteria decision analysis (MCDA) to support regulatory and reimbursement decision making. The EVIDEM framework was developed to provide pragmatic multi-criteria decision support in health care, to estimate the value of healthcare interventions, and to aid in priority-setting. The objectives of this study were to test 1) the influence of different weighting techniques on the overall outcome of an MCDA exercise, 2) the discriminative power in weighting different criteria of such techniques, and 3) whether different techniques result in similar weights in weighting the criteria set proposed by the EVIDEM framework. A sample of 60 Dutch and Canadian students participated in the study. Each student used an online survey to provide weights for 14 criteria with two different techniques: a five-point rating scale and one of the following techniques selected randomly: ranking, point allocation, pairwise comparison and best worst scaling. The results of this study indicate that there is no effect of differences in weights on value estimates at the group level. On an individual level, considerable differences in criteria weights and rank order occur as a result of the weight elicitation method used, and the ability of different techniques to discriminate in criteria importance. Of the five techniques tested, the pair-wise comparison of criteria has the highest ability to discriminate in weights when fourteen criteria are compared. When weights are intended to support group decisions, the choice of elicitation technique has negligible impact on criteria weights and the overall value of an innovation. However, when weights are used to support individual decisions, the choice of elicitation technique influences outcome and studies that use dissimilar techniques cannot be easily compared. Weight elicitation through pairwise comparison of criteria is preferred when taking into account its superior ability to discriminate between criteria and respondents' preferences.

Using structural equation modeling for network meta-analysis.

PubMed

Tu, Yu-Kang; Wu, Yun-Chun

2017-07-14

Network meta-analysis overcomes the limitations of traditional pair-wise meta-analysis by incorporating all available evidence into a general statistical framework for simultaneous comparisons of several treatments. Currently, network meta-analyses are undertaken either within the Bayesian hierarchical linear models or frequentist generalized linear mixed models. Structural equation modeling (SEM) is a statistical method originally developed for modeling causal relations among observed and latent variables. As random effect is explicitly modeled as a latent variable in SEM, it is very flexible for analysts to specify complex random effect structure and to make linear and nonlinear constraints on parameters. The aim of this article is to show how to undertake a network meta-analysis within the statistical framework of SEM. We used an example dataset to demonstrate the standard fixed and random effect network meta-analysis models can be easily implemented in SEM. It contains results of 26 studies that directly compared three treatment groups A, B and C for prevention of first bleeding in patients with liver cirrhosis. We also showed that a new approach to network meta-analysis based on the technique of unrestricted weighted least squares (UWLS) method can also be undertaken using SEM. For both the fixed and random effect network meta-analysis, SEM yielded similar coefficients and confidence intervals to those reported in the previous literature. The point estimates of two UWLS models were identical to those in the fixed effect model but the confidence intervals were greater. This is consistent with results from the traditional pairwise meta-analyses. Comparing to UWLS model with common variance adjusted factor, UWLS model with unique variance adjusted factor has greater confidence intervals when the heterogeneity was larger in the pairwise comparison. The UWLS model with unique variance adjusted factor reflects the difference in heterogeneity within each comparison. SEM provides a very flexible framework for univariate and multivariate meta-analysis, and its potential as a powerful tool for advanced meta-analysis is still to be explored.

Cosmology with the pairwise kinematic SZ effect: Calibration and validation using hydrodynamical simulations

NASA Astrophysics Data System (ADS)

Soergel, Bjoern; Saro, Alexandro; Giannantonio, Tommaso; Efstathiou, George; Dolag, Klaus

2018-05-01

We study the potential of the kinematic SZ effect as a probe for cosmology, focusing on the pairwise method. The main challenge is disentangling the cosmologically interesting mean pairwise velocity from the cluster optical depth and the associated uncertainties on the baryonic physics in clusters. Furthermore, the pairwise kSZ signal might be affected by internal cluster motions or correlations between velocity and optical depth. We investigate these effects using the Magneticum cosmological hydrodynamical simulations, one of the largest simulations of this kind performed to date. We produce tSZ and kSZ maps with an area of ≃ 1600 deg2, and the corresponding cluster catalogues with M500c ≳ 3 × 1013 h-1M⊙ and z ≲ 2. From these data sets we calibrate a scaling relation between the average Compton-y parameter and optical depth. We show that this relation can be used to recover an accurate estimate of the mean pairwise velocity from the kSZ effect, and that this effect can be used as an important probe of cosmology. We discuss the impact of theoretical and observational systematic effects, and find that further work on feedback models is required to interpret future high-precision measurements of the kSZ effect.

Risk of breast cancer with CXCR4-using HIV defined by V3 loop sequencing.

PubMed

Goedert, James J; Swenson, Luke C; Napolitano, Laura A; Haddad, Mojgan; Anastos, Kathryn; Minkoff, Howard; Young, Mary; Levine, Alexandra; Adeyemi, Oluwatoyin; Seaberg, Eric C; Aouizerat, Bradley; Rabkin, Charles S; Harrigan, P Richard; Hessol, Nancy A

2015-01-01

Evaluate the risk of female breast cancer associated with HIV-CXCR4 (X4) tropism as determined by various genotypic measures. A breast cancer case-control study, with pairwise comparisons of tropism determination methods, was conducted. From the Women's Interagency HIV Study repository, one stored plasma specimen was selected from 25 HIV-infected cases near the breast cancer diagnosis date and 75 HIV-infected control women matched for age and calendar date. HIV-gp120 V3 sequences were derived by Sanger population sequencing (PS) and 454-pyro deep sequencing (DS). Sequencing-based HIV-X4 tropism was defined using the geno2pheno algorithm, with both high-stringency DS [false-positive rate (3.5) and 2% X4 cutoff], and lower stringency DS (false-positive rate, 5.75 and 15% X4 cutoff). Concordance of tropism results by PS, DS, and previously performed phenotyping was assessed with kappa (κ) statistics. Case-control comparisons used exact P values and conditional logistic regression. In 74 women (19 cases, 55 controls) with complete results, prevalence of HIV-X4 by PS was 5% in cases vs 29% in controls (P = 0.06; odds ratio, 0.14; confidence interval: 0.003 to 1.03). Smaller case-control prevalence differences were found with high-stringency DS (21% vs 36%, P = 0.32), lower stringency DS (16% vs 35%, P = 0.18), and phenotyping (11% vs 31%, P = 0.10). HIV-X4 tropism concordance was best between PS and lower stringency DS (93%, κ = 0.83). Other pairwise concordances were 82%-92% (κ = 0.56-0.81). Concordance was similar among cases and controls. HIV-X4 defined by population sequencing (PS) had good agreement with lower stringency DS and was significantly associated with lower odds of breast cancer.

Root surface temperature variation during mechanical removal of root canal filling material. An in vitro study.

PubMed

García-Cuerva, Martín; Horvath, Lucía; Pinasco, Laura; Ciparelli, Verónica; Gualtieri, Ariel; Casadoumecq, Ana C; Rodríguez, Pablo; Gonzalez-Zanotto, Carlos

2017-04-01

The aim of this study was to analyze in vitro temperature changes on the outer surface of the dental root during mechanical filling removal procedures. Thirty recently extracted single-rooted lower premolars were cut transversally at 16 mm from the apex in order to standardize sample length. Endodontic treatment was performed on them. The filling material was subsequently removed using Gates Glidden (G1, G2, G3); Peeso (P1, P2, P3) and PostecPlus FRC (FRC) reamers while temperatures were measured on the outer surface using a digital device with thermocouple at 0, 2, 4, 6, 8, 10 and 15 seconds. Temperatures were compared using repeated measures ANOVA followed by pairwise comparison with Tukey's test. All reamers caused significant temperature variation between different times (p<0.05). Pairwise comparisons indicated that temperature increased with time for all reamers (p<0.05). Significant differences in temperature were found between different reamers after 0, 2, 4, 6, 8,10 and 15 seconds (p<0.05). Temperature at the root surface increased considerably. Values higher than 50°C were recorded, the greatest increase from baseline being 16°C. Accordingly, if the procedure were begun at 37°C (physiological temperature), the temperature in the surrounding tissues - cementum, periodontium and bone - would rise to 53°C. An increase in 10°C above body temperature at the root surface may cause lesions in surrounding tissues. While removing filling material, it is essential to cool, control action time and use instruments in perfect condition, all of which may contribute to reducing the heat generated and transmitted to the outer root surface. Sociedad Argentina de Pediatría.

Improving prediction of heterodimeric protein complexes using combination with pairwise kernel.

PubMed

Ruan, Peiying; Hayashida, Morihiro; Akutsu, Tatsuya; Vert, Jean-Philippe

2018-02-19

Since many proteins become functional only after they interact with their partner proteins and form protein complexes, it is essential to identify the sets of proteins that form complexes. Therefore, several computational methods have been proposed to predict complexes from the topology and structure of experimental protein-protein interaction (PPI) network. These methods work well to predict complexes involving at least three proteins, but generally fail at identifying complexes involving only two different proteins, called heterodimeric complexes or heterodimers. There is however an urgent need for efficient methods to predict heterodimers, since the majority of known protein complexes are precisely heterodimers. In this paper, we use three promising kernel functions, Min kernel and two pairwise kernels, which are Metric Learning Pairwise Kernel (MLPK) and Tensor Product Pairwise Kernel (TPPK). We also consider the normalization forms of Min kernel. Then, we combine Min kernel or its normalization form and one of the pairwise kernels by plugging. We applied kernels based on PPI, domain, phylogenetic profile, and subcellular localization properties to predicting heterodimers. Then, we evaluate our method by employing C-Support Vector Classification (C-SVC), carrying out 10-fold cross-validation, and calculating the average F-measures. The results suggest that the combination of normalized-Min-kernel and MLPK leads to the best F-measure and improved the performance of our previous work, which had been the best existing method so far. We propose new methods to predict heterodimers, using a machine learning-based approach. We train a support vector machine (SVM) to discriminate interacting vs non-interacting protein pairs, based on informations extracted from PPI, domain, phylogenetic profiles and subcellular localization. We evaluate in detail new kernel functions to encode these data, and report prediction performance that outperforms the state-of-the-art.

Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal

Highlights: •Transcriptome sequencing yielded 223 mill porcine RNA-seq reads, and 59,000 transcribed locations. •Establishment of unique transcription profiles for ten porcine tissues including four brain tissues. •Comparison of transcription profiles at gene, isoform, promoter and transcription start site level. •Highlights a high level of regulation of neuro-related genes at both gene, isoform, and TSS level. •Our results emphasize the pig as a valuable animal model with respect to human biological issues. -- Abstract: The transcriptome is the absolute set of transcripts in a tissue or cell at the time of sampling. In this study RNA-Seq is employed to enable themore » differential analysis of the transcriptome profile for ten porcine tissues in order to evaluate differences between the tissues at the gene and isoform expression level, together with an analysis of variation in transcription start sites, promoter usage, and splicing. Totally, 223 million RNA fragments were sequenced leading to the identification of 59,930 transcribed gene locations and 290,936 transcript variants using Cufflinks with similarity to approximately 13,899 annotated human genes. Pairwise analysis of tissues for differential expression at the gene level showed that the smallest differences were between tissues originating from the porcine brain. Interestingly, the relative level of differential expression at the isoform level did generally not vary between tissue contrasts. Furthermore, analysis of differential promoter usage between tissues, revealed a proportionally higher variation between cerebellum (CBE) versus frontal cortex and cerebellum versus hypothalamus (HYP) than in the remaining comparisons. In addition, the comparison of differential transcription start sites showed that the number of these sites is generally increased in comparisons including hypothalamus in contrast to other pairwise assessments. A comprehensive analysis of one of the tissue contrasts, i.e. cerebellum versus heart for differential variation at the gene, isoform, and transcription start site (TSS), and promoter level showed that several of the genes differed at all four levels. Interestingly, these genes were mainly annotated to the “electron transport chain” and neuronal differentiation, emphasizing that “tissue important” genes are regulated at several levels. Furthermore, our analysis shows that the “across tissue approach” has a promising potential when screening for possible explanations for variations, such as those observed at the gene expression levels.« less

InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk.

PubMed

Cheng, Liang; Jiang, Yue; Ju, Hong; Sun, Jie; Peng, Jiajie; Zhou, Meng; Hu, Yang

2018-01-19

Since the establishment of the first biomedical ontology Gene Ontology (GO), the number of biomedical ontology has increased dramatically. Nowadays over 300 ontologies have been built including extensively used Disease Ontology (DO) and Human Phenotype Ontology (HPO). Because of the advantage of identifying novel relationships between terms, calculating similarity between ontology terms is one of the major tasks in this research area. Though similarities between terms within each ontology have been studied with in silico methods, term similarities across different ontologies were not investigated as deeply. The latest method took advantage of gene functional interaction network (GFIN) to explore such inter-ontology similarities of terms. However, it only used gene interactions and failed to make full use of the connectivity among gene nodes of the network. In addition, all existent methods are particularly designed for GO and their performances on the extended ontology community remain unknown. We proposed a method InfAcrOnt to infer similarities between terms across ontologies utilizing the entire GFIN. InfAcrOnt builds a term-gene-gene network which comprised ontology annotations and GFIN, and acquires similarities between terms across ontologies through modeling the information flow within the network by random walk. In our benchmark experiments on sub-ontologies of GO, InfAcrOnt achieves a high average area under the receiver operating characteristic curve (AUC) (0.9322 and 0.9309) and low standard deviations (1.8746e-6 and 3.0977e-6) in both human and yeast benchmark datasets exhibiting superior performance. Meanwhile, comparisons of InfAcrOnt results and prior knowledge on pair-wise DO-HPO terms and pair-wise DO-GO terms show high correlations. The experiment results show that InfAcrOnt significantly improves the performance of inferring similarities between terms across ontologies in benchmark set.

PubMed Central

SENNAROĞLU, G.; YÜCEL, E.; BELGIN, E.; MANCINI, P.

2015-01-01

SUMMARY The aim of this study was to investigate the amount of binaural squelch effect (BSE) and head shadow effect (HSE) in children who use unilateral cochlear implants (CI) and contralateral hearing aids (HA). The study group consisted of 19 CI recipient children who consistently wore a contralateral HA. Speech sounds were used to evaluate speech perception performance in noise. Testing was performed in three listening conditions: (1) bimodal listening with noise source on HA side; (2) CI only with noise source contralaterally (HA off); (3) CI only with noise source on the CI side. Statistical analysis revealed a significant difference between the three listening conditions and post hoc tests indicated significant differences for all pairwise comparisons (p < 0.001). The average BSE and HSE were 11.8% and 17.1% respectively. The majority of bimodal CI users showed BSE and HSE with significant speech perception improvement in the presence of noise. PMID:26824917

Evaluation of the Three Gorges Dam project using multi-criteria analysis (MCA) based on a sustainable perspective

NASA Astrophysics Data System (ADS)

Han, Yue; Zheng, Wei; Guo, Junshan; Ma, Yihe; Ding, Junqi; Zhu, Lingkai; Che, Yongqiang; Zhang, Yanpeng

2018-02-01

Abstract . The Three Gorges dam of China is one of the largest and expensive hydropower projects of the world. The four main purposes of the project are flood control,energy production, improved navigation and fresh water supply. The dam project has been completed and running successfully with the potential benefits. However, this project is still a controversial issue among many environmentalists and socialists due to various impacts. This study focuses on the benefit and the impacts of the project, and also evaluates the performance of the project using multi-criteria analysis (MCA) approach from a sustainable perspective. Different sustainability criteria related with the dam project have been identified and used for the ranking and rating process. The final result of MCA comes with this scoring process and pairwise comparison, which evaluates the performance of the project considering different positive and negative aspects.

Protein Kinase Classification with 2866 Hidden Markov Models and One Support Vector Machine

NASA Technical Reports Server (NTRS)

Weber, Ryan; New, Michael H.; Fonda, Mark (Technical Monitor)

2002-01-01

The main application considered in this paper is predicting true kinases from randomly permuted kinases that share the same length and amino acid distributions as the true kinases. Numerous methods already exist for this classification task, such as HMMs, motif-matchers, and sequence comparison algorithms. We build on some of these efforts by creating a vector from the output of thousands of structurally based HMMs, created offline with Pfam-A seed alignments using SAM-T99, which then must be combined into an overall classification for the protein. Then we use a Support Vector Machine for classifying this large ensemble Pfam-Vector, with a polynomial and chisquared kernel. In particular, the chi-squared kernel SVM performs better than the HMMs and better than the BLAST pairwise comparisons, when predicting true from false kinases in some respects, but no one algorithm is best for all purposes or in all instances so we consider the particular strengths and weaknesses of each.

A Procedure for Testing the Difference between Effect Sizes.

ERIC Educational Resources Information Center

Lambert, Richard G.; Flowers, Claudia

A special case of the homogeneity of effect size test, as applied to pairwise comparisons of standardized mean differences, was evaluated. Procedures for comparing pairs of pretest to posttest effect sizes, as well as pairs of treatment versus control group effect sizes, were examined. Monte Carlo simulation was used to generate Type I error rates…

Amphibian Communities Under Diverse Forest Management In The Ouachita Mountains, Arkansas

Treesearch

Stanley F. Fox; Paul A. Shipman; Ronald E. Thill; Joseph P. Phelps; David M. Leslie

2004-01-01

Abstract - From May 1995 to March 1999, we censused amphibians in the Ouachita Mountains, Arkansas, on 60 plots on each of four forested watersheds five times per year, with new plots each year. We found negligible differences in species richness among watersheds, and community similarities were high, even though most pairwise comparisons were...

The Versatility of SpAM: A Fast, Efficient, Spatial Method of Data Collection for Multidimensional Scaling

ERIC Educational Resources Information Center

Hout, Michael C.; Goldinger, Stephen D.; Ferguson, Ryan W.

2013-01-01

Although traditional methods to collect similarity data (for multidimensional scaling [MDS]) are robust, they share a key shortcoming. Specifically, the possible pairwise comparisons in any set of objects grow rapidly as a function of set size. This leads to lengthy experimental protocols, or procedures that involve scaling stimulus subsets. We…

Performance metrics for the assessment of satellite data products: an ocean color case study

PubMed Central

Seegers, Bridget N.; Stumpf, Richard P.; Schaeffer, Blake A.; Loftin, Keith A.; Werdell, P. Jeremy

2018-01-01

Performance assessment of ocean color satellite data has generally relied on statistical metrics chosen for their common usage and the rationale for selecting certain metrics is infrequently explained. Commonly reported statistics based on mean squared errors, such as the coefficient of determination (r2), root mean square error, and regression slopes, are most appropriate for Gaussian distributions without outliers and, therefore, are often not ideal for ocean color algorithm performance assessment, which is often limited by sample availability. In contrast, metrics based on simple deviations, such as bias and mean absolute error, as well as pair-wise comparisons, often provide more robust and straightforward quantities for evaluating ocean color algorithms with non-Gaussian distributions and outliers. This study uses a SeaWiFS chlorophyll-a validation data set to demonstrate a framework for satellite data product assessment and recommends a multi-metric and user-dependent approach that can be applied within science, modeling, and resource management communities. PMID:29609296

A new method of content based medical image retrieval and its applications to CT imaging sign retrieval.

PubMed

Ma, Ling; Liu, Xiabi; Gao, Yan; Zhao, Yanfeng; Zhao, Xinming; Zhou, Chunwu

2017-02-01

This paper proposes a new method of content based medical image retrieval through considering fused, context-sensitive similarity. Firstly, we fuse the semantic and visual similarities between the query image and each image in the database as their pairwise similarities. Then, we construct a weighted graph whose nodes represent the images and edges measure their pairwise similarities. By using the shortest path algorithm over the weighted graph, we obtain a new similarity measure, context-sensitive similarity measure, between the query image and each database image to complete the retrieval process. Actually, we use the fused pairwise similarity to narrow down the semantic gap for obtaining a more accurate pairwise similarity measure, and spread it on the intrinsic data manifold to achieve the context-sensitive similarity for a better retrieval performance. The proposed method has been evaluated on the retrieval of the Common CT Imaging Signs of Lung Diseases (CISLs) and achieved not only better retrieval results but also the satisfactory computation efficiency. Copyright © 2017 Elsevier Inc. All rights reserved.

SVM-dependent pairwise HMM: an application to protein pairwise alignments.

PubMed

Orlando, Gabriele; Raimondi, Daniele; Khan, Taushif; Lenaerts, Tom; Vranken, Wim F

2017-12-15

Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions. Here we present Rigapollo, a highly flexible pairwise alignment method based on a pairwise HMM-SVM that can use any type of information to build alignments. Rigapollo lets the user decide the optimal features to align their protein class of interest. It outperforms current state of the art methods on two well-known benchmark datasets when aligning highly divergent sequences. A Python implementation of the algorithm is available at http://ibsquare.be/rigapollo. wim.vranken@vub.be. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Frequency-Dependent Selection: The High Potential for Permanent Genetic Variation in the Diallelic, Pairwise Interaction Model

PubMed Central

Asmussen, M. A.; Basnayake, E.

1990-01-01

A detailed analytic and numerical study is made of the potential for permanent genetic variation in frequency-dependent models based on pairwise interactions among genotypes at a single diallelic locus. The full equilibrium structure and qualitative gene-frequency dynamics are derived analytically for a symmetric model, in which pairwise fitnesses are chiefly determined by the genetic similarity of the individuals involved. This is supplemented by an extensive numerical investigation of the general model, the symmetric model, and nine other special cases. Together the results show that there is a high potential for permanent genetic diversity in the pairwise interaction model, and provide insight into the extent to which various forms of genotypic interactions enhance or reduce this potential. Technically, although two stable polymorphic equilibria are possible, the increased likelihood of maintaining both alleles, and the poor performance of protected polymorphism conditions as a measure of this likelihood, are primarily due to a greater variety and frequency of equilibrium patterns with one stable polymorphic equilibrium, in conjunction with a disproportionately large domain of attraction for stable internal equilibria. PMID:2341034

Spatial interactions of yarded White-tailed Deer, Odocoileus virginianus

USGS Publications Warehouse

Nelson, M.E.; Sargeant, G.A.

2008-01-01

We examined the spatial interactions of nine female White-tailed Deer (Odocoileus virginianus) in two deeryards (winter aggregations) in northeastern Minnesota during February-April 1999. Global positioning system (GPS) collars yielded seven pair-wise comparisons of deer that were located at the same time (???1 minute apart) and mat used overlapping areas. Deer traveled separately and did not associate with one another. Within overlapping areas, comparisons of distances between deer and distances between random locations indicated deer moved without regard to each other. Similarly, comparisons of observed and expected probabilities of deer using areas overlapping those of other deer also evinced that deer moved independently.

Matrix multiplication operations using pair-wise load and splat operations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eichenberger, Alexandre E.; Gschwind, Michael K.; Gunnels, John A.

Mechanisms for performing a matrix multiplication operation are provided. A vector load operation is performed to load a first vector operand of the matrix multiplication operation to a first target vector register. A pair-wise load and splat operation is performed to load a pair of scalar values of a second vector operand and replicate the pair of scalar values within a second target vector register. An operation is performed on elements of the first target vector register and elements of the second target vector register to generate a partial product of the matrix multiplication operation. The partial product is accumulatedmore » with other partial products and a resulting accumulated partial product is stored. This operation may be repeated for a second pair of scalar values of the second vector operand.« less

Non-rigid multi-frame registration of cell nuclei in live cell fluorescence microscopy image data.

PubMed

Tektonidis, Marco; Kim, Il-Han; Chen, Yi-Chun M; Eils, Roland; Spector, David L; Rohr, Karl

2015-01-01

The analysis of the motion of subcellular particles in live cell microscopy images is essential for understanding biological processes within cells. For accurate quantification of the particle motion, compensation of the motion and deformation of the cell nucleus is required. We introduce a non-rigid multi-frame registration approach for live cell fluorescence microscopy image data. Compared to existing approaches using pairwise registration, our approach exploits information from multiple consecutive images simultaneously to improve the registration accuracy. We present three intensity-based variants of the multi-frame registration approach and we investigate two different temporal weighting schemes. The approach has been successfully applied to synthetic and live cell microscopy image sequences, and an experimental comparison with non-rigid pairwise registration has been carried out. Copyright © 2014 Elsevier B.V. All rights reserved.

Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview.

PubMed

Skinner, Jeff; Kotliarov, Yuri; Varma, Sudhir; Mine, Karina L; Yambartsev, Anatoly; Simon, Richard; Huyen, Yentram; Morgun, Andrey

2011-07-14

DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes. Each significant difference in gene-gene association represents a Differentially Associated Pair (DAP). Our tools include several choices of filtering methods, gene-gene association metrics, statistical testing methods and multiple comparison adjustments. Network results are easily displayed in Cytoscape. Analyses of glioma experiments and microarray simulations demonstrate the utility of these tools. DAPfinder is a new friendly-user tool for reconstruction and comparison of biological networks.

Amino acid positions subject to multiple coevolutionary constraints can be robustly identified by their eigenvector network centrality scores.

PubMed

Parente, Daniel J; Ray, J Christian J; Swint-Kruse, Liskin

2015-12-01

As proteins evolve, amino acid positions key to protein structure or function are subject to mutational constraints. These positions can be detected by analyzing sequence families for amino acid conservation or for coevolution between pairs of positions. Coevolutionary scores are usually rank-ordered and thresholded to reveal the top pairwise scores, but they also can be treated as weighted networks. Here, we used network analyses to bypass a major complication of coevolution studies: For a given sequence alignment, alternative algorithms usually identify different, top pairwise scores. We reconciled results from five commonly-used, mathematically divergent algorithms (ELSC, McBASC, OMES, SCA, and ZNMI), using the LacI/GalR and 1,6-bisphosphate aldolase protein families as models. Calculations used unthresholded coevolution scores from which column-specific properties such as sequence entropy and random noise were subtracted; "central" positions were identified by calculating various network centrality scores. When compared among algorithms, network centrality methods, particularly eigenvector centrality, showed markedly better agreement than comparisons of the top pairwise scores. Positions with large centrality scores occurred at key structural locations and/or were functionally sensitive to mutations. Further, the top central positions often differed from those with top pairwise coevolution scores: instead of a few strong scores, central positions often had multiple, moderate scores. We conclude that eigenvector centrality calculations reveal a robust evolutionary pattern of constraints-detectable by divergent algorithms--that occur at key protein locations. Finally, we discuss the fact that multiple patterns coexist in evolutionary data that, together, give rise to emergent protein functions. © 2015 Wiley Periodicals, Inc.

Retention time alignment of LC/MS data by a divide-and-conquer algorithm.

PubMed

Zhang, Zhongqi

2012-04-01

Liquid chromatography-mass spectrometry (LC/MS) has become the method of choice for characterizing complex mixtures. These analyses often involve quantitative comparison of components in multiple samples. To achieve automated sample comparison, the components of interest must be detected and identified, and their retention times aligned and peak areas calculated. This article describes a simple pairwise iterative retention time alignment algorithm, based on the divide-and-conquer approach, for alignment of ion features detected in LC/MS experiments. In this iterative algorithm, ion features in the sample run are first aligned with features in the reference run by applying a single constant shift of retention time. The sample chromatogram is then divided into two shorter chromatograms, which are aligned to the reference chromatogram the same way. Each shorter chromatogram is further divided into even shorter chromatograms. This process continues until each chromatogram is sufficiently narrow so that ion features within it have a similar retention time shift. In six pairwise LC/MS alignment examples containing a total of 6507 confirmed true corresponding feature pairs with retention time shifts up to five peak widths, the algorithm successfully aligned these features with an error rate of 0.2%. The alignment algorithm is demonstrated to be fast, robust, fully automatic, and superior to other algorithms. After alignment and gap-filling of detected ion features, their abundances can be tabulated for direct comparison between samples.

Efficacy of Proton Pump Inhibitors for Patients with Duodenal Ulcers: A Pairwise and Network Meta-Analysis of Randomized Controlled Trials

PubMed Central

Hu, Zhan-Hong; Shi, Ai-Ming; Hu, Duan-Min; Bao, Jun-Jie

2017-01-01

Background/Aim: To compare the efficacy and tolerance of different proton pump inhibitors (PPIs) in different doses for patients with duodenal ulcers. Materials and Methods: An electronic database was searched to collect all randomized clinical trials (RCTs), and a pairwise and network meta-analysis were performed. Results: A total of 24 RCTs involving 6188 patients were included. The network meta-analysis showed that there were no significant differences for the 4-week healing rate of duodenal ulcer treated with different PPI regimens except pantoprazle 40 mg/d versus lansoprazole 15 mg/d [Relative risk (RR) = 3.57; 95% confidence interval (CI) = 1.36–10.31)] and lansoprazole 30 mg/d versus lansoprazole 15 mg/d (RR = 2.45; 95% CI = 1.01–6.14). In comparison with H2 receptor antagonists (H2 RA), pantoprazole 40 mg/d and lansoprazole 30 mg/d significantly increase the healing rate (RR = 2.96; 95% CI = 1.78–5.14 and RR = 2.04; 95% CI = 1.13–3.53, respectively). There was no significant difference for the rate of adverse events between different regimens, including H2 RA for a duration of 4-week of follow up. Conclusion: There was no significant difference for the efficacy and tolerance between the ordinary doses of different PPIs with the exception of lansoprazle 15 mg/d. PMID:28139495

Dispersion- and Exchange-Corrected Density Functional Theory for Sodium Ion Hydration.

PubMed

Soniat, Marielle; Rogers, David M; Rempe, Susan B

2015-07-14

A challenge in density functional theory is developing functionals that simultaneously describe intermolecular electron correlation and electron delocalization. Recent exchange-correlation functionals address those two issues by adding corrections important at long ranges: an atom-centered pairwise dispersion term to account for correlation and a modified long-range component of the electron exchange term to correct for delocalization. Here we investigate how those corrections influence the accuracy of binding free energy predictions for sodium-water clusters. We find that the dual-corrected ωB97X-D functional gives cluster binding energies closest to high-level ab initio methods (CCSD(T)). Binding energy decomposition shows that the ωB97X-D functional predicts the smallest ion-water (pairwise) interaction energy and larger multibody contributions for a four-water cluster than most other functionals - a trend consistent with CCSD(T) results. Also, ωB97X-D produces the smallest amounts of charge transfer and the least polarizable waters of the density functionals studied, which mimics the lower polarizability of CCSD. When compared with experimental binding free energies, however, the exchange-corrected CAM-B3LYP functional performs best (error <1 kcal/mol), possibly because of its parametrization to experimental formation enthalpies. For clusters containing more than four waters, "split-shell" coordination must be considered to obtain accurate free energies in comparison with experiment.

Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks

PubMed Central

Wadhwab, Gulshan; Upadhyayaa, K. C.

2016-01-01

The amount of data on molecular interactions is growing at an enormous pace, whereas the progress of methods for analysing this data is still lacking behind. Particularly, in the area of comparative analysis of biological networks, where one wishes to explore the similarity between two biological networks, this holds a potential problem. In consideration that the functionality primarily runs at the network level, it advocates the need for robust comparison methods. In this paper, we describe Net2Align, an algorithm for pairwise global alignment that can perform node-to-node correspondences as well as edge-to-edge correspondences into consideration. The uniqueness of our algorithm is in the fact that it is also able to detect the type of interaction, which is essential in case of directed graphs. The existing algorithm is only able to identify the common nodes but not the common edges. Another striking feature of the algorithm is that it is able to remove duplicate entries in case of variable datasets being aligned. This is achieved through creation of a local database which helps exclude duplicate links. In a pervasive computational study on gene regulatory network, we establish that our algorithm surpasses its counterparts in its results. Net2Align has been implemented in Java 7 and the source code is available as supplementary files. PMID:28356678

Dynamic facial expression recognition based on geometric and texture features

NASA Astrophysics Data System (ADS)

Li, Ming; Wang, Zengfu

2018-04-01

Recently, dynamic facial expression recognition in videos has attracted growing attention. In this paper, we propose a novel dynamic facial expression recognition method by using geometric and texture features. In our system, the facial landmark movements and texture variations upon pairwise images are used to perform the dynamic facial expression recognition tasks. For one facial expression sequence, pairwise images are created between the first frame and each of its subsequent frames. Integration of both geometric and texture features further enhances the representation of the facial expressions. Finally, Support Vector Machine is used for facial expression recognition. Experiments conducted on the extended Cohn-Kanade database show that our proposed method can achieve a competitive performance with other methods.

Identification of forgeries in handwritten petitions for ballot propositions

NASA Astrophysics Data System (ADS)

Srihari, Sargur; Ramakrishnan, Veshnu; Malgireddy, Manavender; Ball, Gregory R.

2009-01-01

Many governments have some form of "direct democracy" legislation procedure whereby individual citizens can propose various measures creating or altering laws. Generally, such a process is started with the gathering of a large number of signatures. There is interest in whether or not there are fraudulent signatures present in such a petition, and if so what percentage of the signatures are indeed fraudulent. However, due to the large number of signatures (tens of thousands), it is not feasible to have a document examiner verify the signatures directly. Instead, there is interest in creating a subset of signatures where there is a high probability of fraud that can be verified. We present a method by which a pairwise comparison of signatures can be performed and subsequent sorting can generate such subsets.

Deep Sequencing Reveals a Divergent Ugandan cassava brown streak virus Isolate from Malawi

PubMed Central

Winter, Stephan; Mukasa, Settumba; Tairo, Fred; Sseruwagi, Peter; Ndunguru, Joseph; Duffy, Siobain

2017-01-01

ABSTRACT Illumina sequencing of RNA from a cassava cutting from northern Malawi produced a genome of Ugandan cassava brown streak virus (UCBSV-MW-NB7_2013). Sequence comparisons revealed stronger similarity to an isolate from nearby Tanzania (93.4% pairwise nucleotide identity) than to those previously reported from Malawi (86.9 to 87.0%). PMID:28818908

Entropy production rate as a criterion for inconsistency in decision theory

NASA Astrophysics Data System (ADS)

Dixit, Purushottam D.

2018-05-01

Individual and group decisions are complex, often involving choosing an apt alternative from a multitude of options. Evaluating pairwise comparisons breaks down such complex decision problems into tractable ones. Pairwise comparison matrices (PCMs) are regularly used to solve multiple-criteria decision-making problems, for example, using Saaty’s analytic hierarchy process (AHP) framework. However, there are two significant drawbacks of using PCMs. First, humans evaluate PCMs in an inconsistent manner. Second, not all entries of a large PCM can be reliably filled by human decision makers. We address these two issues by first establishing a novel connection between PCMs and time-irreversible Markov processes. Specifically, we show that every PCM induces a family of dissipative maximum path entropy random walks (MERW) over the set of alternatives. We show that only ‘consistent’ PCMs correspond to detailed balanced MERWs. We identify the non-equilibrium entropy production in the induced MERWs as a metric of inconsistency of the underlying PCMs. Notably, the entropy production satisfies all of the recently laid out criteria for reasonable consistency indices. We also propose an approach to use incompletely filled PCMs in AHP. Potential future avenues are discussed as well.

Consistent linguistic fuzzy preference relations method with ranking fuzzy numbers

NASA Astrophysics Data System (ADS)

Ridzuan, Siti Amnah Mohd; Mohamad, Daud; Kamis, Nor Hanimah

2014-12-01

Multi-Criteria Decision Making (MCDM) methods have been developed to help decision makers in selecting the best criteria or alternatives from the options given. One of the well known methods in MCDM is the Consistent Fuzzy Preference Relation (CFPR) method, essentially utilizes a pairwise comparison approach. This method was later improved to cater subjectivity in the data by using fuzzy set, known as the Consistent Linguistic Fuzzy Preference Relations (CLFPR). The CLFPR method uses the additive transitivity property in the evaluation of pairwise comparison matrices. However, the calculation involved is lengthy and cumbersome. To overcome this problem, a method of defuzzification was introduced by researchers. Nevertheless, the defuzzification process has a major setback where some information may lose due to the simplification process. In this paper, we propose a method of CLFPR that preserves the fuzzy numbers form throughout the process. In obtaining the desired ordering result, a method of ranking fuzzy numbers is utilized in the procedure. This improved procedure for CLFPR is implemented to a case study to verify its effectiveness. This method is useful for solving decision making problems and can be applied to many areas of applications.

Comparison of the ITS1 and ITS2 rDNA in Emeria callospermophili (Apicomplexa: Eimeriidae) from Sciurid Rodents

PubMed Central

Motriuk-Smith, Dagmara; Seville, R Scott; Quealy, Leah; Oliver, Clinton E.

2011-01-01

The taxonomy of the coccidia has historically been morphologically based. The purpose of this study was to establish if conspecificity of isolates of Eimeria callospermophili from 4 ground-dwelling squirrel hosts (Rodentia: Sciuridae) is supported by comparison of rDNA sequence data and to examine how this species relates to eimerian species from other sciurid hosts. Eimeria callospermophili was isolated from 4 wild caught hosts, i.e., Urocitellus elegans, Cynomys leucurus, Marmota flaviventris, and Cynomys ludovicianus. The ITS1 and ITS2 genomic rDNA sequences were PCR generated, sequenced, and analyzed. The highest intraspecific pairwise distance values of 6.0% in ITS1 and 7.1% in ITS2 were observed in C. leucurus. Interspecific pairwise distance values greater than 5% do not support E. callospermophili conspecificity. Generated E. callospermophili sequences were compared to Eimeria lancasterensis from Sciuris niger and Sciurus niger cinereus, and Eimeria ontarioensis from S. niger. A single well-supported clade was formed by E. callospermophili amplicons in Neighbor Joining and Maximum Parsimony analyses. However, within the clade there was little evidence of host or geographic structuring of the species. PMID:21506777

Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers.

PubMed

Galpert, Deborah; Fernández, Alberto; Herrera, Francisco; Antunes, Agostinho; Molina-Ruiz, Reinaldo; Agüero-Chapin, Guillermin

2018-05-03

The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011). Despite several pairwise protein features being combined in a supervised big data approach; they all, to some extent were alignment-based features and the proposed algorithms were evaluated on a unique test set. Here, we aim to evaluate the impact of alignment-free features on the performance of supervised models implemented in the Spark big data platform for pairwise ortholog detection in several related yeast proteomes. The Spark Random Forest and Decision Trees with oversampling and undersampling techniques, and built with only alignment-based similarity measures or combined with several alignment-free pairwise protein features showed the highest classification performance for ortholog detection in three yeast proteome pairs. Although such supervised approaches outperformed traditional methods, there were no significant differences between the exclusive use of alignment-based similarity measures and their combination with alignment-free features, even within the twilight zone of the studied proteomes. Just when alignment-based and alignment-free features were combined in Spark Decision Trees with imbalance management, a higher success rate (98.71%) within the twilight zone could be achieved for a yeast proteome pair that underwent a whole genome duplication. The feature selection study showed that alignment-based features were top-ranked for the best classifiers while the runners-up were alignment-free features related to amino acid composition. The incorporation of alignment-free features in supervised big data models did not significantly improve ortholog detection in yeast proteomes regarding the classification qualities achieved with just alignment-based similarity measures. However, the similarity of their classification performance to that of traditional ortholog detection methods encourages the evaluation of other alignment-free protein pair descriptors in future research.

Sequence comparison alignment-free approach based on suffix tree and L-words frequency.

PubMed

Soares, Inês; Goios, Ana; Amorim, António

2012-01-01

The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

K2 and K2*: efficient alignment-free sequence similarity measurement based on Kendall statistics.

PubMed

Lin, Jie; Adjeroh, Donald A; Jiang, Bing-Hua; Jiang, Yue

2018-05-15

Alignment-free sequence comparison methods can compute the pairwise similarity between a huge number of sequences much faster than sequence-alignment based methods. We propose a new non-parametric alignment-free sequence comparison method, called K2, based on the Kendall statistics. Comparing to the other state-of-the-art alignment-free comparison methods, K2 demonstrates competitive performance in generating the phylogenetic tree, in evaluating functionally related regulatory sequences, and in computing the edit distance (similarity/dissimilarity) between sequences. Furthermore, the K2 approach is much faster than the other methods. An improved method, K2*, is also proposed, which is able to determine the appropriate algorithmic parameter (length) automatically, without first considering different values. Comparative analysis with the state-of-the-art alignment-free sequence similarity methods demonstrates the superiority of the proposed approaches, especially with increasing sequence length, or increasing dataset sizes. The K2 and K2* approaches are implemented in the R language as a package and is freely available for open access (http://community.wvu.edu/daadjeroh/projects/K2/K2_1.0.tar.gz). yueljiang@163.com. Supplementary data are available at Bioinformatics online.

CoCoNUT: an efficient system for the comparison and analysis of genomes

PubMed Central

2008-01-01

Background Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and software to perform pairwise and multiple genome comparisons. Results Most of the software tools available are tailored for one specific task. In contrast, we have developed a novel system CoCoNUT (Computational Comparative geNomics Utility Toolkit) that allows solving several different tasks in a unified framework: (1) finding regions of high similarity among multiple genomic sequences and aligning them, (2) comparing two draft or multi-chromosomal genomes, (3) locating large segmental duplications in large genomic sequences, and (4) mapping cDNA/EST to genomic sequences. Conclusion CoCoNUT is competitive with other software tools w.r.t. the quality of the results. The use of state of the art algorithms and data structures allows CoCoNUT to solve comparative genomics tasks more efficiently than previous tools. With the improved user interface (including an interactive visualization component), CoCoNUT provides a unified, versatile, and easy-to-use software tool for large scale studies in comparative genomics. PMID:19014477

A novel combined approach of diffuse reflectance UV-Vis-NIR spectroscopy and multivariate analysis for non-destructive examination of blue ballpoint pen inks in forensic application.

PubMed

Kumar, Raj; Sharma, Vishal

2017-03-15

The present research is focused on the analysis of writing inks using destructive UV-Vis spectroscopy (dissolution of ink by the solvent) and non-destructive diffuse reflectance UV-Vis-NIR spectroscopy along with Chemometrics. Fifty seven samples of blue ballpoint pen inks were analyzed under optimum conditions to determine the differences in spectral features of inks among same and different manufacturers. Normalization was performed on the spectroscopic data before chemometric analysis. Principal Component Analysis (PCA) and K-mean cluster analysis were used on the data to ascertain whether the blue ballpoint pen inks could be differentiated by their UV-Vis/UV-Vis NIR spectra. The discriminating power is calculated by qualitative analysis by the visual comparison of the spectra (absorbance peaks), produced by the destructive and non-destructive methods. In the latter two methods, the pairwise comparison is made by incorporating the clustering method. It is found that chemometric method provides better discriminating power (98.72% and 99.46%, in destructive and non-destructive, respectively) in comparison to the qualitative analysis (69.67%). Copyright © 2016 Elsevier B.V. All rights reserved.

Analyzing thresholds and efficiency with hierarchical Bayesian logistic regression.

PubMed

Houpt, Joseph W; Bittner, Jennifer L

2018-07-01

Ideal observer analysis is a fundamental tool used widely in vision science for analyzing the efficiency with which a cognitive or perceptual system uses available information. The performance of an ideal observer provides a formal measure of the amount of information in a given experiment. The ratio of human to ideal performance is then used to compute efficiency, a construct that can be directly compared across experimental conditions while controlling for the differences due to the stimuli and/or task specific demands. In previous research using ideal observer analysis, the effects of varying experimental conditions on efficiency have been tested using ANOVAs and pairwise comparisons. In this work, we present a model that combines Bayesian estimates of psychometric functions with hierarchical logistic regression for inference about both unadjusted human performance metrics and efficiencies. Our approach improves upon the existing methods by constraining the statistical analysis using a standard model connecting stimulus intensity to human observer accuracy and by accounting for variability in the estimates of human and ideal observer performance scores. This allows for both individual and group level inferences. Copyright © 2018 Elsevier Ltd. All rights reserved.

Population and forensic genetic analyses of mitochondrial DNA control region variation from six major provinces in the Korean population.

PubMed

Hong, Seung Beom; Kim, Ki Cheol; Kim, Wook

2015-07-01

We generated complete mitochondrial DNA (mtDNA) control region sequences from 704 unrelated individuals residing in six major provinces in Korea. In addition to our earlier survey of the distribution of mtDNA haplogroup variation, a total of 560 different haplotypes characterized by 271 polymorphic sites were identified, of which 473 haplotypes were unique. The gene diversity and random match probability were 0.9989 and 0.0025, respectively. According to the pairwise comparison of the 704 control region sequences, the mean number of pairwise differences between individuals was 13.47±6.06. Based on the result of mtDNA control region sequences, pairwise FST genetic distances revealed genetic homogeneity of the Korean provinces on a peninsular level, except in samples from Jeju Island. This result indicates there may be a need to formulate a local mtDNA database for Jeju Island, to avoid bias in forensic parameter estimates caused by genetic heterogeneity of the population. Thus, the present data may help not only in personal identification but also in determining maternal lineages to provide an expanded and reliable Korean mtDNA database. These data will be available on the EMPOP database via accession number EMP00661. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Detection of the kinematic Sunyaev–Zel'dovich effect with DES Year 1 and SPT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soergel, B.; Flender, S.; Story, K. T.

Here, we detect the kinematic Sunyaev-Zel'dovich (kSZ) effect with a statistical significance ofmore » $$4.2 \\sigma$$ by combining a cluster catalogue derived from the first year data of the Dark Energy Survey (DES) with CMB temperature maps from the South Pole Telescope Sunyaev-Zel'dovich (SPT-SZ) Survey. This measurement is performed with a differential statistic that isolates the pairwise kSZ signal, providing the first detection of the large-scale, pairwise motion of clusters using redshifts derived from photometric data. By fitting the pairwise kSZ signal to a theoretical template we measure the average central optical depth of the cluster sample, $$\\bar{\\tau}_e = (3.75 \\pm 0.89)\\cdot 10^{-3}$$. We compare the extracted signal to realistic simulations and find good agreement with respect to the signal-to-noise, the constraint on $$\\bar{\\tau}_e$$, and the corresponding gas fraction. High-precision measurements of the pairwise kSZ signal with future data will be able to place constraints on the baryonic physics of galaxy clusters, and could be used to probe gravity on scales $$ \\gtrsim 100$$ Mpc.« less

Detection of the kinematic Sunyaev–Zel'dovich effect with DES Year 1 and SPT

DOE PAGES

Soergel, B.; Flender, S.; Story, K. T.; ...

2016-06-17

Here, we detect the kinematic Sunyaev-Zel'dovich (kSZ) effect with a statistical significance ofmore » $$4.2 \\sigma$$ by combining a cluster catalogue derived from the first year data of the Dark Energy Survey (DES) with CMB temperature maps from the South Pole Telescope Sunyaev-Zel'dovich (SPT-SZ) Survey. This measurement is performed with a differential statistic that isolates the pairwise kSZ signal, providing the first detection of the large-scale, pairwise motion of clusters using redshifts derived from photometric data. By fitting the pairwise kSZ signal to a theoretical template we measure the average central optical depth of the cluster sample, $$\\bar{\\tau}_e = (3.75 \\pm 0.89)\\cdot 10^{-3}$$. We compare the extracted signal to realistic simulations and find good agreement with respect to the signal-to-noise, the constraint on $$\\bar{\\tau}_e$$, and the corresponding gas fraction. High-precision measurements of the pairwise kSZ signal with future data will be able to place constraints on the baryonic physics of galaxy clusters, and could be used to probe gravity on scales $$ \\gtrsim 100$$ Mpc.« less

Laparoscopic-guided abdominal wall nerve blocks in the pediatric population: a novel technique with comparison to ultrasound-guided blocks and local wound infiltration alone.

PubMed

Landmann, Alessandra; Visoiu, Mihaela; Malek, Marcus M

2018-03-01

Abdominal wall nerve blocks have been gaining popularity for the treatment of perioperative pain in children. Our aim was to compare a technique of surgeon-performed, laparoscopic abdominal wall nerve blocks to anesthesia-placed, ultrasound-guided abdominal wall nerve blocks and the current standard of local wound infiltration. After institutional review board approval was obtained, a retrospective chart review was performed of pediatric patients treated at a single institution during a 2-year period. Statistics were calculated using analysis of variance with post-hoc Bonferonni t tests for pair-wise comparisons. Included in this study were 380 patients who received ultrasound-guided abdominal wall nerve blocks (n = 125), laparoscopic-guided abdominal wall nerve blocks (n = 88), and local wound infiltration (n = 117). Groups were well matched for age, sex, and weight. There was no significant difference in pain scores within the first 8 hours or narcotic usage between groups. Local wound infiltration demonstrated the shortest overall time required to perform (P < .0001). Patients who received a surgeon-performed abdominal wall nerve block demonstrated a shorter duration of hospital stay when compared to the other groups (P = .02). Our study has demonstrated that laparoscopic-guided abdominal wall nerve blocks show similar efficacy to ultrasound-guided nerve blocks performed by pain management physicians without increasing time in the operating room. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparison of potential method in analytic hierarchy process for multi-attribute of catering service companies

NASA Astrophysics Data System (ADS)

Mamat, Siti Salwana; Ahmad, Tahir; Awang, Siti Rahmah

2017-08-01

Analytic Hierarchy Process (AHP) is a method used in structuring, measuring and synthesizing criteria, in particular ranking of multiple criteria in decision making problems. On the other hand, Potential Method is a ranking procedure in which utilizes preference graph ς (V, A). Two nodes are adjacent if they are compared in a pairwise comparison whereby the assigned arc is oriented towards the more preferred node. In this paper Potential Method is used to solve problem on a catering service selection. The comparison of result by using Potential method is made with Extent Analysis. The Potential Method is found to produce the same rank as Extent Analysis in AHP.

Combined Use of Satellite Observations with Urban Surface Characteristics to Estimate PM Concentrations by Employing Mixed-Effects Models

NASA Astrophysics Data System (ADS)

Beloconi, Anton; Benas, Nikolaos; Chrysoulakis, Nektarios; Kamarianakis, Yiannis

2015-11-01

Linear mixed effects models were developed for the estimation of the average daily Particulate Matter (PM) concentration spatial distribution over the area of Greater London (UK). Both fine (PM2.5) and coarse (PM10) concentrations were predicted for the 2002- 2012 time period, based on satellite data. The latter included Aerosol Optical Thickness (AOT) at 3×3 km spatial resolution, as well as the Surface Relative Humidity, Surface Temperature and K-Index derived from MODIS (Moderate Resolution Imaging Spectroradiometer) sensor. For a meaningful interpretation of the association among these variables, all data were homogenized with regard to spatial support and geographic projection, thus addressing the change of support problem and leading to a valid statistical inference. To this end, spatial (2D) and spatio- temporal (3D) kriging techniques were applied to in-situ particulate matter concentrations and the leave-one- station-out cross-validation was performed on a daily level to gauge the quality of the predictions. Satellite- derived covariates displayed clear seasonal patterns; in order to work with data which is stationary in mean, for each covariate, deviations from its estimated annual profiles were computed using nonlinear least squares and nonlinear absolute deviations. High-resolution land- cover and morphology static datasets were additionally incorporated in the analysis in order to catch the effects of nearby emission sources and sequestration sites. For pairwise comparisons of the particulate matter concentration means at distinct land-cover classes, the pairwise comparisons method for unequal sample sizes, known as Tukey's method, was performed. The use of satellite-derived products allowed better assessment of space-time interactions of PM, since these daily spatial measurements were able to capture differences in PM concentrations between grid cells, while the use of high- resolution land-cover and morphology static datasets allowed accounting for local industrial, domestic and traffic related air pollution. The developed methods are expected to fully exploit ESA's new Sentinel-3 observations to estimate spatial distributions of both PM10 and PM2.5 concentrations in arbitrary cities.

Pairwise adaptive thermostats for improved accuracy and stability in dissipative particle dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leimkuhler, Benedict, E-mail: b.leimkuhler@ed.ac.uk; Shang, Xiaocheng, E-mail: x.shang@brown.edu

2016-11-01

We examine the formulation and numerical treatment of dissipative particle dynamics (DPD) and momentum-conserving molecular dynamics. We show that it is possible to improve both the accuracy and the stability of DPD by employing a pairwise adaptive Langevin thermostat that precisely matches the dynamical characteristics of DPD simulations (e.g., autocorrelation functions) while automatically correcting thermodynamic averages using a negative feedback loop. In the low friction regime, it is possible to replace DPD by a simpler momentum-conserving variant of the Nosé–Hoover–Langevin method based on thermostatting only pairwise interactions; we show that this method has an extra order of accuracy for anmore » important class of observables (a superconvergence result), while also allowing larger timesteps than alternatives. All the methods mentioned in the article are easily implemented. Numerical experiments are performed in both equilibrium and nonequilibrium settings; using Lees–Edwards boundary conditions to induce shear flow.« less

Pairwise Interaction Extended Point-Particle (PIEP) model for multiphase jets and sedimenting particles

NASA Astrophysics Data System (ADS)

Liu, Kai; Balachandar, S.

2017-11-01

We perform a series of Euler-Lagrange direct numerical simulations (DNS) for multiphase jets and sedimenting particles. The forces the flow exerts on the particles in these two-way coupled simulations are computed using the Basset-Bousinesq-Oseen (BBO) equations. These forces do not explicitly account for particle-particle interactions, even though such pairwise interactions induced by the perturbations from neighboring particles may be important especially when the particle volume fraction is high. Such effects have been largely unaddressed in the literature. Here, we implement the Pairwise Interaction Extended Point-Particle (PIEP) model to simulate the effect of neighboring particle pairs. A simple collision model is also applied to avoid unphysical overlapping of solid spherical particles. The simulation results indicate that the PIEP model provides a more elaborative and complicated movement of the dispersed phase (droplets and particles). Office of Naval Research (ONR) Multidisciplinary University Research Initiative (MURI) project N00014-16-1-2617.

Additional considerations are required when preparing a protocol for a systematic review with multiple interventions.

PubMed

Chaimani, Anna; Caldwell, Deborah M; Li, Tianjing; Higgins, Julian P T; Salanti, Georgia

2017-03-01

The number of systematic reviews that aim to compare multiple interventions using network meta-analysis is increasing. In this study, we highlight aspects of a standard systematic review protocol that may need modification when multiple interventions are to be compared. We take the protocol format suggested by Cochrane for a standard systematic review as our reference and compare the considerations for a pairwise review with those required for a valid comparison of multiple interventions. We suggest new sections for protocols of systematic reviews including network meta-analyses with a focus on how to evaluate their assumptions. We provide example text from published protocols to exemplify the considerations. Standard systematic review protocols for pairwise meta-analyses need extensions to accommodate the increased complexity of network meta-analysis. Our suggested modifications are widely applicable to both Cochrane and non-Cochrane systematic reviews involving network meta-analyses. Copyright © 2017 Elsevier Inc. All rights reserved.

OxfordGrid: a web interface for pairwise comparative map views.

PubMed

Yang, Hongyu; Gingle, Alan R

2005-12-01

OxfordGrid is a web application and database schema for storing and interactively displaying genetic map data in a comparative, dot-plot, fashion. Its display is composed of a matrix of cells, each representing a pairwise comparison of mapped probe data for two linkage groups or chromosomes. These are arranged along the axes with one forming grid columns and the other grid rows with the degree and pattern of synteny/colinearity between the two linkage groups manifested in the cell's dot density and structure. A mouse click over the selected grid cell launches an image map-based display for the selected cell. Both individual and linear groups of mapped probes can be selected and displayed. Also, configurable links can be used to access other web resources for mapped probe information. OxfordGrid is implemented in C#/ASP.NET and the package, including MySQL schema creation scripts, is available at ftp://cggc.agtec.uga.edu/OxfordGrid/.

Analysis of laser printer and photocopier toners by spectral properties and chemometrics

NASA Astrophysics Data System (ADS)

Verma, Neha; Kumar, Raj; Sharma, Vishal

2018-05-01

The use of printers to generate falsified documents has become a common practice in today's world. The examination and identification of the printed matter in the suspected documents (civil or criminal cases) may provide important information about the authenticity of the document. In the present study, a total number of 100 black toner samples both from laser printers and photocopiers were examined using diffuse reflectance UV-Vis Spectroscopy. The present research is divided into two parts; visual discrimination and discrimination by using multivariate analysis. A comparison between qualitative and quantitative analysis showed that multivariate analysis (Principal component analysis) provides 99.59%pair-wise discriminating power for laser printer toners while 99.84% pair-wise discriminating power for photocopier toners. The overall results obtained confirm the applicability of UV-Vis spectroscopy and chemometrics, in the nondestructive analysis of toner printed documents while enhancing their evidential value for forensic applications.

Approximate reasoning by pairwise comparisons. "Topodynamics of metastable brains" by Arturo Tozzi, et al.

NASA Astrophysics Data System (ADS)

Kakiashvili, Tamar; Koczkodaj, Waldemar W.; Magnot, Jean-Pierre

2017-07-01

The innovative approach in [1], ;Topodynamics of Metastable Brains; by Arturo Tozzi, James Peters, Andrew Fingelkurts, Alexander Fingelkurts, and Pedro Marijuan has a high potential of becoming a paradigm shift in the brain research. It seems that this study has successfully explored the possibility of applying a celebrated Borsuk-Ulam theorem to the operational architectonics of the fundamental brain-mind processes.

MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level.

PubMed

Chiapello, Hélène; Gendrault, Annie; Caron, Christophe; Blum, Jérome; Petit, Marie-Agnès; El Karoui, Meriem

2008-11-27

The recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. Several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. It is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons. Here we present recent developments on MOSAIC, a generalist comparative bacterial genome database. This database provides the bacteriologist community with easy access to comparisons of complete bacterial genomes at the intra-species level. The strategy we developed for comparison allows us to define two types of regions in bacterial genomes: backbone segments (i.e., regions conserved in all compared strains) and variable segments (i.e., regions that are either specific to or variable in one of the aligned genomes). Definition of these segments at the nucleotide level allows precise comparative and evolutionary analyses of both coding and non-coding regions of bacterial genomes. Such work is easily performed using the MOSAIC Web interface, which allows browsing and graphical visualization of genome comparisons. The MOSAIC database now includes 493 pairwise comparisons and 35 multiple maximal comparisons representing 78 bacterial species. Genome conserved regions (backbones) and variable segments are presented in various formats for further analysis. A graphical interface allows visualization of aligned genomes and functional annotations. The MOSAIC database is available online at http://genome.jouy.inra.fr/mosaic.

Financial incentive strategies for maintenance of weight loss: results from an internet-based randomized controlled trial.

PubMed

Yancy, William S; Shaw, Pamela A; Wesby, Lisa; Hilbert, Victoria; Yang, Lin; Zhu, Jingsan; Troxel, Andrea; Huffman, David; Foster, Gary D; Wojtanowski, Alexis C; Volpp, Kevin G

2018-05-25

Financial incentives can improve initial weight loss; we examined whether financial incentives can improve weight loss maintenance. Participants aged 30-80 years who lost at least 5 kg during the first 4-6 months in a nationally available commercial weight loss program were recruited via the internet into a three-arm randomized trial of two types of financial incentives versus active control during months 1-6 (Phase I) followed by passive monitoring during months 7-12 (Phase II). Interventions were daily self-weighing and text messaging feedback alone (control) or combined with a lottery-based incentive or a direct incentive. The primary outcome was weight change 6 months after initial weight loss. Secondary outcomes included weight change 12 months after initial weight loss (6 months after cessation of maintenance intervention), and self-reported physical activity and eating behaviors. Of 191 participants randomized, the mean age was 49.0 (SD = 10.5) years and weight loss prior to randomization was 11.4 (4.7) kg; 92% were women and 89% were White. Mean weight changes during the next 6 months (Phase I) were: lottery -3.0 (5.8) kg; direct -2.8 (5.8) kg; and control -1.4 (5.8) kg (all pairwise comparisons p > 0.1). Weight changes through the end of 12 months post-weight loss (Phase II) were: lottery -1.8 (10.5) kg; direct -0.7 (10.7) kg; and control -0.3 (9.4) kg (all pairwise comparisons p > 0.1). The percentages of participants who maintained their weight loss (defined as gaining ≤1.36 kg) were: lottery 79%, direct 76%, and control 67% at 6 months and lottery 66%, direct 62%, and control 59% at 12 months (all pairwise comparisons p > 0.1). At 6 and 12 months after initial weight loss, changes in self-reported physical activity or eating behaviors did not differ across arms. Compared with the active control of daily texting based on daily home weighing, lottery-based and direct monetary incentives provided no additional benefit for weight loss maintenance.

The Chiropractic Hospital-Based Interventions Research Outcomes Study: Consistency of Outcomes Between Doctors of Chiropractic Treating Patients With Acute Lower Back Pain.

PubMed

Quon, Jeffrey A; Bishop, Paul B; Arthur, Brian

2015-06-01

The aim of this study was to determine if effectiveness differs between community-based doctors of chiropractic administering standardized evidence-based care that includes high-velocity low-amplitude spinal manipulative therapy (SMT) for acute low back pain (LBP). A secondary analysis of randomized controlled trial and observational pilot study data was performed with nonrandom allocation to 4 DCs. Patients included those with Quebec Task Force categories less than or equal to 2 and acute LBP of 2 to 4 weeks' duration. The intervention provided was clinical practice guidelines-based care including high-velocity low-amplitude SMT. Primary outcomes included changes from baseline in modified Roland Disability Questionnaire (RDQ) at 24 weeks. Comparisons of simple main effects at 24 weeks and of marginal main effects in repeated-measures analyses were performed. Between groups, adjusted point-specific differences in RDQ change were minimally clinically important but not statistically significant at 24 weeks (largest pairwise difference, -3.1; 95% confidence interval, -6.3 to 0.1; overall P = .10). However, in optimal analyses that considered the repeated nature of the measurements for each outcome, significant differences in marginal mean RDQ changes were found between groups (largest pairwise difference, -3.8; 95% confidence interval, -4.9 to 2.6; overall P = .03). Overall, DCs differed modestly in their effectiveness in improving LBP-specific disability. The point estimates mirrored typically reported effect sizes from recent systematic reviews of SMT; however, confidence limits did not exclude clinically negligible effects. Copyright © 2015 National University of Health Sciences. Published by Elsevier Inc. All rights reserved.

A Pairwise Naïve Bayes Approach to Bayesian Classification.

PubMed

Asafu-Adjei, Josephine K; Betensky, Rebecca A

2015-10-01

Despite the relatively high accuracy of the naïve Bayes (NB) classifier, there may be several instances where it is not optimal, i.e. does not have the same classification performance as the Bayes classifier utilizing the joint distribution of the examined attributes. However, the Bayes classifier can be computationally intractable due to its required knowledge of the joint distribution. Therefore, we introduce a "pairwise naïve" Bayes (PNB) classifier that incorporates all pairwise relationships among the examined attributes, but does not require specification of the joint distribution. In this paper, we first describe the necessary and sufficient conditions under which the PNB classifier is optimal. We then discuss sufficient conditions for which the PNB classifier, and not NB, is optimal for normal attributes. Through simulation and actual studies, we evaluate the performance of our proposed classifier relative to the Bayes and NB classifiers, along with the HNB, AODE, LBR and TAN classifiers, using normal density and empirical estimation methods. Our applications show that the PNB classifier using normal density estimation yields the highest accuracy for data sets containing continuous attributes. We conclude that it offers a useful compromise between the Bayes and NB classifiers.

Comparison between available serologic tests for detecting antibodies against Anaplasma phagocytophilum and Borrelia burgdorferi in horses in Canada.

PubMed

Schvartz, Gili; Epp, Tasha; Burgess, Hilary J; Chilton, Neil B; Lohmann, Katharina L

2015-07-01

To investigate the agreement between available serologic tests for the detection of antibodies against Anaplasma phagocytophilum and Borrelia burgdorferi, 50 serum samples from horses of unknown clinical status and at low risk for infection were tested. In addition to a point-of-care enzyme-linked immunosorbent assay (pocELISA), the evaluated tests included 2 indirect fluorescent antibody tests (IFATs) for antibodies against A. phagocytophilum and an IFAT, an ELISA confirmed with Western blot, and the Lyme multiplex assay for antibodies against B. burgdorferi. For each pair-wise comparison between serologic tests, the difference in the proportion of seropositive results as well as kappa and the prevalence-adjusted, bias-adjusted kappa were calculated. The proportion of seropositive results differed significantly in each pairwise comparison of tests for detection of antibodies against A. phagocytophilum, and between the pocELISA and IFAT as well as between the pocELISA and Lyme multiplex assay for detection of antibodies against B. burgdorferi. Agreement based on kappa varied from poor to fair while agreement was improved when evaluating prevalence-adjusted, bias-adjusted kappa. Lack of agreement may be explained by differences in methodology between the evaluated tests, cross-reactivity or false-positive and false-negative tests. In addition to the limitations of serologic test interpretation in the absence of clinical disease, this data suggest that screening of horses for exposure to tick-borne diseases in nonendemic areas may not be warranted. © 2015 The Author(s).

The mobile image quality survey game

NASA Astrophysics Data System (ADS)

Rasmussen, D. René

2012-01-01

In this paper we discuss human assessment of the quality of photographic still images, that are degraded in various manners relative to an original, for example due to compression or noise. In particular, we examine and present results from a technique where observers view images on a mobile device, perform pairwise comparisons, identify defects in the images, and interact with the display to indicate the location of the defects. The technique measures the response time and accuracy of the responses. By posing the survey in a form similar to a game, providing performance feedback to the observer, the technique attempts to increase the engagement of the observers, and to avoid exhausting observers, a factor that is often a problem for subjective surveys. The results are compared with the known physical magnitudes of the defects and with results from similar web-based surveys. The strengths and weaknesses of the technique are discussed. Possible extensions of the technique to video quality assessment are also discussed.

Use of environmental tobacco smoke constituents as markers for exposure

DOE Office of Scientific and Technical Information (OSTI.GOV)

LaKind, J.S.; Jenkins, R.A.; Naiman, D.Q.

1999-06-01

The 16-City Study analyzed for gas-phase environmental tobacco smoke (ETS) constituents (nicotine, 3-ethenyl pyridine [3-EP], and myosmine) and for particulate-phase constituents (respirable particulate matter [RSP], ultraviolet-absorbing particulate matter [UVPM], fluorescing particulate matter [FPM], scopoletin, and solanesol). In this second of three articles, the authors discuss the merits of each constituent as a marker for ETS and report pair-wise comparisons of the markers. Neither nicotine nor UVPM were good predictors for RSP. However, nicotine and UVPM were good qualitative predictors of each other. Nicotine was correlated with other gas-phase constituents. Comparisons between UVPM and other particulate-phase constituents were performed. Its relationmore » with FPM was excellent, with UVPM approximately 1 1/2 times FPM. The correlation between UVPM and solanesol was good, but the relationship between the two was not linear. The relation between UVPM and scopoletin was not good, largely because of noise in the scopoletin measures around its limit of detection. The authors considered the relation between nicotine and saliva cotinine, a metabolite of nicotine. The two were highly correlated on the group level.« less

Quantitative genetic-interaction mapping in mammalian cells

PubMed Central

Roguev, Assen; Talbot, Dale; Negri, Gian Luca; Shales, Michael; Cagney, Gerard; Bandyopadhyay, Sourav; Panning, Barbara; Krogan, Nevan J

2013-01-01

Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ~11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape. PMID:23407553

Application of one-way ANOVA in completely randomized experiments

NASA Astrophysics Data System (ADS)

Wahid, Zaharah; Izwan Latiff, Ahmad; Ahmad, Kartini

2017-12-01

This paper describes an application of a statistical technique one-way ANOVA in completely randomized experiments with three replicates. This technique was employed to a single factor with four levels and multiple observations at each level. The aim of this study is to investigate the relationship between chemical oxygen demand index and location on-sites. Two different approaches are employed for the analyses; critical value and p-value. It also presents key assumptions of the technique to be satisfied by the data in order to obtain valid results. Pairwise comparisons by Turkey method are also considered and discussed to determine where the significant differences among the means is after the ANOVA has been performed. The results revealed that there are statistically significant relationship exist between the chemical oxygen demand index and the location on-sites.

Cardiovascular risk with non-steroidal anti-inflammatory drugs: systematic review of population-based controlled observational studies.

PubMed

McGettigan, Patricia; Henry, David

2011-09-01

Randomised trials have highlighted the cardiovascular risks of non-steroidal anti-inflammatory drugs (NSAIDs) in high doses and sometimes atypical settings. Here, we provide estimates of the comparative risks with individual NSAIDs at typical doses in community settings. We performed a systematic review of community-based controlled observational studies. We conducted comprehensive literature searches, extracted adjusted relative risk (RR) estimates, and pooled the estimates for major cardiovascular events associated with use of individual NSAIDs, in different doses, and in populations with low and high background risks of cardiovascular events. We also compared individual drugs in pair-wise (within study) analyses, generating ratios of RRs (RRRs). Thirty case-control studies included 184,946 cardiovascular events, and 21 cohort studies described outcomes in >2.7 million exposed individuals. Of the extensively studied drugs (ten or more studies), the highest overall risks were seen with rofecoxib, 1.45 (95% CI 1.33, 1.59), and diclofenac, 1.40 (1.27, 1.55), and the lowest with ibuprofen, 1.18 (1.11, 1.25), and naproxen, 1.09 (1.02, 1.16). In a sub-set of studies, risk was elevated with low doses of rofecoxib, 1.37 (1.20, 1.57), celecoxib, 1.26 (1.09, 1.47), and diclofenac, 1.22 (1.12, 1.33), and rose in each case with higher doses. Ibuprofen risk was seen only with higher doses. Naproxen was risk-neutral at all doses. Of the less studied drugs etoricoxib, 2.05 (1.45, 2.88), etodolac, 1.55 (1.28, 1.87), and indomethacin, 1.30 (1.19, 1.41), had the highest risks. In pair-wise comparisons, etoricoxib had a higher RR than ibuprofen, RRR = 1.68 (99% CI 1.14, 2.49), and naproxen, RRR = 1.75 (1.16, 2.64); etodolac was not significantly different from naproxen and ibuprofen. Naproxen had a significantly lower risk than ibuprofen, RRR = 0.92 (0.87, 0.99). RR estimates were constant with different background risks for cardiovascular disease and rose early in the course of treatment. This review suggests that among widely used NSAIDs, naproxen and low-dose ibuprofen are least likely to increase cardiovascular risk. Diclofenac in doses available without prescription elevates risk. The data for etoricoxib were sparse, but in pair-wise comparisons this drug had a significantly higher RR than naproxen or ibuprofen. Indomethacin is an older, rather toxic drug, and the evidence on cardiovascular risk casts doubt on its continued clinical use. Please see later in the article for the Editors' Summary.

Neighbourhood-consensus message passing and its potentials in image processing applications

NASA Astrophysics Data System (ADS)

Ružic, Tijana; Pižurica, Aleksandra; Philips, Wilfried

2011-03-01

In this paper, a novel algorithm for inference in Markov Random Fields (MRFs) is presented. Its goal is to find approximate maximum a posteriori estimates in a simple manner by combining neighbourhood influence of iterated conditional modes (ICM) and message passing of loopy belief propagation (LBP). We call the proposed method neighbourhood-consensus message passing because a single joint message is sent from the specified neighbourhood to the central node. The message, as a function of beliefs, represents the agreement of all nodes within the neighbourhood regarding the labels of the central node. This way we are able to overcome the disadvantages of reference algorithms, ICM and LBP. On one hand, more information is propagated in comparison with ICM, while on the other hand, the huge amount of pairwise interactions is avoided in comparison with LBP by working with neighbourhoods. The idea is related to the previously developed iterated conditional expectations algorithm. Here we revisit it and redefine it in a message passing framework in a more general form. The results on three different benchmarks demonstrate that the proposed technique can perform well both for binary and multi-label MRFs without any limitations on the model definition. Furthermore, it manifests improved performance over related techniques either in terms of quality and/or speed.

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

PubMed Central

Momeni, Babak; Xie, Li; Shou, Wenying

2017-01-01

Pairwise models are commonly used to describe many-species communities. In these models, an individual receives additive fitness effects from pairwise interactions with each species in the community ('additivity assumption'). All pairwise interactions are typically represented by a single equation where parameters reflect signs and strengths of fitness effects ('universality assumption'). Here, we show that a single equation fails to qualitatively capture diverse pairwise microbial interactions. We build mechanistic reference models for two microbial species engaging in commonly-found chemical-mediated interactions, and attempt to derive pairwise models. Different equations are appropriate depending on whether a mediator is consumable or reusable, whether an interaction is mediated by one or more mediators, and sometimes even on quantitative details of the community (e.g. relative fitness of the two species, initial conditions). Our results, combined with potential violation of the additivity assumption in many-species communities, suggest that pairwise modeling will often fail to predict microbial dynamics. DOI: http://dx.doi.org/10.7554/eLife.25051.001 PMID:28350295

Spatially resolved bimodal spectroscopy for classification/evaluation of mouse skin inflammatory and pre-cancerous stages

NASA Astrophysics Data System (ADS)

Díaz-Ayil, Gilberto; Amouroux, Marine; Clanché, Fabien; Granjon, Yves; Blondel, Walter C. P. M.

2009-07-01

Spatially-resolved bimodal spectroscopy (multiple AutoFluorescence AF excitation and Diffuse Reflectance DR), was used in vivo to discriminate various healthy and precancerous skin stages in a pre-clinical model (UV-irradiated mouse): Compensatory Hyperplasia CH, Atypical Hyperplasia AH and Dysplasia D. A specific data preprocessing scheme was applied to intensity spectra (filtering, spectral correction and intensity normalization), and several sets of spectral characteristics were automatically extracted and selected based on their discrimination power, statistically tested for every pair-wise comparison of histological classes. Data reduction with Principal Components Analysis (PCA) was performed and 3 classification methods were implemented (k-NN, LDA and SVM), in order to compare diagnostic performance of each method. Diagnostic performance was studied and assessed in terms of Sensibility (Se) and Specificity (Sp) as a function of the selected features, of the combinations of 3 different inter-fibres distances and of the numbers of principal components, such that: Se and Sp ~ 100% when discriminating CH vs. others; Sp ~ 100% and Se > 95% when discriminating Healthy vs. AH or D; Sp ~ 74% and Se ~ 63% for AH vs. D.

Ar(n)HF van der Waals clusters revisited: II. Energetics and HF vibrational frequency shifts from diffusion Monte Carlo calculations on additive and nonadditive potential-energy surfaces for n=1-12.

PubMed

Jiang, Hao; Xu, Minzhong; Hutson, Jeremy M; Bacić, Zlatko

2005-08-01

The ground-state energies and HF vibrational frequency shifts of Ar(n)HF clusters have been calculated on the nonadditive potential-energy surfaces (PESs) for n=2-7 and on the pairwise-additive PESs for the clusters with n=1-12, using the diffusion Monte Carlo (DMC) method. For n>3, the calculations have been performed for the lowest-energy isomer and several higher-lying isomers which are the closest in energy. They provide information about the isomer dependence of the HF redshift, and enable direct comparison with the experimental data recently obtained in helium nanodroplets. The agreement between theory and experiment is excellent, in particular, for the nonadditive DMC redshifts. The relative, incremental redshifts are reproduced accurately even at the lower level of theory, i.e., the DMC and quantum five-dimensional (rigid Ar(n)) calculations on the pairwise-additive PESs. The nonadditive interactions make a significant contribution to the frequency shift, on the order of 10%-12%, and have to be included in the PESs in order for the theory to yield accurate magnitude of the HF redshift. The energy gaps between the DMC ground states of the cluster isomers are very different from the energy separation of their respective minima on the PES, due to the considerable variations in the intermolecular zero-point energy of different Ar(n)HF isomers.

Evaluation of Goal Programming for the Optimal Assignment of Inspectors to Construction Projects

DTIC Science & Technology

1988-09-01

Inputs ..... .............. 90 Equation Coefficients . ....... .. 90 Weights, Priorities and the AHP . . 91 Right-Hand Side Values ........ .. 91...the AHP Hierarchy with k Levels . . 36 3. Sample Matrix for Pairwise Comparison ........ .. 37 4. Assignment of I and p for Example Problem...Weights for Example Problem ... 61 3. AHP Weights and Coefficient ci, Values. ........ 63 vii AFIT/GEM/LSM/88S-16 Abstract The purpose of this study was

An Adaptive Tutor for Improving Visual Diagnosis

DTIC Science & Technology

2017-10-01

designed to inform the design of the adaptive tutor including a) focus groups to develop a relative “importance” ranking, b) pairwise comparisons by...Goal – Assemble case library X Focus group to verify controlled vocabulary for diagnosis and importance ranking X Assembled corpus of 80,000 cases and...policy or decision unless so designated by other documentation. REPORT DOCUMENTATION PAGE Form Approved OMB No. 0704-0188 Public reporting burden

Which is more effective for suppressing an infectious disease: imperfect vaccination or defense against contagion?

NASA Astrophysics Data System (ADS)

Kuga, Kazuki; Tanimoto, Jun

2018-02-01

We consider two imperfect ways to protect against an infectious disease such as influenza, namely vaccination giving only partial immunity and a defense against contagion such as wearing a mask. We build up a new analytic framework considering those two cases instead of perfect vaccination, conventionally assumed as a premise, with the assumption of an infinite and well-mixed population. Our framework also considers three different strategy-updating rules based on evolutionary game theory: conventional pairwise comparison with one randomly selected agent, another concept of pairwise comparison referring to a social average, and direct alternative selection not depending on the usual copying concept. We successfully obtain a phase diagram in which vaccination coverage at equilibrium can be compared when assuming the model of either imperfect vaccination or a defense against contagion. The obtained phase diagram reveals that a defense against contagion is marginally inferior to an imperfect vaccination as long as the same coefficient value is used. Highlights - We build a new analytical framework for a vaccination game combined with the susceptible-infected-recovered (SIR) model. - Our model can evaluate imperfect provisions such as vaccination giving only partial immunity and a defense against contagion. - We obtain a phase diagram with which to compare the quantitative effects of partial vaccination and a defense against contagion.

A randomized trial to determine the impact on compliance of a psychophysical peripheral cue based on the Elaboration Likelihood Model.

PubMed

Horton, Rachael Jane; Minniti, Antoinette; Mireylees, Stewart; McEntegart, Damian

2008-11-01

Non-compliance in clinical studies is a significant issue, but causes remain unclear. Utilizing the Elaboration Likelihood Model of persuasion, this study assessed the psychophysical peripheral cue 'Interactive Voice Response System (IVRS) call frequency' on compliance. 71 participants were randomized to once daily (OD), twice daily (BID) or three times daily (TID) call schedules over two weeks. Participants completed 30-item cognitive function tests at each call. Compliance was defined as proportion of expected calls within a narrow window (+/- 30 min around scheduled time), and within a relaxed window (-30 min to +4 h). Data were analyzed by ANOVA and pairwise comparisons adjusted by the Bonferroni correction. There was a relationship between call frequency and compliance. Bonferroni adjusted pairwise comparisons showed significantly higher compliance (p=0.03) for the BID (51.0%) than TID (30.3%) for the narrow window; for the extended window, compliance was higher (p=0.04) with OD (59.5%), than TID (38.4%). The IVRS psychophysical peripheral cue call frequency supported the ELM as a route to persuasion. The results also support OD strategy for optimal compliance. Models suggest specific indicators to enhance compliance with medication dosing and electronic patient diaries to improve health outcomes and data integrity respectively.

β-Hydroxy-β-methylbutyrate (HMB) supplementation and resistance exercise significantly reduce abdominal adiposity in healthy elderly men.

PubMed

Stout, Jeffrey R; Fukuda, David H; Kendall, Kristina L; Smith-Ryan, Abbie E; Moon, Jordan R; Hoffman, Jay R

2015-04-01

The effects of 12-weeks of HMB ingestion and resistance training (RT) on abdominal adiposity were examined in 48 men (66-78 yrs). All participants were randomly assigned to 1 of 4 groups: no-training placebo (NT-PL), HMB only (NT-HMB), RT with PL (RT-PL), or HMB with RT (RT-HMB). DXA was used to estimate abdominal fat mass (AFM) by placing the region of interest over the L1-L4 region of the spine. Outcomes were assessed by ANCOVA, with Bonferroni-corrected pairwise comparisons. Baseline AFM values were used as the covariate. The ANCOVA indicated a significant difference (p = 0.013) between group means for the adjusted posttest AFM values (mean (kg) ± SE: NT-PL = 2.59 ± 0.06; NT-HMB = 2.59 ± 0.61; RT-PL = 2.59 ± 0.62; RT-HMB = 2.34 ± 0.61). The pairwise comparisons indicated that AFM following the intervention period in the RT-HMB group was significantly less than NT-PL (p = 0.013), NT-HMB (p = 0.011), and RT-PL (p = 0.010). These data suggested that HMB in combination with 12 weeks of RT decreased AFM in elderly men. Copyright © 2015. Published by Elsevier Inc.

Comparisons of false negative rates from a trend test alone and from a trend test jointly with a control-high groups pairwise test in the determination of the carcinogenicity of new drugs.

PubMed

Lin, Karl K; Rahman, Mohammad A

2018-05-21

Interest has been expressed in using a joint test procedure that requires that the results of both a trend test and a pairwise comparison test between the control and the high groups be statistically significant simultaneously at the levels of significance recommended in the FDA 2001 draft guidance for industry document for the separate tests in order for the drug effect on the development of an individual tumor type to be considered as statistically significant. Results of our simulation studies show that there is a serious consequence of large inflations of the false negative rate through large decreases of false positive rate in the use of the above joint test procedure in the final interpretation of the carcinogenicity potential of a new drug if the levels of significance recommended for separate tests are used. The inflation can be as high as 204.5% of the false negative rate when the trend test alone is required to test if the effect is statistically significant. To correct the problem, new sets of levels of significance have also been developed for those who want to use the joint test in reviews of carcinogenicity studies.

Novel presentational approaches were developed for reporting network meta-analysis.

PubMed

Tan, Sze Huey; Cooper, Nicola J; Bujkiewicz, Sylwia; Welton, Nicky J; Caldwell, Deborah M; Sutton, Alexander J

2014-06-01

To present graphical tools for reporting network meta-analysis (NMA) results aiming to increase the accessibility, transparency, interpretability, and acceptability of NMA analyses. The key components of NMA results were identified based on recommendations by agencies such as the National Institute for Health and Care Excellence (United Kingdom). Three novel graphs were designed to amalgamate the identified components using familiar graphical tools such as the bar, line, or pie charts and adhering to good graphical design principles. Three key components for presentation of NMA results were identified, namely relative effects and their uncertainty, probability of an intervention being best, and between-study heterogeneity. Two of the three graphs developed present results (for each pairwise comparison of interventions in the network) obtained from both NMA and standard pairwise meta-analysis for easy comparison. They also include options to display the probability best, ranking statistics, heterogeneity, and prediction intervals. The third graph presents rankings of interventions in terms of their effectiveness to enable clinicians to easily identify "top-ranking" interventions. The graphical tools presented can display results tailored to the research question of interest, and targeted at a whole spectrum of users from the technical analyst to the nontechnical clinician. Copyright © 2014 Elsevier Inc. All rights reserved.

AlignMe—a membrane protein sequence alignment web server

PubMed Central

Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

2014-01-01

We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

Referring to the social performance promotes cooperation in spatial prisoner's dilemma games

NASA Astrophysics Data System (ADS)

Shigaki, Keizo; Tanimoto, Jun; Wang, Zhen; Kokubo, Satoshi; Hagishima, Aya; Ikegaya, Naoki

2012-09-01

We propose a new pairwise Fermi updating rule by considering a social average payoff when an agent copies a neighbor's strategy. In the update rule, a focal agent compares her payoff with the social average payoff of the same strategy that her pairwise opponent has. This concept might be justified by the fact that people reference global and, somehow, statistical information, not local information when imitating social behaviors. We presume several possible ways for the social average. Simulation results prove that the social average of some limited agents realizes more significant cooperation than that of the entire population.

A lower-extremities kinematic comparison of deep-water running styles and treadmill running.

PubMed

Killgore, Garry L; Wilcox, Anthony R; Caster, Brian L; Wood, Terry M

2006-11-01

The purpose of this investigation was to identify a deep-water running (DWR) style that most closely approximates terrestrial running, particularly relative to the lower extremities. Twenty intercollegiate distance runners (women, N = 12; men, N = 8) were videotaped from the right sagittal view while running on a treadmill (TR) and in deep water at 55-60% of their TR VO(2)max using 2 DWR styles: cross-country (CC) and high-knee (HK). Variables of interest were horizontal (X) and vertical (Y) displacement of the knee and ankle, stride rate (SR), VO(2), heart rate (HR), and rating of perceived exertion (RPE). Multivariate omnibus tests revealed statistically significant differences for RPE (p < 0.001). The post hoc pairwise comparisons revealed significant differences between TR and both DWR styles (p < 0.001). The kinematic variables multivariate omnibus tests were found to be statistically significant (p < 0.001 to p < 0.019). The post hoc pairwise comparisons revealed significant differences in SR (p < 0.001) between TR (1.25 +/- 0.08 Hz) and both DWR styles and also between the CC (0.81 +/- 0.08 Hz) and HK (1.14 +/- 0.10 Hz) styles of DWR. The CC style of DWR was found to be similar to TR with respect to linear ankle displacement, whereas the HK style was significantly different from TR in all comparisons made for ankle and knee displacement. The CC style of DWR is recommended as an adjunct to distance running training if the goal is to mimic the specificity of the ankle linear horizontal displacement of land-based running, but the SR will be slower at a comparable percentage of VO(2)max.

Comparing genomes with rearrangements and segmental duplications.

PubMed

Shao, Mingfu; Moret, Bernard M E

2015-06-15

Large-scale evolutionary events such as genomic rearrange.ments and segmental duplications form an important part of the evolution of genomes and are widely studied from both biological and computational perspectives. A basic computational problem is to infer these events in the evolutionary history for given modern genomes, a task for which many algorithms have been proposed under various constraints. Algorithms that can handle both rearrangements and content-modifying events such as duplications and losses remain few and limited in their applicability. We study the comparison of two genomes under a model including general rearrangements (through double-cut-and-join) and segmental duplications. We formulate the comparison as an optimization problem and describe an exact algorithm to solve it by using an integer linear program. We also devise a sufficient condition and an efficient algorithm to identify optimal substructures, which can simplify the problem while preserving optimality. Using the optimal substructures with the integer linear program (ILP) formulation yields a practical and exact algorithm to solve the problem. We then apply our algorithm to assign in-paralogs and orthologs (a necessary step in handling duplications) and compare its performance with that of the state-of-the-art method MSOAR, using both simulations and real data. On simulated datasets, our method outperforms MSOAR by a significant margin, and on five well-annotated species, MSOAR achieves high accuracy, yet our method performs slightly better on each of the 10 pairwise comparisons. http://lcbb.epfl.ch/softwares/coser. © The Author 2015. Published by Oxford University Press.

Mortality and operator experience with vascular access for percutaneous coronary intervention in patients with acute coronary syndromes: A pairwise and network meta-analysis of randomized controlled trials.

PubMed

Shah, Rahman; Askari, Reza; Haji, Showkat A; Rashid, Abdul

2017-12-01

Recently, several meta-analyses of randomized controlled trials (RCTs) have shown that transradial access (TRA) reduces mortality compared to transfemoral access (TFA). However, a critical appraisal of these RCTs suggests that the findings could have resulted from a greater incidence of adverse events in the TFA groups rather than a beneficial effect of TRA. Scientific databases and websites were searched for RCTs. Patients were divided into groups based on access type and whether the operator was a radial expert (RE) or non-radial expert (NRE). The groups were TFA-RE, TFA-NRE, TRA-RE, and TRA-NRE. Both a traditional meta-analysis and a network meta-analysis using mixed-treatment comparison models were performed. Data from 13 trials including 15,615 patients were analyzed. The mortality rate for TFA-RE (3.54%) was more than double compared to TFA-NRE (1.61%). In pairwise meta-analysis, TFA-RE was associated with increased risk of mortality (RR: 1.72, 95% CI: 1.13-2.62; p=0.011) compared to TFA-NRE. In subgroup analysis, TFA-RE was associated with increased mortality (RR: 1.70, 95% CI: 1.24-2.34; p=0.001) compared to TRA, but TRA-NRE was not. Similarly, in mixed comparison models, TFA-RE was associated with increased mortality compared to TRA-NRE, TRA-RE, and TFA-NRE, but TFA-NRE was not, compared to TRA-RE and TRA-NRE. Recently-reported survival differences between TRA and TFA may have been driven by adverse events in the TFA groups of the RCTs rather than a beneficial effect of TRA. This issue needs further investigation before labeling radial access a lifesaving procedure in invasively-managed patients with ACS. Published by Elsevier B.V.

Risk of Breast Cancer with CXCR4-using HIV Defined by V3-Loop Sequencing

PubMed Central

Goedert, James J.; Swenson, Luke C.; Napolitano, Laura A.; Haddad, Mojgan; Anastos, Kathryn; Minkoff, Howard; Young, Mary; Levine, Alexandra; Adeyemi, Oluwatoyin; Seaberg, Eric C.; Aouizerat, Bradley; Rabkin, Charles S.; Harrigan, P. Richard; Hessol, Nancy A.

2014-01-01

Objective Evaluate the risk of female breast cancer associated with HIV-CXCR4 (X4) tropism as determined by various genotypic measures. Methods A breast cancer case-control study, with pairwise comparisons of tropism determination methods, was conducted. From the Women's Interagency HIV Study repository, one stored plasma specimen was selected from 25 HIV-infected cases near the breast cancer diagnosis date and 75 HIV-infected control women matched for age and calendar date. HIVgp120-V3 sequences were derived by Sanger population sequencing (PS) and 454-pyro deep sequencing (DS). Sequencing-based HIV-X4 tropism was defined using the geno2pheno algorithm, with both high-stringency DS [False-Positive-Rate (FPR 3.5) and 2% X4 cutoff], and lower stringency DS (FPR 5.75, 15% X4 cut-off). Concordance of tropism results by PS, DS, and previously performed phenotyping was assessed with kappa (κ) statistics. Case-control comparisons used exact P-values and conditional logistic regression. Results In 74 women (19 cases, 55 controls) with complete results, prevalence of HIV-X4 by PS was 5% in cases vs 29% in controls (P=0.06, odds ratio 0.14, confidence interval 0.003-1.03). Smaller case-control prevalence differences were found with high-stringency DS (21% vs 36%, P=0.32), lower-stringency DS (16% vs 35%, P=0.18), and phenotyping (11% vs 31%, P=0.10). HIV-X4-tropism concordance was best between PS and lower-stringency DS (93%, κ=0.83). Other pairwise concordances were 82%-92% (κ=0.56-0.81). Concordance was similar among cases and controls. Conclusions HIV-X4 defined by population sequencing (PS) had good agreement with lower stringency deep sequencing and was significantly associated with lower odds of breast cancer. PMID:25321183

Remarkable sequence conservation of the last intron in the PKD1 gene.

PubMed

Rodova, Marianna; Islam, M Rafiq; Peterson, Kenneth R; Calvet, James P

2003-10-01

The last intron of the PKD1 gene (intron 45) was found to have exceptionally high sequence conservation across four mammalian species: human, mouse, rat, and dog. This conservation did not extend to the comparable intron in pufferfish. Pairwise comparisons for intron 45 showed 91% identity (human vs. dog) to 100% identity (mouse vs. rat) for an average for all four species of 94% identity. In contrast, introns 43 and 44 of the PKD1 gene had average pairwise identities of 57% and 54%, and exons 43, 44, and 45 and the coding region of exon 46 had average pairwise identities of 80%, 84%, 82%, and 80%. Intron 45 is 90 to 95 bp in length, with the major region of sequence divergence being in a central 4-bp to 9-bp variable region. RNA secondary structure analysis of intron 45 predicts a branching stem-loop structure in which the central variable region lies in one loop and the putative branch point sequence lies in another loop, suggesting that the intron adopts a specific stem-loop structure that may be important for its removal. Although intron 45 appears to conform to the class of small, G-triplet-containing introns that are spliced by a mechanism utilizing intron definition, its high sequence conservation may be a reflection of constraints imposed by a unique mechanism that coordinates splicing of this last PKD1 intron with polyadenylation.

Profiling cellular protein complexes by proximity ligation with dual tag microarray readout.

PubMed

Hammond, Maria; Nong, Rachel Yuan; Ericsson, Olle; Pardali, Katerina; Landegren, Ulf

2012-01-01

Patterns of protein interactions provide important insights in basic biology, and their analysis plays an increasing role in drug development and diagnostics of disease. We have established a scalable technique to compare two biological samples for the levels of all pairwise interactions among a set of targeted protein molecules. The technique is a combination of the proximity ligation assay with readout via dual tag microarrays. In the proximity ligation assay protein identities are encoded as DNA sequences by attaching DNA oligonucleotides to antibodies directed against the proteins of interest. Upon binding by pairs of antibodies to proteins present in the same molecular complexes, ligation reactions give rise to reporter DNA molecules that contain the combined sequence information from the two DNA strands. The ligation reactions also serve to incorporate a sample barcode in the reporter molecules to allow for direct comparison between pairs of samples. The samples are evaluated using a dual tag microarray where information is decoded, revealing which pairs of tags that have become joined. As a proof-of-concept we demonstrate that this approach can be used to detect a set of five proteins and their pairwise interactions both in cellular lysates and in fixed tissue culture cells. This paper provides a general strategy to analyze the extent of any pairwise interactions in large sets of molecules by decoding reporter DNA strands that identify the interacting molecules.

Population genetic structure of Santa Ynez rainbow trout – 2001 based on microsatellite and mtDNA analyses

USGS Publications Warehouse

Nielsen, Jennifer L.; Zimmerman, Christian E.; Olsen, Jeffrey B.; Wiacek, Talia; Kretschmer, E.J.; Greenwald, Glenn M.; Wenburg, John K.

2003-01-01

Microsatellite allelic and mitochondrial DNA (mtDNA) haplotype diversity are analyzed in eight rainbow trout (Oncorhynchus mykiss) collections: two from tributaries flowing into the upper Santa Ynez River watershed at Gibraltar Reservoir (Camuesa and Gidney creeks); three from tributaries between Gibraltar and Jameson reservoirs (Fox, Blue Canyon, and Alder creeks); one from a tributary above Jameson Reservoir (Juncal Creek); Jameson Reservoir; and one from the mainstem Santa Ynez River above the Jameson Reservoir. Both analyses reveal a high degree of population structure. Thirteen microsatellite loci are amplified from 376 fish. Population pairwise comparisons show significant differences in allelic frequency among all populations with the exception of Juncal Creek and Jameson Reservoir (p = 0.4). Pairwise Fst values range from 0.001 (Juncal Creek and Jameson Reservoir) to 0.17 (Camuesa and Juncal creeks) with an overall value of 0.021. Regression analyses (Slatkin 1993) supports an isolation-bydistance model in the five populations below Jameson Reservoir (intercept = 1.187, slope = -0.41, r2 = 0.67). A neighbor-joining bootstrap value of 100% (based on 2000 replicate trees) separates the populations sampled above and below Juncal Dam. Composite haplotypes from 321 fish generated using mtDNA sequence data (Dloop) reveal four previously described haplotypes (MYS1, MYS3, MYS5 and MYS8; Nielsen et al. 1994a), and one (MYS5) was found in all populations. Mean haplotype diversity is 0.48. Pairwise Fst values from mtDNA range from -0.019 to 0.530 (0.177 over all populations) and are larger than those for microsatellites in 26 of 28 pairwise comparisons. In addition, the mtDNA and microsatellites provide contrasting evidence of the relationship of Fox and Alder creeks to the other six populations. Discrepancies between the two markers are likely due to the unique properties of the two marker types and their value in revealing historic (mtDNA) versus contemporary (microsatellites) genetic relationships. The contrasting results may indicate how relationships among the upper Santa Ynez River populations have changed since the installation of Juncal Dam. Comparisons of mtDNA haplotype frequencies from fish collected for this study with samples analyzed previously in JLN’s laboratory (1993) reveal significant differences in mtDNA haplotypes for Fox and Alder creeks. In the 2001 samples from this study, there is a loss of three haplotypes despite larger sample sizes. AMOVA analysis of what we term “upper” (Alder, Fox, Blue Canyon, Camuesa, Gidney creeks and the upper Santa Ynez mainstem) and “lower” (Hilton, Salsipuedes and the lower mainstem Santa Ynez River) Santa Ynez River populations (1993-2001) reveal that 11% of the variance in haplotypes is found between the upper and lower drainage. A comparison of the mtDNA data from this study with those available for southern California coastal and California hatchery O. mykiss populations yields Fst values of 0.15 and 0.47, respectively. Differentiation of mtDNA haplotypes for population pairs of Santa Ynez River and hatchery fish show no significant differentiation between wild and at least one hatchery strain in Cachuma Reservoir, Hilton Creek, and the Lower Santa Ynez River.

Dali server update.

PubMed

Holm, Liisa; Laakso, Laura M

2016-07-08

The Dali server (http://ekhidna2.biocenter.helsinki.fi/dali) is a network service for comparing protein structures in 3D. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The Dali server has been running in various places for over 20 years and is used routinely by crystallographers on newly solved structures. The latest update of the server provides enhanced analytics for the study of sequence and structure conservation. The server performs three types of structure comparisons: (i) Protein Data Bank (PDB) search compares one query structure against those in the PDB and returns a list of similar structures; (ii) pairwise comparison compares one query structure against a list of structures specified by the user; and (iii) all against all structure comparison returns a structural similarity matrix, a dendrogram and a multidimensional scaling projection of a set of structures specified by the user. Structural superimpositions are visualized using the Java-free WebGL viewer PV. The structural alignment view is enhanced by sequence similarity searches against Uniprot. The combined structure-sequence alignment information is compressed to a stack of aligned sequence logos. In the stack, each structure is structurally aligned to the query protein and represented by a sequence logo. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Pairwise contact energy statistical potentials can help to find probability of point mutations.

PubMed

Saravanan, K M; Suvaithenamudhan, S; Parthasarathy, S; Selvaraj, S

2017-01-01

To adopt a particular fold, a protein requires several interactions between its amino acid residues. The energetic contribution of these residue-residue interactions can be approximated by extracting statistical potentials from known high resolution structures. Several methods based on statistical potentials extracted from unrelated proteins are found to make a better prediction of probability of point mutations. We postulate that the statistical potentials extracted from known structures of similar folds with varying sequence identity can be a powerful tool to examine probability of point mutation. By keeping this in mind, we have derived pairwise residue and atomic contact energy potentials for the different functional families that adopt the (α/β) 8 TIM-Barrel fold. We carried out computational point mutations at various conserved residue positions in yeast Triose phosphate isomerase enzyme for which experimental results are already reported. We have also performed molecular dynamics simulations on a subset of point mutants to make a comparative study. The difference in pairwise residue and atomic contact energy of wildtype and various point mutations reveals probability of mutations at a particular position. Interestingly, we found that our computational prediction agrees with the experimental studies of Silverman et al. (Proc Natl Acad Sci 2001;98:3092-3097) and perform better prediction than i Mutant and Cologne University Protein Stability Analysis Tool. The present work thus suggests deriving pairwise contact energy potentials and molecular dynamics simulations of functionally important folds could help us to predict probability of point mutations which may ultimately reduce the time and cost of mutation experiments. Proteins 2016; 85:54-64. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Multicriteria analysis of product operational effectiveness at design stages

NASA Astrophysics Data System (ADS)

Irzaev, G. Kh

2018-03-01

The multicriteria rapid assessment method of techno-economic parameters of new products is developed. It avoids expensive engineering changes during the operational stages through the analysis of external and internal factors at an early stage in the design that affect the maintainability and manufacturability of the product. The expert selection of the initial multitude of indicators from the five enlarged criteria groups and their subsequent pairwise comparison allow one to distinguish the complex compliance criteria of product design with the average and optimum values of the operational effectiveness. The values comparison provides an opportunity to decide on the continuation of the process for designing and preparation of the product manufacture.

Quantitative assessment of joint position sense recovery in subacute stroke patients: a pilot study.

PubMed

Kattenstroth, Jan-Christoph; Kalisch, Tobias; Kowalewski, Rebecca; Tegenthoff, Martin; Dinse, Hubert R

2013-11-01

To assess joint position sense performance in subacute stroke patients using a novel quantitative assessment. Proof-of-principle pilot study with a group of subacute stroke patients. Assessment at baseline and after 2 weeks of intervention. Additional data for a healthy age-matched control group. Ten subacute stroke patients (aged 65.41 years (standard deviation 2.5), 4 females, 2.3 weeks (standard deviation 0.2)) post-stroke receiving in-patient standard rehabilitation and repetitive electrical stimulation of the affected hand. Joint position sense was assessed based on the ability of correctly perceiving the opening angles of the finger joints. Patients had to report size differences of polystyrene balls of various sizes, whilst the balls were enclosed simultaneously by the affected and the non-affected hands. A total of 21 pairwise size comparisons was used to quantify joint position performance. After 2 weeks of therapeutic intervention a significant improvement in joint position sense performance was observed; however, the performance level was still below that of a healthy control group. The results indicate high feasibility and sensitivity of the joint position test in subacute stroke patients. Testing allowed quantification of both the deficit and the rehabilitation outcome.

Network reciprocity by coexisting learning and teaching strategies

NASA Astrophysics Data System (ADS)

Tanimoto, Jun; Brede, Markus; Yamauchi, Atsuo

2012-03-01

We propose a network reciprocity model in which an agent probabilistically adopts learning or teaching strategies. In the learning adaptation mechanism, an agent may copy a neighbor's strategy through Fermi pairwise comparison. The teaching adaptation mechanism involves an agent imposing its strategy on a neighbor. Our simulations reveal that the reciprocity is significantly affected by the frequency with which learning and teaching agents coexist in a network and by the structure of the network itself.

Full-Thickness Thermal Injury Delays Wound Closure in a Murine Model

DTIC Science & Technology

2015-01-01

Wu, MS Submitted for publication June 9, 2014. Ac- cepted in revised form August 17, 2014. *Correspondence: Dental and Trauma Re- search Detachment...repeated measures ANOVA with pairwise comparison and Tukey–Kramer adjustment, using JMP statistics software (SAS, Cary , NC). Results were presented as...Microbiologist and the Director of Science, and Rodney K. Chan, MD, is a Plastic Surgeon in the Dental and Trauma Research Detachment at US Army

Health-Related Quality of Life in Children and Adolescents with Hereditary Bleeding Disorders and in Children and Adolescents with Stroke: Cross-Sectional Comparison to Siblings and Peers

PubMed Central

Neuner, Bruno; von Mackensen, Sylvia; Holzhauer, Susanne; Funk, Stephanie; Klamroth, Robert; Kurnik, Karin; Krümpel, Anne; Halimeh, Susan; Reinke, Sarah; Frühwald, Michael; Nowak-Göttl, Ulrike

2016-01-01

Objectives. To investigate self-reported health-related quality of life (HrQoL) in children and adolescents with chronic medical conditions compared with siblings/peers. Methods. Group 1 (6 treatment centers) consisted of 74 children/adolescents aged 8–16 years with hereditary bleeding disorders (HBD), 12 siblings, and 34 peers. Group 2 (one treatment center) consisted of 70 children/adolescents with stroke/transient ischemic attack, 14 siblings, and 72 peers. HrQoL was assessed with the “revised KINDer Lebensqualitätsfragebogen” (KINDL-R) questionnaire. Multivariate analyses within groups were done by one-way ANOVA and post hoc pairwise single comparisons by Student's t-tests. Adjusted pairwise comparisons were done by hierarchical linear regressions with individuals nested within treatment centers (group 1) and by linear regressions (group 2), respectively. Results. No differences were found in multivariate analyses of self-reported HrQoL in group 1, while in group 2 differences occurred in overall wellbeing and all subdimensions. These differences were due to differences between patients and peers. After adjusting for age, gender, number of siblings, and treatment center these differences persisted regarding self-worth (p = .0040) and friend-related wellbeing (p < .001). Conclusions. In children with HBD, HrQoL was comparable to siblings and peers. In children with stroke/TIA HrQoL was comparable to siblings while peers, independently of relevant confounder, showed better self-worth and friend-related wellbeing. PMID:27294108

Development and evaluation of learning module on clinical decision-making in Prosthodontics.

PubMed

Deshpande, Saee; Lambade, Dipti; Chahande, Jayashree

2015-01-01

Best practice strategies for helping students learn the reasoning skills of problem solving and critical thinking (CT) remain a source of conjecture, particularly with regard to CT. The dental education literature is fundamentally devoid of research on the cognitive components of clinical decision-making. This study was aimed to develop and evaluate the impact of blended learning module on clinical decision-making skills of dental graduates for planning prosthodontics rehabilitation. An interactive teaching module consisting of didactic lectures on clinical decision-making and a computer-assisted case-based treatment planning software was developed Its impact on cognitive knowledge gain in clinical decision-making was evaluated using an assessment involving problem-based multiple choice questions and paper-based case scenarios. Mean test scores were: Pretest (17 ± 1), posttest 1 (21 ± 2) and posttest 2 (43 ± 3). Comparison of mean scores was done with one-way ANOVA test. There was overall significant difference in between mean scores at all the three points (P < 0.001). A pair-wise comparison of mean scores was done with Bonferroni test. The mean difference is significant at the 0.05 level. The pair-wise comparison shows that posttest 2 score is significantly higher than posttest 1 and posttest 1 is significantly higher than pretest that is, pretest 2 > posttest 1 > pretest. Blended teaching methods employing didactic lectures on the clinical decision-making as well as computer assisted case-based learning can be used to improve quality of clinical decision-making in prosthodontic rehabilitation for dental graduates.

Variation in host specificity and gene content in strains from genetically isolated lineages of the ectomycorrhizal fungus Paxillus involutus s. lat.

PubMed

Hedh, Jenny; Johansson, Tomas; Tunlid, Anders

2009-10-01

Ectomycorrhizal fungi are known to vary in host range. Some fungi can enter into symbiosis with multiple plant species, while others have restricted host ranges. The aim of this study was to examine variation in host specificity among strains from the basidiomycete Paxillus involutus s. lat. Recent studies have shown that this fungus consists of at least four genetically isolated lineages, phylogenetic species (PS) I (which corresponds to the morphological species Paxillus obscurosporus), PS II (P. involutus s. str.), PS III (Paxillus validus), and PS IV (not yet supported by any reference material). Thirty-five Paxillus strains of PS I to IV were examined in microcosms for their capacity to infect birch (Betula pendula) and spruce (Picea abies). Seventeen strains were compatible and formed mycorrhizae with both tree species. Seven strains were incompatible with both birch and spruce. The gene content in three pairs of incompatible and compatible strains PS I, II, and III were compared using microarray-based comparative genomic hybridizations. Of 4,113 P. involutus gene representatives analyzed, 390 varied in copy numbers in at least one of the three pairwise comparisons. Only three reporters showed significant changes in all three pairwise comparisons, and none of these were changed in a similar way in three comparisons. Our data indicate that changes in host range have occurred frequently and independently among strains in P. obscurosporus, P. involutus s. str., and P. validus. No evidence was obtained demonstrating that these changes have been associated with the gain or loss of similar genes in these three species.

Cost-effectiveness of alternative outpatient pelvic inflammatory disease treatment strategies.

PubMed

Smith, Kenneth J; Ness, Roberta B; Wiesenfeld, Harold C; Roberts, Mark S

2007-12-01

Effectiveness differences between outpatient pelvic inflammatory disease (PID) treatment regimens are uncertain, but significant differences in cost exist. To examine the influence of antibiotic costs on PID therapy cost-effectiveness. The authors used a Markov decision model to estimate the cost-effectiveness of recommended antibiotic regimens for PID and performed a value of information analysis to guide future research. Antibiotic costs vary between USD 43 and USD188. Pairwise comparisons, assuming a hypothetical 1% relative risk reduction in PID complications with the more expensive regimen, showed economically reasonable cost-effectiveness ratios. Value of information and sample size considerations support further investigation to detect 10% PID complication rate differences between regimens with >or=USD 50 cost differences. Within the cost range of recommended regimens, use of more expensive antibiotics would be economically reasonable if relatively small decreases in PID complication rates exist. Further investigation of effectiveness differences between regimens is needed.

Surface Hold Advisor Using Critical Sections

NASA Technical Reports Server (NTRS)

Law, Caleb Hoi Kei (Inventor); Hsiao, Thomas Kun-Lung (Inventor); Mittler, Nathan C. (Inventor); Couluris, George J. (Inventor)

2013-01-01

The Surface Hold Advisor Using Critical Sections is a system and method for providing hold advisories to surface controllers to prevent gridlock and resolve crossing and merging conflicts among vehicles traversing a vertex-edge graph representing a surface traffic network on an airport surface. The Advisor performs pair-wise comparisons of current position and projected path of each vehicle with other surface vehicles to detect conflicts, determine critical sections, and provide hold advisories to traffic controllers recommending vehicles stop at entry points to protected zones around identified critical sections. A critical section defines a segment of the vertex-edge graph where vehicles are in crossing or merging or opposite direction gridlock contention. The Advisor detects critical sections without reference to scheduled, projected or required times along assigned vehicle paths, and generates hold advisories to prevent conflicts without requiring network path direction-of-movement rules and without requiring rerouting, rescheduling or other network optimization solutions.

Bayesian learning of visual chunks by human observers

PubMed Central

Orbán, Gergő; Fiser, József; Aslin, Richard N.; Lengyel, Máté

2008-01-01

Efficient and versatile processing of any hierarchically structured information requires a learning mechanism that combines lower-level features into higher-level chunks. We investigated this chunking mechanism in humans with a visual pattern-learning paradigm. We developed an ideal learner based on Bayesian model comparison that extracts and stores only those chunks of information that are minimally sufficient to encode a set of visual scenes. Our ideal Bayesian chunk learner not only reproduced the results of a large set of previous empirical findings in the domain of human pattern learning but also made a key prediction that we confirmed experimentally. In accordance with Bayesian learning but contrary to associative learning, human performance was well above chance when pair-wise statistics in the exemplars contained no relevant information. Thus, humans extract chunks from complex visual patterns by generating accurate yet economical representations and not by encoding the full correlational structure of the input. PMID:18268353

Learning a Markov Logic network for supervised gene regulatory network inference

PubMed Central

2013-01-01

Background Gene regulatory network inference remains a challenging problem in systems biology despite the numerous approaches that have been proposed. When substantial knowledge on a gene regulatory network is already available, supervised network inference is appropriate. Such a method builds a binary classifier able to assign a class (Regulation/No regulation) to an ordered pair of genes. Once learnt, the pairwise classifier can be used to predict new regulations. In this work, we explore the framework of Markov Logic Networks (MLN) that combine features of probabilistic graphical models with the expressivity of first-order logic rules. Results We propose to learn a Markov Logic network, e.g. a set of weighted rules that conclude on the predicate “regulates”, starting from a known gene regulatory network involved in the switch proliferation/differentiation of keratinocyte cells, a set of experimental transcriptomic data and various descriptions of genes all encoded into first-order logic. As training data are unbalanced, we use asymmetric bagging to learn a set of MLNs. The prediction of a new regulation can then be obtained by averaging predictions of individual MLNs. As a side contribution, we propose three in silico tests to assess the performance of any pairwise classifier in various network inference tasks on real datasets. A first test consists of measuring the average performance on balanced edge prediction problem; a second one deals with the ability of the classifier, once enhanced by asymmetric bagging, to update a given network. Finally our main result concerns a third test that measures the ability of the method to predict regulations with a new set of genes. As expected, MLN, when provided with only numerical discretized gene expression data, does not perform as well as a pairwise SVM in terms of AUPR. However, when a more complete description of gene properties is provided by heterogeneous sources, MLN achieves the same performance as a black-box model such as a pairwise SVM while providing relevant insights on the predictions. Conclusions The numerical studies show that MLN achieves very good predictive performance while opening the door to some interpretability of the decisions. Besides the ability to suggest new regulations, such an approach allows to cross-validate experimental data with existing knowledge. PMID:24028533

Learning a Markov Logic network for supervised gene regulatory network inference.

PubMed

Brouard, Céline; Vrain, Christel; Dubois, Julie; Castel, David; Debily, Marie-Anne; d'Alché-Buc, Florence

2013-09-12

Gene regulatory network inference remains a challenging problem in systems biology despite the numerous approaches that have been proposed. When substantial knowledge on a gene regulatory network is already available, supervised network inference is appropriate. Such a method builds a binary classifier able to assign a class (Regulation/No regulation) to an ordered pair of genes. Once learnt, the pairwise classifier can be used to predict new regulations. In this work, we explore the framework of Markov Logic Networks (MLN) that combine features of probabilistic graphical models with the expressivity of first-order logic rules. We propose to learn a Markov Logic network, e.g. a set of weighted rules that conclude on the predicate "regulates", starting from a known gene regulatory network involved in the switch proliferation/differentiation of keratinocyte cells, a set of experimental transcriptomic data and various descriptions of genes all encoded into first-order logic. As training data are unbalanced, we use asymmetric bagging to learn a set of MLNs. The prediction of a new regulation can then be obtained by averaging predictions of individual MLNs. As a side contribution, we propose three in silico tests to assess the performance of any pairwise classifier in various network inference tasks on real datasets. A first test consists of measuring the average performance on balanced edge prediction problem; a second one deals with the ability of the classifier, once enhanced by asymmetric bagging, to update a given network. Finally our main result concerns a third test that measures the ability of the method to predict regulations with a new set of genes. As expected, MLN, when provided with only numerical discretized gene expression data, does not perform as well as a pairwise SVM in terms of AUPR. However, when a more complete description of gene properties is provided by heterogeneous sources, MLN achieves the same performance as a black-box model such as a pairwise SVM while providing relevant insights on the predictions. The numerical studies show that MLN achieves very good predictive performance while opening the door to some interpretability of the decisions. Besides the ability to suggest new regulations, such an approach allows to cross-validate experimental data with existing knowledge.

Application of the Refined Integral Method in the mathematical modeling of drug delivery from one-layer torus-shaped devices.

PubMed

Helbling, Ignacio M; Ibarra, Juan C D; Luna, Julio A

2012-02-28

A mathematical modeling of controlled release of drug from one-layer torus-shaped devices is presented. Analytical solutions based on Refined Integral Method (RIM) are derived. The validity and utility of the model are ascertained by comparison of the simulation results with matrix-type vaginal rings experimental release data reported in the literature. For the comparisons, the pair-wise procedure is used to measure quantitatively the fit of the theoretical predictions to the experimental data. A good agreement between the model prediction and the experimental data is observed. A comparison with a previously reported model is also presented. More accurate results are achieved for small A/C(s) ratios. Copyright © 2011 Elsevier B.V. All rights reserved.

Exploring the roles of cannot-link constraint in community detection via Multi-variance Mixed Gaussian Generative Model.

PubMed

Yang, Liang; Ge, Meng; Jin, Di; He, Dongxiao; Fu, Huazhu; Wang, Jing; Cao, Xiaochun

2017-01-01

Due to the demand for performance improvement and the existence of prior information, semi-supervised community detection with pairwise constraints becomes a hot topic. Most existing methods have been successfully encoding the must-link constraints, but neglect the opposite ones, i.e., the cannot-link constraints, which can force the exclusion between nodes. In this paper, we are interested in understanding the role of cannot-link constraints and effectively encoding pairwise constraints. Towards these goals, we define an integral generative process jointly considering the network topology, must-link and cannot-link constraints. We propose to characterize this process as a Multi-variance Mixed Gaussian Generative (MMGG) Model to address diverse degrees of confidences that exist in network topology and pairwise constraints and formulate it as a weighted nonnegative matrix factorization problem. The experiments on artificial and real-world networks not only illustrate the superiority of our proposed MMGG, but also, most importantly, reveal the roles of pairwise constraints. That is, though the must-link is more important than cannot-link when either of them is available, both must-link and cannot-link are equally important when both of them are available. To the best of our knowledge, this is the first work on discovering and exploring the importance of cannot-link constraints in semi-supervised community detection.

Exploring the roles of cannot-link constraint in community detection via Multi-variance Mixed Gaussian Generative Model

PubMed Central

Ge, Meng; Jin, Di; He, Dongxiao; Fu, Huazhu; Wang, Jing; Cao, Xiaochun

2017-01-01

Due to the demand for performance improvement and the existence of prior information, semi-supervised community detection with pairwise constraints becomes a hot topic. Most existing methods have been successfully encoding the must-link constraints, but neglect the opposite ones, i.e., the cannot-link constraints, which can force the exclusion between nodes. In this paper, we are interested in understanding the role of cannot-link constraints and effectively encoding pairwise constraints. Towards these goals, we define an integral generative process jointly considering the network topology, must-link and cannot-link constraints. We propose to characterize this process as a Multi-variance Mixed Gaussian Generative (MMGG) Model to address diverse degrees of confidences that exist in network topology and pairwise constraints and formulate it as a weighted nonnegative matrix factorization problem. The experiments on artificial and real-world networks not only illustrate the superiority of our proposed MMGG, but also, most importantly, reveal the roles of pairwise constraints. That is, though the must-link is more important than cannot-link when either of them is available, both must-link and cannot-link are equally important when both of them are available. To the best of our knowledge, this is the first work on discovering and exploring the importance of cannot-link constraints in semi-supervised community detection. PMID:28678864

POEM: Identifying Joint Additive Effects on Regulatory Circuits.

PubMed

Botzman, Maya; Nachshon, Aharon; Brodt, Avital; Gat-Viks, Irit

2016-01-01

Expression Quantitative Trait Locus (eQTL) mapping tackles the problem of identifying variation in DNA sequence that have an effect on the transcriptional regulatory network. Major computational efforts are aimed at characterizing the joint effects of several eQTLs acting in concert to govern the expression of the same genes. Yet, progress toward a comprehensive prediction of such joint effects is limited. For example, existing eQTL methods commonly discover interacting loci affecting the expression levels of a module of co-regulated genes. Such "modularization" approaches, however, are focused on epistatic relations and thus have limited utility for the case of additive (non-epistatic) effects. Here we present POEM (Pairwise effect On Expression Modules), a methodology for identifying pairwise eQTL effects on gene modules. POEM is specifically designed to achieve high performance in the case of additive joint effects. We applied POEM to transcription profiles measured in bone marrow-derived dendritic cells across a population of genotyped mice. Our study reveals widespread additive, trans-acting pairwise effects on gene modules, characterizes their organizational principles, and highlights high-order interconnections between modules within the immune signaling network. These analyses elucidate the central role of additive pairwise effect in regulatory circuits, and provide computational tools for future investigations into the interplay between eQTLs. The software described in this article is available at csgi.tau.ac.il/POEM/.

POEM: Identifying Joint Additive Effects on Regulatory Circuits

PubMed Central

Botzman, Maya; Nachshon, Aharon; Brodt, Avital; Gat-Viks, Irit

2016-01-01

Motivation: Expression Quantitative Trait Locus (eQTL) mapping tackles the problem of identifying variation in DNA sequence that have an effect on the transcriptional regulatory network. Major computational efforts are aimed at characterizing the joint effects of several eQTLs acting in concert to govern the expression of the same genes. Yet, progress toward a comprehensive prediction of such joint effects is limited. For example, existing eQTL methods commonly discover interacting loci affecting the expression levels of a module of co-regulated genes. Such “modularization” approaches, however, are focused on epistatic relations and thus have limited utility for the case of additive (non-epistatic) effects. Results: Here we present POEM (Pairwise effect On Expression Modules), a methodology for identifying pairwise eQTL effects on gene modules. POEM is specifically designed to achieve high performance in the case of additive joint effects. We applied POEM to transcription profiles measured in bone marrow-derived dendritic cells across a population of genotyped mice. Our study reveals widespread additive, trans-acting pairwise effects on gene modules, characterizes their organizational principles, and highlights high-order interconnections between modules within the immune signaling network. These analyses elucidate the central role of additive pairwise effect in regulatory circuits, and provide computational tools for future investigations into the interplay between eQTLs. Availability: The software described in this article is available at csgi.tau.ac.il/POEM/. PMID:27148351

Post-Vacuum-Assisted Stereotactic Core Biopsy Clip Displacement: A Comparison Between Commercially Available Clips and Surgical Clip.

PubMed

Yen, Peggy; Dumas, Sandra; Albert, Arianne; Gordon, Paula

2018-02-01

The placement of localization clips following percutaneous biopsy is a standard practice for a variety of situations. Subsequent clip displacement creates challenges for imaging surveillance and surgical planning, and may cause confusion amongst radiologists and between surgeons and radiologists. Many causes have been attributed for this phenomenon including the commonly accepted "accordion effect." Herein, we investigate the performance of a low cost surgical clip system against 4 commercially available clips. We retrospectively reviewed 2112 patients who underwent stereotactic vacuum-assisted core biopsy followed by clip placement between January 2013 and June 2016. The primary performance parameter compared was displacement >10 mm following vacuum-assisted stereotactic core biopsy. Within the group of clips that had displaced, the magnitude of displacement was compared. There was a significant difference in displacement among the clip types (P < .0001) with significant pairwise comparisons between pediatric surgical clips and SecureMark (38% vs 28%; P = .001) and SenoMark (38% vs 27%; P = .0001) in the proportion displaced. The surgical clips showed a significant magnitude of displacement of approximately 25% greater average distance displaced. As a whole, the commercial clips performed better than the surgical clip after stereotactic vacuum-assisted core biopsy suggesting the surrounding outer component acts to anchor the central clip and minimizes clip displacement. The same should apply to tomosynthesis-guided biopsy. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

Relationships Between Potentiation Effects After Ballistic Half-Squats and Bilateral Symmetry.

PubMed

Suchomel, Timothy J; Sato, Kimitake; DeWeese, Brad H; Ebben, William P; Stone, Michael H

2016-05-01

The purposes of this study were to examine the effect of ballistic concentric-only half-squats (COHS) on subsequent squat-jump (SJ) performances at various rest intervals and to examine the relationships between changes in SJ performance and bilateral symmetry at peak performance. Thirteen resistance-trained men performed an SJ immediately and every minute up to 10 min on dual force plates after 2 ballistic COHS repetitions at 90% of their 1-repetition-maximum COHS. SJ peak force, peak power, net impulse, and rate of force development (RFD) were compared using a series of 1-way repeated-measures ANOVAs. The percent change in performance at which peak performance occurred for each variable was correlated with the symmetry index scores at the corresponding time point using Pearson correlation coefficients. Statistical differences in peak power (P = .031) existed between rest intervals; however, no statistically significant pairwise comparisons were present (P > .05). No statistical differences in peak force (P = .201), net impulse (P = .064), and RFD (P = .477) were present between rest intervals. The relationships between changes in SJ performance and bilateral symmetry after the rest interval that produced the greatest performance for peak force (r = .300, P = .319), peak power (r = -.041, P = .894), net impulse (r = -.028, P = .927), and RFD (r = -.434, P = .138) were not statistically significant. Ballistic COHS may enhance SJ performance; however, the changes in performance were not related to bilateral symmetry.

Systematic review and economic modelling of the effectiveness and cost-effectiveness of non-surgical treatments for women with stress urinary incontinence.

PubMed

Imamura, M; Abrams, P; Bain, C; Buckley, B; Cardozo, L; Cody, J; Cook, J; Eustice, S; Glazener, C; Grant, A; Hay-Smith, J; Hislop, J; Jenkinson, D; Kilonzo, M; Nabi, G; N'Dow, J; Pickard, R; Ternent, L; Wallace, S; Wardle, J; Zhu, S; Vale, L

2010-08-01

To assess the clinical effectiveness and cost-effectiveness of non-surgical treatments for women with stress urinary incontinence (SUI) through systematic review and economic modelling. The Cochrane Incontinence Group Specialised Register, electronic databases and the websites of relevant professional organisations and manufacturers, and the following databases: CINAHL, EMBASE, BIOSIS, Science Citation Index and Social Science Citation Index, Current Controlled Trials, ClinicalTrials.gov and the UKCRN Portfolio Database. The study comprised three distinct elements. (1) A survey of 188 women with SUI to identify outcomes of importance to them (activities of daily living; sex, hygiene and lifestyle issues; emotional health; and the availability of services). (2) A systematic review and meta-analysis of non-surgical treatments for SUI to find out which are most effective by comparing results of trials (direct pairwise comparisons) and by modelling results (mixed-treatment comparisons - MTCs). A total of 88 randomised controlled trials (RCTs) and quasi-RCTs reporting data from 9721 women were identified, considering five generic interventions [pelvic floor muscle training (PFMT), electrical stimulation (ES), vaginal cones (VCs), bladder training (BT) and serotonin-noradrenaline reuptake inhibitor (SNRI) medications], in many variations and combinations. Data were available for 37 interventions and 68 treatment comparisons by direct pairwise assessment. Mixed-treatment comparison models compared 14 interventions, using data from 55 trials (6608 women). (3) Economic modelling, using a Markov model, to find out which combinations of treatments (treatment pathways) are most cost-effective for SUI. Titles and abstracts identified were assessed by one reviewer and full-text copies of all potentially relevant reports independently assessed by two reviewers. Any disagreements were resolved by consensus or arbitration by a third person. Direct pairwise comparison and MTC analysis showed that the treatments were more effective than no treatment. Delivering PFMT in a more intense fashion, either through extra sessions or with biofeedback (BF), appeared to be the most effective treatment [PFMT extra sessions vs no treatment (NT) odds ratio (OR) 10.7, 95% credible interval (CrI) 5.03 to 26.2; PFMT + BF vs NT OR 12.3, 95% CrI 5.35 to 32.7]. Only when success was measured in terms of improvement was there evidence that basic PFMT was better than no treatment (PFMT basic vs NT OR 4.47, 95% CrI 2.03 to 11.9). Analysis of cost-effectiveness showed that for cure rates, the strategy using lifestyle changes and PFMT with extra sessions followed by tension-free vaginal tape (TVT) (lifestyle advice-PFMT extra sessions-TVT) had a probability of greater than 70% of being considered cost-effective for all threshold values for willingness to pay for a QALY up to 50,000 pounds. For improvement rates, lifestyle advice-PFMT extra sessions-TVT had a probability of greater than 50% of being considered cost-effective when society's willingness to pay for an additional QALY was more than 10,000 pounds. The results were most sensitive to changes in the long-term performance of PFMT and also in the relative effectiveness of basic PFMT and PFMT with extra sessions. Although a large number of studies were identified, few data were available for most comparisons and long-term data were sparse. Challenges for evidence synthesis were the lack of consensus on the most appropriate method for assessing incontinence and intervention protocols that were complex and varied considerably across studies. More intensive forms of PFMT appear worthwhile, but further research is required to define an optimal form of more intensive therapy that is feasible and efficient for the NHS to provide, along with further definitive evidence from large, well-designed studies.

Development of a methodology for selecting criteria and indicators of sustainable forest management: a case study on participatory assessment.

PubMed

Mendoza, G A; Prabhu, R

2000-12-01

This paper describes an application of multiple criteria analysis (MCA) in assessing criteria and indicators adapted for a particular forest management unit. The methods include: ranking, rating, and pairwise comparisons. These methods were used in a participatory decision-making environment where a team representing various stakeholders and professionals used their expert opinions and judgements in assessing different criteria and indicators (C&I) on the one hand, and how suitable and applicable they are to a forest management unit on the other. A forest concession located in Kalimantan, Indonesia, was used as the site for the case study. Results from the study show that the multicriteria methods are effective tools that can be used as structured decision aids to evaluate, prioritize, and select sets of C&I for a particular forest management unit. Ranking and rating approaches can be used as a screening tool to develop an initial list of C&I. Pairwise comparison, on the other hand, can be used as a finer filter to further reduce the list. In addition to using these three MCA methods, the study also examines two commonly used group decision-making techniques, the Delphi method and the nominal group technique. Feedback received from the participants indicates that the methods are transparent, easy to implement, and provide a convenient environment for participatory decision-making.

Disability Weights for Chronic Mercury Intoxication Resulting from Gold Mining Activities: Results from an Online Pairwise Comparisons Survey.

PubMed

Steckling, Nadine; Devleesschauwer, Brecht; Winkelnkemper, Julia; Fischer, Florian; Ericson, Bret; Krämer, Alexander; Hornberg, Claudia; Fuller, Richard; Plass, Dietrich; Bose-O'Reilly, Stephan

2017-01-10

In artisanal small-scale gold mining, mercury is used for gold-extraction, putting miners and nearby residents at risk of chronic metallic mercury vapor intoxication (CMMVI). Burden of disease (BoD) analyses allow the estimation of the public health relevance of CMMVI, but until now there have been no specific CMMVI disability weights (DWs). The objective is to derive DWs for moderate and severe CMMVI. Disease-specific and generic health state descriptions of 18 diseases were used in a pairwise comparison survey. Mercury and BoD experts were invited to participate in an online survey. Data were analyzed using probit regression. Local regression was used to make the DWs comparable to the Global Burden of Disease (GBD) study. Alternative survey (visual analogue scale) and data analyses approaches (linear interpolation) were evaluated in scenario analyses. A total of 105 participants completed the questionnaire. DWs for moderate and severe CMMVI were 0.368 (0.261-0.484) and 0.588 (0.193-0.907), respectively. Scenario analyses resulted in higher mean values. The results are limited by the sample size, group of interviewees, questionnaire extent, and lack of generally accepted health state descriptions. DWs were derived to improve the data basis of mercury-related BoD estimates, providing useful information for policy-making. Integration of the results into the GBD DWs enhances comparability.

Phylogenetic Relationship of Necoclí Virus to Other South American Hantaviruses (Bunyaviridae: Hantavirus).

PubMed

Montoya-Ruiz, Carolina; Cajimat, Maria N B; Milazzo, Mary Louise; Diaz, Francisco J; Rodas, Juan David; Valbuena, Gustavo; Fulhorst, Charles F

2015-07-01

The results of a previous study suggested that Cherrie's cane rat (Zygodontomys cherriei) is the principal host of Necoclí virus (family Bunyaviridae, genus Hantavirus) in Colombia. Bayesian analyses of complete nucleocapsid protein gene sequences and complete glycoprotein precursor gene sequences in this study confirmed that Necoclí virus is phylogenetically closely related to Maporal virus, which is principally associated with the delicate pygmy rice rat (Oligoryzomys delicatus) in western Venezuela. In pairwise comparisons, nonidentities between the complete amino acid sequence of the nucleocapsid protein of Necoclí virus and the complete amino acid sequences of the nucleocapsid proteins of other hantaviruses were ≥8.7%. Likewise, nonidentities between the complete amino acid sequence of the glycoprotein precursor of Necoclí virus and the complete amino acid sequences of the glycoprotein precursors of other hantaviruses were ≥11.7%. Collectively, the unique association of Necoclí virus with Z. cherriei in Colombia, results of the Bayesian analyses of complete nucleocapsid protein gene sequences and complete glycoprotein precursor gene sequences, and results of the pairwise comparisons of amino acid sequences strongly support the notion that Necoclí virus represents a novel species in the genus Hantavirus. Further work is needed to determine whether Calabazo virus (a hantavirus associated with Z. brevicauda cherriei in Panama) and Necoclí virus are conspecific.

Disability Weights for Chronic Mercury Intoxication Resulting from Gold Mining Activities: Results from an Online Pairwise Comparisons Survey

PubMed Central

Steckling, Nadine; Devleesschauwer, Brecht; Winkelnkemper, Julia; Fischer, Florian; Ericson, Bret; Krämer, Alexander; Hornberg, Claudia; Fuller, Richard; Plass, Dietrich; Bose-O’Reilly, Stephan

2017-01-01

In artisanal small-scale gold mining, mercury is used for gold-extraction, putting miners and nearby residents at risk of chronic metallic mercury vapor intoxication (CMMVI). Burden of disease (BoD) analyses allow the estimation of the public health relevance of CMMVI, but until now there have been no specific CMMVI disability weights (DWs). The objective is to derive DWs for moderate and severe CMMVI. Disease-specific and generic health state descriptions of 18 diseases were used in a pairwise comparison survey. Mercury and BoD experts were invited to participate in an online survey. Data were analyzed using probit regression. Local regression was used to make the DWs comparable to the Global Burden of Disease (GBD) study. Alternative survey (visual analogue scale) and data analyses approaches (linear interpolation) were evaluated in scenario analyses. A total of 105 participants completed the questionnaire. DWs for moderate and severe CMMVI were 0.368 (0.261–0.484) and 0.588 (0.193–0.907), respectively. Scenario analyses resulted in higher mean values. The results are limited by the sample size, group of interviewees, questionnaire extent, and lack of generally accepted health state descriptions. DWs were derived to improve the data basis of mercury-related BoD estimates, providing useful information for policy-making. Integration of the results into the GBD DWs enhances comparability. PMID:28075395

Computer-Based Readability Testing of Information Booklets for German Cancer Patients.

PubMed

Keinki, Christian; Zowalla, Richard; Pobiruchin, Monika; Huebner, Jutta; Wiesner, Martin

2018-04-12

Understandable health information is essential for treatment adherence and improved health outcomes. For readability testing, several instruments analyze the complexity of sentence structures, e.g., Flesch-Reading Ease (FRE) or Vienna-Formula (WSTF). Moreover, the vocabulary is of high relevance for readers. The aim of this study is to investigate the agreement of sentence structure and vocabulary-based (SVM) instruments. A total of 52 freely available German patient information booklets on cancer were collected from the Internet. The mean understandability level L was computed for 51 booklets. The resulting values of FRE, WSTF, and SVM were assessed pairwise for agreement with Bland-Altman plots and two-sided, paired t tests. For the pairwise comparison, the mean L values are L FRE  = 6.81, L WSTF  = 7.39, L SVM  = 5.09. The sentence structure-based metrics gave significantly different scores (P < 0.001) for all assessed booklets, confirmed by the Bland-Altman analysis. The study findings suggest that vocabulary-based instruments cannot be interchanged with FRE/WSTF. However, both analytical aspects should be considered and checked by authors to linguistically refine texts with respect to the individual target group. Authors of health information can be supported by automated readability analysis. Health professionals can benefit by direct booklet comparisons allowing for time-effective selection of suitable booklets for patients.

Kinetic Analysis of Horizontal Plyometric Exercise Intensity.

PubMed

Kossow, Andrew J; Ebben, William P

2018-05-01

Kossow, AJ, DeChiara, TG, Neahous, SM, and Ebben, WP. Kinetic analysis of horizontal plyometric exercise intensity. J Strength Cond Res 32(5): 1222-1229, 2018-Plyometric exercises are frequently performed as part of a strength and conditioning program. Most studies assessed the kinetics of plyometric exercises primarily performed in the vertical plane. The purpose of this study was to evaluate the multiplanar kinetic characteristics of a variety of plyometric exercises, which have a significant horizontal component. This study also sought to assess sex differences in the intensity progression of these exercises. Ten men and 10 women served as subjects. The subjects performed a variety of plyometric exercises including the double-leg hop, standing long jump, single-leg standing long jump, bounding, skipping, power skipping, cone hops, and 45.72-cm hurdle hops. Subjects also performed the countermovement jump for comparison. All plyometric exercises were evaluated using a force platform. Dependent variables included the landing rate of force development and landing ground reaction forces for each exercise in the vertical, frontal, and sagittal planes. A 2-way mixed analysis of variance with repeated-measures for plyometric exercise type demonstrated main effects for exercise type for all dependent variables (p ≤ 0.001). There was no significant interaction between plyometric exercise type and sex for any of the variable assessed. Bonferroni-adjusted pairwise comparisons identified a number of differences between the plyometric exercises for the dependent variables assessed (p ≤ 0.05). These findings should be used to guide practitioners in the progression of plyometric exercise intensity, and thus program design, for those who require significant horizontal power in their sport.

A comparison of the palatability of flavored oral contrasts.

PubMed

Arya, Rajiv; Hansen, Allison; Taira, Breena R; Packy, Theodore; Singer, Adam J

2009-09-01

The aim of this study was to compare the taste of computed tomography (CT) oral contrast diluted with various flavored drinks. We performed a prospective, blinded, controlled trial in healthy adult volunteers. Subjects were assigned to ingest four 250-mL aliquots of oral contrast media diluted in water, Crystal Light Lemonade (Kraft Food, Northfield, Ill), Tropical Punch Kool-Aid (Kraft Food), and Tropicana orange juice (Pepsi Bottling Company, Sommers, NY) in random order; and the taste of the solution was measured with a 100-mm visual analogue scale and 5-point Likert scale from very worst to best. Between-group comparison of the taste scores was performed with repeated-measures analysis of variance and pairwise t tests. The study had 80% power to detect an effect size 0.75 SDs. There were 23 subjects; mean (SD) age was 33 (7.7) and 30% were female. The mean (SD) taste scores were water 12 (5), lemonade 37 (21), Kool-Aid 44 (20), and orange juice 40 (20) (P < .05). The proportion of subjects completely ingesting the contrast in water (65%) was significantly less than that with other 3 study solutions (100% each, P < .001). Dilution of oral contrast media with lemonade, fruit punch, or orange juice is tastier than with water. The choice of the specific juice used to dilute the oral contrast should be individualized based on patient preferences and availability.

SortNet: learning to rank by a neural preference function.

PubMed

Rigutini, Leonardo; Papini, Tiziano; Maggini, Marco; Scarselli, Franco

2011-09-01

Relevance ranking consists in sorting a set of objects with respect to a given criterion. However, in personalized retrieval systems, the relevance criteria may usually vary among different users and may not be predefined. In this case, ranking algorithms that adapt their behavior from users' feedbacks must be devised. Two main approaches are proposed in the literature for learning to rank: the use of a scoring function, learned by examples, that evaluates a feature-based representation of each object yielding an absolute relevance score, a pairwise approach, where a preference function is learned to determine the object that has to be ranked first in a given pair. In this paper, we present a preference learning method for learning to rank. A neural network, the comparative neural network (CmpNN), is trained from examples to approximate the comparison function for a pair of objects. The CmpNN adopts a particular architecture designed to implement the symmetries naturally present in a preference function. The learned preference function can be embedded as the comparator into a classical sorting algorithm to provide a global ranking of a set of objects. To improve the ranking performances, an active-learning procedure is devised, that aims at selecting the most informative patterns in the training set. The proposed algorithm is evaluated on the LETOR dataset showing promising performances in comparison with other state-of-the-art algorithms.

Using landscape topology to compare continuous metaheuristics: a framework and case study on EDAs and ridge structure.

PubMed

Morgan, R; Gallagher, M

2012-01-01

In this paper we extend a previously proposed randomized landscape generator in combination with a comparative experimental methodology to study the behavior of continuous metaheuristic optimization algorithms. In particular, we generate two-dimensional landscapes with parameterized, linear ridge structure, and perform pairwise comparisons of algorithms to gain insight into what kind of problems are easy and difficult for one algorithm instance relative to another. We apply this methodology to investigate the specific issue of explicit dependency modeling in simple continuous estimation of distribution algorithms. Experimental results reveal specific examples of landscapes (with certain identifiable features) where dependency modeling is useful, harmful, or has little impact on mean algorithm performance. Heat maps are used to compare algorithm performance over a large number of landscape instances and algorithm trials. Finally, we perform a meta-search in the landscape parameter space to find landscapes which maximize the performance between algorithms. The results are related to some previous intuition about the behavior of these algorithms, but at the same time lead to new insights into the relationship between dependency modeling in EDAs and the structure of the problem landscape. The landscape generator and overall methodology are quite general and extendable and can be used to examine specific features of other algorithms.

A new compound arithmetic crossover-based genetic algorithm for constrained optimisation in enterprise systems

NASA Astrophysics Data System (ADS)

Jin, Chenxia; Li, Fachao; Tsang, Eric C. C.; Bulysheva, Larissa; Kataev, Mikhail Yu

2017-01-01

In many real industrial applications, the integration of raw data with a methodology can support economically sound decision-making. Furthermore, most of these tasks involve complex optimisation problems. Seeking better solutions is critical. As an intelligent search optimisation algorithm, genetic algorithm (GA) is an important technique for complex system optimisation, but it has internal drawbacks such as low computation efficiency and prematurity. Improving the performance of GA is a vital topic in academic and applications research. In this paper, a new real-coded crossover operator, called compound arithmetic crossover operator (CAC), is proposed. CAC is used in conjunction with a uniform mutation operator to define a new genetic algorithm CAC10-GA. This GA is compared with an existing genetic algorithm (AC10-GA) that comprises an arithmetic crossover operator and a uniform mutation operator. To judge the performance of CAC10-GA, two kinds of analysis are performed. First the analysis of the convergence of CAC10-GA is performed by the Markov chain theory; second, a pair-wise comparison is carried out between CAC10-GA and AC10-GA through two test problems available in the global optimisation literature. The overall comparative study shows that the CAC performs quite well and the CAC10-GA defined outperforms the AC10-GA.

The demodulated band transform

PubMed Central

Kovach, Christopher K.; Gander, Phillip E.

2016-01-01

Background Windowed Fourier decompositions (WFD) are widely used in measuring stationary and non-stationary spectral phenomena and in describing pairwise relationships among multiple signals. Although a variety of WFDs see frequent application in electrophysiological research, including the short-time Fourier transform, continuous wavelets, band-pass filtering and multitaper-based approaches, each carries certain drawbacks related to computational efficiency and spectral leakage. This work surveys the advantages of a WFD not previously applied in electrophysiological settings. New Methods A computationally efficient form of complex demodulation, the demodulated band transform (DBT), is described. Results DBT is shown to provide an efficient approach to spectral estimation with minimal susceptibility to spectral leakage. In addition, it lends itself well to adaptive filtering of non-stationary narrowband noise. Comparison with existing methods A detailed comparison with alternative WFDs is offered, with an emphasis on the relationship between DBT and Thomson's multitaper. DBT is shown to perform favorably in combining computational efficiency with minimal introduction of spectral leakage. Conclusion DBT is ideally suited to efficient estimation of both stationary and non-stationary spectral and cross-spectral statistics with minimal susceptibility to spectral leakage. These qualities are broadly desirable in many settings. PMID:26711370

Comparison between Thermal Desorption Tubes and Stainless Steel Canisters Used for Measuring Volatile Organic Compounds in Petrochemical Factories

PubMed Central

Chang, Cheng-Ping; Lin, Tser-Cheng; Lin, Yu-Wen; Hua, Yi-Chun; Chu, Wei-Ming; Lin, Tzu-Yu; Lin, Yi-Wen; Wu, Jyun-De

2016-01-01

Objective: The purpose of this study was to compare thermal desorption tubes and stainless steel canisters for measuring volatile organic compounds (VOCs) emitted from petrochemical factories. Methods: Twelve petrochemical factories in the Mailiao Industrial Complex were recruited for conducting the measurements of VOCs. Thermal desorption tubes and 6-l specially prepared stainless steel canisters were used to simultaneously perform active sampling of environmental air samples. The sampling time of the environmental air samples was set up on 6h close to a full work shift of the workers. A total of 94 pairwise air samples were collected by using the thermal adsorption tubes and stainless steel canisters in these 12 factories in the petrochemical industrial complex. To maximize the number of comparative data points, all the measurements from all the factories in different sampling times were lumped together to perform a linear regression analysis for each selected VOC. Pearson product–moment correlation coefficient was used to examine the correlation between the pairwise measurements of these two sampling methods. A paired t-test was also performed to examine whether the difference in the concentrations of each selected VOC measured by the two methods was statistically significant. Results: The correlation coefficients of seven compounds, including acetone, n-hexane, benzene, toluene, 1,2-dichloroethane, 1,3-butadiene, and styrene were >0.80 indicating the two sampling methods for these VOCs’ measurements had high consistency. The paired t-tests for the measurements of n-hexane, benzene, m/p-xylene, o-xylene, 1,2-dichloroethane, and 1,3-butadiene showed statistically significant difference (P-value < 0.05). This indicated that the two sampling methods had various degrees of systematic errors. Looking at the results of six chemicals and these systematic errors probably resulted from the differences of the detection limits in the two sampling methods for these VOCs. Conclusions: The comparison between the concentrations of each of the 10 selected VOCs measured by the two sampling methods indicted that the thermal desorption tubes provided high accuracy and precision measurements for acetone, benzene, and 1,3-butadiene. The accuracy and precision of using the thermal desorption tubes for measuring the VOCs can be improved due to new developments in sorbent materials, multi-sorbent designs, and thermal desorption instrumentation. More applications of thermal desorption tubes for measuring occupational and environmental hazardous agents can be anticipated. PMID:26585828

Comparison between Thermal Desorption Tubes and Stainless Steel Canisters Used for Measuring Volatile Organic Compounds in Petrochemical Factories.

PubMed

Chang, Cheng-Ping; Lin, Tser-Cheng; Lin, Yu-Wen; Hua, Yi-Chun; Chu, Wei-Ming; Lin, Tzu-Yu; Lin, Yi-Wen; Wu, Jyun-De

2016-04-01

The purpose of this study was to compare thermal desorption tubes and stainless steel canisters for measuring volatile organic compounds (VOCs) emitted from petrochemical factories. Twelve petrochemical factories in the Mailiao Industrial Complex were recruited for conducting the measurements of VOCs. Thermal desorption tubes and 6-l specially prepared stainless steel canisters were used to simultaneously perform active sampling of environmental air samples. The sampling time of the environmental air samples was set up on 6 h close to a full work shift of the workers. A total of 94 pairwise air samples were collected by using the thermal adsorption tubes and stainless steel canisters in these 12 factories in the petrochemical industrial complex. To maximize the number of comparative data points, all the measurements from all the factories in different sampling times were lumped together to perform a linear regression analysis for each selected VOC. Pearson product-moment correlation coefficient was used to examine the correlation between the pairwise measurements of these two sampling methods. A paired t-test was also performed to examine whether the difference in the concentrations of each selected VOC measured by the two methods was statistically significant. The correlation coefficients of seven compounds, including acetone, n-hexane, benzene, toluene, 1,2-dichloroethane, 1,3-butadiene, and styrene were >0.80 indicating the two sampling methods for these VOCs' measurements had high consistency. The paired t-tests for the measurements of n-hexane, benzene, m/p-xylene, o-xylene, 1,2-dichloroethane, and 1,3-butadiene showed statistically significant difference (P-value < 0.05). This indicated that the two sampling methods had various degrees of systematic errors. Looking at the results of six chemicals and these systematic errors probably resulted from the differences of the detection limits in the two sampling methods for these VOCs. The comparison between the concentrations of each of the 10 selected VOCs measured by the two sampling methods indicted that the thermal desorption tubes provided high accuracy and precision measurements for acetone, benzene, and 1,3-butadiene. The accuracy and precision of using the thermal desorption tubes for measuring the VOCs can be improved due to new developments in sorbent materials, multi-sorbent designs, and thermal desorption instrumentation. More applications of thermal desorption tubes for measuring occupational and environmental hazardous agents can be anticipated. © The Author 2015. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

The impact of wood ice cream sticks' origin on the aroma of exposed ice cream mixes.

PubMed

Jiamyangyuen, S; Delwiche, J F; Harper, W J

2002-02-01

The effect of volatile compounds in white birch sticks obtained from four different geographical locations on the aroma of ice cream mix was investigated. Sensory evaluation, (specifically, a series of warmed-up paired comparisons) was conducted on stick-exposed ice cream mixes to determine whether aroma differences in those mixes could be detected. Batches of ice cream mix were exposed to the sticks and aged for 6 d at 4 degrees C and then assessed by the panelists by pairwise comparison. Findings suggest that differences in aroma of mixes that have been exposed to white birch sticks from four different geographical origins can be distinguished perceptually.

Advanced propulsion for LEO-Moon transport. 1: A method for evaluating advanced propulsion performance

NASA Technical Reports Server (NTRS)

Stern, Martin O.

1992-01-01

This report describes a study to evaluate the benefits of advanced propulsion technologies for transporting materials between low Earth orbit and the Moon. A relatively conventional reference transportation system, and several other systems, each of which includes one advanced technology component, are compared in terms of how well they perform a chosen mission objective. The evaluation method is based on a pairwise life-cycle cost comparison of each of the advanced systems with the reference system. Somewhat novel and economically important features of the procedure are the inclusion not only of mass payback ratios based on Earth launch costs, but also of repair and capital acquisition costs, and of adjustments in the latter to reflect the technological maturity of the advanced technologies. The required input information is developed by panels of experts. The overall scope and approach of the study are presented in the introduction. The bulk of the paper describes the evaluation method; the reference system and an advanced transportation system, including a spinning tether in an eccentric Earth orbit, are used to illustrate it.

Factors that influence the efficiency of beef and dairy cattle recording system in Kenya: A SWOT-AHP analysis.

PubMed

Wasike, Chrilukovian B; Magothe, Thomas M; Kahi, Alexander K; Peters, Kurt J

2011-01-01

Animal recording in Kenya is characterised by erratic producer participation and high drop-out rates from the national recording scheme. This study evaluates factors influencing efficiency of beef and dairy cattle recording system. Factors influencing efficiency of animal identification and registration, pedigree and performance recording, and genetic evaluation and information utilisation were generated using qualitative and participatory methods. Pairwise comparison of factors was done by strengths, weaknesses, opportunities and threats-analytical hierarchical process analysis and priority scores to determine their relative importance to the system calculated using Eigenvalue method. For identification and registration, and evaluation and information utilisation, external factors had high priority scores. For pedigree and performance recording, threats and weaknesses had the highest priority scores. Strengths factors could not sustain the required efficiency of the system. Weaknesses of the system predisposed it to threats. Available opportunities could be explored as interventions to restore efficiency in the system. Defensive strategies such as reorienting the system to offer utility benefits to recording, forming symbiotic and binding collaboration between recording organisations and NARS, and development of institutions to support recording were feasible.

Autogrid-based clustering of kinases: selection of representative conformations for docking purposes.

PubMed

Marzaro, Giovanni; Ferrarese, Alessandro; Chilin, Adriana

2014-08-01

The selection of the most appropriate protein conformation is a crucial aspect in molecular docking experiments. In order to reduce the errors arising from the use of a single protein conformation, several authors suggest the use of several tridimensional structures for the target. However, the selection of the most appropriate protein conformations still remains a challenging goal. The protein 3D-structures selection is mainly performed based on pairwise root-mean-square-deviation (RMSD) values computation, followed by hierarchical clustering. Herein we report an alternative strategy, based on the computation of only two atom affinity map for each protein conformation, followed by multivariate analysis and hierarchical clustering. This methodology was applied on seven different kinases of pharmaceutical interest. The comparison with the classical RMSD-based strategy was based on cross-docking of co-crystallized ligands. In the case of epidermal growth factor receptor kinase, also the docking performance on 220 known ligands were evaluated, followed by 3D-QSAR studies. In all the cases, the herein proposed methodology outperformed the RMSD-based one.

Using a genetic algorithm as an optimal band selector in the mid and thermal infrared (2.5-14 μm) to discriminate vegetation species.

PubMed

Ullah, Saleem; Groen, Thomas A; Schlerf, Martin; Skidmore, Andrew K; Nieuwenhuis, Willem; Vaiphasa, Chaichoke

2012-01-01

Genetic variation between various plant species determines differences in their physio-chemical makeup and ultimately in their hyperspectral emissivity signatures. The hyperspectral emissivity signatures, on the one hand, account for the subtle physio-chemical changes in the vegetation, but on the other hand, highlight the problem of high dimensionality. The aim of this paper is to investigate the performance of genetic algorithms coupled with the spectral angle mapper (SAM) to identify a meaningful subset of wavebands sensitive enough to discriminate thirteen broadleaved vegetation species from the laboratory measured hyperspectral emissivities. The performance was evaluated using an overall classification accuracy and Jeffries Matusita distance. For the multiple plant species, the targeted bands based on genetic algorithms resulted in a high overall classification accuracy (90%). Concentrating on the pairwise comparison results, the selected wavebands based on genetic algorithms resulted in higher Jeffries Matusita (J-M) distances than randomly selected wavebands did. This study concludes that targeted wavebands from leaf emissivity spectra are able to discriminate vegetation species.

Assessing organizational performance in intensive care units: a French experience.

PubMed

Minvielle, Etienne; Aegerter, Philippe; Dervaux, Benoît; Boumendil, Ariane; Retbi, Aurélia; Jars-Guincestre, Marie Claude; Guidet, Bertrand

2008-06-01

The objective of the study was to assess and to explain variation of organizational performance in intensive care units (ICUs). This was a prospective multicenter study. The study involved 26 ICUs located in the Paris area, France, participating in a regional database. Data were collected through answers of 1000 ICU personnel to the Culture, Organization, and Management in Intensive Care questionnaire and from the database. Organizational performance was assessed through a composite score related to 5 dimensions: coordination and adaptation to uncertainty, communication, conflict management, organizational change, and organizational learning, Skills developed in relationship with patients and their families. Statistical comparisons between ICUs were performed by analysis of variance with a Scheffé pairwise procedure. A multilevel regression model was used to analyze both individual and structural variables explaining differences of ICU's organizational performance. The organizational performance score differed among ICUs. Some cultural values were negatively correlated with a high level of organizational performance, suggesting improvement potential. Several individual and structural factors were also related to the quality of ICU organization, including absence of burnout, older staff, satisfaction to work, and high workload (P < .02 for each). A benchmarking approach can be used by ICU managers to assess the organizational performance of their ICU based on a validated questionnaire. Differences are mainly explained by cultural values and individual well-being factors, introducing new requirements for managing human resources in ICUs.

Manipulation of Karyotype in Caenorhabditis elegans Reveals Multiple Inputs Driving Pairwise Chromosome Synapsis During Meiosis

PubMed Central

Roelens, Baptiste; Schvarzstein, Mara; Villeneuve, Anne M.

2015-01-01

Meiotic chromosome segregation requires pairwise association between homologs, stabilized by the synaptonemal complex (SC). Here, we investigate factors contributing to pairwise synapsis by investigating meiosis in polyploid worms. We devised a strategy, based on transient inhibition of cohesin function, to generate polyploid derivatives of virtually any Caenorhabditis elegans strain. We exploited this strategy to investigate the contribution of recombination to pairwise synapsis in tetraploid and triploid worms. In otherwise wild-type polyploids, chromosomes first sort into homolog groups, then multipartner interactions mature into exclusive pairwise associations. Pairwise synapsis associations still form in recombination-deficient tetraploids, confirming a propensity for synapsis to occur in a strictly pairwise manner. However, the transition from multipartner to pairwise association was perturbed in recombination-deficient triploids, implying a role for recombination in promoting this transition when three partners compete for synapsis. To evaluate the basis of synapsis partner preference, we generated polyploid worms heterozygous for normal sequence and rearranged chromosomes sharing the same pairing center (PC). Tetraploid worms had no detectable preference for identical partners, indicating that PC-adjacent homology drives partner choice in this context. In contrast, triploid worms exhibited a clear preference for identical partners, indicating that homology outside the PC region can influence partner choice. Together, our findings, suggest a two-phase model for C. elegans synapsis: an early phase, in which initial synapsis interactions are driven primarily by recombination-independent assessment of homology near PCs and by a propensity for pairwise SC assembly, and a later phase in which mature synaptic interactions are promoted by recombination. PMID:26500263

Cognitive impairments in former patients with work-related stress complaints - one year later.

PubMed

Eskildsen, Anita; Andersen, Lars Peter; Pedersen, Anders Degn; Andersen, Johan Hviid

2016-11-01

Patients on sick leave due to work-related stress often present with cognitive impairments. The aim of this prospective cohort study was to examine the long-term consequences of prolonged work-related stress in terms of cognitive functioning one year after initial professional care seeking. We tested a group of patients with work-related stress with a comprehensive neuropsychological test battery at two occasions, one year apart. At both time points, we compared the performance of patients with healthy controls matched pairwise on sex, age and length of education. This paper presents the results from the one-year follow-up. When adjusting for practice effects, patients improved on measures of prospective memory and processing speed. However, patients continued to perform worse than controls on all tests, though only half of the comparisons reached statistical significance. The effect sizes of the differences between the two groups at one-year follow-up were small to medium. In conclusion, former patients with prolonged work-related stress improved, but they continued to perform worse than controls after one year. In the acute phase, the largest impairments were related to executive function and mental speed but at follow-up memory impairments also became apparent.

Comparing masked target transform volume (MTTV) clutter metric to human observer evaluation of visual clutter

NASA Astrophysics Data System (ADS)

Camp, H. A.; Moyer, Steven; Moore, Richard K.

2010-04-01

The Night Vision and Electronic Sensors Directorate's current time-limited search (TLS) model, which makes use of the targeting task performance (TTP) metric to describe image quality, does not explicitly account for the effects of visual clutter on observer performance. The TLS model is currently based on empirical fits to describe human performance for a time of day, spectrum and environment. Incorporating a clutter metric into the TLS model may reduce the number of these empirical fits needed. The masked target transform volume (MTTV) clutter metric has been previously presented and compared to other clutter metrics. Using real infrared imagery of rural images with varying levels of clutter, NVESD is currently evaluating the appropriateness of the MTTV metric. NVESD had twenty subject matter experts (SME) rank the amount of clutter in each scene in a series of pair-wise comparisons. MTTV metric values were calculated and then compared to the SME observers rankings. The MTTV metric ranked the clutter in a similar manner to the SME evaluation, suggesting that the MTTV metric may emulate SME response. This paper is a first step in quantifying clutter and measuring the agreement to subjective human evaluation.

Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm.

PubMed

Hoffmann, Thomas J; Zhan, Yiping; Kvale, Mark N; Hesselson, Stephanie E; Gollub, Jeremy; Iribarren, Carlos; Lu, Yontao; Mei, Gangwu; Purdy, Matthew M; Quesenberry, Charles; Rowell, Sarah; Shapero, Michael H; Smethurst, David; Somkin, Carol P; Van den Eeden, Stephen K; Walter, Larry; Webster, Teresa; Whitmer, Rachel A; Finn, Andrea; Schaefer, Catherine; Kwok, Pui-Yan; Risch, Neil

2011-12-01

Four custom Axiom genotyping arrays were designed for a genome-wide association (GWA) study of 100,000 participants from the Kaiser Permanente Research Program on Genes, Environment and Health. The array optimized for individuals of European race/ethnicity was previously described. Here we detail the development of three additional microarrays optimized for individuals of East Asian, African American, and Latino race/ethnicity. For these arrays, we decreased redundancy of high-performing SNPs to increase SNP capacity. The East Asian array was designed using greedy pairwise SNP selection. However, removing SNPs from the target set based on imputation coverage is more efficient than pairwise tagging. Therefore, we developed a novel hybrid SNP selection method for the African American and Latino arrays utilizing rounds of greedy pairwise SNP selection, followed by removal from the target set of SNPs covered by imputation. The arrays provide excellent genome-wide coverage and are valuable additions for large-scale GWA studies. Copyright © 2011 Elsevier Inc. All rights reserved.

Cardiovascular Risk with Non-Steroidal Anti-Inflammatory Drugs: Systematic Review of Population-Based Controlled Observational Studies

PubMed Central

McGettigan, Patricia; Henry, David

2011-01-01

Background Randomised trials have highlighted the cardiovascular risks of non-steroidal anti-inflammatory drugs (NSAIDs) in high doses and sometimes atypical settings. Here, we provide estimates of the comparative risks with individual NSAIDs at typical doses in community settings. Methods and Findings We performed a systematic review of community-based controlled observational studies. We conducted comprehensive literature searches, extracted adjusted relative risk (RR) estimates, and pooled the estimates for major cardiovascular events associated with use of individual NSAIDs, in different doses, and in populations with low and high background risks of cardiovascular events. We also compared individual drugs in pair-wise (within study) analyses, generating ratios of RRs (RRRs). Thirty case-control studies included 184,946 cardiovascular events, and 21 cohort studies described outcomes in >2.7 million exposed individuals. Of the extensively studied drugs (ten or more studies), the highest overall risks were seen with rofecoxib, 1.45 (95% CI 1.33, 1.59), and diclofenac, 1.40 (1.27, 1.55), and the lowest with ibuprofen, 1.18 (1.11, 1.25), and naproxen, 1.09 (1.02, 1.16). In a sub-set of studies, risk was elevated with low doses of rofecoxib, 1.37 (1.20, 1.57), celecoxib, 1.26 (1.09, 1.47), and diclofenac, 1.22 (1.12, 1.33), and rose in each case with higher doses. Ibuprofen risk was seen only with higher doses. Naproxen was risk-neutral at all doses. Of the less studied drugs etoricoxib, 2.05 (1.45, 2.88), etodolac, 1.55 (1.28, 1.87), and indomethacin, 1.30 (1.19, 1.41), had the highest risks. In pair-wise comparisons, etoricoxib had a higher RR than ibuprofen, RRR = 1.68 (99% CI 1.14, 2.49), and naproxen, RRR = 1.75 (1.16, 2.64); etodolac was not significantly different from naproxen and ibuprofen. Naproxen had a significantly lower risk than ibuprofen, RRR = 0.92 (0.87, 0.99). RR estimates were constant with different background risks for cardiovascular disease and rose early in the course of treatment. Conclusions This review suggests that among widely used NSAIDs, naproxen and low-dose ibuprofen are least likely to increase cardiovascular risk. Diclofenac in doses available without prescription elevates risk. The data for etoricoxib were sparse, but in pair-wise comparisons this drug had a significantly higher RR than naproxen or ibuprofen. Indomethacin is an older, rather toxic drug, and the evidence on cardiovascular risk casts doubt on its continued clinical use. Please see later in the article for the Editors' Summary PMID:21980265

Structure based alignment and clustering of proteins (STRALCP)

DOEpatents

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Performance analysis of model based iterative reconstruction with dictionary learning in transportation security CT

NASA Astrophysics Data System (ADS)

Haneda, Eri; Luo, Jiajia; Can, Ali; Ramani, Sathish; Fu, Lin; De Man, Bruno

2016-05-01

In this study, we implement and compare model based iterative reconstruction (MBIR) with dictionary learning (DL) over MBIR with pairwise pixel-difference regularization, in the context of transportation security. DL is a technique of sparse signal representation using an over complete dictionary which has provided promising results in image processing applications including denoising,1 as well as medical CT reconstruction.2 It has been previously reported that DL produces promising results in terms of noise reduction and preservation of structural details, especially for low dose and few-view CT acquisitions.2 A distinguishing feature of transportation security CT is that scanned baggage may contain items with a wide range of material densities. While medical CT typically scans soft tissues, blood with and without contrast agents, and bones, luggage typically contains more high density materials (i.e. metals and glass), which can produce severe distortions such as metal streaking artifacts. Important factors of security CT are the emphasis on image quality such as resolution, contrast, noise level, and CT number accuracy for target detection. While MBIR has shown exemplary performance in the trade-off of noise reduction and resolution preservation, we demonstrate that DL may further improve this trade-off. In this study, we used the KSVD-based DL3 combined with the MBIR cost-minimization framework and compared results to Filtered Back Projection (FBP) and MBIR with pairwise pixel-difference regularization. We performed a parameter analysis to show the image quality impact of each parameter. We also investigated few-view CT acquisitions where DL can show an additional advantage relative to pairwise pixel difference regularization.

Aggregating Individual Preferences in the Analytic Hierarchy Process Applied to the 1983 Battelle TAV Study.

DTIC Science & Technology

1985-03-15

elicitation - rankings, ratings, and pairwise comparisons, 2) Value Theory: includes an explanation of the AHP and fuzzy set theory, and 3) Group... AHP are better tools for these " fuzzy " applications. These results apply directly to this thesis. The original Battelle survey used direct ratings to...iridepeindent uf three arggretation toctiiIque5: geometric mean input, arithmetic me;n voctor output, and Majority rle,, output. The AHP consi:3tcncy index was

Regulation of Intracellular Signaling Leading to Gene Expression in Lipopolysaccharide Stimulated Murine Macrophages

DTIC Science & Technology

1995-09-20

parentheses represent the lower and upper values defined by 1 SEM. The LSD test was used for pairwise mean comparisons. c,d,"Means are significantly...different at the 5% level of significance of the LSD test. 100 Table VI: Effect of Calyculin A on LPS-induced TNF and IFN Production Treatment Medium...transfer an antiviral state. Role of endogenous interferon. J. Immun . 139:1991. Gille. H. G., A. D. Sharrocks, and P. E. Shaw . 1992. Phosphorylation

Portable Low Volume Therapy for Severe Blood Loss

DTIC Science & Technology

2016-08-01

loss . 8 24-hour survival showed no statistical differences (p>0.05) between BHB/M (mean survival 21.0 ± 2.74 hrs) and 4 M BHB, 4.3 mM melatonin...in Figure 6 were compared 24 hours and 10 days after 60% blood loss . Pairwise comparisons are summarized in Table 3. No treatment differences were...Award Number: W81XWH-11-1-0409 TITLE: Portable Low-Volume Therapy for Severe Blood Loss PRINCIPAL INVESTIGATOR: Matthew T. Andrews CONTRACTING

Comparing and explaining differences in the magnitude, content, and sensitivity of utilities predicted by the EQ-5D, SF-6D, HUI 3, 15D, QWB, and AQoL-8D multiattribute utility instruments.

PubMed

Richardson, Jeff; Khan, Munir A; Iezzi, Angelo; Maxwell, Aimee

2015-04-01

Cost utility analysis permits the comparison of disparate health services by measuring outcomes in comparable units, namely, quality-adjusted life-years, which equal life-years times the utility of the health state. However, comparability is compromised when different utility instruments predict different utilities for the same health state. The present paper measures the extent of, and reason for, differences between the utilities predicted by the EQ-5D-5L, SF-6D, HUI 3, 15D, QWB, and AQoL-8D. Data were obtained from patients in seven disease areas and members of the healthy public in six countries. Differences between public and patient utilities were estimated using each of the instruments. To explain discrepancies between the estimates, the measurement scales and content of the instruments were compared. The sensitivity of instruments to independently measured health dimensions was measured in pairwise comparisons of all combinations of the instruments. The difference between public and patient utilities varied with the choice of instrument by more than 50% for every disease group and in four of the seven groups by more than 100%. Discrepancies were associated with differences in both the instrument content and their measurement scales. Pairwise comparisons of instruments found that variation in the sensitivity to physical and psychosocial dimensions of health closely reflected the items in the instrument's descriptive systems. Results indicate that instruments measure related but different constructs. They imply that commonly used instruments systematically discriminate against some classes of services, most notably mental health services. Differences in the instrument scales imply the need for transformations between the instruments to increase the comparability of measurement. © The Author(s) 2014.

Interbreed variation in serum serotonin (5-hydroxytryptamine) concentration in healthy dogs.

PubMed

Höglund, K; Häggström, J; Hanås, S; Merveille, A-C; Gouni, V; Wiberg, M; Lundgren Willesen, J; Entee, K Mc; Mejer Sørensen, L; Tiret, L; Seppälä, E H; Lohi, H; Chetboul, V; Fredholm, M; Lequarré, A-S; Ljungvall, I

2018-06-16

Serotonin (5-hydroxytryptamine [5-HT]) has several biological functions. In different species, excessive 5-HT has been linked to valvular lesions, similar to those seen in dogs with myxomatous mitral valve disease. Previous studies suggest higher 5-HT in healthy Cavalier King Charles Spaniels (CKCSs), a breed highly affected by myxomatous mitral valve disease, compared to other breeds. To investigate potential interbreed variation in serum 5-HT in healthy dogs. 483 healthy dogs of nine breeds aged 1-7 years. Dogs were examined at five European centers. Absence of cardiovascular, organ-related, or systemic diseases was ensured by thorough clinical investigations including echocardiography. Serum was frozen and later analyzed by enzyme-linked immunosorbent assay (ELISA). Median 5-HT concentration was 252.5 (interquartile range = 145.5-390.6) ng/mL. Overall breed difference was found (p<0.0001), and 42% of pairwise breed comparisons were significant. Univariate regression analysis showed association between serum 5-HT concentration and breed, center of examination, storage time, and sex, with higher 5-HT in females. In multiple regression analysis, the final model had an adjusted R 2 of 0.27 with breed (p<0.0001), center (p<0.0001), and storage time (p=0.014) remaining significant. Within centers, overall breed differences were found at 3/5 centers (p≤0.028), and pairwise comparisons within those centers showed breed differences in 42% of comparisons. Among the included breeds, Newfoundlands, Belgian Shepherds and CKCSs had highest 5-HT concentrations. Interbreed variation in serum 5-HT concentration was found in healthy dogs aged 1-7 years. These differences should be taken into account when designing clinical studies. Copyright © 2018 Elsevier B.V. All rights reserved.

Performance evaluation of the zero-multipole summation method in modern molecular dynamics software.

PubMed

Sakuraba, Shun; Fukuda, Ikuo

2018-05-04

The zero-multiple summation method (ZMM) is a cutoff-based method for calculating electrostatic interactions in molecular dynamics simulations, utilizing an electrostatic neutralization principle as a physical basis. Since the accuracies of the ZMM have been revealed to be sufficient in previous studies, it is highly desirable to clarify its practical performance. In this paper, the performance of the ZMM is compared with that of the smooth particle mesh Ewald method (SPME), where the both methods are implemented in molecular dynamics software package GROMACS. Extensive performance comparisons against a highly optimized, parameter-tuned SPME implementation are performed for various-sized water systems and two protein-water systems. We analyze in detail the dependence of the performance on the potential parameters and the number of CPU cores. Even though the ZMM uses a larger cutoff distance than the SPME does, the performance of the ZMM is comparable to or better than that of the SPME. This is because the ZMM does not require a time-consuming electrostatic convolution and because the ZMM gains short neighbor-list distances due to the smooth damping feature of the pairwise potential function near the cutoff length. We found, in particular, that the ZMM with quadrupole or octupole cancellation and no damping factor is an excellent candidate for the fast calculation of electrostatic interactions. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

CUFID-query: accurate network querying through random walk based network flow estimation.

PubMed

Jeong, Hyundoo; Qian, Xiaoning; Yoon, Byung-Jun

2017-12-28

Functional modules in biological networks consist of numerous biomolecules and their complicated interactions. Recent studies have shown that biomolecules in a functional module tend to have similar interaction patterns and that such modules are often conserved across biological networks of different species. As a result, such conserved functional modules can be identified through comparative analysis of biological networks. In this work, we propose a novel network querying algorithm based on the CUFID (Comparative network analysis Using the steady-state network Flow to IDentify orthologous proteins) framework combined with an efficient seed-and-extension approach. The proposed algorithm, CUFID-query, can accurately detect conserved functional modules as small subnetworks in the target network that are expected to perform similar functions to the given query functional module. The CUFID framework was recently developed for probabilistic pairwise global comparison of biological networks, and it has been applied to pairwise global network alignment, where the framework was shown to yield accurate network alignment results. In the proposed CUFID-query algorithm, we adopt the CUFID framework and extend it for local network alignment, specifically to solve network querying problems. First, in the seed selection phase, the proposed method utilizes the CUFID framework to compare the query and the target networks and to predict the probabilistic node-to-node correspondence between the networks. Next, the algorithm selects and greedily extends the seed in the target network by iteratively adding nodes that have frequent interactions with other nodes in the seed network, in a way that the conductance of the extended network is maximally reduced. Finally, CUFID-query removes irrelevant nodes from the querying results based on the personalized PageRank vector for the induced network that includes the fully extended network and its neighboring nodes. Through extensive performance evaluation based on biological networks with known functional modules, we show that CUFID-query outperforms the existing state-of-the-art algorithms in terms of prediction accuracy and biological significance of the predictions.

Systematic review with meta-analysis: comparative efficacy of biologics for induction and maintenance of mucosal healing in Crohn's disease and ulcerative colitis controlled trials.

PubMed

Cholapranee, A; Hazlewood, G S; Kaplan, G G; Peyrin-Biroulet, L; Ananthakrishnan, A N

2017-05-01

Mucosal healing is an important therapeutic endpoint in the management of Crohn's disease (CD) and ulcerative colitis (UC). Limited data exist regarding the comparative efficacy of various therapies in achieving this outcome. To perform a systematic review and meta-analysis of biologics for induction and maintenance of mucosal healing in Crohn's disease and ulcerative colitis. We performed a systematic review and meta-analysis of randomised controlled trials (RCT) examining mucosal healing as an endpoint of immunosuppressives, anti-tumour necrosis factor α (anti-TNF) or anti-integrin monoclonal antibody therapy for moderate-to-severe CD or UC. Pooled effect sizes for induction and maintenance of mucosal healing were calculated and pairwise treatment comparisons evaluated using a Bayesian network meta-analysis. A total of 12 RCTs were included in the meta-analysis (CD - 2 induction, 4 maintenance; UC - 8 induction, 5 maintenance). Duration of follow-up was 6-12 weeks for induction and 32-54 weeks for maintenance trials. In CD, anti-TNFs were more effective than placebo for maintaining mucosal healing [28% vs. 1%, Odds ratio (OR) 19.71, 95% confidence interval (CI) 3.51-110.84]. In UC, anti-TNFs and anti-integrins were more effective than placebo for inducing (45% vs. 30%) and maintaining mucosal healing (33% vs. 18%). In network analysis, adalimumab therapy was inferior to infliximab [OR 0.45, 95% credible interval (CrI) 0.25-0.82] and combination infliximab-azathioprine (OR 0.32, 95% CrI 0.12-0.84) for inducing mucosal healing in UC. There was no statistically significant pairwise difference between vedolizumab and anti-TNF agents in UC. Anti-TNF and anti-integrin biological agents are effective in inducing mucosal healing in UC, with adalimumab being inferior to infliximab or combination therapy. Infliximab and adalimumab were similar in CD. © 2017 John Wiley & Sons Ltd.

Monitoring equity in vaccination coverage: A systematic analysis of demographic and health surveys from 45 Gavi-supported countries.

PubMed

Arsenault, Catherine; Harper, Sam; Nandi, Arijit; Mendoza Rodríguez, José M; Hansen, Peter M; Johri, Mira

2017-02-07

(1) To conduct a systematic analysis of inequalities in childhood vaccination coverage in Gavi-supported countries; (2) to comparatively assess alternative measurement approaches and how they may affect cross-country comparisons of the level of inequalities. Using the most recent Demographic and Health Surveys (2005-2014) in 45 Gavi-supported countries, we measured inequalities in vaccination coverage across seven dimensions of social stratification and of vulnerability to poor health outcomes. We quantified inequalities using pairwise comparisons (risk differences and ratios) and whole spectrum measures (slope and relative indices of inequality). To contrast measurement approaches, we pooled the estimates using random-effects meta-analyses, ranked countries by the magnitude of inequality and compared agreement in country ranks. At the aggregate level, maternal education, multidimensional poverty, and wealth index poverty were the dimensions associated with the largest inequalities. In 36 out of 45 countries, inequalities were substantial, with a difference in coverage of 10 percentage points or more between the top and bottom of at least one of these social dimensions. Important inequalities by child sex, child malnutrition and urban/rural residence were also found in a smaller set of countries. The magnitude of inequality and ranking of countries differed across dimension and depending on the measure used. Pairwise comparisons could not be estimated in certain countries. The slope and relative indices of inequality were estimated in all countries and produced more stable country rankings, and should thus facilitate more reliable international comparisons. Inequalities in vaccination coverage persist in a large majority of Gavi-supported countries. Inequalities should be monitored across multiple dimensions of vulnerability. Using whole spectrum measures to quantify inequality across multiple ordered social groups has important advantages. We illustrate these findings using an equity dashboard designed to support decision-making in the Sustainable Development Goals period. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluating the critical source area concept of phosphorus loss from soils to water-bodies in agricultural catchments.

PubMed

Shore, M; Jordan, P; Mellander, P-E; Kelly-Quinn, M; Wall, D P; Murphy, P N C; Melland, A R

2014-08-15

Using data collected from six basins located across two hydrologically contrasting agricultural catchments, this study investigated whether transport metrics alone provide better estimates of storm phosphorus (P) loss from basins than critical source area (CSA) metrics which combine source factors as well. Concentrations and loads of P in quickflow (QF) were measured at basin outlets during four storm events and were compared with dynamic (QF magnitude) and static (extent of highly-connected, poorly-drained soils) transport metrics and a CSA metric (extent of highly-connected, poorly-drained soils with excess plant-available P). Pairwise comparisons between basins with similar CSA risks but contrasting QF magnitudes showed that QF flow-weighted mean TRP (total molybdate-reactive P) concentrations and loads were frequently (at least 11 of 14 comparisons) more than 40% higher in basins with the highest QF magnitudes. Furthermore, static transport metrics reliably discerned relative QF magnitudes between these basins. However, particulate P (PP) concentrations were often (6 of 14 comparisons) higher in basins with the lowest QF magnitudes, most likely due to soil-management activities (e.g. ploughing), in these predominantly arable basins at these times. Pairwise comparisons between basins with contrasting CSA risks and similar QF magnitudes showed that TRP and PP concentrations and loads did not reflect trends in CSA risk or QF magnitude. Static transport metrics did not discern relative QF magnitudes between these basins. In basins with contrasting transport risks, storm TRP concentrations and loads were well differentiated by dynamic or static transport metrics alone, regardless of differences in soil P. In basins with similar transport risks, dynamic transport metrics and P source information additional to soil P may be required to predict relative storm TRP concentrations and loads. Regardless of differences in transport risk, information on land use and management, may be required to predict relative differences in storm PP concentrations between these agricultural basins. Copyright © 2014 Elsevier B.V. All rights reserved.

Torsional stability of interference screws derived from bovine bone - a biomechanical study

PubMed Central

2010-01-01

Background In the present biomechanical study, the torsional stability of different interference screws, made of bovine bone, was tested. Interference screws derived from bovine bone are a possible biological alternative to conventional metallic or bioabsorbable polymer interference screws. Methods In the first part of the study we compared the torsional stability of self-made 8 mm Interference screws (BC) and a commercial 8 mm interference screw (Tutofix®). Furthermore, we compared the torsional strength of BC screws with different diameters. For screwing in, a hexagon head and an octagon head were tested. Maximum breaking torques in polymethyl methacrylate resin were recorded by means of an electronic torque screw driver. In the second part of the study the tibial part of a bone-patellar tendon-bone graft was fixed in porcine test specimens using an 8 mm BC screw and the maximum insertion torques were recorded. Each interference screw type was tested 5 times. Results There was no statistically significant difference between the different 8 mm interference screws (p = 0.121). Pairwise comparisons did not reveal statistically significant differences, either. It was demonstrated for the BC screws, that a larger screw diameter significantly leads to higher torsional stability (p = 9.779 × 10-5). Pairwise comparisons showed a significantly lower torsional stability for the 7 mm BC screw than for the 8 mm BC screw (p = 0.0079) and the 9 mm BC screw (p = 0.0079). Statistically significant differences between the 8 mm and the 9 mm BC screw could not be found (p = 0.15). During screwing into the tibial graft channel of the porcine specimens, insertion torques between 0.5 Nm and 3.2 Nm were recorded. In one case the hexagon head of a BC screw broke off during the last turn. Conclusions The BC screws show comparable torsional stability to Tutofix® interference screws. As expected the torsional strength of the screws increases significantly with the diameter. The safety and in vivo performance of products derived from xenogeneic bone should be the focus of further investigations. PMID:20433761

Time-Frequency Analysis Reveals Pairwise Interactions in Insect Swarms

NASA Astrophysics Data System (ADS)

Puckett, James G.; Ni, Rui; Ouellette, Nicholas T.

2015-06-01

The macroscopic emergent behavior of social animal groups is a classic example of dynamical self-organization, and is thought to arise from the local interactions between individuals. Determining these interactions from empirical data sets of real animal groups, however, is challenging. Using multicamera imaging and tracking, we studied the motion of individual flying midges in laboratory mating swarms. By performing a time-frequency analysis of the midge trajectories, we show that the midge behavior can be segmented into two distinct modes: one that is independent and composed of low-frequency maneuvers, and one that consists of higher-frequency nearly harmonic oscillations conducted in synchrony with another midge. We characterize these pairwise interactions, and make a hypothesis as to their biological function.

Biologicals and small molecules in psoriasis: A systematic review of economic evaluations

PubMed Central

Kromer, Christian; Celis, Daniel; Sonntag, Diana

2018-01-01

Biological therapy for moderate-to-severe psoriasis is highly effective but cost-intensive. This systematic review aimed at analyzing evidence on the cost-effectiveness of biological treatment of moderate-to-severe psoriasis. A literature search was conducted until 30/06/2017 in PubMed, Cochrane Library, LILACS, and EconLit. The quality of identified studies was assessed with the checklist by the Centre for Reviews and Dissemination guidance. Out of 482 records, 53 publications were eligible for inclusion. Half of the studies met between 20 and 25 of the quality checklist items, displaying moderate quality. Due to heterogeneity of studies, a qualitative synthesis was conducted. Cost ranges per outcome were enormous across different studies due to diversity in assumptions and model design. Pairwise comparisons of biologicals revealed conflicting results. Overall, adalimumab appeared to be most cost-effective (100% of all aggregated pairwise comparisons), followed by ustekinumab (66.7%), and infliximab (60%). However, in study conclusions most recent publications favored secukinumab and apremilast (75% and 60% of the studies investigating these medications). Accepted willingness-to-pay thresholds varied between 30,000 and 50,000 USD/Quality-Adjusted Life Year (QALY). Three-quarters of studies were financially supported, and in 90% of those, results were consistent with the funder’s interest. Economic evaluation of biologicals is crucial for responsible allocation of health care resources. In addition to summarizing the actual evidence this review highlights gaps and needs for future research. PMID:29298315

Dynamically heterogenous partitions and phylogenetic inference: an evaluation of analytical strategies with cytochrome b and ND6 gene sequences in cranes.

PubMed

Krajewski, C; Fain, M G; Buckley, L; King, D G

1999-11-01

ki ctes over whether molecular sequence data should be partitioned for phylogenetic analysis often confound two types of heterogeneity among partitions. We distinguish historical heterogeneity (i.e., different partitions have different evolutionary relationships) from dynamic heterogeneity (i.e., different partitions show different patterns of sequence evolution) and explore the impact of the latter on phylogenetic accuracy and precision with a two-gene, mitochondrial data set for cranes. The well-established phylogeny of cranes allows us to contrast tree-based estimates of relevant parameter values with estimates based on pairwise comparisons and to ascertain the effects of incorporating different amounts of process information into phylogenetic estimates. We show that codon positions in the cytochrome b and NADH dehydrogenase subunit 6 genes are dynamically heterogenous under both Poisson and invariable-sites + gamma-rates versions of the F84 model and that heterogeneity includes variation in base composition and transition bias as well as substitution rate. Estimates of transition-bias and relative-rate parameters from pairwise sequence comparisons were comparable to those obtained as tree-based maximum likelihood estimates. Neither rate-category nor mixed-model partitioning strategies resulted in a loss of phylogenetic precision relative to unpartitioned analyses. We suggest that weighted-average distances provide a computationally feasible alternative to direct maximum likelihood estimates of phylogeny for mixed-model analyses of large, dynamically heterogenous data sets. Copyright 1999 Academic Press.

Age-Related Changes in Pharyngeal Lumen Size: A Retrospective MRI Analysis.

PubMed

Molfenter, Sonja M; Amin, M R; Branski, R C; Brumm, J D; Hagiwara, M; Roof, S A; Lazarus, C L

2015-06-01

Age-related loss of muscle bulk and strength (sarcopenia) is often cited as a potential mechanism underlying age-related changes in swallowing. Our goal was to explore this phenomenon in the pharynx, specifically, by measuring pharyngeal wall thickness and pharyngeal lumen area in a sample of young versus older women. MRI scans of the neck were retrospectively reviewed from 60 women equally stratified into three age groups (20s, 60s, 70+). Four de-identified slices were extracted per scan for randomized, blinded analysis: one mid-sagittal and three axial slices were selected at the anterior inferior border of C2 and C3, and at the pit of the vallecula. Pixel-based measures of pharyngeal wall thickness and pharyngeal lumen area were completed using ImageJ and then converted to metric units. Measures of pharyngeal wall thickness and pharyngeal lumen area were compared between age groups with one-way ANOVAs using Sidak adjustments for post-hoc pairwise comparisons. A significant main effect for age was observed across all variables whereby pharyngeal wall thickness decreased and pharyngeal lumen area increased with advancing age. Pairwise comparisons revealed significant differences between 20s versus 70+ for all variables and 20s versus 60s for all variables except those measured at C2. Effect sizes ranged from 0.54 to 1.34. Consistent with existing sacropenia literature, the pharyngeal muscles appear to atrophy with age and consequently, the size of the pharyngeal lumen increases.

Leaf habit does not determine the investment in both physical and chemical defences and pair-wise correlations between these defensive traits.

PubMed

Moreira, X; Pearse, I S

2017-05-01

Plant life-history strategies associated with resource acquisition and economics (e.g. leaf habit) are thought to be fundamental determinants of the traits and mechanisms that drive herbivore pressure, resource allocation to plant defensive traits, and the simultaneous expression (positive correlations) or trade-offs (negative correlations) between these defensive traits. In particular, it is expected that evergreen species - which usually grow slower and support constant herbivore pressure in comparison with deciduous species - will exhibit higher levels of both physical and chemical defences and a higher predisposition to the simultaneous expression of physical and chemical defensive traits. Here, by using a dataset which included 56 oak species (Quercus genus), we investigated whether leaf habit of plant species governs the investment in both physical and chemical defences and pair-wise correlations between these defensive traits. Our results showed that leaf habit does not determine the production of most leaf physical and chemical defences. Although evergreen oak species had higher levels of leaf toughness and specific leaf mass (physical defences) than deciduous oak species, both traits are essentially prerequisites for evergreenness. Similarly, our results also showed that leaf habit does not determine pair-wise correlations between defensive traits because most physical and chemical defensive traits were simultaneously expressed in both evergreen and deciduous oak species. Our findings indicate that leaf habit does not substantially contribute to oak species differences in plant defence investment. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

Comparison of the AJCC, MSTS, and Modified Spanier Systems for Clinical and Pathologic Staging of Osteosarcoma.

PubMed

Cates, Justin M M

2017-03-01

The prognostic performance of the 2 most commonly used staging systems for skeletal sarcoma (the American Joint Committee on Cancer [AJCC] and Musculoskeletal Tumor Society [MSTS] systems) have never been compared analytically. Another staging system originally proposed by Spanier has not yet been validated. Given the recent release of the 8th edition of the AJCC Cancer Staging Manual, this study was designed to directly compare these anatomic staging systems in a series of 153 high-grade, intramedullary osteosarcomas. Kaplan-Meier curves were plotted and pairwise comparisons between each stage category were performed. Predictive accuracy of each staging system for determining 5-year disease-free survival was evaluated by comparing areas under receiver-operating characteristic curves generated from logistic regression analysis. Multiple concordance indices were calculated using bootstrapping methods (200 replications). ρk and R were estimated as measures of the variation in survival outcomes explained by the regression models. The AJCC, MSTS, and a modified version of the Spanier staging systems showed similar discriminatory abilities and no significant differences in the levels of contrast between different tumor stages across staging systems. Addition of T-category information from each staging system contributed significant prognostic information compared with a Cox proportional hazard regression model consisting only of the presence or absence of metastatic disease as a measure of disease extent. Concordance indices and predictive accuracy for 5-year disease-free survival were not significantly different among the different staging systems either. Similar findings were observed after accounting for other important prognostic variables. Additional studies are necessary to determine performance parameters of each staging system for other types of skeletal sarcoma. Prognostic performance of osteosarcoma staging systems would also be improved by incorporating nonanatomic prognostic variables into staging algorithms.

Prediction of microsleeps using pairwise joint entropy and mutual information between EEG channels.

PubMed

Baseer, Abdul; Weddell, Stephen J; Jones, Richard D

2017-07-01

Microsleeps are involuntary and brief instances of complete loss of responsiveness, typically of 0.5-15 s duration. They adversely affect performance in extended attention-driven jobs and can be fatal. Our aim was to predict microsleeps from 16 channel EEG signals. Two information theoretic concepts - pairwise joint entropy and mutual information - were independently used to continuously extract features from EEG signals. k-nearest neighbor (kNN) with k = 3 was used to calculate both joint entropy and mutual information. Highly correlated features were discarded and the rest were ranked using Fisher score followed by an average of 3-fold cross-validation area under the curve of the receiver operating characteristic (AUC ROC ). Leave-one-out method (LOOM) was performed to test the performance of microsleep prediction system on independent data. The best prediction for 0.25 s ahead was AUCROC, sensitivity, precision, geometric mean (GM), and φ of 0.93, 0.68, 0.33, 0.75, and 0.38 respectively with joint entropy using single linear discriminant analysis (LDA) classifier.

COMPARISON OF LAPAROSCOPIC SKILLS PERFORMANCE USING SINGLE-SITE ACCESS (SSA) DEVICES VS. AN INDEPENDENT-PORT SSA APPROACH

PubMed Central

Schill, Matthew R.; Varela, J. Esteban; Frisella, Margaret M.; Brunt, L. Michael

2015-01-01

Background We compared performance of validated laparoscopic tasks on four commercially available single site access (SSA) access devices (AD) versus an independent port (IP) SSA set-up. Methods A prospective, randomized comparison of laparoscopic skills performance on four AD (GelPOINT™, SILS™ Port, SSL Access System™, TriPort™) and one IP SSA set-up was conducted. Eighteen medical students (2nd–4th year), four surgical residents, and five attending surgeons were trained to proficiency in multi-port laparoscopy using four laparoscopic drills (peg transfer, bean drop, pattern cutting, extracorporeal suturing) in a laparoscopic trainer box. Drills were then performed in random order on each IP-SSA and AD-SSA set-up using straight laparoscopic instruments. Repetitions were timed and errors recorded. Data are mean ± SD, and statistical analysis was by two-way ANOVA with Tukey HSD post-hoc tests. Results Attending surgeons had significantly faster total task times than residents or students (p< 0.001), but the difference between residents and students was NS. Pair-wise comparisons revealed significantly faster total task times for the IP-SSA set-up compared to all four AD-SSA’s within the student group only (p<0.05). Total task times for residents and attending surgeons showed a similar profile, but the differences were NS. When data for the three groups was combined, the total task time was less for the IP-SSA set-up than for each of the four AD-SSA set-ups (p < 0.001). Similarly,, the IP-SSA set-up was significantly faster than 3 of 4 AD-SSA set-ups for peg transfer, 3 of 4 for pattern cutting, and 2 of 4 for suturing. No significant differences in error rates between IP-SSA and AD-SSA set-ups were detected. Conclusions When compared to an IP-SSA laparoscopic set-up, single site access devices are associated with longer task performance times in a trainer box model, independent of level of training. Task performance was similar across different SSA devices. PMID:21993938

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daily, Jeffrey A.

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

DOE PAGES

Daily, Jeffrey A.

2016-02-10

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less

Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations.

PubMed

Zgarbová, Marie; Otyepka, Michal; Sponer, Jirí; Hobza, Pavel; Jurecka, Petr

2010-09-21

The intermolecular interaction energy components for several molecular complexes were calculated using force fields available in the AMBER suite of programs and compared with Density Functional Theory-Symmetry Adapted Perturbation Theory (DFT-SAPT) values. The extent to which such comparison is meaningful is discussed. The comparability is shown to depend strongly on the intermolecular distance, which means that comparisons made at one distance only are of limited value. At large distances the coulombic and van der Waals 1/r(6) empirical terms correspond fairly well with the DFT-SAPT electrostatics and dispersion terms, respectively. At the onset of electronic overlap the empirical values deviate from the reference values considerably. However, the errors in the force fields tend to cancel out in a systematic manner at equilibrium distances. Thus, the overall performance of the force fields displays errors an order of magnitude smaller than those of the individual interaction energy components. The repulsive 1/r(12) component of the van der Waals expression seems to be responsible for a significant part of the deviation of the force field results from the reference values. We suggest that further improvement of the force fields for intermolecular interactions would require replacement of the nonphysical 1/r(12) term by an exponential function. Dispersion anisotropy and its effects are discussed. Our analysis is intended to show that although comparing the empirical and non-empirical interaction energy components is in general problematic, it might bring insights useful for the construction of new force fields. Our results are relevant to often performed force-field-based interaction energy decompositions.

Functional connectivity analysis in resting state fMRI with echo-state networks and non-metric clustering for network structure recovery

NASA Astrophysics Data System (ADS)

Wismüller, Axel; DSouza, Adora M.; Abidin, Anas Z.; Wang, Xixi; Hobbs, Susan K.; Nagarajan, Mahesh B.

2015-03-01

Echo state networks (ESN) are recurrent neural networks where the hidden layer is replaced with a fixed reservoir of neurons. Unlike feed-forward networks, neuron training in ESN is restricted to the output neurons alone thereby providing a computational advantage. We demonstrate the use of such ESNs in our mutual connectivity analysis (MCA) framework for recovering the primary motor cortex network associated with hand movement from resting state functional MRI (fMRI) data. Such a framework consists of two steps - (1) defining a pair-wise affinity matrix between different pixel time series within the brain to characterize network activity and (2) recovering network components from the affinity matrix with non-metric clustering. Here, ESNs are used to evaluate pair-wise cross-estimation performance between pixel time series to create the affinity matrix, which is subsequently subject to non-metric clustering with the Louvain method. For comparison, the ground truth of the motor cortex network structure is established with a task-based fMRI sequence. Overlap between the primary motor cortex network recovered with our model free MCA approach and the ground truth was measured with the Dice coefficient. Our results show that network recovery with our proposed MCA approach is in close agreement with the ground truth. Such network recovery is achieved without requiring low-pass filtering of the time series ensembles prior to analysis, an fMRI preprocessing step that has courted controversy in recent years. Thus, we conclude our MCA framework can allow recovery and visualization of the underlying functionally connected networks in the brain on resting state fMRI.

Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations.

PubMed

Panteva, Maria T; Giambaşu, George M; York, Darrin M

2015-05-15

The prevalence of Mg(2+) ions in biology and their essential role in nucleic acid structure and function has motivated the development of various Mg(2+) ion models for use in molecular simulations. Currently, the most widely used models in biomolecular simulations represent a nonbonded metal ion as an ion-centered point charge surrounded by a nonelectrostatic pairwise potential that takes into account dispersion interactions and exchange effects that give rise to the ion's excluded volume. One strategy toward developing improved models for biomolecular simulations is to first identify a Mg(2+) model that is consistent with the simulation force fields that closely reproduces a range of properties in aqueous solution, and then, in a second step, balance the ion-water and ion-solute interactions by tuning parameters in a pairwise fashion where necessary. The present work addresses the first step in which we compare 17 different nonbonded single-site Mg(2+) ion models with respect to their ability to simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. None of the models based on a 12-6 nonelectrostatic nonbonded potential was able to reproduce the experimental radial distribution function, solvation free energy, exchange barrier and diffusion constant. The models based on a 12-6-4 potential offered improvement, and one model in particular, in conjunction with the SPC/E water model, performed exceptionally well for all properties. The results reported here establish useful benchmark calculations for Mg(2+) ion models that provide insight into the origin of the behavior in aqueous solution, and may aid in the development of next-generation models that target specific binding sites in biomolecules. © 2015 Wiley Periodicals, Inc.

Mapping hydrological signatures in the tropical Andes using a network of paired catchments

NASA Astrophysics Data System (ADS)

Ochoa-Tocachi, B. F.; Buytaert, W.; De Bièvre, B.

2016-12-01

The complexity and data scarcity of tropical Andean catchments make regional hydrological predictions very challenging. The strong spatiotemporal patterns of the local climate contrast with the inadequate coverage, especially of remote areas, by the national monitoring networks. We present an approach to regionalize the hydrological impacts of land-use and land-cover (LUC) using a network of 24 headwater catchments in a pairwise comparison approach. We monitored precipitation and streamflow through an informal partnership of stakeholders in the Andes, known as iMHEA. Using a `trading-space-for-time' approach, our design aims at strengthening the statistical significance of LUC signals. To test our hypothesis, we summarized the hydrological responses using a set of indices, which are then regionalized against catchment properties including land-use. Lastly, the regionalization model is then used to generate distributed maps of hydrological signatures in ungauged areas. Our results clearly reflect the dominant regional climate patterns of the tropical Andes and the associated wide spectrum of hydrological responses. Although the hydrological impacts of LUC are equally diverse, we find consistent trends within different biomes. Contrary to earlier studies, we find that incorporating LUC variables in the regionalization increases significantly the performance of the regression model and its predictive capacity, which makes it possible to generate regional maps that predict the dynamics and propagation of streamflow signatures in complex regions with an explicit report of uncertainty. We attribute the robust regionalization results to the regional pairwise setup that covers diverse physiographic characteristics, contrasting LUC types, and degrees of conservation/alteration. As such, it may be a useful strategy to optimize data collection, leverage commonly available geographical information, and understand the major controls of hydrological response in data-scarce regions.

Blood-Based Gene Expression Profiles Models for Classification of Subsyndromal Symptomatic Depression and Major Depressive Disorder

PubMed Central

Yu, Shunying; Yuan, Chengmei; Hong, Wu; Wang, Zuowei; Cui, Jian; Shi, Tieliu; Fang, Yiru

2012-01-01

Subsyndromal symptomatic depression (SSD) is a subtype of subthreshold depressive and also lead to significant psychosocial functional impairment as same as major depressive disorder (MDD). Several studies have suggested that SSD is a transitory phenomena in the depression spectrum and is thus considered a subtype of depression. However, the pathophysioloy of depression remain largely obscure and studies on SSD are limited. The present study compared the expression profile and made the classification with the leukocytes by using whole-genome cRNA microarrays among drug-free first-episode subjects with SSD, MDD, and matched controls (8 subjects in each group). Support vector machines (SVMs) were utilized for training and testing on candidate signature expression profiles from signature selection step. Firstly, we identified 63 differentially expressed SSD signatures in contrast to control (P< = 5.0E-4) and 30 differentially expressed MDD signatures in contrast to control, respectively. Then, 123 gene signatures were identified with significantly differential expression level between SSD and MDD. Secondly, in order to conduct priority selection for biomarkers for SSD and MDD together, we selected top gene signatures from each group of pair-wise comparison results, and merged the signatures together to generate better profiles used for clearly classify SSD and MDD sets in the same time. In details, we tried different combination of signatures from the three pair-wise compartmental results and finally determined 48 gene expression signatures with 100% accuracy. Our finding suggested that SSD and MDD did not exhibit the same expressed genome signature with peripheral blood leukocyte, and blood cell–derived RNA of these 48 gene models may have significant value for performing diagnostic functions and classifying SSD, MDD, and healthy controls. PMID:22348066

Phylogenomic analysis of the species of the Mycobacterium tuberculosis complex demonstrates that Mycobacterium africanum, Mycobacterium bovis, Mycobacterium caprae, Mycobacterium microti and Mycobacterium pinnipedii are later heterotypic synonyms of Mycobacterium tuberculosis.

PubMed

Riojas, Marco A; McGough, Katya J; Rider-Riojas, Cristin J; Rastogi, Nalin; Hazbón, Manzour Hernando

2018-01-01

The species within the Mycobacterium tuberculosis Complex (MTBC) have undergone numerous taxonomic and nomenclatural changes, leaving the true structure of the MTBC in doubt. We used next-generation sequencing (NGS), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) to investigate the relationship between these species. The type strains of Mycobacterium africanum, Mycobacterium bovis, Mycobacterium caprae, Mycobacterium microti and Mycobacterium pinnipedii were sequenced via NGS. Pairwise dDDH and ANI comparisons between these, previously sequenced MTBC type strain genomes (including 'Mycobacterium canettii', 'Mycobacterium mungi' and 'Mycobacterium orygis') and M. tuberculosis H37Rv T were performed. Further, all available genome sequences in GenBank for species in or putatively in the MTBC were compared to H37Rv T . Pairwise results indicated that all of the type strains of the species are extremely closely related to each other (dDDH: 91.2-99.2 %, ANI: 99.21-99.92 %), greatly exceeding the respective species delineation thresholds, thus indicating that they belong to the same species. Results from the GenBank genomes indicate that all the strains examined are within the circumscription of H37Rv T (dDDH: 83.5-100 %). We, therefore, formally propose a union of the species of the MTBC as M. tuberculosis. M. africanum, M. bovis, M. caprae, M. microti and M. pinnipedii are reclassified as later heterotypic synonyms of M. tuberculosis. 'M. canettii', 'M. mungi', and 'M. orygis' are classified as strains of the species M. tuberculosis. We further recommend use of the infrasubspecific term 'variant' ('var.') and infrasubspecific designations that generally retain the historical nomenclature associated with the groups or otherwise convey such characteristics, e.g. M. tuberculosis var. bovis.

Maternal ADHD, parenting, and psychopathology among mothers of adolescents with ADHD

PubMed Central

Babinski, Dara E.; Pelham, William E.; Molina, Brooke S.G.; Gnagy, Elizabeth M.; Waschbusch, Daniel A.; Wymbs, Brian T.; Sibley, Margaret H.; Derefinko, Karen J.; Kuriyan, Aparajita B.

2012-01-01

Objective This study describes the parenting and psychopathology of mothers with ADHD of adolescents with ADHD (MCA), non-ADHD mothers of adolescents with ADHD (CA), and non-ADHD mothers of adolescents without ADHD (COMP). Method Two sets of pairwise comparisons: 1) COMP vs. CA and 2) CA vs. MCA were conducted. We hypothesized that CA would experience greater distress in parenting and psychopathology compared to COMP, and that MCA would experience even more impairment compared to CA. Results Few differences emerged in comparisons of CA and COMP, with the exception of CA reporting greater parent-adolescent conflict and internalizing problems. In contrast, differences consistently emerged in comparisons of MCA and CA showing more difficulty for MCA in parenting and psychopathology. Conclusion These findings underscore the need for treatments that address parental ADHD when adolescent ADHD is the intended target. PMID:23160485

Pairwise gene GO-based measures for biclustering of high-dimensional expression data.

PubMed

Nepomuceno, Juan A; Troncoso, Alicia; Nepomuceno-Chamorro, Isabel A; Aguilar-Ruiz, Jesús S

2018-01-01

Biclustering algorithms search for groups of genes that share the same behavior under a subset of samples in gene expression data. Nowadays, the biological knowledge available in public repositories can be used to drive these algorithms to find biclusters composed of groups of genes functionally coherent. On the other hand, a distance among genes can be defined according to their information stored in Gene Ontology (GO). Gene pairwise GO semantic similarity measures report a value for each pair of genes which establishes their functional similarity. A scatter search-based algorithm that optimizes a merit function that integrates GO information is studied in this paper. This merit function uses a term that addresses the information through a GO measure. The effect of two possible different gene pairwise GO measures on the performance of the algorithm is analyzed. Firstly, three well known yeast datasets with approximately one thousand of genes are studied. Secondly, a group of human datasets related to clinical data of cancer is also explored by the algorithm. Most of these data are high-dimensional datasets composed of a huge number of genes. The resultant biclusters reveal groups of genes linked by a same functionality when the search procedure is driven by one of the proposed GO measures. Furthermore, a qualitative biological study of a group of biclusters show their relevance from a cancer disease perspective. It can be concluded that the integration of biological information improves the performance of the biclustering process. The two different GO measures studied show an improvement in the results obtained for the yeast dataset. However, if datasets are composed of a huge number of genes, only one of them really improves the algorithm performance. This second case constitutes a clear option to explore interesting datasets from a clinical point of view.

Tools for Protecting the Privacy of Specific Individuals in Video

NASA Astrophysics Data System (ADS)

Chen, Datong; Chang, Yi; Yan, Rong; Yang, Jie

2007-12-01

This paper presents a system for protecting the privacy of specific individuals in video recordings. We address the following two problems: automatic people identification with limited labeled data, and human body obscuring with preserved structure and motion information. In order to address the first problem, we propose a new discriminative learning algorithm to improve people identification accuracy using limited training data labeled from the original video and imperfect pairwise constraints labeled from face obscured video data. We employ a robust face detection and tracking algorithm to obscure human faces in the video. Our experiments in a nursing home environment show that the system can obtain a high accuracy of people identification using limited labeled data and noisy pairwise constraints. The study result indicates that human subjects can perform reasonably well in labeling pairwise constraints with the face masked data. For the second problem, we propose a novel method of body obscuring, which removes the appearance information of the people while preserving rich structure and motion information. The proposed approach provides a way to minimize the risk of exposing the identities of the protected people while maximizing the use of the captured data for activity/behavior analysis.

Random Partition Distribution Indexed by Pairwise Information

PubMed Central

Dahl, David B.; Day, Ryan; Tsai, Jerry W.

2017-01-01

We propose a random partition distribution indexed by pairwise similarity information such that partitions compatible with the similarities are given more probability. The use of pairwise similarities, in the form of distances, is common in some clustering algorithms (e.g., hierarchical clustering), but we show how to use this type of information to define a prior partition distribution for flexible Bayesian modeling. A defining feature of the distribution is that it allocates probability among partitions within a given number of subsets, but it does not shift probability among sets of partitions with different numbers of subsets. Our distribution places more probability on partitions that group similar items yet keeps the total probability of partitions with a given number of subsets constant. The distribution of the number of subsets (and its moments) is available in closed-form and is not a function of the similarities. Our formulation has an explicit probability mass function (with a tractable normalizing constant) so the full suite of MCMC methods may be used for posterior inference. We compare our distribution with several existing partition distributions, showing that our formulation has attractive properties. We provide three demonstrations to highlight the features and relative performance of our distribution. PMID:29276318

Impaired inference in a case of developmental amnesia.

PubMed

D'Angelo, Maria C; Rosenbaum, R Shayna; Ryan, Jennifer D

2016-10-01

Amnesia is associated with impairments in relational memory, which is critically supported by the hippocampus. By adapting the transitivity paradigm, we previously showed that age-related impairments in inference were mitigated when judgments could be predicated on known pairwise relations, however, such advantages were not observed in the adult-onset amnesic case D.A. Here, we replicate and extend this finding in a developmental amnesic case (N.C.), who also shows impaired relational learning and transitive expression. Unlike D.A., N.C.'s damage affected the extended hippocampal system and diencephalic structures, and does not extend to neocortical areas that are affected in D.A. Critically, despite their differences in etiology and affected structures, N.C. and D.A. perform similarly on the task. N.C. showed intact pairwise knowledge, suggesting that he is able to use existing semantic information, but this semantic knowledge was insufficient to support transitive expression. The present results suggest a critical role for regions connected to the hippocampus and/or medial prefrontal cortex in inference beyond learning of pairwise relations. © 2016 The Authors Hippocampus Published by Wiley Periodicals, Inc. © 2016 The Authors. Wiley Periodicals, Inc.

A DNA microarray-based methylation-sensitive (MS)-AFLP hybridization method for genetic and epigenetic analyses.

PubMed

Yamamoto, F; Yamamoto, M

2004-07-01

We previously developed a PCR-based DNA fingerprinting technique named the Methylation Sensitive (MS)-AFLP method, which permits comparative genome-wide scanning of methylation status with a manageable number of fingerprinting experiments. The technique uses the methylation sensitive restriction enzyme NotI in the context of the existing Amplified Fragment Length Polymorphism (AFLP) method. Here we report the successful conversion of this gel electrophoresis-based DNA fingerprinting technique into a DNA microarray hybridization technique (DNA Microarray MS-AFLP). By performing a total of 30 (15 x 2 reciprocal labeling) DNA Microarray MS-AFLP hybridization experiments on genomic DNA from two breast and three prostate cancer cell lines in all pairwise combinations, and Southern hybridization experiments using more than 100 different probes, we have demonstrated that the DNA Microarray MS-AFLP is a reliable method for genetic and epigenetic analyses. No statistically significant differences were observed in the number of differences between the breast-prostate hybridization experiments and the breast-breast or prostate-prostate comparisons.

Phagonaute: A web-based interface for phage synteny browsing and protein function prediction.

PubMed

Delattre, Hadrien; Souiai, Oussema; Fagoonee, Khema; Guerois, Raphaël; Petit, Marie-Agnès

2016-09-01

Distant homology search tools are of great help to predict viral protein functions. However, due to the lack of profile databases dedicated to viruses, they can lack sensitivity. We constructed HMM profiles for more than 80,000 proteins from both phages and archaeal viruses, and performed all pairwise comparisons with HHsearch program. The whole resulting database can be explored through a user-friendly "Phagonaute" interface to help predict functions. Results are displayed together with their genetic context, to strengthen inferences based on remote homology. Beyond function prediction, this tool permits detections of co-occurrences, often indicative of proteins completing a task together, and observation of conserved patterns across large evolutionary distances. As a test, Herpes simplex virus I was added to Phagonaute, and 25% of its proteome matched to bacterial or archaeal viral protein counterparts. Phagonaute should therefore help virologists in their quest for protein functions and evolutionary relationships. Copyright © 2016 Elsevier Inc. All rights reserved.

Regularities and irregularities in order flow data

NASA Astrophysics Data System (ADS)

Theissen, Martin; Krause, Sebastian M.; Guhr, Thomas

2017-11-01

We identify and analyze statistical regularities and irregularities in the recent order flow of different NASDAQ stocks, focusing on the positions where orders are placed in the order book. This includes limit orders being placed outside of the spread, inside the spread and (effective) market orders. Based on the pairwise comparison of the order flow of different stocks, we perform a clustering of stocks into groups with similar behavior. This is useful to assess systemic aspects of stock price dynamics. We find that limit order placement inside the spread is strongly determined by the dynamics of the spread size. Most orders, however, arrive outside of the spread. While for some stocks order placement on or next to the quotes is dominating, deeper price levels are more important for other stocks. As market orders are usually adjusted to the quote volume, the impact of market orders depends on the order book structure, which we find to be quite diverse among the analyzed stocks as a result of the way limit order placement takes place.

pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling.

PubMed

Gil, Víctor A; Guallar, Víctor

2013-09-15

We introduce pyRMSD, an open source standalone Python package that aims at offering an integrative and efficient way of performing Root Mean Square Deviation (RMSD)-related calculations of large sets of structures. It is specially tuned to do fast collective RMSD calculations, as pairwise RMSD matrices, implementing up to three well-known superposition algorithms. pyRMSD provides its own symmetric distance matrix class that, besides the fact that it can be used as a regular matrix, helps to save memory and increases memory access speed. This last feature can dramatically improve the overall performance of any Python algorithm using it. In addition, its extensibility, testing suites and documentation make it a good choice to those in need of a workbench for developing or testing new algorithms. The source code (under MIT license), installer, test suites and benchmarks can be found at https://pele.bsc.es/ under the tools section. victor.guallar@bsc.es Supplementary data are available at Bioinformatics online.

Design and implementation of a hybrid MPI-CUDA model for the Smith-Waterman algorithm.

PubMed

Khaled, Heba; Faheem, Hossam El Deen Mostafa; El Gohary, Rania

2015-01-01

This paper provides a novel hybrid model for solving the multiple pair-wise sequence alignment problem combining message passing interface and CUDA, the parallel computing platform and programming model invented by NVIDIA. The proposed model targets homogeneous cluster nodes equipped with similar Graphical Processing Unit (GPU) cards. The model consists of the Master Node Dispatcher (MND) and the Worker GPU Nodes (WGN). The MND distributes the workload among the cluster working nodes and then aggregates the results. The WGN performs the multiple pair-wise sequence alignments using the Smith-Waterman algorithm. We also propose a modified implementation to the Smith-Waterman algorithm based on computing the alignment matrices row-wise. The experimental results demonstrate a considerable reduction in the running time by increasing the number of the working GPU nodes. The proposed model achieved a performance of about 12 Giga cell updates per second when we tested against the SWISS-PROT protein knowledge base running on four nodes.

Hospital consolidation and costs: another look at the evidence.

PubMed

Dranove, David; Lindrooth, Richard

2003-11-01

We investigate whether pairwise hospital consolidation leads to cost savings. We use a unified empirical methodology to assess both systems and mergers. Our comparison group for each consolidation consists of 10 'pseudo-mergers' chosen based on propensity scores. Cost function estimates reveal that consolidation into systems does not generate savings, even after 4 years. Mergers in which hospitals consolidate financial reporting and licenses generate savings of approximately 14%: 2, 3, and 4 years after merger. The system consolidation and merger results are very robust to changes in the specification and the sample.

Enzyme markers in inbred rat strains: genetics of new markers and strain profiles.

PubMed

Adams, M; Baverstock, P R; Watts, C H; Gutman, G A

1984-08-01

Twenty-six inbred strains of the laboratory rat (Rattus norvegicus) were examined for electrophoretic variation at an estimated 97 genetic loci. In addition to previously documented markers, variation was observed for the enzymes aconitase, aldehyde dehydrogenase, and alkaline phosphatase. The genetic basis of these markers (Acon-1, Ahd-2, and Akp-1) was confirmed. Linkage analysis between 35 pairwise comparisons revealed that the markers Fh-1 and Pep-3 are linked. The strain profiles of the 25 inbred strains at 11 electrophoretic markers are given.

Hepatic Transcriptome Responses of Domesticated and Wild Turkey Embryos to Aflatoxin B₁.

PubMed

Monson, Melissa S; Cardona, Carol J; Coulombe, Roger A; Reed, Kent M

2016-01-06

The mycotoxin, aflatoxin B₁ (AFB₁) is a hepatotoxic, immunotoxic, and mutagenic contaminant of food and animal feeds. In poultry, AFB₁ can be maternally transferred to embryonated eggs, affecting development, viability and performance after hatch. Domesticated turkeys (Meleagris gallopavo) are especially sensitive to aflatoxicosis, while Eastern wild turkeys (M. g. silvestris) are likely more resistant. In ovo exposure provided a controlled AFB₁ challenge and comparison of domesticated and wild turkeys. Gene expression responses to AFB₁ in the embryonic hepatic transcriptome were examined using RNA-sequencing (RNA-seq). Eggs were injected with AFB₁ (1 μg) or sham control and dissected for liver tissue after 1 day or 5 days of exposure. Libraries from domesticated turkey (n = 24) and wild turkey (n = 15) produced 89.2 Gb of sequence. Approximately 670 M reads were mapped to a turkey gene set. Differential expression analysis identified 1535 significant genes with |log₂ fold change| ≥ 1.0 in at least one pair-wise comparison. AFB₁ effects were dependent on exposure time and turkey type, occurred more rapidly in domesticated turkeys, and led to notable up-regulation in cell cycle regulators, NRF2-mediated response genes and coagulation factors. Further investigation of NRF2-response genes may identify targets to improve poultry resistance.

SpecOMS: A Full Open Modification Search Method Performing All-to-All Spectra Comparisons within Minutes.

PubMed

David, Matthieu; Fertin, Guillaume; Rogniaux, Hélène; Tessier, Dominique

2017-08-04

The analysis of discovery proteomics experiments relies on algorithms that identify peptides from their tandem mass spectra. The almost exhaustive interpretation of these spectra remains an unresolved issue. At present, an important number of missing interpretations is probably due to peptides displaying post-translational modifications and variants that yield spectra that are particularly difficult to interpret. However, the emergence of a new generation of mass spectrometers that provide high fragment ion accuracy has paved the way for more efficient algorithms. We present a new software, SpecOMS, that can handle the computational complexity of pairwise comparisons of spectra in the context of large volumes. SpecOMS can compare a whole set of experimental spectra generated by a discovery proteomics experiment to a whole set of theoretical spectra deduced from a protein database in a few minutes on a standard workstation. SpecOMS can ingeniously exploit those capabilities to improve the peptide identification process, allowing strong competition between all possible peptides for spectrum interpretation. Remarkably, this software resolves the drawbacks (i.e., efficiency problems and decreased sensitivity) that usually accompany open modification searches. We highlight this promising approach using results obtained from the analysis of a public human data set downloaded from the PRIDE (PRoteomics IDEntification) database.

HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts

PubMed Central

Laffy, Patrick W.; Wood-Charlson, Elisha M.; Turaev, Dmitrij; Weynberg, Karen D.; Botté, Emmanuelle S.; van Oppen, Madeleine J. H.; Webster, Nicole S.; Rattei, Thomas

2016-01-01

Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments. PMID:27375564

A network meta-analysis of randomized controlled trials for comparing the effectiveness and safety profile of treatments with marketing authorization for relapsing multiple sclerosis.

PubMed

Hadjigeorgiou, G M; Doxani, C; Miligkos, M; Ziakas, P; Bakalos, G; Papadimitriou, D; Mprotsis, T; Grigoriadis, N; Zintzaras, E

2013-12-01

The relative effectiveness and safety profile of the treatments with marketing authorization for relapsing multiple sclerosis (MS) are not well known because randomized controlled trials with head-to-head comparisons between these treatments do not exist. Thus, a network of multiple-treatments meta-analysis was performed using four clinical outcomes: 'patients free of relapse', 'patients without disease progression', 'patients without MRI progression' and 'patients with adverse events'. Randomized controlled trials (RCTs) on MS were systematically searched in PubMed and Cochrane Central Register of Controlled Trial. The network analysis performed pairwise comparisons between the marketed treatments (Betaferon 250mcg, Avonex 30mcg, Rebif 44mcg, Rebif 22mcg, Aubagio 7 mg, Aubagio 14 mg, Copaxone 20 mg, Tysabri 300 mg, Gilenya 0·5 mg and Novantrone 12 mg/m(2)) using direct and indirect analyses. The analysis included 48 articles, involving 20 455 patients with MS. The direct analysis showed better response for more than one outcome for Gilenya compared with Avonex ('patients free of relapse' and 'patients without MRI progression') and for Betaferon compared with Avonex ('patients without disease progression' and 'patients without MRI progression'). The indirect analysis indicated that Tysabri may have better relative effectiveness compared with the other treatments for two outcomes: 'patients free of relapse' and 'patients without MRI progression'. Regarding 'patients with adverse events', no data were available for all comparisons to make fair inferences. This was an attempt, for the first time, to compare the efficacy and safety profile of existing approved treatments for relapsing MS. Although some treatments have shown better response, the results of the network analysis should be interpreted with caution because of the lack of RCTs with head-to-head comparisons between treatments. © 2013 John Wiley & Sons Ltd.

Meta-Analysis Comparing Complete Revascularization Versus Infarct-Related Only Strategies for Patients With ST-Segment Elevation Myocardial Infarction and Multivessel Coronary Artery Disease.

PubMed

Shah, Rahman; Berzingi, Chalak; Mumtaz, Mubashir; Jasper, John B; Goswami, Rohan; Morsy, Mohamed S; Ramanathan, Kodangudi B; Rao, Sunil V

2016-11-15

Several recent randomized controlled trials (RCTs) demonstrated better outcomes with multivessel complete revascularization (CR) than with infarct-related artery-only revascularization (IRA-OR) in patients with ST-segment elevation myocardial infarction. It is unclear whether CR should be performed during the index procedure (IP) at the time of primary percutaneous coronary intervention (PCI) or as a staged procedure (SP). Therefore, we performed a pairwise meta-analysis using a random-effects model and network meta-analysis using mixed-treatment comparison models to compare the efficacies of 3 revascularization strategies (IRA-OR, CR-IP, and CR-SP). Scientific databases and websites were searched to find RCTs. Data from 9 RCTs involving 2,176 patients were included. In mixed-comparison models, CR-IP decreased the risk of major adverse cardiac events (MACEs; odds ratio [OR] 0.36, 95% CI 0.25 to 0.54), recurrent myocardial infarction (MI; OR 0.50, 95% CI 0.24 to 0.91), revascularization (OR 0.24, 95% CI 0.15 to 0.38), and cardiovascular (CV) mortality (OR 0.44, 95% CI 0.20 to 0.87). However, only the rates of MACEs, MI, and CV mortality were lower with CR-SP than with IRA-OR. Similarly, in direct-comparison meta-analysis, the risk of MI was 66% lower with CR-IP than with IRA-OR, but this advantage was not seen with CR-SP. There were no differences in all-cause mortality between the 3 revascularization strategies. In conclusion, this meta-analysis shows that in patients with ST-segment elevation myocardial infarction and multivessel coronary artery disease, CR either during primary PCI or as an SP results in lower occurrences of MACE, revascularization, and CV mortality than IRA-OR. CR performed during primary PCI also results in lower rates of recurrent MI and seems the most efficacious revascularization strategy of the 3. Published by Elsevier Inc.

Direct comparison of coronary bare metal vs. drug-eluting stents: same platform, different mechanics?

PubMed

Schmidt, Wolfram; Lanzer, Peter; Behrens, Peter; Brandt-Wunderlich, Christoph; Öner, Alper; Ince, Hüseyin; Schmitz, Klaus-Peter; Grabow, Niels

2018-01-08

Drug-eluting stents (DES) compared to bare metal stents (BMS) have shown superior clinical performance, but are considered less suitable in complex cases. Most studies do not distinguish between DES and BMS with respect to their mechanical performance. The objective was to obtain mechanical parameters for direct comparison of BMS and DES. In vitro bench tests evaluated crimped stent profiles, crossability in stenosis models, elastic recoil, bending stiffness (crimped and expanded), and scaffolding properties. The study included five pairs of BMS and DES each with the same stent platforms (all n = 5; PRO-Kinetic Energy, Orsiro: BIOTRONIK AG, Bülach, Switzerland; MULTI-LINK 8, XIENCE Xpedition: Abbott Vascular, Temecula, CA; REBEL Monorail, Promus PREMIER, Boston Scientific, Marlborough, MA; Integrity, Resolute Integrity, Medtronic, Minneapolis, MN; Kaname, Ultimaster: Terumo Corporation, Tokyo, Japan). Statistical analysis used pooled variance t tests for pairwise comparison of BMS with DES. Crimped profiles in BMS groups ranged from 0.97 ± 0.01 mm (PRO-Kinetic Energy) to 1.13 ± 0.01 mm (Kaname) and in DES groups from 1.02 ± 0.01 mm (Orsiro) to 1.13 ± 0.01 mm (Ultimaster). Crossability was best for low profile stent systems. Elastic recoil ranged from 4.07 ± 0.22% (Orsiro) to 5.87 ± 0.54% (REBEL Monorail) including both BMS and DES. The bending stiffness of crimped and expanded stents showed no systematic differences between BMS and DES neither did the scaffolding. Based on in vitro measurements BMS appear superior to DES in some aspects of mechanical performance, yet the differences are small and not class uniform. The data provide assistance in selecting the optimal system for treatment and assessment of new generations of bioresorbable scaffolds. not applicable.

Blocking Strategies for Performing Entity Resolution in a Distributed Computing Environment

ERIC Educational Resources Information Center

Wang, Pei

2016-01-01

Entity resolution (ER) is an O(n[superscript 2]) problem where n is the number of records to be processed. The pair-wise nature of ER makes it impractical to perform on large datasets without the use of a technique called blocking. In blocking the records are separated into groups (called blocks) in such a way the records most likely to match are…

Influence of the Smile Line on Smile Attractiveness in Short and Long Face Individuals.

PubMed

Al Taki, Amjad; Hayder Mohammed, Thar; Mohammad Hamdan, Ahmad

2017-01-01

The study assessed the impact of facial height on attractiveness of smile, in association with the maxillary gingival display. This research was performed by dental professionals and laypersons. Frontal extraoral photographs were captured for both short and long faces. The photographs were modified using software for image-processing and three rater groups (orthodontists, dentists, and laypersons) evaluated the smile attractiveness, with 30 subjects in each group. Differences in ratings of the different smiles among the different experimental groups were examined using the Kruskal-Wallis test. The Mann-Whitney U test was performed for pairwise comparisons between the experimental groups. Dentists and laypeople were most likely to agree. For the short face, laypeople and dentists both rated the +2 mm gingival display smile as the most attractive smile whilst orthodontists ranked the 0 mm gingival display smile as the most attractive smile. For the long face, laypeople and dentists ranked the 0 mm gingival display smile as the most attractive smile, whilst orthodontists ranked the +2 mm gingival display as the most attractive. Smile line of both short and long face subjects was found to influence the smile attractiveness rating by the three rater groups.

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.

PubMed

Kelly, Brendan J; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe

2015-08-01

The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence-absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA. We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

PubMed Central

Joyce, Blake L.; Haug-Baltzell, Asher K.; Hulvey, Jonathan P.; McCarthy, Fiona; Devisetty, Upendra Kumar; Lyons, Eric

2017-01-01

This workflow allows novice researchers to leverage advanced computational resources such as cloud computing to carry out pairwise comparative transcriptomics. It also serves as a primer for biologists to develop data scientist computational skills, e.g. executing bash commands, visualization and management of large data sets. All command line code and further explanations of each command or step can be found on the wiki (https://wiki.cyverse.org/wiki/x/dgGtAQ). The Discovery Environment and Atmosphere platforms are connected together through the CyVerse Data Store. As such, once the initial raw sequencing data has been uploaded there is no more need to transfer large data files over an Internet connection, minimizing the amount of time needed to conduct analyses. This protocol is designed to analyze only two experimental treatments or conditions. Differential gene expression analysis is conducted through pairwise comparisons, and will not be suitable to test multiple factors. This workflow is also designed to be manual rather than automated. Each step must be executed and investigated by the user, yielding a better understanding of data and analytical outputs, and therefore better results for the user. Once complete, this protocol will yield de novo assembled transcriptome(s) for underserved (non-model) organisms without the need to map to previously assembled reference genomes (which are usually not available in underserved organism). These de novo transcriptomes are further used in pairwise differential gene expression analysis to investigate genes differing between two experimental conditions. Differentially expressed genes are then functionally annotated to understand the genetic response organisms have to experimental conditions. In total, the data derived from this protocol is used to test hypotheses about biological responses of underserved organisms. PMID:28518075

Propensity-score matching in economic analyses: comparison with regression models, instrumental variables, residual inclusion, differences-in-differences, and decomposition methods.

PubMed

Crown, William H

2014-02-01

This paper examines the use of propensity score matching in economic analyses of observational data. Several excellent papers have previously reviewed practical aspects of propensity score estimation and other aspects of the propensity score literature. The purpose of this paper is to compare the conceptual foundation of propensity score models with alternative estimators of treatment effects. References are provided to empirical comparisons among methods that have appeared in the literature. These comparisons are available for a subset of the methods considered in this paper. However, in some cases, no pairwise comparisons of particular methods are yet available, and there are no examples of comparisons across all of the methods surveyed here. Irrespective of the availability of empirical comparisons, the goal of this paper is to provide some intuition about the relative merits of alternative estimators in health economic evaluations where nonlinearity, sample size, availability of pre/post data, heterogeneity, and missing variables can have important implications for choice of methodology. Also considered is the potential combination of propensity score matching with alternative methods such as differences-in-differences and decomposition methods that have not yet appeared in the empirical literature.

Concentrations of MUC16 and MUC5AC using three tear collection methods

PubMed Central

Nichols, Jason J.

2017-01-01

Purpose To determine the optimal tear collection method for analysis of ocular surface mucins MUC5AC and MUC16. Methods Fifteen subjects without ocular surface disease were recruited. Subjects presented for tear collection on three separate days for three different tear collection methods with the order of method randomized. Methods used to collect tears from right and left eyes included Schirmer’s strip, basal tear collection, and flush tear collection. All samples from the right eyes were individually analyzed for MUC5AC whereas the left eye samples were individually analyzed for MUC16. For each individual sample, 10 μg of protein were loaded per lane into a 1% (w/v) agarose gel and run in electrophoresis buffer for 2 h. After overnight capillary transfer, membranes were incubated with either MUC5AC antibody CLH2 or MUC16 antibody OC125 for western blot analysis. Blots were developed with enhanced chemiluminescence (ECL) and signals captured with the Odyssey Fc (LI-COR). The relative amounts of MUC5AC and MUC16 were quantified with densitometry using software and compared for statistically significant differences between tear collection methods using the Kruskal–Wallis test in SPSS 22 and GraphPad Prism 7.02. Dunn’s multiple comparisons test was used for pairwise post-hoc comparisons. Results Samples containing less than 10 μg of total protein were not used for analysis which left eight samples (out of 45) unusable. The calculated MUC5AC median signal intensities from Schirmer’s strip, basal tears, and flush tears were 2.86 (n = 15, the interquartile range [IQR] = 2.54–3.21), 1.65 (n = 14, IQR = 1.34–3.1), and 1.67 (n = 9, IQR = 1.42–1.72), respectively (H = 9.5, p = 0.009). Post-hoc pairwise comparisons showed a statistically significant difference between Schirmer’s strip and flush tears (p = 0.01). The calculated MUC16 median signal intensities from Schirmer’s strip, basal tears, and flush tears were 1.88 (n = 14, IQR = 1.43–2.61), 5.24 (n = 15, IQR = 4.16–6.21), and 2.45 (n = 7, IQR = 1.85–2.48), respectively (H = 18.1, p = 0.001). Post-hoc pairwise comparison showed statistically significant differences between basal tears and Schirmer’s strip (p = 0.0003) and between basal tears and flush tears (p = 0.006). Conclusions MUC5AC and MUC16 are present in human tear fluid and can be captured using various tear collection methods. Although basal tear collection yielded the highest relative concentration of MUC16, Schirmer’s strip tear collection yielded the highest MUC5AC concentration. Therefore, the tear collection method chosen depends on the mucin of interest. PMID:28761326

Selection of a suitable method for the preparation of polymeric nanoparticles: multi-criteria decision making approach.

PubMed

Krishnamoorthy, Kannan; Mahalingam, Manikandan

2015-03-01

The present study is aimed to select the suitable method for preparation of camptothecin loaded polymeric nanoparticles by utilizing the multi-criteria decision making method. Novel approaches of drug delivery by formulation using nanotechnology are revolutionizing the future of medicine. Recent years have witnessed unprecedented growth of research and application in the area of nanotechnology. Nanoparticles have become an important area of research in the field of drug delivery because they have the ability to deliver a wide range of drug to varying areas of body. Despite of extensive research and development, polymeric nanoparticles are frequently used to improve the therapeutic effect of drugs. A number of techniques are available for the preparation of polymeric nanoparticles. The Analytical Hierarchy Process (AHP) is a method for decision making, which are derived from individual judgements for qualitative factors, using the pair-wise comparison matrix. In AHP, a decision hierarchy is constructed with a goal, criteria and alternatives. The model uses three main criteria 1) Instrument, 2) Process and Output and 3) Cost. In addition, there are eight sub-criteria's as well as eight alternatives. Pair-wise comparison matrixes are used to obtain the overall priority weight and ranking for the selection of suitable method. Nanoprecipitation technique is the most suitable method for the preparation of camptothecin loaded polymeric nanoparticles with the highest overall priority weight of 0.297 CONCLUSION: In particular, the result indicates that the priority weights obtained from AHP could be defined as a multiple output for finding out the most suitable method for preparation of camptothecin loaded polymeric nanoparticles.

Validation of environmental content in the Young Children's Participation and Environment Measure.

PubMed

Khetani, Mary A

2015-02-01

To evaluate the concurrent validity of the environment content in the newly developed Young Children's Participation and Environment Measure (YC-PEM). Cross-sectional study. Data were collected online. Convenience and snowball sampling methods were used to survey caregivers of children (N=381; 85 children with developmental disabilities and delays and 296 children without developmental disabilities and delays) aged 0 and 5 years (mean age, 36.49±20.18 mo). Not applicable. The YC-PEM includes an assessment of the effect of environment on children's participation for 3 settings: home, daycare/preschool, and community. Pearson and Spearman correlational analyses were used to examine the concurrent validity of the YC-PEM environmental content according to a criterion measure, the Craig Hospital Inventory of Environmental Factors-Child and Parent Version (CHIEF-CP). The YC-PEM and the CHIEF-CP items were first mapped to the International Classification of Functioning, Disability, and Health-Children and Youth Version to identify items for pairwise comparison. We found small to moderate negative associations for 51 of 66 pairwise comparisons involving CHIEF-CP and YC-PEM environment items (r=-.13 to -.39; P<.01). Significant associations were found for items in all 5 International Classification of Functioning, Disability and Health-Children and Youth Version environmental domains. Results lend further support for the use of the YC-PEM for valid caregiver assessment of the physical, social, attitudinal, and institutional features of environments in terms of their effect on young children's participation within the home, daycare/preschool, and community settings. Copyright © 2015 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Diel variation in detection and vocalization rates of king (Rallus elegans) and clapper (Rallus crepitans) rails in intracoastal waterways

USGS Publications Warehouse

Stiffler, Lydia L.; Anderson, James T.; Welsh, Amy B.; Harding, Sergio R.; Costanzo, Gary R.; Katzner, Todd

2017-01-01

Surveys for secretive marsh birds could be improved with refinements to address regional and species-specific variation in detection probabilities and optimal times of day to survey. Diel variation in relation to naïve occupancy, detection rates, and vocalization rates of King (Rallus elegans) and Clapper (R. crepitans) rails were studied in intracoastal waterways in Virginia, USA. Autonomous acoustic devices recorded vocalizations of King and Clapper rails at 75 locations for 48-hr periods within a marsh complex. Naïve King and Clapper rail occupancy did not vary hourly at either the marsh or the study area level. Combined King and Clapper rail detections and vocalizations varied across marshes, decreased as the sampling season progressed, and, for detections, was greatest during low rising tides (P < 0.01). Hourly variation in vocalization and detection rates did not show a pattern but occurred between 7.8% of pairwise comparisons for detections and 10.5% of pairwise comparisons for vocalizations (P < 0.01). Higher rates of detections and vocalizations occurred during the hours of 00:00–00:59, 05:00–05:59, 14:00–15:59, and lower rates during the hours of 07:00–09:59. Although statistically significant, because there were no patterns in these hourly differences, they may not be biologically relevant and are of little use to management. In fact, these findings demonstrate that surveys for King and Clapper rails in Virginia intracoastal waterways may be effectively conducted throughout the day.

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts.

PubMed

Göke, Jonathan; Schulz, Marcel H; Lasserre, Julia; Vingron, Martin

2012-03-01

The identity of cells and tissues is to a large degree governed by transcriptional regulation. A major part is accomplished by the combinatorial binding of transcription factors at regulatory sequences, such as enhancers. Even though binding of transcription factors is sequence-specific, estimating the sequence similarity of two functionally similar enhancers is very difficult. However, a similarity measure for regulatory sequences is crucial to detect and understand functional similarities between two enhancers and will facilitate large-scale analyses like clustering, prediction and classification of genome-wide datasets. We present the standardized alignment-free sequence similarity measure N2, a flexible framework that is defined for word neighbourhoods. We explore the usefulness of adding reverse complement words as well as words including mismatches into the neighbourhood. On simulated enhancer sequences as well as functional enhancers in mouse development, N2 is shown to outperform previous alignment-free measures. N2 is flexible, faster than competing methods and less susceptible to single sequence noise and the occurrence of repetitive sequences. Experiments on the mouse enhancers reveal that enhancers active in different tissues can be separated by pairwise comparison using N2. N2 represents an improvement over previous alignment-free similarity measures without compromising speed, which makes it a good candidate for large-scale sequence comparison of regulatory sequences. The software is part of the open-source C++ library SeqAn (www.seqan.de) and a compiled version can be downloaded at http://www.seqan.de/projects/alf.html. Supplementary data are available at Bioinformatics online.

A multisite validation of whole slide imaging for primary diagnosis using standardized data collection and analysis.

PubMed

Wack, Katy; Drogowski, Laura; Treloar, Murray; Evans, Andrew; Ho, Jonhan; Parwani, Anil; Montalto, Michael C

2016-01-01

Text-based reporting and manual arbitration for whole slide imaging (WSI) validation studies are labor intensive and do not allow for consistent, scalable, and repeatable data collection or analysis. The objective of this study was to establish a method of data capture and analysis using standardized codified checklists and predetermined synoptic discordance tables and to use these methods in a pilot multisite validation study. Fifteen case report form checklists were generated from the College of American Pathology cancer protocols. Prior to data collection, all hypothetical pairwise comparisons were generated, and a level of harm was determined for each possible discordance. Four sites with four pathologists each generated 264 independent reads of 33 cases. Preestablished discordance tables were applied to determine site by site and pooled accuracy, intrareader/intramodality, and interreader intramodality error rates. Over 10,000 hypothetical pairwise comparisons were evaluated and assigned harm in discordance tables. The average difference in error rates between WSI and glass, as compared to ground truth, was 0.75% with a lower bound of 3.23% (95% confidence interval). Major discordances occurred on challenging cases, regardless of modality. The average inter-reader agreement across sites for glass was 76.5% (weighted kappa of 0.68) and for digital it was 79.1% (weighted kappa of 0.72). These results demonstrate the feasibility and utility of employing standardized synoptic checklists and predetermined discordance tables to gather consistent, comprehensive diagnostic data for WSI validation studies. This method of data capture and analysis can be applied in large-scale multisite WSI validations.

Colony-level variation in pollen collection and foraging preferences among wild-caught bumble bees (Hymenoptera: Apidae).

PubMed

Saifuddin, Mustafa; Jha, Shalene

2014-04-01

Given that many pollinators have exhibited dramatic declines related to habitat destruction, an improved understanding of pollinator resource collection across human-altered landscapes is essential to conservation efforts. Despite the importance of bumble bees (Bombus spp.) as global pollinators, little is known regarding how pollen collection patterns vary between individuals, colonies, and landscapes. In this study, Vosnesensky bumble bees (Bombus vosnesenskii Radoszkowski) were collected from a range of human-altered and natural landscapes in northern California. Extensive vegetation surveys and Geographic Information System (GIS)-based habitat classifications were conducted at each site, bees were genotyped to identify colony mates, and pollen loads were examined to identify visited plants. In contrast to predictions based on strong competitive interactions, pollen load composition was significantly more similar for bees captured in a shared study region compared with bees throughout the research area but was not significantly more similar for colony mates. Preference analyses revealed that pollen loads were not composed of the most abundant plant species per study region. The majority of ranked pollen preference lists were significantly correlated for pairwise comparisons of colony mates and individuals within a study region, whereas the majority of pairwise comparisons of ranked pollen preference lists between individuals located at separate study regions were uncorrelated. Results suggest that pollen load composition and foraging preferences are similar for bees throughout a shared landscape regardless of colony membership. The importance of native plant species in pollen collection is illustrated through preference analyses, and we suggest prioritization of specific rare native plant species for enhanced bumble bee pollen collection.

Enabling task-based information prioritization via semantic web encodings

NASA Astrophysics Data System (ADS)

Michaelis, James R.

2016-05-01

Modern Soldiers rely upon accurate and actionable information technology to achieve mission objectives. While increasingly rich sensor networks for Areas of Operation (AO) can offer many directions for aiding Soldiers, limitations are imposed by current tactical edge systems on the rate that content can be transmitted. Furthermore, mission tasks will often require very specific sets of information which may easily be drowned out by other content sources. Prior research on Quality and Value of Information (QoI/VoI) has aimed to define ways to prioritize information objects based on their intrinsic attributes (QoI) and perceived value to a consumer (VoI). As part of this effort, established ranking approaches for obtaining Subject Matter Expert (SME) recommendations, such as the Analytic Hierarchy Process (AHP) have been considered. However, limited work has been done to tie Soldier context - such as descriptions of their mission and tasks - back to intrinsic attributes of information objects. As a first step toward addressing the above challenges, this work introduces an ontology-backed approach - rooted in Semantic Web publication practices - for expressing both AHP decision hierarchies and corresponding SME feedback. Following a short discussion on related QoI/VoI research, an ontology-based data structure is introduced for supporting evaluation of Information Objects, using AHP rankings designed to facilitate information object prioritization. Consistent with alternate AHP approaches, prioritization in this approach is based on pairwise comparisons between Information Objects with respect to established criteria, as well as on pairwise comparison of the criteria to assess their relative importance. The paper concludes with a discussion of both ongoing and future work.

Bispectral pairwise interacting source analysis for identifying systems of cross-frequency interacting brain sources from electroencephalographic or magnetoencephalographic signals

NASA Astrophysics Data System (ADS)

Chella, Federico; Pizzella, Vittorio; Zappasodi, Filippo; Nolte, Guido; Marzetti, Laura

2016-05-01

Brain cognitive functions arise through the coordinated activity of several brain regions, which actually form complex dynamical systems operating at multiple frequencies. These systems often consist of interacting subsystems, whose characterization is of importance for a complete understanding of the brain interaction processes. To address this issue, we present a technique, namely the bispectral pairwise interacting source analysis (biPISA), for analyzing systems of cross-frequency interacting brain sources when multichannel electroencephalographic (EEG) or magnetoencephalographic (MEG) data are available. Specifically, the biPISA makes it possible to identify one or many subsystems of cross-frequency interacting sources by decomposing the antisymmetric components of the cross-bispectra between EEG or MEG signals, based on the assumption that interactions are pairwise. Thanks to the properties of the antisymmetric components of the cross-bispectra, biPISA is also robust to spurious interactions arising from mixing artifacts, i.e., volume conduction or field spread, which always affect EEG or MEG functional connectivity estimates. This method is an extension of the pairwise interacting source analysis (PISA), which was originally introduced for investigating interactions at the same frequency, to the study of cross-frequency interactions. The effectiveness of this approach is demonstrated in simulations for up to three interacting source pairs and for real MEG recordings of spontaneous brain activity. Simulations show that the performances of biPISA in estimating the phase difference between the interacting sources are affected by the increasing level of noise rather than by the number of the interacting subsystems. The analysis of real MEG data reveals an interaction between two pairs of sources of central mu and beta rhythms, localizing in the proximity of the left and right central sulci.

Pair-Wise Trajectory Management-Oceanic (PTM-O) . [Concept of Operations—Version 3.9

NASA Technical Reports Server (NTRS)

Jones, Kenneth M.

2014-01-01

This document describes the Pair-wise Trajectory Management-Oceanic (PTM-O) Concept of Operations (ConOps). Pair-wise Trajectory Management (PTM) is a concept that includes airborne and ground-based capabilities designed to enable and to benefit from, airborne pair-wise distance-monitoring capability. PTM includes the capabilities needed for the controller to issue a PTM clearance that resolves a conflict for a specific pair of aircraft. PTM avionics include the capabilities needed for the flight crew to manage their trajectory relative to specific designated aircraft. Pair-wise Trajectory Management PTM-Oceanic (PTM-O) is a regional specific application of the PTM concept. PTM is sponsored by the National Aeronautics and Space Administration (NASA) Concept and Technology Development Project (part of NASA's Airspace Systems Program). The goal of PTM is to use enhanced and distributed communications and surveillance along with airborne tools to permit reduced separation standards for given aircraft pairs, thereby increasing the capacity and efficiency of aircraft operations at a given altitude or volume of airspace.

A pairwise maximum entropy model accurately describes resting-state human brain networks

PubMed Central

Watanabe, Takamitsu; Hirose, Satoshi; Wada, Hiroyuki; Imai, Yoshio; Machida, Toru; Shirouzu, Ichiro; Konishi, Seiki; Miyashita, Yasushi; Masuda, Naoki

2013-01-01

The resting-state human brain networks underlie fundamental cognitive functions and consist of complex interactions among brain regions. However, the level of complexity of the resting-state networks has not been quantified, which has prevented comprehensive descriptions of the brain activity as an integrative system. Here, we address this issue by demonstrating that a pairwise maximum entropy model, which takes into account region-specific activity rates and pairwise interactions, can be robustly and accurately fitted to resting-state human brain activities obtained by functional magnetic resonance imaging. Furthermore, to validate the approximation of the resting-state networks by the pairwise maximum entropy model, we show that the functional interactions estimated by the pairwise maximum entropy model reflect anatomical connexions more accurately than the conventional functional connectivity method. These findings indicate that a relatively simple statistical model not only captures the structure of the resting-state networks but also provides a possible method to derive physiological information about various large-scale brain networks. PMID:23340410

A new graph-based method for pairwise global network alignment

PubMed Central

Klau, Gunnar W

2009-01-01

Background In addition to component-based comparative approaches, network alignments provide the means to study conserved network topology such as common pathways and more complex network motifs. Yet, unlike in classical sequence alignment, the comparison of networks becomes computationally more challenging, as most meaningful assumptions instantly lead to NP-hard problems. Most previous algorithmic work on network alignments is heuristic in nature. Results We introduce the graph-based maximum structural matching formulation for pairwise global network alignment. We relate the formulation to previous work and prove NP-hardness of the problem. Based on the new formulation we build upon recent results in computational structural biology and present a novel Lagrangian relaxation approach that, in combination with a branch-and-bound method, computes provably optimal network alignments. The Lagrangian algorithm alone is a powerful heuristic method, which produces solutions that are often near-optimal and – unlike those computed by pure heuristics – come with a quality guarantee. Conclusion Computational experiments on the alignment of protein-protein interaction networks and on the classification of metabolic subnetworks demonstrate that the new method is reasonably fast and has advantages over pure heuristics. Our software tool is freely available as part of the LISA library. PMID:19208162

An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species

PubMed Central

Galpert, Deborah; del Río, Sara; Herrera, Francisco; Ancede-Gallardo, Evys; Antunes, Agostinho; Agüero-Chapin, Guillermin

2015-01-01

Orthology detection requires more effective scaling algorithms. In this paper, a set of gene pair features based on similarity measures (alignment scores, sequence length, gene membership to conserved regions, and physicochemical profiles) are combined in a supervised pairwise ortholog detection approach to improve effectiveness considering low ortholog ratios in relation to the possible pairwise comparison between two genomes. In this scenario, big data supervised classifiers managing imbalance between ortholog and nonortholog pair classes allow for an effective scaling solution built from two genomes and extended to other genome pairs. The supervised approach was compared with RBH, RSD, and OMA algorithms by using the following yeast genome pairs: Saccharomyces cerevisiae-Kluyveromyces lactis, Saccharomyces cerevisiae-Candida glabrata, and Saccharomyces cerevisiae-Schizosaccharomyces pombe as benchmark datasets. Because of the large amount of imbalanced data, the building and testing of the supervised model were only possible by using big data supervised classifiers managing imbalance. Evaluation metrics taking low ortholog ratios into account were applied. From the effectiveness perspective, MapReduce Random Oversampling combined with Spark SVM outperformed RBH, RSD, and OMA, probably because of the consideration of gene pair features beyond alignment similarities combined with the advances in big data supervised classification. PMID:26605337

The use of a modified pairwise comparison method in evaluating critical success factors for community-based rural homestay programmes

NASA Astrophysics Data System (ADS)

Daud, Shahidah Md; Ramli, Razamin; Kasim, Maznah Mat; Kayat, Kalsom; Razak, Rafidah Abd

2014-12-01

Tourism industry has become the highlighted sector which has amazingly increased the national income level. Despite the tourism industry being one of the highest income generating sectors, Homestay Programme as a Community-Based Tourism (CBT) product in Malaysia does not absorbed much of the incoming wealth. Homestay Programme refers to a programme in a community where a tourist stays together with a host family and experiences the everyday way of life of the family in both direct and indirect manner. There are over 100 Homestay Programme currently being registered with the Ministry of Culture and Tourism Malaysia which mostly are located in rural areas, but only a few excel and enjoying the fruit of the booming industry. Hence, this article seeks to identify the critical success factors for a Community-Based Rural Homestay Programme in Malaysia. A modified pairwise method is utilized to further evaluate the identified success factors in a more meaningful way. The findings will help Homestay Programme function as a community development tool that manages tourism resources. Thus, help the community in improving local economy and creating job opportunities.

An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species.

PubMed

Galpert, Deborah; Del Río, Sara; Herrera, Francisco; Ancede-Gallardo, Evys; Antunes, Agostinho; Agüero-Chapin, Guillermin

2015-01-01

Orthology detection requires more effective scaling algorithms. In this paper, a set of gene pair features based on similarity measures (alignment scores, sequence length, gene membership to conserved regions, and physicochemical profiles) are combined in a supervised pairwise ortholog detection approach to improve effectiveness considering low ortholog ratios in relation to the possible pairwise comparison between two genomes. In this scenario, big data supervised classifiers managing imbalance between ortholog and nonortholog pair classes allow for an effective scaling solution built from two genomes and extended to other genome pairs. The supervised approach was compared with RBH, RSD, and OMA algorithms by using the following yeast genome pairs: Saccharomyces cerevisiae-Kluyveromyces lactis, Saccharomyces cerevisiae-Candida glabrata, and Saccharomyces cerevisiae-Schizosaccharomyces pombe as benchmark datasets. Because of the large amount of imbalanced data, the building and testing of the supervised model were only possible by using big data supervised classifiers managing imbalance. Evaluation metrics taking low ortholog ratios into account were applied. From the effectiveness perspective, MapReduce Random Oversampling combined with Spark SVM outperformed RBH, RSD, and OMA, probably because of the consideration of gene pair features beyond alignment similarities combined with the advances in big data supervised classification.

Combining large number of weak biomarkers based on AUC.

PubMed

Yan, Li; Tian, Lili; Liu, Song

2015-12-20

Combining multiple biomarkers to improve diagnosis and/or prognosis accuracy is a common practice in clinical medicine. Both parametric and non-parametric methods have been developed for finding the optimal linear combination of biomarkers to maximize the area under the receiver operating characteristic curve (AUC), primarily focusing on the setting with a small number of well-defined biomarkers. This problem becomes more challenging when the number of observations is not order of magnitude greater than the number of variables, especially when the involved biomarkers are relatively weak. Such settings are not uncommon in certain applied fields. The first aim of this paper is to empirically evaluate the performance of existing linear combination methods under such settings. The second aim is to propose a new combination method, namely, the pairwise approach, to maximize AUC. Our simulation studies demonstrated that the performance of several existing methods can become unsatisfactory as the number of markers becomes large, while the newly proposed pairwise method performs reasonably well. Furthermore, we apply all the combination methods to real datasets used for the development and validation of MammaPrint. The implication of our study for the design of optimal linear combination methods is discussed. Copyright © 2015 John Wiley & Sons, Ltd.

Combining large number of weak biomarkers based on AUC

PubMed Central

Yan, Li; Tian, Lili; Liu, Song

2018-01-01

Combining multiple biomarkers to improve diagnosis and/or prognosis accuracy is a common practice in clinical medicine. Both parametric and non-parametric methods have been developed for finding the optimal linear combination of biomarkers to maximize the area under the receiver operating characteristic curve (AUC), primarily focusing on the setting with a small number of well-defined biomarkers. This problem becomes more challenging when the number of observations is not order of magnitude greater than the number of variables, especially when the involved biomarkers are relatively weak. Such settings are not uncommon in certain applied fields. The first aim of this paper is to empirically evaluate the performance of existing linear combination methods under such settings. The second aim is to propose a new combination method, namely, the pairwise approach, to maximize AUC. Our simulation studies demonstrated that the performance of several existing methods can become unsatisfactory as the number of markers becomes large, while the newly proposed pairwise method performs reasonably well. Furthermore, we apply all the combination methods to real datasets used for the development and validation of MammaPrint. The implication of our study for the design of optimal linear combination methods is discussed. PMID:26227901

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

PubMed Central

Kelly, Brendan J.; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D.; Collman, Ronald G.; Bushman, Frederic D.; Li, Hongzhe

2015-01-01

Motivation: The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence–absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA. Results: We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study. Availability and implementation: http://github.com/brendankelly/micropower. Contact: brendank@mail.med.upenn.edu or hongzhe@upenn.edu PMID:25819674

[Experiment study on ultrashort wave for treating vascular crisis after rat tail replantation].

PubMed

Tan, Long; Gao, Wenshan; Xi, Ali; Wang, Cong; Chen, Shouying; Zhao, Yanyan; Di, Keqian; Yang, Xincai; Weng, Shengbin

2012-10-01

To explore the effect and mechanism of ultrashort wave (USW) for prevention and treatment of vascular crisis after rat tail replantation. Eighty 3-month old female Sprague Dawley rats (weighing 232.8-289.6 g) were randomly divided into 5 groups. In each group, based on the caudal vein and the coccyx was retained, the tail was cut off. The tail artery was ligated in group A; the tail artery was anastomosed in groups B, C, D, and E to establish the tail replantation model. After surgery, the rats of group B were given normal management; the rats of group C were immediately given intraperitoneal injection (3.125 mL/kg) of diluted papaverine hydrochloride injection (1 mg/mL); the rats of groups D and E were immediately given the local USW treatment (once a day) at anastomotic site for 5 days at the dosage of 3 files and 50 mA for 20 minutes (group D) and 2 files and 28 mA for 20 minutes (group E). The survival rate of the rat tails was observed for 10 days after the tail replantation. The tail skin temperature difference between proximal and distal anastomosis was measured at pre- and post-operation; the change between postoperative and preoperative temperature difference was calculated. The blood plasma specimens were collected from the inner canthus before operation and from the tip of the tail at 8 hours after operation to measure the content of nitric oxide (NO). The survival rates of the rat tails were 0 (0/14), 36.4% (8/22), 57.1% (8/14), 22.2% (4/18), and 75.0% (9/12) in groups A, B, C, D, and E, respectively, showing significant overall differences among 5 groups (chi2 = 19.935, P = 0.001); the survival rate of group E was significantly higher than that of group B at 7 days (P < 0.05), but no significant difference was found between the other groups by pairwise comparison (P > 0.05). At preoperation, there was no significant difference in tail skin temperature difference among 5 groups (P > 0.05); at 8 hours, 5 days, 6 days, and 7 days after operation, significant overall difference was found in the change of the skin temperature difference among groups (P < 0.05); pairwise comparison showed significant differences after operation (P < 0.05): group B > group D at 8 hours, group C > group D at 5 days, groups A, B, and C > group D at 6 days, groups B and C > groups A and E, and group B > group D at 7 days; but no significant difference was found between the other groups at the other time points (P > 0.05). Preoperative plasma NO content between each group had no significant difference (P > 0.05). The overall differences had significance in the NO content at postopoerative 8 hours and in the change of the NO content at pre- and post-operation among groups (P < 0.05). Significant differences were found by pairwise comparison (P < 0.05): group D > groups A, B, and C in the plasma NO content, group D > groups A and B in the change of the NO content at pre- and post-operation; but no significant difference was found between the other groups by pairwise comparison (P > 0.05). Rat tail replantation model in this experiment is feasible. USW therapy can increase the survival rate of replanted rat tails, reduce skin temperature at 7 days, improve blood supply, increase the content of nitric oxide at the early period and prevent vascular crisis.

Pharmacokinetic analysis and comparison of caffeine administered rapidly or slowly in coffee chilled or hot versus chilled energy drink in healthy young adults.

PubMed

White, John R; Padowski, Jeannie M; Zhong, Yili; Chen, Gang; Luo, Shaman; Lazarus, Philip; Layton, Matthew E; McPherson, Sterling

2016-01-01

There is a paucity of data describing the impact of type of beverage (coffee versus energy drink), different rates of consumption and different temperature of beverages on the pharmacokinetic disposition of caffeine. Additionally, there is concern that inordinately high levels of caffeine may result from the rapid consumption of cold energy drinks. The objective of this study was to compare the pharmacokinetics of caffeine under various drink temperature, rate of consumption and vehicle (coffee versus energy drink) conditions. Five caffeine (dose = 160 mg) conditions were evaluated in an open-label, group-randomized, crossover fashion. After the administration of each caffeine dose, 10 serial plasma samples were harvested. Caffeine concentration was measured via liquid chromatography-mass spectrometry (LC-MS), and those concentrations were assessed by non-compartmental pharmacokinetic analysis. The calculated mean pharmacokinetic parameters were analyzed statistically by one-way repeated measures analysis of variance (RM ANOVA). If differences were found, each group was compared to the other by all pair-wise multiple comparison. Twenty-four healthy subjects ranging in age from 18 to 30 completed the study. The mean caffeine concentration time profiles were similar with overlapping SDs at all measured time points. The ANOVA revealed significant differences in mean Cmax and Vd ss/F, but no pair-wise comparisons reached statistical significance. No other differences in pharmacokinetic parameters were found. The results of this study are consistent with previous caffeine pharmacokinetic studies and suggest that while rate of consumption, temperature of beverage and vehicle (coffee versus energy drink) may be associated with slightly different pharmacokinetic parameters, the overall impact of these variables is small. This study suggests that caffeine absorption and exposure from coffee and energy drink is similar irrespective of beverage temperature or rate of consumption.

T2-Weighted Liver MRI Using the MultiVane Technique at 3T: Comparison with Conventional T2-Weighted MRI

PubMed Central

Kang, Kyung A; Kim, EunJu; Jeong, Woo Kyoung; Choi, Dongil; Lee, Won Jae; Jung, Sin-Ho; Baek, Sun-Young

2015-01-01

Objective To assess the value of applying MultiVane to liver T2-weighted imaging (T2WI) compared with conventional T2WIs with emphasis on detection of focal liver lesions. Materials and Methods Seventy-eight patients (43 men and 35 women) with 86 hepatic lesions and 20 pancreatico-biliary diseases underwent MRI including T2WIs acquired using breath-hold (BH), respiratory-triggered (RT), and MultiVane technique at 3T. Two reviewers evaluated each T2WI with respect to artefacts, organ sharpness, and conspicuity of intrahepatic vessels, hilar duct, and main lesion using five-point scales, and made pairwise comparisons between T2WI sequences for these categories. Diagnostic accuracy (Az) and sensitivity for hepatic lesion detection were evaluated using alternative free-response receiver operating characteristic analysis. Results MultiVane T2WI was significantly better than BH-T2WI or RT-T2WI for organ sharpness and conspicuity of intrahepatic vessels and main lesion in both separate reviews and pairwise comparisons (p < 0.001). With regard to motion artefacts, MultiVane T2WI or BH-T2WI was better than RT-T2WI (p < 0.001). Conspicuity of hilar duct was better with BH-T2WI than with MultiVane T2WI (p = 0.030) or RT-T2WI (p < 0.001). For detection of 86 hepatic lesions, sensitivity (mean, 97.7%) of MultiVane T2WI was significantly higher than that of BH-T2WI (mean, 89.5%) (p = 0.008) or RT-T2WI (mean, 84.9%) (p = 0.001). Conclusion Applying the MultiVane technique to T2WI of the liver is a promising approach to improving image quality that results in increased detection of focal liver lesions compared with conventional T2WI. PMID:26357498

Pharmacokinetic analysis and comparison of caffeine administered rapidly or slowly in coffee chilled or hot versus chilled energy drink in healthy young adults

PubMed Central

White, John R.; Padowski, Jeannie M.; Zhong, Yili; Chen, Gang; Luo, Shaman; Lazarus, Philip; Layton, Matthew E.; McPherson, Sterling

2016-01-01

Abstract Context: There is a paucity of data describing the impact of type of beverage (coffee versus energy drink), different rates of consumption and different temperature of beverages on the pharmacokinetic disposition of caffeine. Additionally, there is concern that inordinately high levels of caffeine may result from the rapid consumption of cold energy drinks. Objective: The objective of this study was to compare the pharmacokinetics of caffeine under various drink temperature, rate of consumption and vehicle (coffee versus energy drink) conditions. Materials: Five caffeine (dose = 160 mg) conditions were evaluated in an open-label, group-randomized, crossover fashion. After the administration of each caffeine dose, 10 serial plasma samples were harvested. Caffeine concentration was measured via liquid chromatography–mass spectrometry (LC–MS), and those concentrations were assessed by non-compartmental pharmacokinetic analysis. The calculated mean pharmacokinetic parameters were analyzed statistically by one-way repeated measures analysis of variance (RM ANOVA). If differences were found, each group was compared to the other by all pair-wise multiple comparison. Results: Twenty-four healthy subjects ranging in age from 18 to 30 completed the study. The mean caffeine concentration time profiles were similar with overlapping SDs at all measured time points. The ANOVA revealed significant differences in mean C max and V d ss/F, but no pair-wise comparisons reached statistical significance. No other differences in pharmacokinetic parameters were found. Discussion: The results of this study are consistent with previous caffeine pharmacokinetic studies and suggest that while rate of consumption, temperature of beverage and vehicle (coffee versus energy drink) may be associated with slightly different pharmacokinetic parameters, the overall impact of these variables is small. Conclusion: This study suggests that caffeine absorption and exposure from coffee and energy drink is similar irrespective of beverage temperature or rate of consumption. PMID:27100333

Comparison of prognostic nomograms based on different nodal staging systems in patients with resected gastric cancer.

PubMed

Wang, Zi-Xian; Qiu, Miao-Zhen; Jiang, Yu-Ming; Zhou, Zhi-Wei; Li, Guo-Xin; Xu, Rui-Hua

2017-01-01

Purpose: Previous studies addressing the optimal nodal staging system in patients with resected gastric cancer have shown inconsistent results, and the optimal system for development of prognostic nomograms remains unclear. In this study, we compared prognostic nomograms based on the metastatic lymph node (MLN) count, lymph node ratio (LNR), and log odds of metastatic lymph nodes (LODDS) to predict the 5-year overall survival in patients with resected gastric cancer. Methods: We analysed 15,320 patients with resected gastric cancer in the Surveillance, Epidemiology, and End Results (SEER) database between 1988 and 2010. Missing data were handled using multiple imputation. When assessed as a continuous covariate with restricted cubic splines, each MLN, LNR, and LODDS variable was incorporated into a nomogram with other significant prognosticators to predict the 5-year overall survival. A two-centre Chinese dataset (1,595 cases) was used as external validation data. Results: The discriminatory abilities of the MLN-, LNR-, and LODDS-based nomograms were comparable (concordance indices: 0.744, 0.741, and 0.744, respectively, in the SEER set, P > 0.152 for all pairwise comparisons; 0.715, 0.712, and 0.713, respectively, in the Chinese set, P > 0.445 for all pairwise comparisons). The discriminatory abilities of the three nomograms were all superior to the American Joint Committee on Cancer (AJCC) TNM classification (concordance indices: 0.713, P < 0.001 for all in the SEER set; and 0.693, P < 0.001 for all in the Chinese set). The discriminatory abilities of the nomograms were comparable regardless of the number of nodes examined. Moreover, decision curve analyses indicated similar net benefits of using the nomograms. Conclusion: MLN-, LNR-, and LODDS should be considered equally in the development of multivariate prognostic models and nomograms to refine the prediction of survival among patients with resected gastric cancer.

Can a clinical placement influence stigma? An analysis of measures of social distance.

PubMed

Moxham, Lorna; Taylor, Ellie; Patterson, Christopher; Perlman, Dana; Brighton, Renee; Sumskis, Susan; Keough, Emily; Heffernan, Tim

2016-09-01

The way people who experience mental illness are perceived by health care professionals, which often includes stigmatising attitudes, can have a significant impact on treatment outcomes and on their quality of life. To determine whether stigma towards people with mental illness varied for undergraduate nursing students who attended a non-traditional clinical placement called Recovery Camp compared to students who attended a 'typical' mental health clinical placement. Quasi-experimental. Seventy-nine third-year nursing students were surveyed; n=40 attended Recovery Camp (intervention), n=39 (comparison group) attended a 'typical' mental health clinical placement. All students completed the Social Distance Scale (SDS) pre- and post-placement and at three-month follow-up. Data analysis consisted of a one-way repeated measures analysis of variance (ANOVA) exploring parameter estimates between group scores across three time points. Two secondary repeated measures ANOVAs were performed to demonstrate the differences in SDS scores for each group across time. Pairwise comparisons demonstrated the differences between time intervals. A statistically significant difference in ratings of stigma between the intervention group and the comparison group existed. Parameter estimates revealed that stigma ratings for the intervention group were significantly reduced post-placement and remained consistently low at three-month follow-up. There was no significant difference in ratings of stigma for the comparison group over time. Students who attended Recovery Camp reported significant decreases in stigma towards people with a mental illness over time, compared to the typical placement group. Findings suggest that a therapeutic recreation based clinical placement was more successful in reducing stigma regarding mental illness in undergraduate nursing students compared to those who attended typical mental health clinical placements. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparison of Six Generic Vancomycin Products for Treatment of Methicillin-Resistant Staphylococcus aureus Experimental Endocarditis in Rabbits

PubMed Central

Tattevin, P.; Saleh-Mghir, A.; Davido, B.; Ghout, I.; Massias, L.; Garcia de la Maria, C.; Miró, J. M.; Perronne, C.; Laurent, F.

2013-01-01

Concerns have recently emerged about the potency and the quality of generic vancomycin (VAN) products approved for use in humans, based on experiments in a neutropenic mouse thigh infection model. However, other animal models may be more appropriate to decipher the bactericidal activities of VAN generics in vivo and to predict their efficacy in humans. We aimed to compare the bactericidal activities of six generic VAN products currently used in France (Mylan and Sandoz), Spain (Hospira), Switzerland (Teva), and the United States (Akorn-Strides and American Pharmaceutical Products [APP]) in a rabbit model of aortic valve endocarditis induced by 8 × 107 CFU of methicillin-resistant Staphylococcus aureus (MRSA) strain COL (VAN MIC, 1.5 μg/ml). In vitro, there were no significant differences in the time-kill curve studies performed with the six generic VAN products. Ten rabbits in each group were treated with intravenous (i.v.) VAN, 60 mg/kg of body weight twice a day (b.i.d.) for 4 days. Mean peak serum VAN levels, measured 45 min after the last injection, ranged from 35.5 (APP) to 45.9 μg/ml (Teva). Mean trough serum VAN levels, measured 12 h after the last injection, ranged from 2.3 (Hospira) to 9.2 (APP) μg/ml. All generic VAN products were superior to controls (no treatment) in terms of residual organisms in vegetations (P < 0.02 for each comparison) and in the spleen (P < 0.005 for each comparison). Pairwise comparisons of generic VAN products found no significant differences. In conclusion, a stringent MRSA endocarditis model found no significant differences in the bactericidal activities of six generic VAN products currently used in Europe and America. PMID:23254435

Ultrafast Comparison of Personal Genomes via Precomputed Genome Fingerprints.

PubMed

Glusman, Gustavo; Mauldin, Denise E; Hood, Leroy E; Robinson, Max

2017-01-01

We present an ultrafast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into "genome fingerprints" via locality sensitive hashing. The resulting genome fingerprints can be meaningfully compared even when the input data were obtained using different sequencing technologies, processed using different pipelines, represented in different data formats and relative to different reference versions. Furthermore, genome fingerprints are robust to up to 30% missing data. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. For example, we could compute all-against-all pairwise comparisons among the 2504 genomes in the 1000 Genomes data set in 67 s at high quality (21 μs per comparison, on a single processor), and achieved a lower quality approximation in just 11 s. Efficient computation enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative sequenced genomes in a set, population reconstruction, and many others. The original genome representation cannot be reconstructed from its fingerprint, effectively decoupling genome comparison from genome interpretation; the method thus has significant implications for privacy-preserving genome analytics.

Automatic identification of individual killer whales.

PubMed

Brown, Judith C; Smaragdis, Paris; Nousek-McGregor, Anna

2010-09-01

Following the successful use of HMM and GMM models for classification of a set of 75 calls of northern resident killer whales into call types [Brown, J. C., and Smaragdis, P., J. Acoust. Soc. Am. 125, 221-224 (2009)], the use of these same methods has been explored for the identification of vocalizations from the same call type N2 of four individual killer whales. With an average of 20 vocalizations from each of the individuals the pairwise comparisons have an extremely high success rate of 80 to 100% and the identifications within the entire group yield around 78%.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelbe, David; Oak Ridge National Lab.; van Aardt, Jan

Terrestrial laser scanning has demonstrated increasing potential for rapid comprehensive measurement of forest structure, especially when multiple scans are spatially registered in order to reduce the limitations of occlusion. Although marker-based registration techniques (based on retro-reflective spherical targets) are commonly used in practice, a blind marker-free approach is preferable, insofar as it supports rapid operational data acquisition. To support these efforts, we extend the pairwise registration approach of our earlier work, and develop a graph-theoretical framework to perform blind marker-free global registration of multiple point cloud data sets. Pairwise pose estimates are weighted based on their estimated error, in ordermore » to overcome pose conflict while exploiting redundant information and improving precision. The proposed approach was tested for eight diverse New England forest sites, with 25 scans collected at each site. Quantitative assessment was provided via a novel embedded confidence metric, with a mean estimated root-mean-square error of 7.2 cm and 89% of scans connected to the reference node. Lastly, this paper assesses the validity of the embedded multiview registration confidence metric and evaluates the performance of the proposed registration algorithm.« less

Harnessing Reddit to Understand the Written-Communication Challenges Experienced by Individuals With Mental Health Disorders: Analysis of Texts From Mental Health Communities.

PubMed

Park, Albert; Conway, Mike

2018-04-10

Mental disorders such as depression, bipolar disorder, and schizophrenia are common, incapacitating, and have the potential to be fatal. Despite the prevalence and gravity of mental disorders, our knowledge concerning everyday challenges associated with them is relatively limited. One of the most studied deficits related to everyday challenges is language impairment, yet we do not know how mental disorders can impact common forms of written communication, for example, social media. The aims of this study were to investigate written communication challenges manifest in online mental health communities focusing on depression, bipolar disorder, and schizophrenia, as well as the impact of participating in these online mental health communities on written communication. As the control, we selected three online health communities focusing on positive emotion, exercising, and weight management. We examined lexical diversity and readability, both important features for measuring the quality of writing. We used four well-established readability metrics that consider word frequencies and syntactic complexity to measure writers' written communication ability. We then measured the lexical diversity by calculating the percentage of unique words in posts. To compare lexical diversity and readability among communities, we first applied pairwise independent sample t tests, followed by P value adjustments using the prespecified Hommel procedure to adjust for multiple comparison. To measure the changes, we applied linear least squares regression to the readability and lexical diversity scores against the interaction sequence for each member, followed by pairwise independent sample t tests and P value adjustments. Given the large sample of members, we also report effect sizes and 95% CIs for the pairwise comparisons. On average, members of depression, bipolar disorder, and schizophrenia communities showed indications of difficulty expressing their ideas compared with three other online health communities. Our results also suggest that participating in these platforms has the potential to improve members' written communication. For example, members of all three mental health communities showed statistically significant improvement in both lexical diversity and readability compared with members of the OHC focusing on positive emotion. We provide new insights into the written communication challenges faced by individuals suffering from depression, bipolar disorder, and schizophrenia. A comparison with three other online health communities suggests that written communication in mental health communities is significantly more difficult to read, while also consisting of a significantly less diverse lexicon. We contribute practical suggestions for utilizing our findings in Web-based communication settings to enhance members' communicative experience. We consider these findings to be an important step toward understanding and addressing everyday written communication challenges among individuals suffering from mental disorders. ©Albert Park, Mike Conway. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 10.04.2018.

The effect of applied transducer force on acoustic radiation force impulse quantification within the left lobe of the liver.

PubMed

Porra, Luke; Swan, Hans; Ho, Chien

2015-08-01

Introduction: Acoustic Radiation Force Impulse (ARFI) Quantification measures shear wave velocities (SWVs) within the liver. It is a reliable method for predicting the severity of liver fibrosis and has the potential to assess fibrosis in any part of the liver, but previous research has found ARFI quantification in the right lobe more accurate than in the left lobe. A lack of standardised applied transducer force when performing ARFI quantification in the left lobe of the liver may account for some of this inaccuracy. The research hypothesis of this present study predicted that an increase in applied transducer force would result in an increase in SWVs measured. Methods: ARFI quantification within the left lobe of the liver was performed within a group of healthy volunteers (n = 28). During each examination, each participant was subjected to ARFI quantification at six different levels of transducer force applied to the epigastric abdominal wall. Results: A repeated measures ANOVA test showed that ARFI quantification was significantly affected by applied transducer force (p = 0.002). Significant pairwise comparisons using Bonferroni correction for multiple comparisons showed that with an increase in applied transducer force, there was a decrease in SWVs. Conclusion: Applied transducer force has a significant effect on SWVs within the left lobe of the liver and it may explain some of the less accurate and less reliable results in previous studies where transducer force was not taken into consideration. Future studies in the left lobe of the liver should take this into account and control for applied transducer force.

Pre-calculated protein structure alignments at the RCSB PDB website.

PubMed

Prlic, Andreas; Bliven, Spencer; Rose, Peter W; Bluhm, Wolfgang F; Bizon, Chris; Godzik, Adam; Bourne, Philip E

2010-12-01

With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user. A web user interface is available at http://www.rcsb.org/pdb/workbench/workbench.do. The source code is available under the LGPL license from http://www.biojava.org. A source bundle, prepared for local execution, is available from http://source.rcsb.org andreas@sdsc.edu; pbourne@ucsd.edu.

Amino acid sequences of ribosomal proteins S11 from Bacillus stearothermophilus and S19 from Halobacterium marismortui. Comparison of the ribosomal protein S11 family.

PubMed

Kimura, M; Kimura, J; Hatakeyama, T

1988-11-21

The complete amino acid sequences of ribosomal proteins S11 from the Gram-positive eubacterium Bacillus stearothermophilus and of S19 from the archaebacterium Halobacterium marismortui have been determined. A search for homologous sequences of these proteins revealed that they belong to the ribosomal protein S11 family. Homologous proteins have previously been sequenced from Escherichia coli as well as from chloroplast, yeast and mammalian ribosomes. A pairwise comparison of the amino acid sequences showed that Bacillus protein S11 shares 68% identical residues with S11 from Escherichia coli and a slightly lower homology (52%) with the homologous chloroplast protein. The halophilic protein S19 is more related to the eukaryotic (45-49%) than to the eubacterial counterparts (35%).

Interpreting indirect treatment comparisons and network meta-analysis for health-care decision making: report of the ISPOR Task Force on Indirect Treatment Comparisons Good Research Practices: part 1.

PubMed

Jansen, Jeroen P; Fleurence, Rachael; Devine, Beth; Itzler, Robbin; Barrett, Annabel; Hawkins, Neil; Lee, Karen; Boersma, Cornelis; Annemans, Lieven; Cappelleri, Joseph C

2011-06-01

Evidence-based health-care decision making requires comparisons of all relevant competing interventions. In the absence of randomized, controlled trials involving a direct comparison of all treatments of interest, indirect treatment comparisons and network meta-analysis provide useful evidence for judiciously selecting the best choice(s) of treatment. Mixed treatment comparisons, a special case of network meta-analysis, combine direct and indirect evidence for particular pairwise comparisons, thereby synthesizing a greater share of the available evidence than a traditional meta-analysis. This report from the ISPOR Indirect Treatment Comparisons Good Research Practices Task Force provides guidance on the interpretation of indirect treatment comparisons and network meta-analysis to assist policymakers and health-care professionals in using its findings for decision making. We start with an overview of how networks of randomized, controlled trials allow multiple treatment comparisons of competing interventions. Next, an introduction to the synthesis of the available evidence with a focus on terminology, assumptions, validity, and statistical methods is provided, followed by advice on critically reviewing and interpreting an indirect treatment comparison or network meta-analysis to inform decision making. We finish with a discussion of what to do if there are no direct or indirect treatment comparisons of randomized, controlled trials possible and a health-care decision still needs to be made. Copyright © 2011 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances.

PubMed

Gil, Manuel

2014-01-01

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances

PubMed Central

2014-01-01

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error. PMID:25279263

Saxagliptin efficacy and safety in patients with type 2 diabetes mellitus stratified by cardiovascular disease history and cardiovascular risk factors: analysis of 3 clinical trials.

PubMed

Cook, William; Minervini, Gianmaria; Bryzinski, Brian; Hirshberg, Boaz

2014-10-01

To test the effectiveness and safety of saxagliptin 5 mg/d in patients with type 2 diabetes mellitus (T2DM) with and without history of cardiovascular disease (CVD) or cardiovascular (CV) risk factors. The authors conducted a post hoc analysis of data from 3 randomized studies that compared saxagliptin versus placebo as initial combination therapy with metformin for 24 weeks (N = 648) and versus placebo as an add-on to insulin with and without metformin for 24 weeks (N = 455), and assessed noninferiority to glipizide as an add-on to metformin for 52 weeks (N = 858). Efficacy outcomes were the adjusted mean change from baseline in glycated hemoglobin (HbA1c) level, fasting plasma glucose concentration, and body weight and the proportion of patients achieving an HbA1c level < 7%. Pairwise comparisons were performed in subgroups with 1) history/no history of CVD, 2) ≥ 2 versus 0 to 1 CV risk factors, 3) hypertension/no hypertension, and 4) statin use/no statin use. Adverse events (AE) and hypoglycemia were monitored. In the initial combination therapy study, reductions in HbA1c level from baseline were greater with saxagliptin versus placebo in all subgroups (difference [saxagliptin - placebo], -0.38% to -0.67%). In the add-on to insulin ± metformin study, differences in adjusted mean change in HbA1c level versus placebo ranged from -0.23% to -0.58% across subgroups. In the noninferiority to glipizide study, adjusted mean changes in HbA1c level were comparable between saxagliptin and glipizide, across subgroups (difference, 0.08%-0.21%). No evidence suggested clinically relevant treatment-by-subgroup interactions in pairwise comparison. Incidences of ≥ 1 AE were comparable across subgroups. Incidences of confirmed hypoglycemia with saxagliptin were 0 in both metformin add-on studies and 1.2% to 7.8% with saxagliptin + insulin ± metformin. In patients with T2DM, saxagliptin 5 mg/d was similarly effective in improving glycemic control, with an AE profile similar to that of placebo, irrespective of CVD history, number of CV risk factors, hypertension, or statin use. www.ClinicalTrials.gov identifiers: NCT00327015, NCT00575588, NCT00757588.

Genetic basis of pyrethroid resistance in a population of Anopheles arabiensis, the primary malaria vector in Lower Moshi, north-eastern Tanzania.

PubMed

Matowo, Johnson; Jones, Christopher M; Kabula, Bilali; Ranson, Hilary; Steen, Keith; Mosha, Franklin; Rowland, Mark; Weetman, David

2014-06-19

Pyrethroid resistance has been slower to emerge in Anopheles arabiensis than in An. gambiae s.s and An. funestus and, consequently, studies are only just beginning to unravel the genes involved. Permethrin resistance in An. arabiensis in Lower Moshi, Tanzania has been linked to elevated levels of both P450 monooxygenases and β-esterases. We have conducted a gene expression study to identify specific genes linked with metabolic resistance in the Lower Moshi An. arabiensis population. Microarray experiments employing an An. gambiae whole genome expression chip were performed on An. arabiensis, using interwoven loop designs. Permethrin-exposed survivors were compared to three separate unexposed mosquitoes from the same or a nearby population. A subsection of detoxification genes were chosen for subsequent quantitative real-time PCR (qRT-PCR). Microarray analysis revealed significant over expression of 87 probes and under expression of 85 probes (in pairwise comparisons between permethrin survivors and unexposed sympatric and allopatric samples from Dar es Salaam (controls). For qRT-PCR we targeted over expressed ABC transporter genes (ABC '2060'), a glutathione-S-transferase, P450s and esterases. Design of efficient, specific primers was successful for ABC '2060'and two P450s (CYP6P3, CYP6M2). For the CYP4G16 gene, we used the primers that were previously used in a microarray study of An. arabiensis from Zanzibar islands. Over expression of CYP4G16 and ABC '2060' was detected though with contrasting patterns in pairwise comparisons between survivors and controls. CYP4G16 was only up regulated in survivors, whereas ABC '2060' was similar in survivors and controls but over expressed in Lower Moshi samples compared to the Dar es Salaam samples. Increased transcription of CYP4G16 and ABC '2060' are linked directly and indirectly respectively, with permethrin resistance in Lower Moshi An. arabiensis. Increased transcription of a P450 (CYP4G16) and an ABC transporter (ABC 2060) are linked directly and indirectly respectively, with permethrin resistance in Lower Moshi An. arabiensis. Our study provides replication of CYP4G16 as a candidate gene for pyrethroid resistance in An. arabiensis, although its role may not be in detoxification, and requires further investigation.

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.

PubMed

Li, Ying; Shi, Xiaohu; Liang, Yanchun; Xie, Juan; Zhang, Yu; Ma, Qin

2017-01-21

RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis. Existing algorithms mainly fall into two categories: alignment-based and alignment-free. The alignment-free algorithms of RNA comparison usually have lower time complexity than alignment-based algorithms. An alignment-free RNA comparison algorithm was proposed, in which novel numerical representations RNA-TVcurve (triple vector curve representation) of RNA sequence and corresponding secondary structure features are provided. Then a multi-scale similarity score of two given RNAs was designed based on wavelet decomposition of their numerical representation. In support of RNA mutation and phylogenetic analysis, a web server (RNA-TVcurve) was designed based on this alignment-free RNA comparison algorithm. It provides three functional modules: 1) visualization of numerical representation of RNA secondary structure; 2) detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and multiple RNA secondary structures. The inputs of the web server require RNA primary sequences, while corresponding secondary structures are optional. For the primary sequences alone, the web server can compute the secondary structures using free energy minimization algorithm in terms of RNAfold tool from Vienna RNA package. RNA-TVcurve is the first integrated web server, based on an alignment-free method, to deliver a suite of RNA analysis functions, including visualization, mutation analysis and multiple RNAs structure comparison. The comparison results with two popular RNA comparison tools, RNApdist and RNAdistance, showcased that RNA-TVcurve can efficiently capture subtle relationships among RNAs for mutation detection and non-coding RNA classification. All the relevant results were shown in an intuitive graphical manner, and can be freely downloaded from this server. RNA-TVcurve, along with test examples and detailed documents, are available at: http://ml.jlu.edu.cn/tvcurve/ .

Comparative safety and efficacy of vasopressors for mortality in septic shock: A network meta-analysis.

PubMed

Nagendran, Myura; Maruthappu, Mahiben; Gordon, Anthony C; Gurusamy, Kurinchi S

2016-05-01

Septic shock is a life-threatening condition requiring vasopressor agents to support the circulatory system. Several agents exist with choice typically guided by the specific clinical scenario. We used a network meta-analysis approach to rate the comparative efficacy and safety of vasopressors for mortality and arrhythmia incidence in septic shock patients. We performed a comprehensive electronic database search including Medline, Embase, Science Citation Index Expanded and the Cochrane database. Randomised trials investigating vasopressor agents in septic shock patients and specifically assessing 28-day mortality or arrhythmia incidence were included. A Bayesian network meta-analysis was performed using Markov chain Monte Carlo methods. Thirteen trials of low to moderate risk of bias in which 3146 patients were randomised were included. There was no pairwise evidence to suggest one agent was superior over another for mortality. In the network meta-analysis, vasopressin was significantly superior to dopamine (OR 0.68 (95% CI 0.5 to 0.94)) for mortality. For arrhythmia incidence, standard pairwise meta-analyses confirmed that dopamine led to a higher incidence of arrhythmias than norepinephrine (OR 2.69 (95% CI 2.08 to 3.47)). In the network meta-analysis, there was no evidence of superiority of one agent over another. In this network meta-analysis, vasopressin was superior to dopamine for 28-day mortality in septic shock. Existing pairwise information supports the use of norepinephrine over dopamine. Our findings suggest that dopamine should be avoided in patients with septic shock and that other vasopressor agents should continue to be based on existing guidelines and clinical judgement of the specific presentation of the patient.

Exponential series approaches for nonparametric graphical models

NASA Astrophysics Data System (ADS)

Janofsky, Eric

Markov Random Fields (MRFs) or undirected graphical models are parsimonious representations of joint probability distributions. This thesis studies high-dimensional, continuous-valued pairwise Markov Random Fields. We are particularly interested in approximating pairwise densities whose logarithm belongs to a Sobolev space. For this problem we propose the method of exponential series which approximates the log density by a finite-dimensional exponential family with the number of sufficient statistics increasing with the sample size. We consider two approaches to estimating these models. The first is regularized maximum likelihood. This involves optimizing the sum of the log-likelihood of the data and a sparsity-inducing regularizer. We then propose a variational approximation to the likelihood based on tree-reweighted, nonparametric message passing. This approximation allows for upper bounds on risk estimates, leverages parallelization and is scalable to densities on hundreds of nodes. We show how the regularized variational MLE may be estimated using a proximal gradient algorithm. We then consider estimation using regularized score matching. This approach uses an alternative scoring rule to the log-likelihood, which obviates the need to compute the normalizing constant of the distribution. For general continuous-valued exponential families, we provide parameter and edge consistency results. As a special case we detail a new approach to sparse precision matrix estimation which has statistical performance competitive with the graphical lasso and computational performance competitive with the state-of-the-art glasso algorithm. We then describe results for model selection in the nonparametric pairwise model using exponential series. The regularized score matching problem is shown to be a convex program; we provide scalable algorithms based on consensus alternating direction method of multipliers (ADMM) and coordinate-wise descent. We use simulations to compare our method to others in the literature as well as the aforementioned TRW estimator.

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.

PubMed

Daily, Jeff

2016-02-10

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 24-core processor system, the highest reported for an implementation based on Farrar's 'striped' approach. Rognes's SWIPE optimal database search application is still generally the fastest available at 1.2 to at best 2.4 times faster than Parasail for sequences shorter than 500 amino acids. However, Parasail was faster for longer sequences. For global alignments, Parasail's prefix scan implementation is generally the fastest, faster even than Farrar's 'striped' approach, however the opal library is faster for single-threaded applications. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

Methods, procedures, and contextual characteristics of health technology assessment and health policy decision making: comparison of health technology assessment agencies in Germany, United Kingdom, France, and Sweden.

PubMed

Schwarzer, Ruth; Siebert, Uwe

2009-07-01

The objectives of this study were (i) to develop a systematic framework for describing and comparing different features of health technology assessment (HTA) agencies, (ii) to identify and describe similarities and differences between the agencies, and (iii) to draw conclusions both for producers and users of HTA in research, policy, and practice. We performed a systematic literature search, added information from HTA agencies, and developed a conceptual framework comprising eight main domains: organization, scope, processes, methods, dissemination, decision, implementation, and impact. We grouped relevant items of these domains in an evidence table and chose five HTA agencies to test our framework: DAHTA@DIMDI, HAS, IQWiG, NICE, and SBU. Item and domain similarity was assessed using the percentage of identical characteristics in pairwise comparisons across agencies. RESULTS were interpreted across agencies by demonstrating similarities and differences. Based on 306 included documents, we identified 90 characteristics of eight main domains appropriate for our framework. After applying the framework to the five agencies, we were able to show 40 percent similarities in "dissemination," 38 percent in "scope," 35 percent in "organization," 29 percent in "methods," 26 percent in "processes," 23 percent in "impact," 19 percent in "decision," and 17 percent in "implementation." We found considerably more differences than similarities of HTA features across agencies and countries. Our framework and comparison provides insights and clarification into the need for harmonization. Our findings could serve as descriptive database facilitating communication between producers and users.

Towards unbiased benchmarking of evolutionary and hybrid algorithms for real-valued optimisation

NASA Astrophysics Data System (ADS)

MacNish, Cara

2007-12-01

Randomised population-based algorithms, such as evolutionary, genetic and swarm-based algorithms, and their hybrids with traditional search techniques, have proven successful and robust on many difficult real-valued optimisation problems. This success, along with the readily applicable nature of these techniques, has led to an explosion in the number of algorithms and variants proposed. In order for the field to advance it is necessary to carry out effective comparative evaluations of these algorithms, and thereby better identify and understand those properties that lead to better performance. This paper discusses the difficulties of providing benchmarking of evolutionary and allied algorithms that is both meaningful and logistically viable. To be meaningful the benchmarking test must give a fair comparison that is free, as far as possible, from biases that favour one style of algorithm over another. To be logistically viable it must overcome the need for pairwise comparison between all the proposed algorithms. To address the first problem, we begin by attempting to identify the biases that are inherent in commonly used benchmarking functions. We then describe a suite of test problems, generated recursively as self-similar or fractal landscapes, designed to overcome these biases. For the second, we describe a server that uses web services to allow researchers to 'plug in' their algorithms, running on their local machines, to a central benchmarking repository.

Fixation of strategies driven by switching probabilities in evolutionary games

NASA Astrophysics Data System (ADS)

Xu, Zimin; Zhang, Jianlei; Zhang, Chunyan; Chen, Zengqiang

2016-12-01

We study the evolutionary dynamics of strategies in finite populations which are homogeneous and well mixed by means of the pairwise comparison process, the core of which is the proposed switching probability. Previous studies about this subject are usually based on the known payoff comparison of the related players, which is an ideal assumption. In real social systems, acquiring the accurate payoffs of partners at each round of interaction may be not easy. So we bypass the need of explicit knowledge of payoffs, and encode the payoffs into the willingness of any individual shift from her current strategy to the competing one, and the switching probabilities are wholly independent of payoffs. Along this way, the strategy updating can be performed when game models are fixed and payoffs are unclear, expected to extend ideal assumptions to be more realistic one. We explore the impact of the switching probability on the fixation probability and derive a simple formula which determines the fixation probability. Moreover we find that cooperation dominates defection if the probability of cooperation replacing defection is always larger than the probability of defection replacing cooperation in finite populations. Last, we investigate the influences of model parameters on the fixation of strategies in the framework of three concrete game models: prisoner's dilemma, snowdrift game and stag-hunt game, which effectively portray the characteristics of cooperative dilemmas in real social systems.

Evidence for holistic episodic recollection via hippocampal pattern completion.

PubMed

Horner, Aidan J; Bisby, James A; Bush, Daniel; Lin, Wen-Jing; Burgess, Neil

2015-07-02

Recollection is thought to be the hallmark of episodic memory. Here we provide evidence that the hippocampus binds together the diverse elements forming an event, allowing holistic recollection via pattern completion of all elements. Participants learn complex 'events' from multiple overlapping pairs of elements, and are tested on all pairwise associations. At encoding, element 'types' (locations, people and objects/animals) produce activation in distinct neocortical regions, while hippocampal activity predicts memory performance for all within-event pairs. When retrieving a pairwise association, neocortical activity corresponding to all event elements is reinstated, including those incidental to the task. Participant's degree of incidental reinstatement correlates with their hippocampal activity. Our results suggest that event elements, represented in distinct neocortical regions, are bound into coherent 'event engrams' in the hippocampus that enable episodic recollection--the re-experiencing or holistic retrieval of all aspects of an event--via a process of hippocampal pattern completion and neocortical reinstatement.

R-based Tool for a Pairwise Structure-activity Relationship Analysis.

PubMed

Klimenko, Kyrylo

2018-04-01

The Structure-Activity Relationship analysis is a complex process that can be enhanced by computational techniques. This article describes a simple tool for SAR analysis that has a graphic user interface and a flexible approach towards the input of molecular data. The application allows calculating molecular similarity represented by Tanimoto index & Euclid distance, as well as, determining activity cliffs by means of Structure-Activity Landscape Index. The calculation is performed in a pairwise manner either for the reference compound and other compounds or for all possible pairs in the data set. The results of SAR analysis are visualized using two types of plot. The application capability is demonstrated by the analysis of a set of COX2 inhibitors with respect to Isoxicam. This tool is available online: it includes manual and input file examples. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Beyond pairwise strategy updating in the prisoner's dilemma game

NASA Astrophysics Data System (ADS)

Wang, Xiaofeng; Perc, Matjaž; Liu, Yongkui; Chen, Xiaojie; Wang, Long

2012-10-01

In spatial games players typically alter their strategy by imitating the most successful or one randomly selected neighbor. Since a single neighbor is taken as reference, the information stemming from other neighbors is neglected, which begets the consideration of alternative, possibly more realistic approaches. Here we show that strategy changes inspired not only by the performance of individual neighbors but rather by entire neighborhoods introduce a qualitatively different evolutionary dynamics that is able to support the stable existence of very small cooperative clusters. This leads to phase diagrams that differ significantly from those obtained by means of pairwise strategy updating. In particular, the survivability of cooperators is possible even by high temptations to defect and over a much wider uncertainty range. We support the simulation results by means of pair approximations and analysis of spatial patterns, which jointly highlight the importance of local information for the resolution of social dilemmas.

Video-based depression detection using local Curvelet binary patterns in pairwise orthogonal planes.

PubMed

Pampouchidou, Anastasia; Marias, Kostas; Tsiknakis, Manolis; Simos, Panagiotis; Fan Yang; Lemaitre, Guillaume; Meriaudeau, Fabrice

2016-08-01

Depression is an increasingly prevalent mood disorder. This is the reason why the field of computer-based depression assessment has been gaining the attention of the research community during the past couple of years. The present work proposes two algorithms for depression detection, one Frame-based and the second Video-based, both employing Curvelet transform and Local Binary Patterns. The main advantage of these methods is that they have significantly lower computational requirements, as the extracted features are of very low dimensionality. This is achieved by modifying the previously proposed algorithm which considers Three-Orthogonal-Planes, to only Pairwise-Orthogonal-Planes. Performance of the algorithms was tested on the benchmark dataset provided by the Audio/Visual Emotion Challenge 2014, with the person-specific system achieving 97.6% classification accuracy, and the person-independed one yielding promising preliminary results of 74.5% accuracy. The paper concludes with open issues, proposed solutions, and future plans.

Ultrahigh-Dimensional Multiclass Linear Discriminant Analysis by Pairwise Sure Independence Screening

PubMed Central

Pan, Rui; Wang, Hansheng; Li, Runze

2016-01-01

This paper is concerned with the problem of feature screening for multi-class linear discriminant analysis under ultrahigh dimensional setting. We allow the number of classes to be relatively large. As a result, the total number of relevant features is larger than usual. This makes the related classification problem much more challenging than the conventional one, where the number of classes is small (very often two). To solve the problem, we propose a novel pairwise sure independence screening method for linear discriminant analysis with an ultrahigh dimensional predictor. The proposed procedure is directly applicable to the situation with many classes. We further prove that the proposed method is screening consistent. Simulation studies are conducted to assess the finite sample performance of the new procedure. We also demonstrate the proposed methodology via an empirical analysis of a real life example on handwritten Chinese character recognition. PMID:28127109

The use of many-body expansions and geometry optimizations in fragment-based methods.

PubMed

Fedorov, Dmitri G; Asada, Naoya; Nakanishi, Isao; Kitaura, Kazuo

2014-09-16

Conspectus Chemists routinely work with complex molecular systems: solutions, biochemical molecules, and amorphous and composite materials provide some typical examples. The questions one often asks are what are the driving forces for a chemical phenomenon? How reasonable are our views of chemical systems in terms of subunits, such as functional groups and individual molecules? How can one quantify the difference in physicochemical properties of functional units found in a different chemical environment? Are various effects on functional units in molecular systems additive? Can they be represented by pairwise potentials? Are there effects that cannot be represented in a simple picture of pairwise interactions? How can we obtain quantitative values for these effects? Many of these questions can be formulated in the language of many-body effects. They quantify the properties of subunits (fragments), referred to as one-body properties, pairwise interactions (two-body properties), couplings of two-body interactions described by three-body properties, and so on. By introducing the notion of fragments in the framework of quantum chemistry, one obtains two immense benefits: (a) chemists can finally relate to quantum chemistry, which now speaks their language, by discussing chemically interesting subunits and their interactions and (b) calculations become much faster due to a reduced computational scaling. For instance, the somewhat academic sounding question of the importance of three-body effects in water clusters is actually another way of asking how two hydrogen bonds affect each other, when they involve three water molecules. One aspect of this is the many-body charge transfer (CT), because the charge transfers in the two hydrogen bonds are coupled to each other (not independent). In this work, we provide a generalized view on the use of many-body expansions in fragment-based methods, focusing on the general aspects of the property expansion and a contraction of a many-body expansion in a formally two-body series, as exemplified in the development of the fragment molecular orbital (FMO) method. Fragment-based methods have been very successful in delivering the properties of fragments, as well as the fragment interactions, providing insights into complex chemical processes in large molecular systems. We briefly review geometry optimizations performed with fragment-based methods and present an efficient geometry optimization method based on the combination of FMO with molecular mechanics (MM), applied to the complex of a subunit of protein kinase 2 (CK2) with a ligand. FMO results are discussed in comparison with experimental and MM-optimized structures.

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

PubMed

Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

2012-09-01

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

An Energy-Efficient Spectrum-Aware Reinforcement Learning-Based Clustering Algorithm for Cognitive Radio Sensor Networks

PubMed Central

Mustapha, Ibrahim; Ali, Borhanuddin Mohd; Rasid, Mohd Fadlee A.; Sali, Aduwati; Mohamad, Hafizal

2015-01-01

It is well-known that clustering partitions network into logical groups of nodes in order to achieve energy efficiency and to enhance dynamic channel access in cognitive radio through cooperative sensing. While the topic of energy efficiency has been well investigated in conventional wireless sensor networks, the latter has not been extensively explored. In this paper, we propose a reinforcement learning-based spectrum-aware clustering algorithm that allows a member node to learn the energy and cooperative sensing costs for neighboring clusters to achieve an optimal solution. Each member node selects an optimal cluster that satisfies pairwise constraints, minimizes network energy consumption and enhances channel sensing performance through an exploration technique. We first model the network energy consumption and then determine the optimal number of clusters for the network. The problem of selecting an optimal cluster is formulated as a Markov Decision Process (MDP) in the algorithm and the obtained simulation results show convergence, learning and adaptability of the algorithm to dynamic environment towards achieving an optimal solution. Performance comparisons of our algorithm with the Groupwise Spectrum Aware (GWSA)-based algorithm in terms of Sum of Square Error (SSE), complexity, network energy consumption and probability of detection indicate improved performance from the proposed approach. The results further reveal that an energy savings of 9% and a significant Primary User (PU) detection improvement can be achieved with the proposed approach. PMID:26287191

An Energy-Efficient Spectrum-Aware Reinforcement Learning-Based Clustering Algorithm for Cognitive Radio Sensor Networks.

PubMed

Mustapha, Ibrahim; Mohd Ali, Borhanuddin; Rasid, Mohd Fadlee A; Sali, Aduwati; Mohamad, Hafizal

2015-08-13

It is well-known that clustering partitions network into logical groups of nodes in order to achieve energy efficiency and to enhance dynamic channel access in cognitive radio through cooperative sensing. While the topic of energy efficiency has been well investigated in conventional wireless sensor networks, the latter has not been extensively explored. In this paper, we propose a reinforcement learning-based spectrum-aware clustering algorithm that allows a member node to learn the energy and cooperative sensing costs for neighboring clusters to achieve an optimal solution. Each member node selects an optimal cluster that satisfies pairwise constraints, minimizes network energy consumption and enhances channel sensing performance through an exploration technique. We first model the network energy consumption and then determine the optimal number of clusters for the network. The problem of selecting an optimal cluster is formulated as a Markov Decision Process (MDP) in the algorithm and the obtained simulation results show convergence, learning and adaptability of the algorithm to dynamic environment towards achieving an optimal solution. Performance comparisons of our algorithm with the Groupwise Spectrum Aware (GWSA)-based algorithm in terms of Sum of Square Error (SSE), complexity, network energy consumption and probability of detection indicate improved performance from the proposed approach. The results further reveal that an energy savings of 9% and a significant Primary User (PU) detection improvement can be achieved with the proposed approach.

Bimodal spectroscopic evaluation of ultra violet-irradiated mouse skin inflammatory and precancerous stages: instrumentation, spectral feature extraction/selection and classification (k-NN, LDA and SVM)

NASA Astrophysics Data System (ADS)

Díaz-Ayil, G.; Amouroux, M.; Blondel, W. C. P. M.; Bourg-Heckly, G.; Leroux, A.; Guillemin, F.; Granjon, Y.

2009-07-01

This paper deals with the development and application of in vivo spatially-resolved bimodal spectroscopy (AutoFluorescence AF and Diffuse Reflectance DR), to discriminate various stages of skin precancer in a preclinical model (UV-irradiated mouse): Compensatory Hyperplasia CH, Atypical Hyperplasia AH and Dysplasia D. A programmable instrumentation was developed for acquiring AF emission spectra using 7 excitation wavelengths: 360, 368, 390, 400, 410, 420 and 430 nm, and DR spectra in the 390-720 nm wavelength range. After various steps of intensity spectra preprocessing (filtering, spectral correction and intensity normalization), several sets of spectral characteristics were extracted and selected based on their discrimination power statistically tested for every pair-wise comparison of histological classes. Data reduction with Principal Components Analysis (PCA) was performed and 3 classification methods were implemented (k-NN, LDA and SVM), in order to compare diagnostic performance of each method. Diagnostic performance was studied and assessed in terms of sensitivity (Se) and specificity (Sp) as a function of the selected features, of the combinations of 3 different inter-fibers distances and of the numbers of principal components, such that: Se and Sp ≈ 100% when discriminating CH vs. others; Sp ≈ 100% and Se > 95% when discriminating Healthy vs. AH or D; Sp ≈ 74% and Se ≈ 63%for AH vs. D.

The National Football League-225 Bench Press Test and the Size-Weight Illusion.

PubMed

Luebbers, Paul E; Buckingham, Gavin; Butler, Michael S

2017-06-01

The purpose of this study was to test reports that size and arrangement manipulations of weight plates (i.e., inducing a size-weight illusion [SWI]) effect athletic weightlifting performance. The participants were 72 experienced, weight-trained collegiate American football players. Across three weeks, each athlete performed three different repetitions-to-fatigue bench press tests (NFL-225, SWI-225, and SWI-215). A multiple regression revealed a positive association between participants' strength relative to the test load and repetitions for NFL-225 and SWI-215, but no association with SWI-225. To explore these results, players were ranked into quartiles based on their one-repetition maximum relative to 102.27 kg (225 lb), and a 3 × 4 repeated measures analysis of variance was conducted. The primary finding was a significant Test Condition × Quartile interaction ( p = .004). Bonferroni-corrected pairwise comparisons revealed that Quartile 4 (those with lowest strength relative to test load) completed more repetitions for SWI-225 compared with NFL-225 ( p = .049). These results suggest that alternate weight plate arrangements may be beneficial for those whose bench press load is near the lifter's one-repetition maximum. However, variations of the SWI do not appear to affect the performance of repetitions-to-fatigue bench press tests for the majority of collegiate American football players.

A Demonstration of ‘Broken’ Visual Space

PubMed Central

Gilson, Stuart

2012-01-01

It has long been assumed that there is a distorted mapping between real and ‘perceived’ space, based on demonstrations of systematic errors in judgements of slant, curvature, direction and separation. Here, we have applied a direct test to the notion of a coherent visual space. In an immersive virtual environment, participants judged the relative distance of two squares displayed in separate intervals. On some trials, the virtual scene expanded by a factor of four between intervals although, in line with recent results, participants did not report any noticeable change in the scene. We found that there was no consistent depth ordering of objects that can explain the distance matches participants made in this environment (e.g. A>B>D yet also A

Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference.

PubMed

Yang, Yunfeng; Zhu, Mengxia; Wu, Liyou; Zhou, Jizhong

2008-09-16

Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories. Conflicting results have been reported with regard to the reliability of microarray results using this method. To explain it, we hypothesize that data processing is a critical element that impacts the data quality. Microarray experiments were performed in a gamma-proteobacterium Shewanella oneidensis. Pair-wise comparison of three experimental conditions was obtained either with two labeled cDNA samples co-hybridized to the same array, or by employing Shewanella genomic DNA as a standard reference. Various data processing techniques were exploited to reduce the amount of inconsistency between both methods and the results were assessed. We discovered that data quality was significantly improved by imposing the constraint of minimal number of replicates, logarithmic transformation and random error analyses. These findings demonstrate that data processing significantly influences data quality, which provides an explanation for the conflicting evaluation in the literature. This work could serve as a guideline for microarray data analysis using genomic DNA as a standard reference.

Temporal processing impairment in children with attention-deficit-hyperactivity disorder.

PubMed

Huang, Jia; Yang, Bin-rang; Zou, Xiao-bing; Jing, Jin; Pen, Gang; McAlonan, Gráinne M; Chan, Raymond C K

2012-01-01

The current study aimed to investigate temporal processing in Chinese children with Attention-Deficit-Hyperactivity Disorder(ADHD) using time production, time reproduction paradigm and duration discrimination tasks. A battery of tests specifically designed to measure temporal processing was administered to 94 children with ADHD and 100 demographically matched healthy children. A multivariate analysis of variance (MANOVA) and a repeated measure MANOVA indicated that children with ADHD were impaired in time processing functions. The results of pairwise comparisons showed that the probands with a family history of ADHD performed significantly worse than those without family history in the time production tasks and the time reproduction task. Logistic regression analysis showed duration discrimination had a significant role in predicting whether the children were suffering from ADHD or not, while temporal processing had a significant role in predicting whether the ADHD children had a family history or not. This study provides further support for the existence of a generic temporal processing impairment in ADHD children and suggests that abnormalities in time processing and ADHD share some common genetic factors. Copyright © 2011 Elsevier Ltd. All rights reserved.

Manganese chloride tetrahydrate (CMC-001) enhanced liver MRI: evaluation of efficacy and safety in healthy volunteers.

PubMed

Albiin, Nils; Kartalis, Nikolaos; Bergquist, Annika; Sadigh, Bita; Brismar, Torkel B

2012-10-01

To evaluate the efficacy of three dose levels of the oral hepatobiliary manganese-based magnetic resonance imaging (MRI) contrast agent CMC-001, and assess its safety profile and patient acceptability. After ethics committee approval, 32 healthy volunteers (males/females: 18/14) were included. Liver MRI was performed before and 3 h after ingestion of 0.8, 0.4, and 0.2 g of CMC-001 on separate occasions. Liver-to-muscle signal intensity (SI) ratio from baseline to post-contrast and image quality was assessed. Adverse drug reactions/adverse events (ADRs/AEs) and clinico-laboratory tests were monitored. The increase in liver-to-muscle SI ratio was significantly higher after 0.8 g (0.696) compared to 0.4 g (0.458) and 0.2 g (0.223) (in all pair-wise comparisons, P < 0.0001). The overall image quality was superior after 0.8 g. ADRs/AEs were dose-related and predominantly of mild intensity. Liver MRI using 0.8 g CMC-001 has the highest efficacy and still acceptable ADRs and should therefore be preferred.

A binary linear programming formulation of the graph edit distance.

PubMed

Justice, Derek; Hero, Alfred

2006-08-01

A binary linear programming formulation of the graph edit distance for unweighted, undirected graphs with vertex attributes is derived and applied to a graph recognition problem. A general formulation for editing graphs is used to derive a graph edit distance that is proven to be a metric, provided the cost function for individual edit operations is a metric. Then, a binary linear program is developed for computing this graph edit distance, and polynomial time methods for determining upper and lower bounds on the solution of the binary program are derived by applying solution methods for standard linear programming and the assignment problem. A recognition problem of comparing a sample input graph to a database of known prototype graphs in the context of a chemical information system is presented as an application of the new method. The costs associated with various edit operations are chosen by using a minimum normalized variance criterion applied to pairwise distances between nearest neighbors in the database of prototypes. The new metric is shown to perform quite well in comparison to existing metrics when applied to a database of chemical graphs.

EGSIEM: Combination of GRACE monthly gravity models on normal equation level

NASA Astrophysics Data System (ADS)

Meyer, Ulrich; Jean, Yoomin; Jäggi, Adrian; Mayer-Gürr, Torsten; Neumayer, Hans; Lemoine, Jean-Michel

2016-04-01

One of the three geodetic services to be realized in the frame of the EGSIEM project is a scientific combination service. Each associated processing center (AC) will follow a set of common processing standards but will apply its own, independent analysis method. Therefore the quality, robustness and reliability of the combined monthly gravity fields is expected to improve significantly compared to the individual solutions. The Monthly GRACE gravity fields of all ACs are combined on normal equation level. The individual normal equations are weighted depending on pairwise comparisons of the individual gravity field solutions. To derive these weights and for quality control of the individual contributions first a combination of the monthly gravity fields on solution level is performed. The concept of weighting and of the combination on normal equation level is introduced and the formats used for normal equation exchange and gravity field solutions is described. First results of the combination on normal equation level are presented and compared to the corresponding combinations on solution level. EGSIEM has an open data policy and all processing centers of GRACE gravity fields are invited to participate in the combination.

Alignment-independent comparison of binding sites based on DrugScore potential fields encoded by 3D Zernike descriptors.

PubMed

Nisius, Britta; Gohlke, Holger

2012-09-24

Analyzing protein binding sites provides detailed insights into the biological processes proteins are involved in, e.g., into drug-target interactions, and so is of crucial importance in drug discovery. Herein, we present novel alignment-independent binding site descriptors based on DrugScore potential fields. The potential fields are transformed to a set of information-rich descriptors using a series expansion in 3D Zernike polynomials. The resulting Zernike descriptors show a promising performance in detecting similarities among proteins with low pairwise sequence identities that bind identical ligands, as well as within subfamilies of one target class. Furthermore, the Zernike descriptors are robust against structural variations among protein binding sites. Finally, the Zernike descriptors show a high data compression power, and computing similarities between binding sites based on these descriptors is highly efficient. Consequently, the Zernike descriptors are a useful tool for computational binding site analysis, e.g., to predict the function of novel proteins, off-targets for drug candidates, or novel targets for known drugs.

Neonatal Outcomes of Very Low Birth Weight and Very Preterm Neonates: An International Comparison.

PubMed

Shah, Prakesh S; Lui, Kei; Sjörs, Gunnar; Mirea, Lucia; Reichman, Brian; Adams, Mark; Modi, Neena; Darlow, Brian A; Kusuda, Satoshi; San Feliciano, Laura; Yang, Junmin; Håkansson, Stellan; Mori, Rintaro; Bassler, Dirk; Figueras-Aloy, Josep; Lee, Shoo K

2016-10-01

To compare rates of a composite outcome of mortality or major morbidity in very-preterm/very low birth weight infants between 8 members of the International Network for Evaluating Outcomes. We included 58 004 infants born weighing <1500 g at 24(0)-31(6) weeks' gestation from databases in Australia/New Zealand, Canada, Israel, Japan, Spain, Sweden, Switzerland, and the United Kingdom. We compared a composite outcome (mortality or any of grade ≥3 peri-intraventricular hemorrhage, periventricular echodensity/echolucency, bronchopulmonary dysplasia, or treated retinopathy of prematurity) between each country and all others by using standardized ratios and pairwise using logistic regression analyses. Despite differences in population coverage, included neonates were similar at baseline. Composite outcome rates varied from 26% to 42%. The overall mortality rate before discharge was 10% (range: 5% [Japan]-17% [Spain]). The standardized ratio (99% CIs) estimates for the composite outcome were significantly greater for Spain 1.09 (1.04-1.14) and the United Kingdom 1.16 (1.11-1.21), lower for Australia/New Zealand 0.93 (0.89-0.97), Japan 0.89 (0.86-0.93), Sweden 0.81 (0.73-0.90), and Switzerland 0.77 (0.69-0.87), and nonsignificant for Canada 1.04 (0.99-1.09) and Israel 1.00 (0.93-1.07). The adjusted odds of the composite outcome varied significantly in pairwise comparisons. We identified marked variations in neonatal outcomes between countries. Further collaboration and exploration is needed to reduce variations in population coverage, data collection, and case definitions. The goal would be to identify care practices and health care organizational factors, which has the potential to improve neonatal outcomes. Copyright © 2016 Elsevier Inc. All rights reserved.

Selection of a Suitable Method for the Preparation of Polymeric Nanoparticles: Multi-Criteria Decision Making Approach

PubMed Central

Krishnamoorthy, Kannan; Mahalingam, Manikandan

2015-01-01

Purpose: The present study is aimed to select the suitable method for preparation of camptothecin loaded polymeric nanoparticles by utilizing the multi-criteria decision making method. Novel approaches of drug delivery by formulation using nanotechnology are revolutionizing the future of medicine. Recent years have witnessed unprecedented growth of research and application in the area of nanotechnology. Nanoparticles have become an important area of research in the field of drug delivery because they have the ability to deliver a wide range of drug to varying areas of body. Methods: Despite of extensive research and development, polymeric nanoparticles are frequently used to improve the therapeutic effect of drugs. A number of techniques are available for the preparation of polymeric nanoparticles. The Analytical Hierarchy Process (AHP) is a method for decision making, which are derived from individual judgements for qualitative factors, using the pair-wise comparison matrix. In AHP, a decision hierarchy is constructed with a goal, criteria and alternatives. Results: The model uses three main criteria 1) Instrument, 2) Process and Output and 3) Cost. In addition, there are eight sub-criteria’s as well as eight alternatives. Pair-wise comparison matrixes are used to obtain the overall priority weight and ranking for the selection of suitable method. Nanoprecipitation technique is the most suitable method for the preparation of camptothecin loaded polymeric nanoparticles with the highest overall priority weight of 0.297 Conclusion: In particular, the result indicates that the priority weights obtained from AHP could be defined as a multiple output for finding out the most suitable method for preparation of camptothecin loaded polymeric nanoparticles. PMID:25789220

Qualitative and quantitative evaluation of solvent systems for countercurrent separation.

PubMed

Friesen, J Brent; Ahmed, Sana; Pauli, Guido F

2015-01-16

Rational solvent system selection for countercurrent chromatography and centrifugal partition chromatography technology (collectively known as countercurrent separation) studies continues to be a scientific challenge as the fundamental questions of comparing polarity range and selectivity within a solvent system family and between putative orthogonal solvent systems remain unanswered. The current emphasis on metabolomic investigations and analysis of complex mixtures necessitates the use of successive orthogonal countercurrent separation (CS) steps as part of complex fractionation protocols. Addressing the broad range of metabolite polarities demands development of new CS solvent systems with appropriate composition, polarity (π), selectivity (σ), and suitability. In this study, a mixture of twenty commercially available natural products, called the GUESSmix, was utilized to evaluate both solvent system polarity and selectively characteristics. Comparisons of GUESSmix analyte partition coefficient (K) values give rise to a measure of solvent system polarity range called the GUESSmix polarity index (GUPI). Solvatochromic dye and electrical permittivity measurements were also evaluated in quantitatively assessing solvent system polarity. The relative selectivity of solvent systems were evaluated with the GUESSmix by calculating the pairwise resolution (αip), the number of analytes found in the sweet spot (Nsw), and the pairwise resolution of those sweet spot analytes (αsw). The combination of these parameters allowed for both intra- and inter-family comparison of solvent system selectivity. Finally, 2-dimensional reciprocal shifted symmetry plots (ReSS(2)) were created to visually compare both the polarities and selectivities of solvent system pairs. This study helps to pave the way to the development of new solvent systems that are amenable to successive orthogonal CS protocols employed in metabolomic studies. Copyright © 2014 Elsevier B.V. All rights reserved.

Electromyography and Mechanomyography Signals During Swallowing in Healthy Adults and Head and Neck Cancer Survivors.

PubMed

Constantinescu, Gabriela; Hodgetts, William; Scott, Dylan; Kuffel, Kristina; King, Ben; Brodt, Chris; Rieger, Jana

2017-02-01

Surface electromyography (sEMG) is used as an adjuvant to dysphagia therapy to demonstrate the activity of submental muscles during swallowing exercises. Mechanomyography (MMG) has been suggested as a potential superior alternative to sEMG; however, this advantage is not confirmed for signal acquired from submental muscles. This study compared the signal-to-noise ratio (SNR) obtained from sEMG and MMG sensors during swallowing tasks, in healthy participants and those with a history of head and neck cancer (HNC), a population with altered anatomy and a high incidence of dysphagia. Twenty-two healthy adults and 10 adults with a history of HNC participated in this study. sEMG and MMG signals were acquired during dry, thin liquid, effortful, and Mendelsohn maneuver swallows. SNR was compared between the two sensors using repeated measures ANOVAs and subsequent planned pairwise comparisons. Test-retest measures were collected on 20 % of participants. In healthy participants, MMG SNR was higher than that of sEMG for dry [t(21) = -3.02, p = 0.007] and thin liquid swallows [t(21) = -4.24, p < 0.001]. Although a significant difference for sensor was found in HNC participants F(1,9) = 5.54, p = 0.043, planned pairwise comparisons by task revealed no statistically significant difference between the two sensors. sEMG also showed much better test-retest reliability than MMG. Biofeedback provided as an adjuvant to dysphagia therapy in patients with HNC should employ sEMG technology, as this sensor type yielded better SNR and overall test-retest reliability. Poor MMG test-retest reliability was noted in both healthy and HNC participants and may have been related to differences in sensor application.

Conarticular congruence of the hominoid subtalar joint complex with implications for joint function in Plio-Pleistocene hominins.

PubMed

Prang, Thomas C

2016-07-01

The purpose of this study is to test the hypothesis that conarticular surfaces areas and curvatures are correlates of mobility at the hominoid talocalcaneal and talonavicular joints. Articular surface areas and curvatures of the talonavicular, anterior talocalcaneal, and posterior talocalcaneal joints were quantified using a total of 425 three-dimensional surface models of extant hominoid and fossil hominin tali, calcanei, and naviculars. Quadric surface fitting was used to calculate curvatures, pairwise comparisons were used to evaluate statistical differences between taxa, and regression was used to test for the effects of allometry. Pairwise comparisons show that the distributions of values for joint curvature indices follow the predicted arboreal-terrestrial morphocline in hominoid primates with no effect of body mass (PGLS p > 0.05). OH 8 (Homo habilis) and LB 1 (Homo floresiensis) can be accommodated within the range of human variation for the talonavicular joint, whereas MH2 (Australopithecus sediba) falls within the ranges of variation for Pan troglodytes and Gorilla gorilla in measures of posterior talocalcaneal joint congruity. Joint curvature indices are better discriminators than joint surface area indices, which may reflect a greater contribution of rotation, rather than translation, to joint movement in plantigrade taxa due to discrepancies in conarticular congruence and the "convex-concave" rule. The pattern of joint congruence in Au. sediba contributes to other data on the foot and ankle suggesting that the lateral side of the foot was more mobile than the medial side, which is consistent with suggestions of increased medial weight transfer associated with hyperpronation. Am J Phys Anthropol 160:446-457, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Test Scatter on the WISC-R in Learning Disabled Children.

ERIC Educational Resources Information Center

Tabachnick, Barbara Gerson

Scatter on the revised Wechsler Intelligence Scale for children (WISC-R) was evaluated for 105 learning disabled (LD) children. Scatter was defined as range of scaled scores on: (1) five regular verbal tests; (2) five regular performance tests; and (3) all 10 regular subtests. Pairwise combinations of 11 subtests were also evaluated for deviations…

Automatic segmentation of mitochondria in EM data using pairwise affinity factorization and graph-based contour searching.

PubMed

Ghita, Ovidiu; Dietlmeier, Julia; Whelan, Paul F

2014-10-01

In this paper, we investigate the segmentation of closed contours in subcellular data using a framework that primarily combines the pairwise affinity grouping principles with a graph partitioning contour searching approach. One salient problem that precluded the application of these methods to large scale segmentation problems is the onerous computational complexity required to generate comprehensive representations that include all pairwise relationships between all pixels in the input data. To compensate for this problem, a practical solution is to reduce the complexity of the input data by applying an over-segmentation technique prior to the application of the computationally demanding strands of the segmentation process. This approach opens the opportunity to build specific shape and intensity models that can be successfully employed to extract the salient structures in the input image which are further processed to identify the cycles in an undirected graph. The proposed framework has been applied to the segmentation of mitochondria membranes in electron microscopy data which are characterized by low contrast and low signal-to-noise ratio. The algorithm has been quantitatively evaluated using two datasets where the segmentation results have been compared with the corresponding manual annotations. The performance of the proposed algorithm has been measured using standard metrics, such as precision and recall, and the experimental results indicate a high level of segmentation accuracy.

Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hardy, David J., E-mail: dhardy@illinois.edu; Schulten, Klaus; Wolff, Matthew A.

2016-03-21

The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation methodmore » (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle–mesh Ewald method falls short.« less

Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations.

PubMed

Hardy, David J; Wolff, Matthew A; Xia, Jianlin; Schulten, Klaus; Skeel, Robert D

2016-03-21

The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle-mesh Ewald method falls short.

Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Hardy, David J.; Wolff, Matthew A.; Xia, Jianlin; Schulten, Klaus; Skeel, Robert D.

2016-03-01

The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle-mesh Ewald method falls short.

Particle-based simulations of self-motile suspensions

NASA Astrophysics Data System (ADS)

Hinz, Denis F.; Panchenko, Alexander; Kim, Tae-Yeon; Fried, Eliot

2015-11-01

A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific class of self-motile bacterial suspensions is considered as a modeling scenario. To mimic the rod-like geometry of a bacterium, two dissipative particle dynamics particles are connected by a stiff harmonic spring to form an aggregate dissipative particle dynamics molecule. Bacterial motility is modeled through a constant self-propulsion force applied along the axis of each such aggregate molecule. The model accounts for hydrodynamic interactions between self-propelled agents through the pairwise dissipative interactions conventional to dissipative particle dynamics. Numerical simulations are performed using a customized version of the open-source software package LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) software package. Detailed studies of the influence of agent concentration, pairwise dissipative interactions, and Stokes friction on the statistics of the system are provided. The simulations are used to explore the influence of hydrodynamic interactions in active suspensions. For high agent concentrations in combination with dominating pairwise dissipative forces, strongly correlated motion patterns and a fluid-like spectral distributions of kinetic energy are found. In contrast, systems dominated by Stokes friction exhibit weaker spatial correlations of the velocity field. These results indicate that hydrodynamic interactions may play an important role in the formation of spatially extended structures in active suspensions.

Nanopore DNA Sequencing and Genome Assembly on the International Space Station.

PubMed

Castro-Wallace, Sarah L; Chiu, Charles Y; John, Kristen K; Stahl, Sarah E; Rubins, Kathleen H; McIntyre, Alexa B R; Dworkin, Jason P; Lupisella, Mark L; Smith, David J; Botkin, Douglas J; Stephenson, Timothy A; Juul, Sissel; Turner, Daniel J; Izquierdo, Fernando; Federman, Scot; Stryke, Doug; Somasekar, Sneha; Alexander, Noah; Yu, Guixia; Mason, Christopher E; Burton, Aaron S

2017-12-21

We evaluated the performance of the MinION DNA sequencer in-flight on the International Space Station (ISS), and benchmarked its performance off-Earth against the MinION, Illumina MiSeq, and PacBio RS II sequencing platforms in terrestrial laboratories. Samples contained equimolar mixtures of genomic DNA from lambda bacteriophage, Escherichia coli (strain K12, MG1655) and Mus musculus (female BALB/c mouse). Nine sequencing runs were performed aboard the ISS over a 6-month period, yielding a total of 276,882 reads with no apparent decrease in performance over time. From sequence data collected aboard the ISS, we constructed directed assemblies of the ~4.6 Mb E. coli genome, ~48.5 kb lambda genome, and a representative M. musculus sequence (the ~16.3 kb mitochondrial genome), at 100%, 100%, and 96.7% consensus pairwise identity, respectively; de novo assembly of the E. coli genome from raw reads yielded a single contig comprising 99.9% of the genome at 98.6% consensus pairwise identity. Simulated real-time analyses of in-flight sequence data using an automated bioinformatic pipeline and laptop-based genomic assembly demonstrated the feasibility of sequencing analysis and microbial identification aboard the ISS. These findings illustrate the potential for sequencing applications including disease diagnosis, environmental monitoring, and elucidating the molecular basis for how organisms respond to spaceflight.

FunShift: a database of function shift analysis on protein subfamilies

PubMed Central

Abhiman, Saraswathi; Sonnhammer, Erik L. L.

2005-01-01

Members of a protein family normally have a general biochemical function in common, but frequently one or more subgroups have evolved a slightly different function, such as different substrate specificity. It is important to detect such function shifts for a more accurate functional annotation. The FunShift database described here is a compilation of function shift analysis performed between subfamilies in protein families. It consists of two main components: (i) subfamilies derived from protein domain families and (ii) pairwise subfamily comparisons analyzed for function shift. The present release, FunShift 12, was derived from Pfam 12 and consists of 151 934 subfamilies derived from 7300 families. We carried out function shift analysis by two complementary methods on families with up to 500 members. From a total of 179 210 subfamily pairs, 62 384 were predicted to be functionally shifted in 2881 families. Each subfamily pair is provided with a markup of probable functional specificity-determining sites. Tools for searching and exploring the data are provided to make this database a valuable resource for protein function annotation. Knowledge of these functionally important sites will be useful for experimental biologists performing functional mutation studies. FunShift is available at http://FunShift.cgb.ki.se. PMID:15608176

Influence of the Smile Line on Smile Attractiveness in Short and Long Face Individuals

PubMed Central

Hayder Mohammed, Thar; Mohammad Hamdan, Ahmad

2017-01-01

Objectives The study assessed the impact of facial height on attractiveness of smile, in association with the maxillary gingival display. This research was performed by dental professionals and laypersons. Materials and Methods Frontal extraoral photographs were captured for both short and long faces. The photographs were modified using software for image-processing and three rater groups (orthodontists, dentists, and laypersons) evaluated the smile attractiveness, with 30 subjects in each group. Differences in ratings of the different smiles among the different experimental groups were examined using the Kruskal-Wallis test. The Mann–Whitney U test was performed for pairwise comparisons between the experimental groups. Results Dentists and laypeople were most likely to agree. For the short face, laypeople and dentists both rated the +2 mm gingival display smile as the most attractive smile whilst orthodontists ranked the 0 mm gingival display smile as the most attractive smile. For the long face, laypeople and dentists ranked the 0 mm gingival display smile as the most attractive smile, whilst orthodontists ranked the +2 mm gingival display as the most attractive. Conclusion Smile line of both short and long face subjects was found to influence the smile attractiveness rating by the three rater groups. PMID:28928770

Dose reduction potential of iterative reconstruction algorithms in neck CTA-a simulation study.

PubMed

Ellmann, Stephan; Kammerer, Ferdinand; Allmendinger, Thomas; Brand, Michael; Janka, Rolf; Hammon, Matthias; Lell, Michael M; Uder, Michael; Kramer, Manuel

2016-10-01

This study aimed to determine the degree of radiation dose reduction in neck CT angiography (CTA) achievable with Sinogram-affirmed iterative reconstruction (SAFIRE) algorithms. 10 consecutive patients scheduled for neck CTA were included in this study. CTA images of the external carotid arteries either were reconstructed with filtered back projection (FBP) at full radiation dose level or underwent simulated dose reduction by proprietary reconstruction software. The dose-reduced images were reconstructed using either SAFIRE 3 or SAFIRE 5 and compared with full-dose FBP images in terms of vessel definition. 5 observers performed a total of 3000 pairwise comparisons. SAFIRE allowed substantial radiation dose reductions in neck CTA while maintaining vessel definition. The possible levels of radiation dose reduction ranged from approximately 34 to approximately 90% and depended on the SAFIRE algorithm strength and the size of the vessel of interest. In general, larger vessels permitted higher degrees of radiation dose reduction, especially with higher SAFIRE strength levels. With small vessels, the superiority of SAFIRE 5 over SAFIRE 3 was lost. Neck CTA can be performed with substantially less radiation dose when SAFIRE is applied. The exact degree of radiation dose reduction should be adapted to the clinical question, in particular to the smallest vessel needing excellent definition.

Independent EEG Sources Are Dipolar

PubMed Central

Delorme, Arnaud; Palmer, Jason; Onton, Julie; Oostenveld, Robert; Makeig, Scott

2012-01-01

Independent component analysis (ICA) and blind source separation (BSS) methods are increasingly used to separate individual brain and non-brain source signals mixed by volume conduction in electroencephalographic (EEG) and other electrophysiological recordings. We compared results of decomposing thirteen 71-channel human scalp EEG datasets by 22 ICA and BSS algorithms, assessing the pairwise mutual information (PMI) in scalp channel pairs, the remaining PMI in component pairs, the overall mutual information reduction (MIR) effected by each decomposition, and decomposition ‘dipolarity’ defined as the number of component scalp maps matching the projection of a single equivalent dipole with less than a given residual variance. The least well-performing algorithm was principal component analysis (PCA); best performing were AMICA and other likelihood/mutual information based ICA methods. Though these and other commonly-used decomposition methods returned many similar components, across 18 ICA/BSS algorithms mean dipolarity varied linearly with both MIR and with PMI remaining between the resulting component time courses, a result compatible with an interpretation of many maximally independent EEG components as being volume-conducted projections of partially-synchronous local cortical field activity within single compact cortical domains. To encourage further method comparisons, the data and software used to prepare the results have been made available (http://sccn.ucsd.edu/wiki/BSSComparison). PMID:22355308

A comparison of two indices for the intraclass correlation coefficient.

PubMed

Shieh, Gwowen

2012-12-01

In the present study, we examined the behavior of two indices for measuring the intraclass correlation in the one-way random effects model: the prevailing ICC(1) (Fisher, 1938) and the corrected eta-squared (Bliese & Halverson, 1998). These two procedures differ both in their methods of estimating the variance components that define the intraclass correlation coefficient and in their performance of bias and mean squared error in the estimation of the intraclass correlation coefficient. In contrast with the natural unbiased principle used to construct ICC(1), in the present study it was analytically shown that the corrected eta-squared estimator is identical to the maximum likelihood estimator and the pairwise estimator under equal group sizes. Moreover, the empirical results obtained from the present Monte Carlo simulation study across various group structures revealed the mutual dominance relationship between their truncated versions for negative values. The corrected eta-squared estimator performs better than the ICC(1) estimator when the underlying population intraclass correlation coefficient is small. Conversely, ICC(1) has a clear advantage over the corrected eta-squared for medium and large magnitudes of population intraclass correlation coefficient. The conceptual description and numerical investigation provide guidelines to help researchers choose between the two indices for more accurate reliability analysis in multilevel research.

π-π stacking tackled with density functional theory

PubMed Central

Swart, Marcel; van der Wijst, Tushar; Fonseca Guerra, Célia

2007-01-01

Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing π-π interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson–Crick pairs. Our main purpose is to find a robust and computationally efficient density functional to be used specifically and only for describing π-π stacking interactions in DNA and other biological molecules in the framework of our recently developed QM/QM approach "QUILD". In line with previous studies, most standard density functionals recover, at best, only part of the favorable stacking interactions. An exception is the new KT1 functional, which correctly yields bound π-stacked structures. Surprisingly, a similarly good performance is achieved with the computationally very robust and efficient local density approximation (LDA). Furthermore, we show that classical electrostatic interactions determine the shape and depth of the π-π stacking potential energy surface. Figure Additivity approximation for the π-π interaction between two stacked Watson–Crick base pairs in terms of pairwise interactions between individual bases Electronic supplementary material The online version of this article (doi:10.1007/s00894-007-0239-y) contains supplementary material, which is available to authorized users. PMID:17874150

Intransitivity is infrequent and fails to promote annual plant coexistence without pairwise niche differences.

PubMed

Godoy, Oscar; Stouffer, Daniel B; Kraft, Nathan J B; Levine, Jonathan M

2017-05-01

Intransitive competition is often projected to be a widespread mechanism of species coexistence in ecological communities. However, it is unknown how much of the coexistence we observe in nature results from this mechanism when species interactions are also stabilized by pairwise niche differences. We combined field-parameterized models of competition among 18 annual plant species with tools from network theory to quantify the prevalence of intransitive competitive relationships. We then analyzed the predicted outcome of competitive interactions with and without pairwise niche differences. Intransitive competition was found for just 15-19% of the 816 possible triplets, and this mechanism was never sufficient to stabilize the coexistence of the triplet when the pair-wise niche differences between competitors were removed. Of the transitive and intransitive triplets, only four were predicted to coexist and these were more similar in multidimensional trait space defined by 11 functional traits than non-coexisting triplets. Our results argue that intransitive competition may be less frequent than recently posed, and that even when it does operate, pairwise niche differences may be key to possible coexistence. © 2017 by the Ecological Society of America.

Dynamics of pairwise motions in the Cosmic Web

NASA Astrophysics Data System (ADS)

Hellwing, Wojciech A.

2016-10-01

We present results of analysis of the dark matter (DM) pairwise velocity statistics in different Cosmic Web environments. We use the DM velocity and density field from the Millennium 2 simulation together with the NEXUS+ algorithm to segment the simulation volume into voxels uniquely identifying one of the four possible environments: nodes, filaments, walls or cosmic voids. We show that the PDFs of the mean infall velocities v 12 as well as its spatial dependence together with the perpendicular and parallel velocity dispersions bear a significant signal of the large-scale structure environment in which DM particle pairs are embedded. The pairwise flows are notably colder and have smaller mean magnitude in wall and voids, when compared to much denser environments of filaments and nodes. We discuss on our results, indicating that they are consistent with a simple theoretical predictions for pairwise motions as induced by gravitational instability mechanism. Our results indicate that the Cosmic Web elements are coherent dynamical entities rather than just temporal geometrical associations. In addition it should be possible to observationally test various Cosmic Web finding algorithms by segmenting available peculiar velocity data and studying resulting pairwise velocity statistics.

A comparison of two instructional methods for drawing Lewis Structures

NASA Astrophysics Data System (ADS)

Terhune, Kari

Two instructional methods for teaching Lewis structures were compared -- the Direct Octet Rule Method (DORM) and the Commonly Accepted Method (CAM). The DORM gives the number of bonds and the number of nonbonding electrons immediately, while the CAM involves moving electron pairs from nonbonding to bonding electrons, if necessary. The research question was as follows: Will high school chemistry students draw more accurate Lewis structures using the DORM or the CAM? Students in Regular Chemistry 1 (N = 23), Honors Chemistry 1 (N = 51) and Chemistry 2 (N = 15) at an urban high school were the study participants. An identical pretest and posttest was given before and after instruction. Students were given instruction with either the DORM (N = 45), the treatment method, or the CAM (N = 44), the control for two days. After the posttest, 15 students were interviewed, using a semistructured interview process. The pretest/posttest consisted of 23 numerical response questions and 2 to 6 free response questions that were graded using a rubric. A two-way ANOVA showed a significant interaction effect between the groups and the methods, F (1, 70) = 10.960, p = 0.001. Post hoc comparisons using the Bonferroni pairwise comparison showed that Reg Chem 1 students demonstrated larger gain scores when they had been taught the CAM (Mean difference = 3.275, SE = 1.324, p < 0.05), while Hon Chem 1 students demonstrated larger gain scores after learning the DORM (Mean difference = 1.931, SE = 0.848, p < 0.05). The DORM requires five mathematical operations, while the CAM only requires one. Honors Chemistry 1 students performed better with the DORM, perhaps due to better math skills, enhanced working memory, and better metacognitive skills. Regular Chemistry 1 students performed better with the CAM, perhaps because it is more visual. Teachers may want to use the CAM or a direct-pairing method to introduce the topic and use the DORM in advanced classes when a correct structure is needed quickly.

Prospective evaluation of cardiac ultrasound performance by general internal medicine physicians during a 6-month faculty development curriculum.

PubMed

Smith, Christopher J; Morad, Abdulrahman; Balwanz, Christopher; Lyden, Elizabeth; Matthias, Tabatha

2018-04-24

Point-of-care (POCUS) education is rapidly expanding within medical schools and internal medicine residency programs, but lack of trained faculty is a major barrier. While POCUS training can improve short-term outcomes, knowledge and skills rapidly decay without deliberate practice and feedback. The purpose of this study was to evaluate the performance of focused cardiac ultrasound (FCU) by volunteer general internal medicine (GIM) faculty participating in a longitudinal POCUS curriculum. Participants: Nine GIM clinician-educators participated in a 6-month POCUS curriculum. Faculty performance was compared to three cardiology fellows. Three diagnostic cardiac sonographers (DCS) were also evaluated and served as the gold standard. the primary outcome was a FCU efficiency score, calculated by dividing image quality score by exam duration. FCU exams were conducted on three standardized patients after completion of an introductory workshop, at 3 months, and at 6 months. Two blinded cardiologists scored the exams. mean efficiency scores were compared using a linear mixed effects model, followed by pairwise comparisons using Tukey's test. GIM faculty's FCU efficiency scores were maintained over the 6-month period (2.2, SE 1.0 vs. 3.8, SE 1.0, p = 0.076). Their scores at each session were similar to cardiology fellows (p > 0.69), but inferior to DCSs (p < 0.0001). GIM faculty participating in a POCUS curriculum maintained their FCU performance over 6 months with efficiency scores comparable to experienced cardiology fellows.

Population structure and covariate analysis based on pairwise microsatellite allele matching frequencies.

PubMed

Givens, Geof H; Ozaksoy, Isin

2007-01-01

We describe a general model for pairwise microsatellite allele matching probabilities. The model can be used for analysis of population substructure, and is particularly focused on relating genetic correlation to measurable covariates. The approach is intended for cases when the existence of subpopulations is uncertain and a priori assignment of samples to hypothesized subpopulations is difficult. Such a situation arises, for example, with western Arctic bowhead whales, where genetic samples are available only from a possibly mixed migratory assemblage. We estimate genetic structure associated with spatial, temporal, or other variables that may confound the detection of population structure. In the bowhead case, the model permits detection of genetic patterns associated with a temporally pulsed multi-population assemblage in the annual migration. Hypothesis tests for population substructure and for covariate effects can be carried out using permutation methods. Simulated and real examples illustrate the effectiveness and reliability of the approach and enable comparisons with other familiar approaches. Analysis of the bowhead data finds no evidence for two temporally pulsed subpopulations using the best available data, although a significant pattern found by other researchers using preliminary data is also confirmed here. Code in the R language is available from www.stat.colostate.edu/~geof/gammmp.html.

Application of a time-dependent coalescence process for inferring the history of population size changes from DNA sequence data.

PubMed

Polanski, A; Kimmel, M; Chakraborty, R

1998-05-12

Distribution of pairwise differences of nucleotides from data on a sample of DNA sequences from a given segment of the genome has been used in the past to draw inferences about the past history of population size changes. However, all earlier methods assume a given model of population size changes (such as sudden expansion), parameters of which (e.g., time and amplitude of expansion) are fitted to the observed distributions of nucleotide differences among pairwise comparisons of all DNA sequences in the sample. Our theory indicates that for any time-dependent population size, N(tau) (in which time tau is counted backward from present), a time-dependent coalescence process yields the distribution, p(tau), of the time of coalescence between two DNA sequences randomly drawn from the population. Prediction of p(tau) and N(tau) requires the use of a reverse Laplace transform known to be unstable. Nevertheless, simulated data obtained from three models of monotone population change (stepwise, exponential, and logistic) indicate that the pattern of a past population size change leaves its signature on the pattern of DNA polymorphism. Application of the theory to the published mtDNA sequences indicates that the current mtDNA sequence variation is not inconsistent with a logistic growth of the human population.

Asynchrony in the inter-annual recruitment of lake whitefish Coregonus clupeaformis in the Great Lakes region

USGS Publications Warehouse

Zischke, Mitchell T.; Bunnell, David B.; Troy, Cary D.; Berglund, Eric K.; Caroffino, David C.; Ebener, Mark P.; He, Ji X.; Sitar, Shawn P.; Hook, Tomas O.

2017-01-01

Spatially separated fish populations may display synchrony in annual recruitment if the factors that drive recruitment success, particularly abiotic factors such as temperature, are synchronised across broad spatial scales. We examined inter-annual variation in recruitment among lake whitefish (Coregonus clupeaformis) populations in lakes Huron, Michigan and Superior using fishery-dependent and -independent data from 1971 to 2014. Relative year-class strength (RYCS) was calculated from catch-curve residuals for each year class across multiple sampling years. Pairwise comparison of RYCS among datasets revealed no significant associations either within or between lakes, suggesting that recruitment of lake whitefish is spatially asynchronous. There was no consistent correlation between pairwise agreement and the distance between datasets, and models to estimate the spatial scale of recruitment synchrony did not fit well to these data. This suggests that inter-annual recruitment variation of lake whitefish is asynchronous across broad spatial scales in the Great Lakes. While our method primarily evaluated year-to-year recruitment variation, it is plausible that recruitment of lake whitefish varies at coarser temporal scales (e.g. decadal). Nonetheless, our findings differ from research on some other Coregonus species and suggest that local biotic or density-dependent factors may contribute strongly to lake whitefish recruitment rather than inter-annual variability in broad-scale abiotic factors.

Multiple Quantum Coherences (MQ) NMR and Entanglement Dynamics in the Mixed-Three-Spin XXX Heisenberg Model with Single-Ion Anisotropy

NASA Astrophysics Data System (ADS)

Hamid, Arian Zad

2016-12-01

We analytically investigate Multiple Quantum (MQ) NMR dynamics in a mixed-three-spin (1/2,1,1/2) system with XXX Heisenberg model at the front of an external homogeneous magnetic field B. A single-ion anisotropy property ζ is considered for the spin-1. The intensities dependence of MQ NMR coherences on their orders (zeroth and second orders) for two pairs of spins (1,1/2) and (1/2,1/2) of the favorite tripartite system are obtained. It is also investigated dynamics of the pairwise quantum entanglement for the bipartite (sub)systems (1,1/2) and (1/2,1/2) permanently coupled by, respectively, coupling constants J}1 and J}2, by means of concurrence and fidelity. Then, some straightforward comparisons are done between these quantities and the intensities of MQ NMR coherences and ultimately some interesting results are reported. We also show that the time evolution of MQ coherences based on the reduced density matrix of the pair spins (1,1/2) is closely connected with the dynamics of the pairwise entanglement. Finally, we prove that one can introduce MQ coherence of the zeroth order corresponds to the pair spins (1,1/2) as an entanglement witness at some special time intervals.

Interspecific analysis of covariance structure in the masticatory apparatus of galagos.

PubMed

Vinyard, Christopher J

2007-01-01

The primate masticatory apparatus (MA) is a functionally integrated set of features, each of which performs important functions in biting, ingestive, and chewing behaviors. A comparison of morphological covariance structure among species for these MA features will help us to further understand the evolutionary history of this region. In this exploratory analysis, the covariance structure of the MA is compared across seven galago species to investigate 1) whether there are differences in covariance structure in this region, and 2) if so, how has this covariation changed with respect to size, MA form, diet, and/or phylogeny? Ten measurements of the MA functionally related to bite force production and load resistance were obtained from 218 adults of seven galago species. Correlation matrices were generated for these 10 dimensions and compared among species via matrix correlations and Mantel tests. Subsequently, pairwise covariance disparity in the MA was estimated as a measure of difference in covariance structure between species. Covariance disparity estimates were correlated with pairwise distances related to differences in body size, MA size and shape, genetic distance (based on cytochrome-b sequences) and percentage of dietary foods to determine whether one or more of these factors is linked to differences in covariance structure. Galagos differ in MA covariance structure. Body size appears to be a major factor correlated with differences in covariance structure among galagos. The largest galago species, Otolemur crassicaudatus, exhibits large differences in body mass and covariance structure relative to other galagos, and thus plays a primary role in creating this association. MA size and shape do not correlate with covariance structure when body mass is held constant. Diet also shows no association. Genetic distance is significantly negatively correlated with covariance disparity when body mass is held constant, but this correlation appears to be a function of the small body size and large genetic distance for Galagoides demidoff. These exploratory results indicate that changing body size may have been a key factor in the evolution of the galago MA.

Abnormal functional network connectivity among resting-state networks in children with frontal lobe epilepsy.

PubMed

Widjaja, E; Zamyadi, M; Raybaud, C; Snead, O C; Smith, M L

2013-12-01

Epilepsy is considered a disorder of neural networks. The aims of this study were to assess functional connectivity within resting-state networks and functional network connectivity across resting-state networks by use of resting-state fMRI in children with frontal lobe epilepsy and to relate changes in resting-state networks with neuropsychological function. Fifteen patients with frontal lobe epilepsy and normal MR imaging and 14 healthy control subjects were recruited. Spatial independent component analysis was used to identify the resting-state networks, including frontal, attention, default mode network, sensorimotor, visual, and auditory networks. The Z-maps of resting-state networks were compared between patients and control subjects. The relation between abnormal connectivity and neuropsychological function was assessed. Correlations from all pair-wise combinations of independent components were performed for each group and compared between groups. The frontal network was the only network that showed reduced connectivity in patients relative to control subjects. The remaining 5 networks demonstrated both reduced and increased functional connectivity within resting-state networks in patients. There was a weak association between connectivity in frontal network and executive function (P = .029) and a significant association between sensorimotor network and fine motor function (P = .004). Control subjects had 79 pair-wise independent components that showed significant temporal coherence across all resting-state networks except for default mode network-auditory network. Patients had 66 pairs of independent components that showed significant temporal coherence across all resting-state networks. Group comparison showed reduced functional network connectivity between default mode network-attention, frontal-sensorimotor, and frontal-visual networks and increased functional network connectivity between frontal-attention, default mode network-sensorimotor, and frontal-visual networks in patients relative to control subjects. We found abnormal functional connectivity within and across resting-state networks in children with frontal lobe epilepsy. Impairment in functional connectivity was associated with impaired neuropsychological function.

Systematic review with meta-analysis: Comparative efficacy of biologics for induction and maintenance of mucosal healing in Crohn’s disease and ulcerative colitis controlled trials

PubMed Central

Cholapranee, Aurada; Hazlewood, Glen S; Kaplan, Gilaad G.; Peyrin-Biroulet, Laurent; Ananthakrishnan, Ashwin N

2017-01-01

Background Mucosal healing is an important therapeutic endpoint in the management of Crohn’s disease (CD) and ulcerative colitis (UC). Limited data exists regarding the comparative efficacy of various therapies in achieving this outcome. Methods We performed a systematic review and meta-analysis of randomized controlled trials (RCT) examining mucosal healing as an endpoint of immunosuppressives, anti-tumor necrosis factor α (anti-TNF) or anti-integrin monoclonal antibody therapy for moderate-to-severe CD or UC. Pooled effect sizes for induction and maintenance of mucosal healing were calculated and pair-wise treatment comparisons evaluated using a Bayesian network meta-analysis. Results A total of 12 RCTs were included in the meta-analysis (CD – 2 induction, 4 maintenance; UC – 8 induction, 5 maintenance). Duration of follow-up was 6–12 weeks for induction and 32–54 weeks for maintenance trials. In CD, anti-TNFs were more effective than placebo for maintaining mucosal healing (28% vs. 1%, Odds ratio (OR) 19.71, 95% confidence interval (CI) 3.51 – 110.84). In UC, anti-TNFs and anti-integrins were more effective than placebo for inducing (45% vs. 30%) and maintaining mucosal healing (33% vs. 18%). In network analysis, adalimumab therapy was inferior to infliximab (OR 0.45, 95% credible interval (CrI) 0.25 – 0.82) and combination infliximab-azathioprine (OR 0.32, 95% CrI 0.12 – 0.84) for inducing mucosal healing in UC. There was no statistically significant pairwise difference between vedolizumab and anti-TNF agents in UC. Conclusion Anti-TNF and anti-integrin biologic agents are effective in inducing mucosal healing in UC with adalimumab being inferior to infliximab or combination therapy. Infliximab and adalimumab were similar in CD. PMID:28326566

Comparisons of diabetic retinopathy events associated with glucose-lowering drugs in patients with type 2 diabetes mellitus: A network meta-analysis.

PubMed

Tang, Huilin; Li, Guangyao; Zhao, Ying; Wang, Fei; Gower, Emily W; Shi, Luwen; Wang, Tiansheng

2018-05-01

To assess the comparative effects of glucose-lowering drugs (GLDs) on the risk of diabetic retinopathy (DR) in patients with type 2 diabetes mellitus (T2DM). We systematically searched Cochrane Central Register of Controlled Trials, PUBMED and EMBASE from inception to January 17, 2017 to identify randomized controlled trials (RCTs) that reported DR events among T2DM patients receiving any GLD. Random-effects pairwise and network meta-analyses were performed to calculate odds ratios (ORs) with 95% confidence intervals (CIs). A total of 37 independent RCTs with 1806 DR events among 100 928 patients with T2DM were included. The mean duration of diabetes was 8.7 years and mean baseline HbA1c was 8.2% (SD, 0.5%). Our network meta-analysis found that DPP-4i (OR, 1.20; 95% CI, 0.87-1.65), GLP-1RA (OR, 1.19; 95% CI, 0.94-1.52) and SGLT2 inhibitors (OR, 0.79; 95% CI, 0.49-1.28) were not associated with a higher risk of DR than placebo; however, a significantly increased risk of DR was associated with DPP-4i in the pairwise meta-analysis (OR, 1.27; 95% CI, 1.05-1.53). Sulfonylureas, on the other hand, were associated with a significantly increased risk of DR compared to placebo (OR, 1.67; 95% CI, 1.01-2.76). Current evidence indicates that the association between DPP-4i, GLP-1RA or SGLT2 inhibitors and risk of DR remains uncertain in patients with T2DM. Some evidence suggests that sulfonylureas may be associated with increased risk of DR. However, given that DR events were not systematically assessed, these effects should be explored further in large-scale, well-designed studies. © 2018 John Wiley & Sons Ltd.

Adulthood depression, anxiety, and trauma symptoms: a comparison of women with nonabusive, abusive, and absent father figures in childhood.

PubMed

Downs, William R; Rindels, Barb

2004-12-01

We collected data from 447 women (aged 18 or higher) from seven domestic violence programs and five substance use disorder treatment programs in a midwestern state. Women who reported a nonabusive natural/adoptive father or stepfather (N=185), abusive natural/adoptive father or stepfather (N=200), or absent father figure (N=40) were compared on a series of mental health measures with multivariate analysis of variance and pairwise post hoc comparisons using the Bonferroni test. Women with absent father figures were found to have significantly lower mean scores on the Beck Anxiety Inventory, Beck Depression Inventory, and Trauma Symptom Checklist-40 (TSC-40) than women with abusive fathers. There were no significant differences between women with absent father figures and women with nonabusive father figures on the Beck Anxiety Inventory, Beck Depression Inventory, and TSC-40. Implications for research, practice, and policy are discussed.

Geographic Profiling to Assess the Risk of Rare Plant Poaching in Natural Areas

NASA Astrophysics Data System (ADS)

Young, John A.; van Manen, Frank T.; Thatcher, Cindy A.

2011-09-01

We demonstrate the use of an expert-assisted spatial model to examine geographic factors influencing the poaching risk of a rare plant (American ginseng, Panax quinquefolius L.) in Shenandoah National Park, Virginia, USA. Following principles of the analytic hierarchy process (AHP), we identified a hierarchy of 11 geographic factors deemed important to poaching risk and requested law enforcement personnel of the National Park Service to rank those factors in a series of pair-wise comparisons. We used those comparisons to determine statistical weightings of each factor and combined them into a spatial model predicting poaching risk. We tested the model using 69 locations of previous poaching incidents recorded by law enforcement personnel. These locations occurred more frequently in areas predicted by the model to have a higher risk of poaching than random locations. The results of our study can be used to evaluate resource protection strategies and to target law enforcement activities.

Evaluation of motion artifact metrics for coronary CT angiography.

PubMed

Ma, Hongfeng; Gros, Eric; Szabo, Aniko; Baginski, Scott G; Laste, Zachary R; Kulkarni, Naveen M; Okerlund, Darin; Schmidt, Taly G

2018-02-01

This study quantified the performance of coronary artery motion artifact metrics relative to human observer ratings. Motion artifact metrics have been used as part of motion correction and best-phase selection algorithms for Coronary Computed Tomography Angiography (CCTA). However, the lack of ground truth makes it difficult to validate how well the metrics quantify the level of motion artifact. This study investigated five motion artifact metrics, including two novel metrics, using a dynamic phantom, clinical CCTA images, and an observer study that provided ground-truth motion artifact scores from a series of pairwise comparisons. Five motion artifact metrics were calculated for the coronary artery regions on both phantom and clinical CCTA images: positivity, entropy, normalized circularity, Fold Overlap Ratio (FOR), and Low-Intensity Region Score (LIRS). CT images were acquired of a dynamic cardiac phantom that simulated cardiac motion and contained six iodine-filled vessels of varying diameter and with regions of soft plaque and calcifications. Scans were repeated with different gantry start angles. Images were reconstructed at five phases of the motion cycle. Clinical images were acquired from 14 CCTA exams with patient heart rates ranging from 52 to 82 bpm. The vessel and shading artifacts were manually segmented by three readers and combined to create ground-truth artifact regions. Motion artifact levels were also assessed by readers using a pairwise comparison method to establish a ground-truth reader score. The Kendall's Tau coefficients were calculated to evaluate the statistical agreement in ranking between the motion artifacts metrics and reader scores. Linear regression between the reader scores and the metrics was also performed. On phantom images, the Kendall's Tau coefficients of the five motion artifact metrics were 0.50 (normalized circularity), 0.35 (entropy), 0.82 (positivity), 0.77 (FOR), 0.77(LIRS), where higher Kendall's Tau signifies higher agreement. The FOR, LIRS, and transformed positivity (the fourth root of the positivity) were further evaluated in the study of clinical images. The Kendall's Tau coefficients of the selected metrics were 0.59 (FOR), 0.53 (LIRS), and 0.21 (Transformed positivity). In the study of clinical data, a Motion Artifact Score, defined as the product of FOR and LIRS metrics, further improved agreement with reader scores, with a Kendall's Tau coefficient of 0.65. The metrics of FOR, LIRS, and the product of the two metrics provided the highest agreement in motion artifact ranking when compared to the readers, and the highest linear correlation to the reader scores. The validated motion artifact metrics may be useful for developing and evaluating methods to reduce motion in Coronary Computed Tomography Angiography (CCTA) images. © 2017 American Association of Physicists in Medicine.

Effect of interacting second- and third-order stimulus-dependent correlations on population-coding asymmetries.

PubMed

Montangie, Lisandro; Montani, Fernando

2016-10-01

Spike correlations among neurons are widely encountered in the brain. Although models accounting for pairwise interactions have proved able to capture some of the most important features of population activity at the level of the retina, the evidence shows that pairwise neuronal correlation analysis does not resolve cooperative population dynamics by itself. By means of a series expansion for short time scales of the mutual information conveyed by a population of neurons, the information transmission can be broken down into firing rate and correlational components. In a proposed extension of this framework, we investigate the information components considering both second- and higher-order correlations. We show that the existence of a mixed stimulus-dependent correlation term defines a new scenario for the interplay between pairwise and higher-than-pairwise interactions in noise and signal correlations that would lead either to redundancy or synergy in the information-theoretic sense.

Shaped Ceria Nanocrystals Catalyze Efficient and Selective Para-Hydrogen-Enhanced Polarization.

PubMed

Zhao, Evan W; Zheng, Haibin; Zhou, Ronghui; Hagelin-Weaver, Helena E; Bowers, Clifford R

2015-11-23

Intense para-hydrogen-enhanced NMR signals are observed in the hydrogenation of propene and propyne over ceria nanocubes, nano-octahedra, and nanorods. The well-defined ceria shapes, synthesized by a hydrothermal method, expose different crystalline facets with various oxygen vacancy densities, which are known to play a role in hydrogenation and oxidation catalysis. While the catalytic activity of the hydrogenation of propene over ceria is strongly facet-dependent, the pairwise selectivity is low (2.4% at 375 °C), which is consistent with stepwise H atom transfer, and it is the same for all three nanocrystal shapes. Selective semi-hydrogenation of propyne over ceria nanocubes yields hyperpolarized propene with a similar pairwise selectivity of (2.7% at 300 °C), indicating product formation predominantly by a non-pairwise addition. Ceria is also shown to be an efficient pairwise replacement catalyst for propene. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pairwise Force Smoothed Particle Hydrodynamics model for multiphase flow: Surface tension and contact line dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tartakovsky, Alexandre M.; Panchenko, Alexander

2016-01-01

We present a novel formulation of the Pairwise Force Smoothed Particle Hydrodynamics Model (PF-SPH) and use it to simulate two- and three-phase flows in bounded domains. In the PF-SPH model, the Navier-Stokes equations are discretized with the Smoothed Particle Hydrodynamics (SPH) method and the Young-Laplace boundary condition at the fluid-fluid interface and the Young boundary condition at the fluid-fluid-solid interface are replaced with pairwise forces added into the Navier-Stokes equations. We derive a relationship between the parameters in the pairwise forces and the surface tension and static contact angle. Next, we demonstrate the accuracy of the model under static andmore » dynamic conditions. Finally, to demonstrate the capabilities and robustness of the model we use it to simulate flow of three fluids in a porous material.« less

Conducting indirect-treatment-comparison and network-meta-analysis studies: report of the ISPOR Task Force on Indirect Treatment Comparisons Good Research Practices: part 2.

PubMed

Hoaglin, David C; Hawkins, Neil; Jansen, Jeroen P; Scott, David A; Itzler, Robbin; Cappelleri, Joseph C; Boersma, Cornelis; Thompson, David; Larholt, Kay M; Diaz, Mireya; Barrett, Annabel

2011-06-01

Evidence-based health care decision making requires comparison of all relevant competing interventions. In the absence of randomized controlled trials involving a direct comparison of all treatments of interest, indirect treatment comparisons and network meta-analysis provide useful evidence for judiciously selecting the best treatment(s). Mixed treatment comparisons, a special case of network meta-analysis, combine direct evidence and indirect evidence for particular pairwise comparisons, thereby synthesizing a greater share of the available evidence than traditional meta-analysis. This report from the International Society for Pharmacoeconomics and Outcomes Research Indirect Treatment Comparisons Good Research Practices Task Force provides guidance on technical aspects of conducting network meta-analyses (our use of this term includes most methods that involve meta-analysis in the context of a network of evidence). We start with a discussion of strategies for developing networks of evidence. Next we briefly review assumptions of network meta-analysis. Then we focus on the statistical analysis of the data: objectives, models (fixed-effects and random-effects), frequentist versus Bayesian approaches, and model validation. A checklist highlights key components of network meta-analysis, and substantial examples illustrate indirect treatment comparisons (both frequentist and Bayesian approaches) and network meta-analysis. A further section discusses eight key areas for future research. Copyright © 2011 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

GOSAP: Gene Ontology-Based Semantic Alignment of Biological Pathways.

PubMed

Gamalielsson, Jonas; Olsson, Bjorn

2008-01-01

We present a new method for semantic comparison of biological pathways, aiming to discover evolutionary conservation of pathways between species. Our method uses all three sub-ontologies of Gene Ontology (GO) and a measure of semantic similarity to calculate match scores between gene products. These scores are used for finding local pairwise pathway alignments. This approach has the advantage of being applicable to all types of pathways where nodes are gene products, e.g., regulatory pathways, signalling pathways and metabolic enzyme-to-enzyme pathways. We demonstrate the usefulness of the method using regulatory and metabolic pathways from E. coli and S. cerevisiae as examples.

Multi-criteria analysis of potential recovery facilities in a reverse supply chain

NASA Astrophysics Data System (ADS)

Nukala, Satish; Gupta, Surendra M.

2005-11-01

Analytic Hierarchy Process (AHP) has been employed by researchers for solving multi-criteria analysis problems. However, AHP is often criticized for its unbalanced scale of judgments and failure to precisely handle the inherent uncertainty and vagueness in carrying out the pair-wise comparisons. With an objective to address these drawbacks, in this paper, we employ a fuzzy approach in selecting potential recovery facilities in the strategic planning of a reverse supply chain network that addresses the decision maker's level of confidence in the fuzzy assessments and his/her attitude towards risk. A numerical example is considered to illustrate the methodology.

Chronic hydrocarbon exposure of harlequin ducks in areas affected by the Selendang Ayu oil spill at Unalaska Island, Alaska

USGS Publications Warehouse

Flint, Paul L.; Schamber, J.L.; Trust, K.A.; Miles, A.K.; Henderson, J.D.; Wilson, B.W.

2012-01-01

We evaluated chronic exposure of harlequin ducks (Histrionicus histrionicus) to hydrocarbons associated with the 2004 M/V Selendang Ayu oil spill at Unalaska Island, Alaska. We measured levels of hepatic 7-ethoxyresorufin-O-deethylase activity (EROD) in liver biopsy samples as an indicator of hydrocarbon exposure in three oiled bays and one reference bay in 2005, 2006, and 2008. Median EROD activity in ducks from oiled bays was significantly higher than in the reference bay in seven of nine pairwise comparisons. These results indicated that harlequin ducks were exposed to lingering hydrocarbons more than three years after the spill.

Is central dogma a global property of cellular information flow?

PubMed Central

Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar

2012-01-01

The central dogma of molecular biology has come under scrutiny in recent years. Here, we reviewed high-throughput mRNA and protein expression data of Escherichia coli, Saccharomyces cerevisiae, and several mammalian cells. At both single cell and population scales, the statistical comparisons between the entire transcriptomes and proteomes show clear correlation structures. In contrast, the pair-wise correlations of single transcripts to proteins show nullity. These data suggest that the organizing structure guiding cellular processes is observed at omics-wide scale, and not at single molecule level. The central dogma, thus, globally emerges as an average integrated flow of cellular information. PMID:23189060

Is central dogma a global property of cellular information flow?

PubMed

Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar

2012-01-01

The central dogma of molecular biology has come under scrutiny in recent years. Here, we reviewed high-throughput mRNA and protein expression data of Escherichia coli, Saccharomyces cerevisiae, and several mammalian cells. At both single cell and population scales, the statistical comparisons between the entire transcriptomes and proteomes show clear correlation structures. In contrast, the pair-wise correlations of single transcripts to proteins show nullity. These data suggest that the organizing structure guiding cellular processes is observed at omics-wide scale, and not at single molecule level. The central dogma, thus, globally emerges as an average integrated flow of cellular information.

Efficient molecular dynamics simulations with many-body potentials on graphics processing units

NASA Astrophysics Data System (ADS)

Fan, Zheyong; Chen, Wei; Vierimaa, Ville; Harju, Ari

2017-09-01

Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently (Fan et al., 2015). In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potential, the double precision performance of GPUMD using a Tesla K40 card is equivalent to that of the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics code running with about 100 CPU cores (Intel Xeon CPU X5670 @ 2.93 GHz).

Strategies for informed sample size reduction in adaptive controlled clinical trials

NASA Astrophysics Data System (ADS)

Arandjelović, Ognjen

2017-12-01

Clinical trial adaptation refers to any adjustment of the trial protocol after the onset of the trial. The main goal is to make the process of introducing new medical interventions to patients more efficient. The principal challenge, which is an outstanding research problem, is to be found in the question of how adaptation should be performed so as to minimize the chance of distorting the outcome of the trial. In this paper, we propose a novel method for achieving this. Unlike most of the previously published work, our approach focuses on trial adaptation by sample size adjustment, i.e. by reducing the number of trial participants in a statistically informed manner. Our key idea is to select the sample subset for removal in a manner which minimizes the associated loss of information. We formalize this notion and describe three algorithms which approach the problem in different ways, respectively, using (i) repeated random draws, (ii) a genetic algorithm, and (iii) what we term pair-wise sample compatibilities. Experiments on simulated data demonstrate the effectiveness of all three approaches, with a consistently superior performance exhibited by the pair-wise sample compatibilities-based method.

Multiview marker-free registration of forest terrestrial laser scanner data with embedded confidence metrics

DOE PAGES

Kelbe, David; Oak Ridge National Lab.; van Aardt, Jan; ...

2016-10-18

Terrestrial laser scanning has demonstrated increasing potential for rapid comprehensive measurement of forest structure, especially when multiple scans are spatially registered in order to reduce the limitations of occlusion. Although marker-based registration techniques (based on retro-reflective spherical targets) are commonly used in practice, a blind marker-free approach is preferable, insofar as it supports rapid operational data acquisition. To support these efforts, we extend the pairwise registration approach of our earlier work, and develop a graph-theoretical framework to perform blind marker-free global registration of multiple point cloud data sets. Pairwise pose estimates are weighted based on their estimated error, in ordermore » to overcome pose conflict while exploiting redundant information and improving precision. The proposed approach was tested for eight diverse New England forest sites, with 25 scans collected at each site. Quantitative assessment was provided via a novel embedded confidence metric, with a mean estimated root-mean-square error of 7.2 cm and 89% of scans connected to the reference node. Lastly, this paper assesses the validity of the embedded multiview registration confidence metric and evaluates the performance of the proposed registration algorithm.« less

NIST-NRC Comparison of Total Immersion Liquid-in-Glass Thermometers

NASA Astrophysics Data System (ADS)

Hill, K. D.; Gee, D. J.; Cross, C. D.; Strouse, G. F.

2009-02-01

The use of liquid-in-glass (LIG) thermometers is described in many documentary standards in the fields of environmental testing, material testing, and material transfer. Many national metrology institutes, including the National Institute of Standards and Technology (NIST) and the National Research Council of Canada (NRC), list calibration services for these thermometers among the Calibration Measurement Capabilities of Appendix C of the BIPM Key Comparison Database. NIST and NRC arranged a bilateral comparison of a set of total-immersion ASTM-type LIG thermometers to validate their uncertainty claims. Two each of ASTM thermometer types 62C through 69C were calibrated at NIST and at NRC at four temperatures distributed over the range appropriate to each thermometer, in addition to the ice point. Collectively, the thermometers span a temperature range of - 38 °C to 305 °C. In total, 160 measurements (80 pairs) comprise the comparison data set. Pair-wise differences ( T NIST- T NRC) were formed for each thermometer at each temperature. For 8 of the 80 pairs (10 %), the differences exceed the k = 2 combined uncertainties. These results support the claimed capabilities of NIST and NRC for the calibration of LIG thermometers.

Ultrafast Comparison of Personal Genomes via Precomputed Genome Fingerprints

PubMed Central

Glusman, Gustavo; Mauldin, Denise E.; Hood, Leroy E.; Robinson, Max

2017-01-01

We present an ultrafast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into “genome fingerprints” via locality sensitive hashing. The resulting genome fingerprints can be meaningfully compared even when the input data were obtained using different sequencing technologies, processed using different pipelines, represented in different data formats and relative to different reference versions. Furthermore, genome fingerprints are robust to up to 30% missing data. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. For example, we could compute all-against-all pairwise comparisons among the 2504 genomes in the 1000 Genomes data set in 67 s at high quality (21 μs per comparison, on a single processor), and achieved a lower quality approximation in just 11 s. Efficient computation enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative sequenced genomes in a set, population reconstruction, and many others. The original genome representation cannot be reconstructed from its fingerprint, effectively decoupling genome comparison from genome interpretation; the method thus has significant implications for privacy-preserving genome analytics. PMID:29018478

Baseline neurocognitive testing in sports-related concussions: the importance of a prior night's sleep.

PubMed

McClure, D Jake; Zuckerman, Scott L; Kutscher, Scott J; Gregory, Andrew J; Solomon, Gary S

2014-02-01

The management of sports-related concussions (SRCs) utilizes serial neurocognitive assessments and self-reported symptom inventories to assess recovery and safety for return to play (RTP). Because postconcussive RTP goals include symptom resolution and a return to neurocognitive baseline levels, clinical decisions rest in part on understanding modifiers of this baseline. Several studies have reported age and sex to influence baseline neurocognitive performance, but few have assessed the potential effect of sleep. We chose to investigate the effect of reported sleep duration on baseline Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) performance and the number of patient-reported symptoms. We hypothesized that athletes receiving less sleep before baseline testing would perform worse on neurocognitive metrics and report more symptoms. Cross-sectional study; Level of evidence, 3. We retrospectively reviewed 3686 nonconcussed athletes (2371 male, 1315 female; 3305 high school, 381 college) with baseline symptom and ImPACT neurocognitive scores. Patients were stratified into 3 groups based on self-reported sleep duration the night before testing: (1) short, <7 hours; (2) intermediate, 7-9 hours; and (3) long, ≥9 hours. A multivariate analysis of covariance (MANCOVA) with an α level of .05 was used to assess the influence of sleep duration on baseline ImPACT performance. A univariate ANCOVA was performed to investigate the influence of sleep on total self-reported symptoms. When controlling for age and sex as covariates, the MANCOVA revealed significant group differences on ImPACT reaction time, verbal memory, and visual memory scores but not visual-motor (processing) speed scores. An ANCOVA also revealed significant group differences in total reported symptoms. For baseline symptoms and ImPACT scores, subsequent pairwise comparisons revealed these associations to be most significant when comparing the short and intermediate sleep groups. Our results indicate that athletes sleeping fewer than 7 hours before baseline testing perform worse on 3 of 4 ImPACT scores and report more symptoms. Because SRC management and RTP decisions hinge on the comparison with a reliable baseline evaluation, clinicians should consider sleep duration before baseline neurocognitive testing as a potential factor in the assessment of athletes' recovery.

Selection and study performance: comparing three admission processes within one medical school.

PubMed

Schripsema, Nienke R; van Trigt, Anke M; Borleffs, Jan C C; Cohen-Schotanus, Janke

2014-12-01

This study was conducted to: (i) analyse whether students admitted to one medical school based on top pre-university grades, a voluntary multifaceted selection process, or lottery, respectively, differed in study performance; (ii) examine whether students who were accepted in the multifaceted selection process outperformed their rejected peers, and (iii) analyse whether participation in the multifaceted selection procedure was related to performance. We examined knowledge test and professionalism scores, study progress and dropout in three cohorts of medical students admitted to the University of Groningen, the Netherlands in 2009, 2010 and 2011 (n = 1055). We divided the lottery-admitted group into, respectively, students who had not participated and students who had been rejected in the multifaceted selection process. We used ancova modelling, logistic regression and Bonferroni post hoc multiple-comparison tests and controlled for gender and cohort. The top pre-university grade group achieved higher knowledge test scores and more Year 1 course credits than all other groups (p < 0.05). This group received the highest possible professionalism score more often than the lottery-admitted group that had not participated in the multifaceted selection process (p < 0.05). The group of students accepted in the multifaceted selection process obtained higher written test scores than the lottery-admitted group that had not participated (p < 0.05) and achieved the highest possible professionalism score more often than both lottery-admitted groups. The lottery-admitted group that had not participated in the multifaceted selection process earned fewer Year 1 and 2 course credits than all other groups (p < 0.05). Dropout rates differed among the groups (p < 0.05), but correction for multiple comparisons rendered all pairwise differences non-significant. A top pre-university grade point average was the best predictor of performance. For so-called non-academic performance, the multifaceted selection process was efficient in identifying applicants with suitable skills. Participation in the multifaceted selection procedure seems to be predictive of higher performance. Further research is needed to assess whether our results are generalisable to other medical schools. © 2014 John Wiley & Sons Ltd.

The Yo-Yo intermittent recovery test level 1 is reliable in young high-level soccer players.

PubMed

Deprez, D; Fransen, J; Lenoir, M; Philippaerts, Rm; Vaeyens, R

2015-03-01

The aim of the study was to investigate test reliability of the Yo-Yo intermittent recovery test level 1 (YYIR1) in 36 high-level youth soccer players, aged between 13 and 18 years. Players were divided into three age groups (U15, U17 and U19) and completed three YYIR1 in three consecutive weeks. Pairwise comparisons were used to investigate test reliability (for distances and heart rate responses) using technical error (TE), coefficient of variation (CV), intra-class correlation (ICC) and limits of agreement (LOA) with Bland-Altman plots. The mean YYIR1 distances for the U15, U17 and U19 groups were 2024 ± 470 m, 2404 ± 347 m and 2547 ± 337 m, respectively. The results revealed that the TEs varied between 74 and 172 m, CVs between 3.0 and 7.5%, and ICCs between 0.87 and 0.95 across all age groups for the YYIR1 distance. For heart rate responses, the TEs varied between 1 and 6 bpm, CVs between 0.7 and 4.8%, and ICCs between 0.73 and 0.97. The small ratio LOA revealed that any two YYIR1 performances in one week will not differ by more than 9 to 28% due to measurement error. In summary, the YYIR1 performance and the physiological responses have proven to be highly reliable in a sample of Belgian high-level youth soccer players, aged between 13 and 18 years. The demonstrated high level of intermittent endurance capacity in all age groups may be used for comparison of other prospective young soccer players.

Performance profile of NCAA Division I men's basketball games and training sessions.

PubMed

Conte, D; Tessitore, A; Smiley, K; Thomas, C; Favero, T G

2016-06-01

This study aimed to analyse live and stoppage time phases, their ratio, and action played on half and full court in college basketball games. Differences were assessed for the entire games and between halves. Moreover, differences of the live/stoppage time ratio were analysed between games and game-based conditioning drills. Ten games as well as fifteen defensive, fourteen offensive and six scrimmage-type drills of the same division I men's college team (13 players) were analysed using time-motion analysis technique. Live and stoppage time were classified in five classes of duration: 1-20, 21-40, 41-60, 61-80, >80 seconds. Half court actions started and finished in the same half court. Full court actions were classified as transfer (TR) phases when at least 3 teammates crossed the mid-court line. TR phases were then classified in 5 classes of frequency: 1TR, 2TR, 3TR, 4TR, and >4TR. The results revealed no statistically significant differences between games or between halves for the considered parameters. The only significant difference was observed for live/stoppage time ratio between halves (p<0.001). Furthermore, a significant difference of the live/stoppage ratio was found between games and game-based drills (p<0.01). Post-hoc analysis demonstrated significant differences of scrimmage-type drills in comparison to games, and defensive and offensive drills (p<0.05), whereas no differences emerged for the other pairwise comparisons. The absence of differences between games in the analysed parameters might be important to characterize the model of performance in division I men's college games. Furthermore, these results encourage coaches to use game-based conditioning drills to replicate the LT/ST ratio documented during games.

The effect of ketoconazole on whole blood and skin ciclosporin concentrations in dogs.

PubMed

Gray, Laura L; Hillier, Andrew; Cole, Lynette K; Rajala-Schultz, Päivi J

2013-02-01

Ciclosporin (CSA) is approved for the treatment of canine atopic dermatitis. Ciclosporin is metabolized by liver cytochrome P450 enzymes, a process inhibited by ketoconazole (KTZ). The aims of this study were to determine skin and blood CSA concentrations when CSA was administered alone at 5.0 (Treatment 1) or 2.5 mg/kg (Treatment 2) and when CSA was administered at 2.5 mg/kg concurrently with KTZ at 5 (Treatment 3) or 2.5 mg/kg (Treatment 4). We hypothesized that skin and blood CSA concentrations in Treatment 1 would not differ from those obtained with T3 or T4. In a randomized cross-over study, six healthy research dogs received each of the treatments (Treatment 1, 2, 3 and 4) once daily for 7 days. After the first, fourth and seventh dose for each treatment, a peak and trough skin punch biopsy sample and whole blood sample were collected and analysed with high-performance liquid chromatography-tandem mass spectrometry. Data were analysed using a repeated measures approach with PROC MIXED in SAS. Pairwise comparisons were performed with least squares means and Tukey-Kramer adjustment for multiple comparisons. Mean blood CSA concentrations in Treatment 1 were not different from those in Treatment 2 or 4, but were less than in Treatment 3. Mean skin CSA concentrations in Treatment 1 were greater than in Treatment 2, not different from those in Treatment 4, and less than those in Treatment 3. Administration of CSA and KTZ concurrently at 2.5 mg/kg each may be as effective as CSA alone at 5.0 mg/kg for treatment of canine atopic dermatitis. © 2013 The Authors. Veterinary Dermatology © 2013 ESVD and ACVD.

Comparison of Minimalist Footwear Strategies for Simulating Barefoot Running: A Randomized Crossover Study

PubMed Central

Hollander, Karsten; Argubi-Wollesen, Andreas; Reer, Rüdiger; Zech, Astrid

2015-01-01

Possible benefits of barefoot running have been widely discussed in recent years. Uncertainty exists about which footwear strategy adequately simulates barefoot running kinematics. The objective of this study was to investigate the effects of athletic footwear with different minimalist strategies on running kinematics. Thirty-five distance runners (22 males, 13 females, 27.9 ± 6.2 years, 179.2 ± 8.4 cm, 73.4 ± 12.1 kg, 24.9 ± 10.9 km.week-1) performed a treadmill protocol at three running velocities (2.22, 2.78 and 3.33 m.s-1) using four footwear conditions: barefoot, uncushioned minimalist shoes, cushioned minimalist shoes, and standard running shoes. 3D kinematic analysis was performed to determine ankle and knee angles at initial foot-ground contact, rate of rear-foot strikes, stride frequency and step length. Ankle angle at foot strike, step length and stride frequency were significantly influenced by footwear conditions (p<0.001) at all running velocities. Posthoc pairwise comparisons showed significant differences (p<0.001) between running barefoot and all shod situations as well as between the uncushioned minimalistic shoe and both cushioned shoe conditions. The rate of rear-foot strikes was lowest during barefoot running (58.6% at 3.33 m.s-1), followed by running with uncushioned minimalist shoes (62.9%), cushioned minimalist (88.6%) and standard shoes (94.3%). Aside from showing the influence of shod conditions on running kinematics, this study helps to elucidate differences between footwear marked as minimalist shoes and their ability to mimic barefoot running adequately. These findings have implications on the use of footwear applied in future research debating the topic of barefoot or minimalist shoe running. PMID:26011042

Comparison of minimalist footwear strategies for simulating barefoot running: a randomized crossover study.

PubMed

Hollander, Karsten; Argubi-Wollesen, Andreas; Reer, Rüdiger; Zech, Astrid

2015-01-01

Possible benefits of barefoot running have been widely discussed in recent years. Uncertainty exists about which footwear strategy adequately simulates barefoot running kinematics. The objective of this study was to investigate the effects of athletic footwear with different minimalist strategies on running kinematics. Thirty-five distance runners (22 males, 13 females, 27.9 ± 6.2 years, 179.2 ± 8.4 cm, 73.4 ± 12.1 kg, 24.9 ± 10.9 km x week(-1)) performed a treadmill protocol at three running velocities (2.22, 2.78 and 3.33 m x s(-1)) using four footwear conditions: barefoot, uncushioned minimalist shoes, cushioned minimalist shoes, and standard running shoes. 3D kinematic analysis was performed to determine ankle and knee angles at initial foot-ground contact, rate of rear-foot strikes, stride frequency and step length. Ankle angle at foot strike, step length and stride frequency were significantly influenced by footwear conditions (p<0.001) at all running velocities. Posthoc pairwise comparisons showed significant differences (p<0.001) between running barefoot and all shod situations as well as between the uncushioned minimalistic shoe and both cushioned shoe conditions. The rate of rear-foot strikes was lowest during barefoot running (58.6% at 3.33 m x s(-1)), followed by running with uncushioned minimalist shoes (62.9%), cushioned minimalist (88.6%) and standard shoes (94.3%). Aside from showing the influence of shod conditions on running kinematics, this study helps to elucidate differences between footwear marked as minimalist shoes and their ability to mimic barefoot running adequately. These findings have implications on the use of footwear applied in future research debating the topic of barefoot or minimalist shoe running.

Task-Driven Tube Current Modulation and Regularization Design in Computed Tomography with Penalized-Likelihood Reconstruction.

PubMed

Gang, G J; Siewerdsen, J H; Stayman, J W

2016-02-01

This work applies task-driven optimization to design CT tube current modulation and directional regularization in penalized-likelihood (PL) reconstruction. The relative performance of modulation schemes commonly adopted for filtered-backprojection (FBP) reconstruction were also evaluated for PL in comparison. We adopt a task-driven imaging framework that utilizes a patient-specific anatomical model and information of the imaging task to optimize imaging performance in terms of detectability index ( d' ). This framework leverages a theoretical model based on implicit function theorem and Fourier approximations to predict local spatial resolution and noise characteristics of PL reconstruction as a function of the imaging parameters to be optimized. Tube current modulation was parameterized as a linear combination of Gaussian basis functions, and regularization was based on the design of (directional) pairwise penalty weights for the 8 in-plane neighboring voxels. Detectability was optimized using a covariance matrix adaptation evolutionary strategy algorithm. Task-driven designs were compared to conventional tube current modulation strategies for a Gaussian detection task in an abdomen phantom. The task-driven design yielded the best performance, improving d' by ~20% over an unmodulated acquisition. Contrary to FBP, PL reconstruction using automatic exposure control and modulation based on minimum variance (in FBP) performed worse than the unmodulated case, decreasing d' by 16% and 9%, respectively. This work shows that conventional tube current modulation schemes suitable for FBP can be suboptimal for PL reconstruction. Thus, the proposed task-driven optimization provides additional opportunities for improved imaging performance and dose reduction beyond that achievable with conventional acquisition and reconstruction.

Hormonal responses to a long duration exploration in a cave of 700 m depth.

PubMed

Stenner, Elisabetta; Gianoli, Elisabetta; Piccinini, Clara; Biasioli, Bruno; Bussani, Andrea; Delbello, Giorgio

2007-05-01

We studied the hypothalamus-pituitary adrenocortical, hypothalamus-pituitary and hypothalamus-pituitary thyroid system responses to a long duration activity (about 20 h) practiced in a demanding environment, characterized by darkness, low temperature and high humidity, namely alpine potholing. We performed four blood drawings in five elite potholers: (1) the morning before the performance, (2) at the bottom of the cave (-700 m), (3) at the end of the ascent, and (4) after 24 h of recovery. Two blood drawings as controls were performed on the same potholers, at the same resting time and with the same experimental procedures as the previous ones. Friedman two-way ANOVA test evidenced significant changes through the different time intervals for detrended (i.e., test values minus control values) growth hormone (GH) (P = 0.003), detrended cortisol (P = 0.004) and FT4 (P = 0.002), while this was not true for TSH and FT3. Successively pairwise comparisons were done both through the different time intervals and between test and control values. The rise of GH values during the performance underlines the great intensity and long duration characteristic of potholing as well as the possibility that the climbing sit harness can cause problems due to vascular hypo-perfusion. Cortisol data, peaking before entering the cave, suggest that there was a marked anticipatory stress reaction followed by less stressing phase during the performance. Finally, the rise of FT4 is likely due to the typical increase of free fatty acids that usually occurs during endurance exercise.

The optimal hormonal replacement modality selection for multiple organ procurement from brain-dead organ donors

PubMed Central

Mi, Zhibao; Novitzky, Dimitri; Collins, Joseph F; Cooper, David KC

2015-01-01

The management of brain-dead organ donors is complex. The use of inotropic agents and replacement of depleted hormones (hormonal replacement therapy) is crucial for successful multiple organ procurement, yet the optimal hormonal replacement has not been identified, and the statistical adjustment to determine the best selection is not trivial. Traditional pair-wise comparisons between every pair of treatments, and multiple comparisons to all (MCA), are statistically conservative. Hsu’s multiple comparisons with the best (MCB) – adapted from the Dunnett’s multiple comparisons with control (MCC) – has been used for selecting the best treatment based on continuous variables. We selected the best hormonal replacement modality for successful multiple organ procurement using a two-step approach. First, we estimated the predicted margins by constructing generalized linear models (GLM) or generalized linear mixed models (GLMM), and then we applied the multiple comparison methods to identify the best hormonal replacement modality given that the testing of hormonal replacement modalities is independent. Based on 10-year data from the United Network for Organ Sharing (UNOS), among 16 hormonal replacement modalities, and using the 95% simultaneous confidence intervals, we found that the combination of thyroid hormone, a corticosteroid, antidiuretic hormone, and insulin was the best modality for multiple organ procurement for transplantation. PMID:25565890

Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs

PubMed Central

Lin, Chun-Yuan; Wang, Chung-Hung; Hung, Che-Lun; Lin, Yu-Shiang

2015-01-01

Compound comparison is an important task for the computational chemistry. By the comparison results, potential inhibitors can be found and then used for the pharmacy experiments. The time complexity of a pairwise compound comparison is O(n 2), where n is the maximal length of compounds. In general, the length of compounds is tens to hundreds, and the computation time is small. However, more and more compounds have been synthesized and extracted now, even more than tens of millions. Therefore, it still will be time-consuming when comparing with a large amount of compounds (seen as a multiple compound comparison problem, abbreviated to MCC). The intrinsic time complexity of MCC problem is O(k 2 n 2) with k compounds of maximal length n. In this paper, we propose a GPU-based algorithm for MCC problem, called CUDA-MCC, on single- and multi-GPUs. Four LINGO-based load-balancing strategies are considered in CUDA-MCC in order to accelerate the computation speed among thread blocks on GPUs. CUDA-MCC was implemented by C+OpenMP+CUDA. CUDA-MCC achieved 45 times and 391 times faster than its CPU version on a single NVIDIA Tesla K20m GPU card and a dual-NVIDIA Tesla K20m GPU card, respectively, under the experimental results. PMID:26491652

Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs.

PubMed

Lin, Chun-Yuan; Wang, Chung-Hung; Hung, Che-Lun; Lin, Yu-Shiang

2015-01-01

Compound comparison is an important task for the computational chemistry. By the comparison results, potential inhibitors can be found and then used for the pharmacy experiments. The time complexity of a pairwise compound comparison is O(n (2)), where n is the maximal length of compounds. In general, the length of compounds is tens to hundreds, and the computation time is small. However, more and more compounds have been synthesized and extracted now, even more than tens of millions. Therefore, it still will be time-consuming when comparing with a large amount of compounds (seen as a multiple compound comparison problem, abbreviated to MCC). The intrinsic time complexity of MCC problem is O(k (2) n (2)) with k compounds of maximal length n. In this paper, we propose a GPU-based algorithm for MCC problem, called CUDA-MCC, on single- and multi-GPUs. Four LINGO-based load-balancing strategies are considered in CUDA-MCC in order to accelerate the computation speed among thread blocks on GPUs. CUDA-MCC was implemented by C+OpenMP+CUDA. CUDA-MCC achieved 45 times and 391 times faster than its CPU version on a single NVIDIA Tesla K20m GPU card and a dual-NVIDIA Tesla K20m GPU card, respectively, under the experimental results.

Online Pairwise Learning Algorithms.

PubMed

Ying, Yiming; Zhou, Ding-Xuan

2016-04-01

Pairwise learning usually refers to a learning task that involves a loss function depending on pairs of examples, among which the most notable ones are bipartite ranking, metric learning, and AUC maximization. In this letter we study an online algorithm for pairwise learning with a least-square loss function in an unconstrained setting of a reproducing kernel Hilbert space (RKHS) that we refer to as the Online Pairwise lEaRning Algorithm (OPERA). In contrast to existing works (Kar, Sriperumbudur, Jain, & Karnick, 2013 ; Wang, Khardon, Pechyony, & Jones, 2012 ), which require that the iterates are restricted to a bounded domain or the loss function is strongly convex, OPERA is associated with a non-strongly convex objective function and learns the target function in an unconstrained RKHS. Specifically, we establish a general theorem that guarantees the almost sure convergence for the last iterate of OPERA without any assumptions on the underlying distribution. Explicit convergence rates are derived under the condition of polynomially decaying step sizes. We also establish an interesting property for a family of widely used kernels in the setting of pairwise learning and illustrate the convergence results using such kernels. Our methodology mainly depends on the characterization of RKHSs using its associated integral operators and probability inequalities for random variables with values in a Hilbert space.

The effect of design modifications to the typographical layout of the New York State elementary science learning standards on user preference and process time

NASA Astrophysics Data System (ADS)

Arnold, Jeffery E.

The purpose of this study was to determine the effect of four different design layouts of the New York State elementary science learning standards on user processing time and preference. Three newly developed layouts contained the same information as the standards core curriculum. In this study, the layout of the core guide is referred to as Book. The layouts of the new documents are referred to as Chart, Map, and Tabloid based on the format used to convey content hierarchy information. Most notably, all the new layouts feature larger page sizes, color, page tabs, and an icon based navigation system (IBNS). A convenience sample of 48 New York State educators representing three educator types (16 pre-service teachers, 16 in-service teachers, and 16 administrators) participated in the study. After completing timed tasks accurately, participants scored each layout based on preference. Educator type and layout were the independent variables, and process time and user preference were the dependent variables. A two-factor experimental design with Educator Type as the between variable and with repeated measures on Layout, the within variable, showed a significant difference in process time for Educator Type and Layout. The main effect for Educator Type (F(2, 45) = 8.03, p <.001) was significant with an observed power of .94, and an effect size of .26. The pair-wise comparisons for process time showed that pre-service teachers (p = .02) and administrators (p =.009) completed the assigned tasks more quickly when compared to in-service teachers. The main effect for Layout (F(3, 135) = 4.47, p =.01) was also significant with an observed power of .80, and an effect size of .09. Pair-wise comparisons showed that the newly developed Chart (p = .019) and Map (p = .032) layouts reduced overall process time when compared to the existing state learning standards (Book). The Layout X Educator type interaction was not significant. The same two-factor experimental design on preference, showed the main effect for Layout (F(3, 135) = 28.43, p =.001) was significant. The observed power was 1.0, with an effect size of .39. Pair-wise comparisons for preference scores showed that the Chart (p = .001), Map (p = .001), and Tabloid (p = .001) were preferred over the Book layout. The Layout Type X Educator Type interaction and the main effect for Educator Type were not significant. This study provides evidence that the newly developed design layouts improve usability (as measured by process time and preference scores) of the New York State elementary science learning standard documents. Features in the new layout design, such as the IBNS, may provide a foundation for a visual language and aid users in navigating standard documents across grade level and subject areas. Implications for the next generation of standard documents are presented.

Evaluation of variability in high-resolution protein structures by global distance scoring.

PubMed

Anzai, Risa; Asami, Yoshiki; Inoue, Waka; Ueno, Hina; Yamada, Koya; Okada, Tetsuji

2018-01-01

Systematic analysis of the statistical and dynamical properties of proteins is critical to understanding cellular events. Extraction of biologically relevant information from a set of high-resolution structures is important because it can provide mechanistic details behind the functional properties of protein families, enabling rational comparison between families. Most of the current structural comparisons are pairwise-based, which hampers the global analysis of increasing contents in the Protein Data Bank. Additionally, pairing of protein structures introduces uncertainty with respect to reproducibility because it frequently accompanies other settings for superimposition. This study introduces intramolecular distance scoring for the global analysis of proteins, for each of which at least several high-resolution structures are available. As a pilot study, we have tested 300 human proteins and showed that the method is comprehensively used to overview advances in each protein and protein family at the atomic level. This method, together with the interpretation of the model calculations, provide new criteria for understanding specific structural variation in a protein, enabling global comparison of the variability in proteins from different species.

Reliability and effect of sodium bicarbonate: buffering and 2000-m rowing performance.

PubMed

Carr, Amelia J; Slater, Gary J; Gore, Christopher J; Dawson, Brian; Burke, Louise M

2012-06-01

The aim of this study was to determine the effect and reliability of acute and chronic sodium bicarbonate ingestion for 2000-m rowing ergometer performance (watts) and blood bicarbonate concentration [HCO3-]. In a crossover study, 7 well-trained rowers performed paired 2000-m rowing ergometer trials under 3 double-blinded conditions: (1) 0.3 grams per kilogram of body mass (g/kg BM) acute bicarbonate; (2) 0.5 g/kg BM daily chronic bicarbonate for 3 d; and (3) calcium carbonate placebo, in semi-counterbalanced order. For 2000-m performance and [HCO3-], we examined differences in effects between conditions via pairwise comparisons, with differences interpreted in relation to the likelihood of exceeding smallest worthwhile change thresholds for each variable. We also calculated the within-subject variation (percent typical error). There were only trivial differences in 2000-m performance between placebo (277 ± 60 W), acute bicarbonate (280 ± 65 W) and chronic bicarbonate (282 ± 65 W); however, [HCO3-] was substantially greater after acute bicarbonate, than with chronic loading and placebo. Typical error for 2000-m mean power was 2.1% (90% confidence interval 1.4 to 4.0%) for acute bicarbonate, 3.6% (2.5 to 7.0%) for chronic bicarbonate, and 1.6% (1.1 to 3.0%) for placebo. Postsupplementation [HCO3-] typical error was 7.3% (5.0 to 14.5%) for acute bicarbonate, 2.9% (2.0 to 5.7%) for chronic bicarbonate and 6.0% (1.4 to 11.9%) for placebo. Performance in 2000-m rowing ergometer trials may not substantially improve after acute or chronic bicarbonate loading. However, performances will be reliable with both acute and chronic bicarbonate loading protocols.

A comparison of scoring weights for the EuroQol derived from patients and the general public.

PubMed

Polsky, D; Willke, R J; Scott, K; Schulman, K A; Glick, H A

2001-01-01

General health state classification systems, such as the EuroQol instrument, have been developed to improve the systematic measurement and comparability of health state preferences. In this paper we generate valuations for EuroQol health states using responses to this instrument's visual analogue scale made by patients enrolled in a randomized clinical trial evaluating tirilazad mesylate, a new drug used to treat subarachnoid haemorrhage. We then compare these valuations derived from patients with published valuations derived from responses made by a sample from the general public. The data were derived from two sources: (1) responses to the EuroQol instrument from 649 patients 3 months after enrollment in the clinical trial, and (2) from a published study reporting a scoring rule for the EuroQol instrument that was based upon responses made by the general public. We used a linear regression model to develop an additive scoring rule. This rule enables direct valuation of all 243 EuroQol health states using patients' scores for their own health states elicited using a visual analogue scale. We then compared predicted scores generated using our scoring rule with predicted scores derived from a sample from the general public. The predicted scores derived using the additive scoring rules met convergent validity criteria and explained a substantial amount of the variation in visual analogue scale scores (R(2)=0.57). In the pairwise comparison of the predicted scores derived from the study sample with those derived from the general public, we found that the former set of scores were higher for 223 of the 243 states. Despite the low level of correspondence in the pairwise comparison, the overall correlation between the two sets of scores was 87%. The model presented in this paper demonstrated that scoring weights for the EuroQol instrument can be derived directly from patient responses from a clinical trial and that these weights can explain a substantial amount of variation in health valuations. Scoring weights based on patient responses are significantly higher than those derived from the general public. Further research is required to understand the source of these differences. Copyright 2001 John Wiley & Sons, Ltd.

Serial MRI and CSF biomarkers in normal aging, MCI, and AD

PubMed Central

Vemuri, P.; Wiste, H.J.; Weigand, S.D.; Knopman, D.S.; Trojanowski, J.Q.; Shaw, L.M.; Bernstein, M.A.; Aisen, P.S.; Weiner, M.; Petersen, R.C; Jack, C.R

2010-01-01

Objective: To compare the annual change in MRI and CSF biomarkers in cognitively normal (CN), amnestic mild cognitive impairment (aMCI), and Alzheimer disease (AD). Comparisons were based on intergroup discrimination, correlation with concurrent cognitive/functional changes, relationships to APOE genotype, and sample sizes for clinical trials. Methods: We used data from the Alzheimer's Disease Neuroimaging Initiative study consisting of CN, aMCI, and AD cohorts with both baseline and 12-month follow-up CSF and MRI. The annual change in CSF (total-tau [t-tau], Aβ1-42) and MRI (change in ventricular volume) was obtained in 312 subjects (92 CN, 149 aMCI, 71 AD). Results: There was no significant average annual change in either CSF biomarker in any clinical group except t-tau in CN; moreover, the annual change did not differ by clinical group in pairwise comparisons. In contrast, annual increase in ventricular volume increased in the following order, AD > aMCI > CN, and differences were significant between all clinical groups in pairwise comparisons. Ventricular volume increase correlated with concurrent worsening on cognitive/functional indices in aMCI and AD whereas evidence of a similar correlation with change in CSF measures was unclear. The annual changes in MRI differed by APOE ε4 status overall and among aMCI while annual changes in CSF biomarkers did not. Estimated sample sizes for clinical trials are notably less for MRI than the CSF or clinical measures. Conclusions: Unlike the CSF biomarkers evaluated, changes in serial structural MRI are correlated with concurrent change on general cognitive and functional indices in impaired subjects, track with clinical disease stage, and are influenced by APOE genotype. GLOSSARY AD = Alzheimer disease; ADAS-Cog = Alzheimer's Disease Assessment Scale–cognitive subscale; ADNI = Alzheimer's Disease Neuroimaging Initiative; aMCI = amnestic mild cognitive impairment; AUROC = area under the receiver operator characteristic curve; BSI = boundary shift integral; CDR-SB = Clinical Dementia Rating–sum of boxes; CN = cognitively normal; MMSE = Mini-Mental State Examination; NFT = neurofibrillary tangle; NT = neuropil thread; PiB = Pittsburgh compound B; t-tau = total-tau. PMID:20625167

Comparison of lipid and calorie loss from donor human milk among 3 methods of simulated gavage feeding: one-hour, 2-hour, and intermittent gravity feedings.

PubMed

Brooks, Christine; Vickers, Amy Manning; Aryal, Subhash

2013-04-01

The objective of this study was to compare the differences in lipid loss from 24 samples of banked donor human milk (DHM) among 3 feeding methods: DHM given by syringe pump over 1 hour, 2 hours, and by bolus/gravity gavage. Comparative, descriptive. There were no human subjects. Twenty-four samples of 8 oz of DHM were divided into four 60-mL aliquots. Timed feedings were given by Medfusion 2001 syringe pumps with syringes connected to narrow-lumened extension sets designed for enteral feedings and connected to standard silastic enteral feeding tubes. Gravity feedings were given using the identical syringes connected to the same silastic feeding tubes. All aliquots were analyzed with the York Dairy Analyzer. Univariate repeated-measures analyses of variance were used for the omnibus testing for overall differences between the feeding methods. Lipid content expressed as grams per deciliter at the end of each feeding method was compared with the prefed control samples using the Dunnett's test. The Tukey correction was used for other pairwise multiple comparisons. The univariate repeated-measures analysis of variance conducted to test for overall differences between feeding methods showed a significant difference between the methods (F = 58.57, df = 3, 69, P < .0001). Post hoc analysis using the Dunnett's approach revealed that there was a significant difference in fat content between the control sample and the 1-hour and 2-hours feeding methods (P < .0001), but we did not find any significant difference in fat content between the control and the gravity feeding methods (P = .3296). Pairwise comparison using the Tukey correction revealed a significant difference between both gravity and 1-hour feeding methods (P < .0001), and gravity and 2-hour feeding method (P < .0001). There was no significant difference in lipid content between the 1-hour and 2-hour feeding methods (P = .2729). Unlike gravity feedings, the timed feedings resulted in a statistically significant loss of fat as compared with their controls. These findings should raise questions about how those infants in the neonatal intensive care unit are routinely gavage fed.

Multimodal description of whole brain connectivity: A comparison of resting state MEG, fMRI, and DWI.

PubMed

Garcés, Pilar; Pereda, Ernesto; Hernández-Tamames, Juan A; Del-Pozo, Francisco; Maestú, Fernando; Pineda-Pardo, José Ángel

2016-01-01

Structural and functional connectivity (SC and FC) have received much attention over the last decade, as they offer unique insight into the coordination of brain functioning. They are often assessed independently with three imaging modalities: SC using diffusion-weighted imaging (DWI), FC using functional magnetic resonance imaging (fMRI), and magnetoencephalography/electroencephalography (MEG/EEG). DWI provides information about white matter organization, allowing the reconstruction of fiber bundles. fMRI uses blood-oxygenation level-dependent (BOLD) contrast to indirectly map neuronal activation. MEG and EEG are direct measures of neuronal activity, as they are sensitive to the synchronous inputs in pyramidal neurons. Seminal studies have targeted either the electrophysiological substrate of BOLD or the anatomical basis of FC. However, multimodal comparisons have been scarcely performed, and the relation between SC, fMRI-FC, and MEG-FC is still unclear. Here we present a systematic comparison of SC, resting state fMRI-FC, and MEG-FC between cortical regions, by evaluating their similarities at three different scales: global network, node, and hub distribution. We obtained strong similarities between the three modalities, especially for the following pairwise combinations: SC and fMRI-FC; SC and MEG-FC at theta, alpha, beta and gamma bands; and fMRI-FC and MEG-FC in alpha and beta. Furthermore, highest node similarity was found for regions of the default mode network and primary motor cortex, which also presented the highest hubness score. Distance was partially responsible for these similarities since it biased all three connectivity estimates, but not the unique contributor, since similarities remained after controlling for distance. © 2015 Wiley Periodicals, Inc.

Flocculation of copper(II) and tetracycline from water using a novel pH- and temperature-responsive flocculants.

PubMed

Yang, Zhen; Jia, Shuying; Zhuo, Ning; Yang, Weiben; Wang, Yuping

2015-12-01

Insufficient research is available on flocculation of combined pollutants of heavy metals and antibiotics, which widely exist in livestock wastewaters. Aiming at solving difficulties in flocculation of this sort of combined pollution, a novel pH- and temperature-responsive biomass-based flocculant, carboxymethyl chitosan-graft-poly(N-isoproyl acrylamide-co-diallyl dimethyl ammonium chloride) (denoted as CND) with two responsive switches [lower critical solution temperature (LCST) and isoelectric point (IEP)], was designed and synthesized. Its flocculation performance at different temperatures and pHs was evaluated using copper(II) and tetracycline (TC) as model contaminants. CND exhibited high efficiency for coremoval of both contaminants, whereas two commercial flocculants (polyaluminum chloride and polyacrylamide) did not. Especially, flocculation performance of the dual-responsive flocculant under conditions of temperature>LCST and IEP(contaminants)

Interobserver variability of radiation therapists aligning to fiducial markers for prostate radiation therapy.

PubMed

Deegan, Timothy; Owen, Rebecca; Holt, Tanya; Roberts, Lisa; Biggs, Jennifer; McCarthy, Alicia; Parfitt, Matthew; Fielding, Andrew

2013-08-01

As the use of fiducial markers (FMs) for the localisation of the prostate during external beam radiation therapy (EBRT) has become part of routine practice, radiation therapists (RTs) have become increasingly responsible for online image interpretation. The aim of this investigation was to quantify the limits of agreement (LoA) between RTs when localising to FMs with orthogonal kilovoltage (kV) imaging. Six patients receiving prostate EBRT utilising FMs were included in this study. Treatment localisation was performed using kV imaging prior to each fraction. Online stereoscopic assessment of FMs, performed by the treating RTs, was compared with the offline assessment by three RTs. Observer agreement was determined by pairwise Bland-Altman analysis. Stereoscopic analysis of 225 image pairs was performed online at the time of treatment, and offline by three RT observers. Eighteen pairwise Bland-Altman analyses were completed to assess the level of agreement between observers. Localisation by RTs was found to be within clinically acceptable 95% LoAs. Small differences between RTs, in both the online and offline setting, were found to be within clinically acceptable limits. RTs were able to make consistent and reliable judgements when matching FMs on planar kV imaging. © 2013 The Authors. Journal of Medical Imaging and Radiation Oncology © 2013 The Royal Australian and New Zealand College of Radiologists.

Maximally informative pairwise interactions in networks

PubMed Central

Fitzgerald, Jeffrey D.; Sharpee, Tatyana O.

2010-01-01

Several types of biological networks have recently been shown to be accurately described by a maximum entropy model with pairwise interactions, also known as the Ising model. Here we present an approach for finding the optimal mappings between input signals and network states that allow the network to convey the maximal information about input signals drawn from a given distribution. This mapping also produces a set of linear equations for calculating the optimal Ising-model coupling constants, as well as geometric properties that indicate the applicability of the pairwise Ising model. We show that the optimal pairwise interactions are on average zero for Gaussian and uniformly distributed inputs, whereas they are nonzero for inputs approximating those in natural environments. These nonzero network interactions are predicted to increase in strength as the noise in the response functions of each network node increases. This approach also suggests ways for how interactions with unmeasured parts of the network can be inferred from the parameters of response functions for the measured network nodes. PMID:19905153

Threesomes destabilise certain relationships: multispecies interactions between wood decay fungi in natural resources

PubMed Central

Savoury, Melanie; Toledo, Selin; Kingscott-Edmunds, James; Bettridge, Aimee; Waili, Nasra Al; Boddy, Lynne

2017-01-01

Abstract Understanding interspecific interactions is key to explaining and modelling community development and associated ecosystem function. Most interactions research has focused on pairwise combinations, overlooking the complexity of multispecies communities. This study investigated three-way interactions between saprotrophic fungi in wood and across soil, and indicated that pairwise combinations are often inaccurate predictors of the outcomes of multispecies competition in wood block interactions. This inconsistency was especially true of intransitive combinations, resulting in increased species coexistence within the resource. Furthermore, the addition of a third competitor frequently destabilised the otherwise consistent outcomes of pairwise combinations in wood blocks, which occasionally resulted in altered resource decomposition rates, depending on the relative decay abilities of the species involved. Conversely, interaction outcomes in soil microcosms were unaffected by the presence of a third combatant. Multispecies interactions promoted species diversity within natural resources, and made community dynamics less consistent than could be predicted from pairwise interaction studies. PMID:28175239

Unbiased and robust quantification of synchronization between spikes and local field potential.

PubMed

Li, Zhaohui; Cui, Dong; Li, Xiaoli

2016-08-30

In neuroscience, relating the spiking activity of individual neurons to the local field potential (LFP) of neural ensembles is an increasingly useful approach for studying rhythmic neuronal synchronization. Many methods have been proposed to measure the strength of the association between spikes and rhythms in the LFP recordings, and most existing measures are dependent upon the total number of spikes. In the present work, we introduce a robust approach for quantifying spike-LFP synchronization which performs reliably for limited samples of data. The measure is termed as spike-triggered correlation matrix synchronization (SCMS), which takes LFP segments centered on each spike as multi-channel signals and calculates the index of spike-LFP synchronization by constructing a correlation matrix. The simulation based on artificial data shows that the SCMS output almost does not change with the sample size. This property is of crucial importance when making comparisons between different experimental conditions. When applied to actual neuronal data recorded from the monkey primary visual cortex, it is found that the spike-LFP synchronization strength shows orientation selectivity to drifting gratings. In comparison to another unbiased method, pairwise phase consistency (PPC), the proposed SCMS behaves better for noisy spike trains by means of numerical simulations. This study demonstrates the basic idea and calculating process of the SCMS method. Considering its unbiasedness and robustness, the measure is of great advantage to characterize the synchronization between spike trains and rhythms present in LFP. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of endpoints relevant to toxicity assessments in 3 generations of CD-1 mice fed irradiated natural and purified ingredient diets with varying soy protein and isoflavone contents.

PubMed

Camacho, Luísa; Lewis, Sherry M; Vanlandingham, Michelle M; Juliar, Beth E; Olson, Greg R; Patton, Ralph E; Gamboa da Costa, Gonçalo; Woodling, Kellie; Sepehr, Estatira; Bryant, Matthew S; Doerge, Daniel R; Basavarajappa, Mallikarjuna S; Felton, Robert P; Delclos, K Barry

2016-08-01

Diet is an important variable in toxicology. There are mixed reports on the impact of soy components on energy utilization, fat deposition, and reproductive parameters. Three generations of CD-1 mice were fed irradiated natural ingredient diets with varying levels of soy (NIH-41, 5K96, or 5008/5001), purified irradiated AIN-93 diet, or the AIN-93 formulation modified with ethanol-washed soy protein concentrate (SPC) or SPC with isoflavones (SPC-IF). NIH-41 was the control for pairwise comparisons. Minimal differences were observed among natural ingredient diet groups. F0 males fed AIN-93, SPC, and SPC-IF diets had elevated glucose levels and lower insulin levels compared with the NIH-41 group. In both sexes of the F1 and F2 generations, the SPC and SPC-IF groups had lower body weight gains than the NIH-41 controls and the AIN-93 group had an increased percent body fat at postnatal day 21. AIN-93 F1 pups had higher baseline glucose than NIH-41 controls, but diet did not significantly affect breeding performance or responses to glucose or uterotrophic challenges. Reduced testes weight and sperm in the AIN-93 group may be related to low thiamine levels. Our observations underline the importance of careful selection, manufacturing procedures, and nutritional characterization of diets used in toxicological studies. Published by Elsevier Ltd.

Transcriptional profile of isoproterenol-induced cardiomyopathy and comparison to exercise-induced cardiac hypertrophy and human cardiac failure

PubMed Central

2009-01-01

Background Isoproterenol-induced cardiac hypertrophy in mice has been used in a number of studies to model human cardiac disease. In this study, we compared the transcriptional response of the heart in this model to other animal models of heart failure, as well as to the transcriptional response of human hearts suffering heart failure. Results We performed microarray analyses on RNA from mice with isoproterenol-induced cardiac hypertrophy and mice with exercise-induced physiological hypertrophy and identified 865 and 2,534 genes that were significantly altered in pathological and physiological cardiac hypertrophy models, respectively. We compared our results to 18 different microarray data sets (318 individual arrays) representing various other animal models and four human cardiac diseases and identified a canonical set of 64 genes that are generally altered in failing hearts. We also produced a pairwise similarity matrix to illustrate relatedness of animal models with human heart disease and identified ischemia as the human condition that most resembles isoproterenol treatment. Conclusion The overall patterns of gene expression are consistent with observed structural and molecular differences between normal and maladaptive cardiac hypertrophy and support a role for the immune system (or immune cell infiltration) in the pathology of stress-induced hypertrophy. Cross-study comparisons such as the results presented here provide targets for further research of cardiac disease that might generally apply to maladaptive cardiac stresses and are also a means of identifying which animal models best recapitulate human disease at the transcriptional level. PMID:20003209

Comparing the efficacy of xylitol-containing and conventional chewing gums in reducing salivary counts of Streptococcus mutans: An in vivo study

PubMed Central

Haghgoo, Rosa; Afshari, Elahe; Ghanaat, Tahere; Aghazadeh, Samaneh

2015-01-01

Objective: Dental caries is among the most common chronic diseases in humans. Streptococcus mutans is generally responsible for most cases of dental caries. The present study sought to compare the effects of xylitol-containing and conventional chewing gums on salivary levels of S. mutans. Materials and Methods: This study adopted a crossover design. Two type of chewing gums (one containing 70% xylitol and approved by the Iranian Dental Association, and another containing sucrose) were purchased. The participants were 32 individuals aged 18–35 years whose oral hygiene was categorized as moderate or poor based on a caries risk assessment table. Salivary levels of S. mutans were measured at baseline, after the first and second phases of chewing gums, and after the washout period. The measurements were performed on blood agar and mitis salivarius-bacitracin agar (MSBA). Pairwise comparisons were then used to analyze the collected data. Results: Salivary levels of S. mutans in both groups were significantly higher during the two stages of chewing gum than in the washout period or baseline. Moreover, comparisons between the two types of gums suggested that chewing xylitol-containing gums led to greater reductions in S. mutans counts. This effect was more apparent in subjects with poor oral hygiene than in those with moderate oral hygiene. Conclusions: Xylitol-containing chewing gums are more effective than conventional gums in reducing salivary levels of S. mutans in individuals with poor–moderate oral hygiene. PMID:26942114

COMPARISON OF CURRENT METHODS FOR THE DETECTION OF CHRONIC MYCOPLASMAL URTD IN WILD POPULATIONS OF THE MOJAVE DESERT TORTOISE (GOPHERUS AGASSIZII).

PubMed

Sandmeier, Franziska C; Weitzman, Chava L; Maloney, K Nichole; Tracy, C Richard; Nieto, Nathan; Teglas, Mike B; Hunter, Kenneth W; DuPré, Sally; Gienger, C M; Tuma, Michael W

2017-01-01

Pathogens that cause subclinical diseases or exhibit low infection intensities are difficult to quantify in wild populations. Mojave desert tortoises ( Gopherus agassizii ) have been the focus of much research aimed at measuring the presence of upper respiratory disease (URTD) and URTD-associated pathogens, and techniques used to quantify disease in Gopherus species have also been used for disease surveillance in other species of turtles and tortoises of conservation concern. Published surveys of G. agassizii populations have found a relatively low prevalence of URTD, with most URTD-positive animals exhibiting moderate, intermittent signs of morbidity. Therefore, multiple tests have been developed to quantify URTD including genetic detection of the pathogens Mycoplasma agassizii and Mycoplasma testudineum , detection of M. agassizii -specific antibodies, and standardized quantification of clinical signs of URTD and body condition. These diagnostic tests have only been compared in diseased or moribund, semicaptive animals. We compared diagnostic techniques (TaqMan® and SYBR™ Green qPCR, serology, and visible examination) to detect M. agassizii -associated URTD in 126 wild desert tortoises sampled in Nevada and California, US in 2010. All had healthy body condition indices and none exhibited more than mild-to-moderate visual signs of URTD. Pairwise comparisons of diagnostic techniques indicated poor performance in diagnosing disease in individual animals. We found stronger, but inconsistent, statistical associations among diagnostic techniques at the population level. Our findings have implications for quantifying subclinical respiratory disease in tortoises.

Effects of two different knee tape procedures on lower-limb kinematics and kinetics in recreational runners.

PubMed

Howe, A; Campbell, A; Ng, L; Hall, T; Hopper, D

2015-08-01

The purpose of this study was to compare the effects of Mulligan's tape (MT) and kinesio tape (KT) with no tape (NT) on hip and knee kinematics and kinetics during running. Twenty-nine female recreational runners performed a series of 'run-throughs' along a 10-m runway under the three taping conditions. Two force plates and a 14-camera Vicon motion analysis system (Oxford Metrics, Inc., Oxford, UK) captured kinematic and kinetic data for each dependent variable from ground contact to toe off. Comparisons of each dependent variable under three taping conditions were assessed through Statistical Package for the Social Sciences (SPSS; SPSS, Inc., Chicago, Illinois, USA; P-value < 0.01) using repeated measure analyses of variance. For each dependent variable with a P-value < 0.01, repeated measures with pairwise comparisons and Bonferroni adjustment were conducted to compare the three taping conditions. MT induced a significant reduction in anterior and posterior hip forces, knee flexion angular velocity, knee extensor moments, and hip flexion and extension moments compared with NT and KT (P = 0.001). There was no difference in hip or knee, kinematics or kinetics, between KT and NT (P = 1.000). MT appears to influence hip and knee biomechanics during running in an asymptomatic sample, whereas KT appeared to be biomechanically not different from NT. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Comparison of endpoints relevant to toxicity assessments in 3 generations of CD-1 mice fed irradiated natural and purified ingredient diets with varying soy protein and isoflavone contents

PubMed Central

Camacho, Luísa; Lewis, Sherry M.; Vanlandingham, Michelle M.; Juliar, Beth E.; Olson, Greg R.; Patton, Ralph E.; da Costa, Gonçalo Gamboa; Woodling, Kellie; Sepehr, Estatira; Bryant, Matthew S.; Doerge, Daniel R.; Basavarajappa, Mallikarjuna S.; Felton, Robert P.; Delclos, K. Barry

2016-01-01

Diet is an important variable in toxicology. There are mixed reports on the impact of soy components on energy utilization, fat deposition, and reproductive parameters. Three generations of CD-1 mice were fed irradiated natural ingredient diets with varying levels of soy (NIH-41, 5K96, or 5008/5001), purified irradiated AIN-93 diet, or the AIN-93 formulation modified with ethanol-washed soy protein concentrate (SPC) or SPC with isoflavones (SPC-IF). NIH-41 was the control for pairwise comparisons. Minimal differences were observed among natural ingredient diet groups. F0 males fed AIN-93, SPC, and SPC-IF diets had elevated glucose levels and lower insulin levels compared with the NIH-41 group. In both sexes of the F1 and F2 generations, the SPC and SPC-IF groups had lower body weight gains than the NIH-41 controls and the AIN-93 group had an increased percent body fat at postnatal day 21. AIN-93 F1 pups had higher baseline glucose than NIH-41 controls, but diet did not significantly affect breeding performance or responses to glucose or uterotrophic challenges. Reduced testes weight and sperm in the AIN-93 group may be related to low thiamine levels. Our observations underline the importance of careful selection, manufacturing procedures, and nutritional characterization of diets used in toxicological studies. PMID:27234134

Communicating with sentences: A multi-word naming game model

NASA Astrophysics Data System (ADS)

Lou, Yang; Chen, Guanrong; Hu, Jianwei

2018-01-01

Naming game simulates the process of naming an object by a single word, in which a population of communicating agents can reach global consensus asymptotically through iteratively pair-wise conversations. We propose an extension of the single-word model to a multi-word naming game (MWNG), simulating the case of describing a complex object by a sentence (multiple words). Words are defined in categories, and then organized as sentences by combining them from different categories. We refer to a formatted combination of several words as a pattern. In such an MWNG, through a pair-wise conversation, it requires the hearer to achieve consensus with the speaker with respect to both every single word in the sentence as well as the sentence pattern, so as to guarantee the correct meaning of the saying; otherwise, they fail reaching consensus in the interaction. We validate the model in three typical topologies as the underlying communication network, and employ both conventional and man-designed patterns in performing the MWNG.

The Gaussian streaming model and convolution Lagrangian effective field theory

DOE PAGES

Vlah, Zvonimir; Castorina, Emanuele; White, Martin

2016-12-05

We update the ingredients of the Gaussian streaming model (GSM) for the redshift-space clustering of biased tracers using the techniques of Lagrangian perturbation theory, effective field theory (EFT) and a generalized Lagrangian bias expansion. After relating the GSM to the cumulant expansion, we present new results for the real-space correlation function, mean pairwise velocity and pairwise velocity dispersion including counter terms from EFT and bias terms through third order in the linear density, its leading derivatives and its shear up to second order. We discuss the connection to the Gaussian peaks formalism. We compare the ingredients of the GSM tomore » a suite of large N-body simulations, and show the performance of the theory on the low order multipoles of the redshift-space correlation function and power spectrum. We highlight the importance of a general biasing scheme, which we find to be as important as higher-order corrections due to non-linear evolution for the halos we consider on the scales of interest to us.« less

Graph Curvature for Differentiating Cancer Networks

PubMed Central

Sandhu, Romeil; Georgiou, Tryphon; Reznik, Ed; Zhu, Liangjia; Kolesov, Ivan; Senbabaoglu, Yasin; Tannenbaum, Allen

2015-01-01

Cellular interactions can be modeled as complex dynamical systems represented by weighted graphs. The functionality of such networks, including measures of robustness, reliability, performance, and efficiency, are intrinsically tied to the topology and geometry of the underlying graph. Utilizing recently proposed geometric notions of curvature on weighted graphs, we investigate the features of gene co-expression networks derived from large-scale genomic studies of cancer. We find that the curvature of these networks reliably distinguishes between cancer and normal samples, with cancer networks exhibiting higher curvature than their normal counterparts. We establish a quantitative relationship between our findings and prior investigations of network entropy. Furthermore, we demonstrate how our approach yields additional, non-trivial pair-wise (i.e. gene-gene) interactions which may be disrupted in cancer samples. The mathematical formulation of our approach yields an exact solution to calculating pair-wise changes in curvature which was computationally infeasible using prior methods. As such, our findings lay the foundation for an analytical approach to studying complex biological networks. PMID:26169480

The Gaussian streaming model and convolution Lagrangian effective field theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vlah, Zvonimir; Castorina, Emanuele; White, Martin, E-mail: zvlah@stanford.edu, E-mail: ecastorina@berkeley.edu, E-mail: mwhite@berkeley.edu

We update the ingredients of the Gaussian streaming model (GSM) for the redshift-space clustering of biased tracers using the techniques of Lagrangian perturbation theory, effective field theory (EFT) and a generalized Lagrangian bias expansion. After relating the GSM to the cumulant expansion, we present new results for the real-space correlation function, mean pairwise velocity and pairwise velocity dispersion including counter terms from EFT and bias terms through third order in the linear density, its leading derivatives and its shear up to second order. We discuss the connection to the Gaussian peaks formalism. We compare the ingredients of the GSM tomore » a suite of large N-body simulations, and show the performance of the theory on the low order multipoles of the redshift-space correlation function and power spectrum. We highlight the importance of a general biasing scheme, which we find to be as important as higher-order corrections due to non-linear evolution for the halos we consider on the scales of interest to us.« less

Pairwise Force SPH Model for Real-Time Multi-Interaction Applications.

PubMed

Yang, Tao; Martin, Ralph R; Lin, Ming C; Chang, Jian; Hu, Shi-Min

2017-10-01

In this paper, we present a novel pairwise-force smoothed particle hydrodynamics (PF-SPH) model to enable simulation of various interactions at interfaces in real time. Realistic capture of interactions at interfaces is a challenging problem for SPH-based simulations, especially for scenarios involving multiple interactions at different interfaces. Our PF-SPH model can readily handle multiple types of interactions simultaneously in a single simulation; its basis is to use a larger support radius than that used in standard SPH. We adopt a novel anisotropic filtering term to further improve the performance of interaction forces. The proposed model is stable; furthermore, it avoids the particle clustering problem which commonly occurs at the free surface. We show how our model can be used to capture various interactions. We also consider the close connection between droplets and bubbles, and show how to animate bubbles rising in liquid as well as bubbles in air. Our method is versatile, physically plausible and easy-to-implement. Examples are provided to demonstrate the capabilities and effectiveness of our approach.

Ultrasound measurement of inferior vena cava diameters by emergency department nurses.

PubMed

De Lorenzo, Robert A; Holbrook-Emmons, Victoria L

2014-01-01

Sonographic measurement of the inferior vena cava (IVC) diameter is a potentially important noninvasive estimate of fluid status. We researched whether nurses without prior ultrasonography experience could accurately obtain vena cava diameter measurements on models and subjects in comparison with those obtained by an expert sonographer. The design was a prospective educational study using a pre- and posttest of knowledge and a comparison of imaging performance between a subject and an expert sonographer. The setting was an urban teaching medical center with emergency nurses and a convenience sample of volunteer patients selected from the emergency department (ED). Nurses completed a written survey and a pretest to document prior training and experience in ultrasonography and assess baseline knowledge. A structured training program (3.5 hr in length) was provided over three sessions. Training consisted of didactic presentations, practice on phantoms (manikin models designed to provide the sonographic image of the human body when scanned by a trainee) and classmates, and one volunteer patient in the ED. Each nurse then measured IVC diameters on three different volunteer patients in transverse and longitudinal orientations using frozen images. An expert sonographer, blinded to subject results, performed the same examination. Correlations were determined, and a posttraining written examination was completed and results compared with the pretest using a pair-wise t test. Fourteen nurses, with a mean of 8 years' nursing experience (range = 2-18 years), participated. Nurse-expert R value correlation for the longitudinal orientation was 0.68 (95% confidence interval [CI] [0.35, 0.76]) and 0.59 (95% CI [0.47, 0.81]) for the transverse orientation. Posttest scores improved 8.2 percentage points (95% CI [4.0, 12.4]) from 83.3% to 91.5%. Following a brief training course, nurses with no prior sonography experience show moderately good correlation measuring the IVC diameter as compared with expert measurements, with better performance demonstrated in the longitudinal orientation.

Performance of freestanding inpatient rehabilitation hospitals before and after the rehabilitation prospective payment system.

PubMed

Thompson, Jon M; McCue, Michael J

2010-01-01

Inpatient rehabilitation hospitals provide important services to patients to restore physical and cognitive functioning. Historically, these hospitals have been reimbursed by Medicare under a cost-based system; but in 2002, Medicare implemented a rehabilitation prospective payment system (PPS). Despite the implementation of a PPS for rehabilitation, there is limited published research that addresses the operating and financial performance of these hospitals. We examined operating and financial performance in the pre- and post-PPS periods for for-profit and nonprofit freestanding inpatient rehabilitation hospitals to test for pre- and post-PPS differences within the ownership groups. We identified freestanding inpatient rehabilitation hospitals from the Centers for Medicare and Medicaid Services Health Care Cost Report Information System database for the first two fiscal years under PPS. We excluded facilities that had fiscal years less than 270 days, facilities with missing data, and government facilities. We computed average values for performance variables for the facilities in the two consecutive fiscal years post-PPS. For the pre-PPS period, we collected data on these same facilities and, once facilities with missing data and fiscal years less than 270 days were excluded, computed average values for the two consecutive fiscal years pre-PPS. Our final sample of 140 inpatient rehabilitation facilities was composed of 44 nonprofit hospitals and 96 for-profit hospitals both pre- and post-PPS. We utilized a pairwise comparison test (t-test comparison) to measure the significance of differences on each performance variable between pre- and post-PPS periods within each ownership group. Findings show that both nonprofit and for-profit freestanding inpatient rehabilitation hospitals reduced length of stay, increased discharges, and increased profitability. Within the for-profit ownership group, the percentage of Medicare discharges increased and operating expense per adjusted discharge decreased. Findings suggest that managers of these hospitals have adapted their administrative practices to conform with the financial incentives of the rehabilitation PPS. Managers must continue to control costs, increase discharges, and reduce length of stay to remain financially viable under the rehabilitation PPS.

The structure of pairwise correlation in mouse primary visual cortex reveals functional organization in the absence of an orientation map.

PubMed

Denman, Daniel J; Contreras, Diego

2014-10-01

Neural responses to sensory stimuli are not independent. Pairwise correlation can reduce coding efficiency, occur independent of stimulus representation, or serve as an additional channel of information, depending on the timescale of correlation and the method of decoding. Any role for correlation depends on its magnitude and structure. In sensory areas with maps, like the orientation map in primary visual cortex (V1), correlation is strongly related to the underlying functional architecture, but it is unclear whether this correlation structure is an essential feature of the system or arises from the arrangement of cells in the map. We assessed the relationship between functional architecture and pairwise correlation by measuring both synchrony and correlated spike count variability in mouse V1, which lacks an orientation map. We observed significant pairwise synchrony, which was organized by distance and relative orientation preference between cells. We also observed nonzero correlated variability in both the anesthetized (0.16) and awake states (0.18). Our results indicate that the structure of pairwise correlation is maintained in the absence of an underlying anatomical organization and may be an organizing principle of the mammalian visual system preserved by nonrandom connectivity within local networks. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't

PubMed Central

Roudi, Yasser; Nirenberg, Sheila; Latham, Peter E.

2009-01-01

One of the most critical problems we face in the study of biological systems is building accurate statistical descriptions of them. This problem has been particularly challenging because biological systems typically contain large numbers of interacting elements, which precludes the use of standard brute force approaches. Recently, though, several groups have reported that there may be an alternate strategy. The reports show that reliable statistical models can be built without knowledge of all the interactions in a system; instead, pairwise interactions can suffice. These findings, however, are based on the analysis of small subsystems. Here, we ask whether the observations will generalize to systems of realistic size, that is, whether pairwise models will provide reliable descriptions of true biological systems. Our results show that, in most cases, they will not. The reason is that there is a crossover in the predictive power of pairwise models: If the size of the subsystem is below the crossover point, then the results have no predictive power for large systems. If the size is above the crossover point, then the results may have predictive power. This work thus provides a general framework for determining the extent to which pairwise models can be used to predict the behavior of large biological systems. Applied to neural data, the size of most systems studied so far is below the crossover point. PMID:19424487

Forensic parameters of the Investigator DIPplex kit (Qiagen) in six Mexican populations.

PubMed

Martínez-Cortés, G; García-Aceves, M; Favela-Mendoza, A F; Muñoz-Valle, J F; Velarde-Felix, J S; Rangel-Villalobos, H

2016-05-01

Allele frequencies and statistical parameters of forensic efficiency for 30 deletion-insertion polymorphisms (DIPs) were estimated in six Mexican populations. For this purpose, 421 unrelated individuals were analyzed with the Investigator DIPplex kit. The Hardy-Weinberg and linkage equilibrium was demonstrated for this 30-plex system in all six populations. We estimated the combined power of discrimination (PD ≥ 99.999999%) and combined power of exclusion (PE ≥ 98.632705%) for this genetic system. A low but significant genetic structure was demonstrated among these six populations by pairwise comparisons and AMOVA (F ST ≥ 0.7054; p ≤ 0.0007), which allows clustering populations in agreement with geographical criteria: Northwest, Center, and Southeast.

Sequence determination and analysis of the NSs genes of two tospoviruses.

PubMed

Hallwass, Mariana; Leastro, Mikhail O; Lima, Mirtes F; Inoue-Nagata, Alice K; Resende, Renato O

2012-03-01

The tospoviruses groundnut ringspot virus (GRSV) and zucchini lethal chlorosis virus (ZLCV) cause severe losses in many crops, especially in solanaceous and cucurbit species. In this study, the non-structural NSs gene and the 5'UTRs of these two biologically distinct tospoviruses were cloned and sequenced. The NSs sequence of GRSV and ZLCV were both 1,404 nucleotides long. Pairwise comparison showed that the NSs amino acid sequence of GRSV shared 69.6% identity with that of ZLCV and 75.9% identity with that of TSWV, while the NSs sequence of ZLCV and TSWV shared 67.9% identity. Phylogenetic analysis based on NSs sequences confirmed that these viruses cluster in the American clade.

Insights into the genetic structure of the rabbitfish Chimaera monstrosa (Holocephali) across the Atlantic-Mediterranean transition zone.

PubMed

Catarino, D; Stanković, D; Menezes, G; Stefanni, S

2017-10-01

A comparison of the genetic structure of Chimaera monstrosa populations from the Atlantic Ocean and the Mediterranean Sea was carried out using mitochondrial DNA analysis. Results indicate high and significant pairwise Φ ST values with no shared haplotypes between the two areas. Furthermore, migration rate estimates suggested absence of gene flow between the two basins. These findings, coupled with the species vertical distribution, suggest that the shallow depth of the Strait of Gibraltar may act as a barrier limiting the dispersal capabilities of these populations, which likely became separated at the end of the middle Pleistocene. © 2017 The Fisheries Society of the British Isles.

Forensic parameters of the X-STR Decaplex system in Mexican populations.

PubMed

Mariscal Ramos, C; Martínez-Cortes, G; Ramos-González, B; Rangel-Villalobos, H

2018-03-01

We studied the X-STR decaplex system in 529 DNA female samples of Mexican populations from five geographic regions. Allele frequencies and forensic parameters were estimated in each region and in the pooled Mexican population. Genotype distribution by locus was in agreement with Hardy-Weinberg expectations in each Mexican population sample. Similarly, linkage equilibrium was demonstrated between pair of loci. Pairwise comparisons and genetic distances between Mexican, Iberoamerican and one African populations were estimated and graphically represented. Interestingly, a non-significant interpopulation differentiation was detected (Fst = 0.0021; p = .74389), which allows using a global Mexican database for forensic interpretation of X-STR genotypes. Copyright © 2017 Elsevier B.V. All rights reserved.

Patterns of text reuse in a scientific corpus

PubMed Central

Citron, Daniel T.; Ginsparg, Paul

2015-01-01

We consider the incidence of text “reuse” by researchers via a systematic pairwise comparison of the text content of all articles deposited to arXiv.org from 1991 to 2012. We measure the global frequencies of three classes of text reuse and measure how chronic text reuse is distributed among authors in the dataset. We infer a baseline for accepted practice, perhaps surprisingly permissive compared with other societal contexts, and a clearly delineated set of aberrant authors. We find a negative correlation between the amount of reused text in an article and its influence, as measured by subsequent citations. Finally, we consider the distribution of countries of origin of articles containing large amounts of reused text. PMID:25489072

Host switch during evolution of a genetically distinct hantavirus in the American shrew mole (Neurotrichus gibbsii)

PubMed Central

Kang, Hae Ji; Bennett, Shannon N.; Dizney, Laurie; Sumibcay, Laarni; Arai, Satoru; Ruedas, Luis A.; Song, Jin-Won; Yanagihara, Richard

2009-01-01

A genetically distinct hantavirus, designated Oxbow virus (OXBV), was detected in tissues of an American shrew mole (Neurotrichus gibbsii), captured in Gresham, Oregon, in September 2003. Pairwise analysis of full-length S- and M- and partial L-segment nucleotide and amino acid sequences of OXBV indicated low sequence similarity with rodent-borne hantaviruses. Phylogenetic analyses using maximum-likelihood and Bayesian methods, and host-parasite evolutionary comparisons, showed that OXBV and Asama virus, a hantavirus recently identified from the Japanese shrew mole (Urotrichus talpoides), were related to soricine shrew-borne hantaviruses from North America and Eurasia, respectively, suggesting parallel evolution associated with cross-species transmission. PMID:19394994

Divergent ancestral lineages of newfound hantaviruses harbored by phylogenetically related crocidurine shrew species in Korea

PubMed Central

Arai, Satoru; Gu, Se Hun; Baek, Luck Ju; Tabara, Kenji; Bennett, Shannon; Oh, Hong-Shik; Takada, Nobuhiro; Kang, Hae Ji; Tanaka-Taya, Keiko; Morikawa, Shigeru; Okabe, Nobuhiko; Yanagihara, Richard; Song, Jin-Won

2012-01-01

Spurred by the recent isolation of a novel hantavirus, named Imjin virus (MJNV), from the Ussuri white-toothed shrew (Crocidura lasiura), targeted trapping was conducted for the phylogenetically related Asian lesser white-toothed shrew (Crocidura shantungensis). Pair-wise alignment and comparison of the S, M and L segments of a newfound hantavirus, designated Jeju virus (JJUV), indicated remarkably low nucleotide and amino acid sequence similarity with MJNV. Phylogenetic analyses, using maximum likelihood and Bayesian methods, showed divergent ancestral lineages for JJUV and MJNV, despite the close phylogenetic relationship of their reservoir soricid hosts. Also, no evidence of host switching was apparent in tanglegrams, generated by TreeMap 2.0β. PMID:22230701

A shape prior-based MRF model for 3D masseter muscle segmentation

NASA Astrophysics Data System (ADS)

Majeed, Tahir; Fundana, Ketut; Lüthi, Marcel; Beinemann, Jörg; Cattin, Philippe

2012-02-01

Medical image segmentation is generally an ill-posed problem that can only be solved by incorporating prior knowledge. The ambiguities arise due to the presence of noise, weak edges, imaging artifacts, inhomogeneous interior and adjacent anatomical structures having similar intensity profile as the target structure. In this paper we propose a novel approach to segment the masseter muscle using the graph-cut incorporating additional 3D shape priors in CT datasets, which is robust to noise; artifacts; and shape deformations. The main contribution of this paper is in translating the 3D shape knowledge into both unary and pairwise potentials of the Markov Random Field (MRF). The segmentation task is casted as a Maximum-A-Posteriori (MAP) estimation of the MRF. Graph-cut is then used to obtain the global minimum which results in the segmentation of the masseter muscle. The method is tested on 21 CT datasets of the masseter muscle, which are noisy with almost all possessing mild to severe imaging artifacts such as high-density artifacts caused by e.g. the very common dental fillings and dental implants. We show that the proposed technique produces clinically acceptable results to the challenging problem of muscle segmentation, and further provide a quantitative and qualitative comparison with other methods. We statistically show that adding additional shape prior into both unary and pairwise potentials can increase the robustness of the proposed method in noisy datasets.

Many-body dispersion effects in the binding of adsorbates on metal surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maurer, Reinhard J.; Ruiz, Victor G.; Tkatchenko, Alexandre

2015-09-14

A correct description of electronic exchange and correlation effects for molecules in contact with extended (metal) surfaces is a challenging task for first-principles modeling. In this work, we demonstrate the importance of collective van der Waals dispersion effects beyond the pairwise approximation for organic–inorganic systems on the example of atoms, molecules, and nanostructures adsorbed on metals. We use the recently developed many-body dispersion (MBD) approach in the context of density-functional theory [Tkatchenko et al., Phys. Rev. Lett. 108, 236402 (2012) and Ambrosetti et al., J. Chem. Phys. 140, 18A508 (2014)] and assess its ability to correctly describe the binding ofmore » adsorbates on metal surfaces. We briefly review the MBD method and highlight its similarities to quantum-chemical approaches to electron correlation in a quasiparticle picture. In particular, we study the binding properties of xenon, 3,4,9,10-perylene-tetracarboxylic acid, and a graphene sheet adsorbed on the Ag(111) surface. Accounting for MBD effects, we are able to describe changes in the anisotropic polarizability tensor, improve the description of adsorbate vibrations, and correctly capture the adsorbate–surface interaction screening. Comparison to other methods and experiment reveals that inclusion of MBD effects improves adsorption energies and geometries, by reducing the overbinding typically found in pairwise additive dispersion-correction approaches.« less

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems

PubMed Central

Williams, Ryan J.; Howe, Adina; Hofmockel, Kirsten S.

2014-01-01

Co-occurrence patterns are used in ecology to explore interactions between organisms and environmental effects on coexistence within biological communities. Analysis of co-occurrence patterns among microbial communities has ranged from simple pairwise comparisons between all community members to direct hypothesis testing between focal species. However, co-occurrence patterns are rarely studied across multiple ecosystems or multiple scales of biological organization within the same study. Here we outline an approach to produce co-occurrence analyses that are focused at three different scales: co-occurrence patterns between ecosystems at the community scale, modules of co-occurring microorganisms within communities, and co-occurring pairs within modules that are nested within microbial communities. To demonstrate our co-occurrence analysis approach, we gathered publicly available 16S rRNA amplicon datasets to compare and contrast microbial co-occurrence at different taxonomic levels across different ecosystems. We found differences in community composition and co-occurrence that reflect environmental filtering at the community scale and consistent pairwise occurrences that may be used to infer ecological traits about poorly understood microbial taxa. However, we also found that conclusions derived from applying network statistics to microbial relationships can vary depending on the taxonomic level chosen and criteria used to build co-occurrence networks. We present our statistical analysis and code for public use in analysis of co-occurrence patterns across microbial communities. PMID:25101065

Development and Characterization of 18 Novel EST-SSRs from the Western Flower Thrips, Frankliniella occidentalis (Pergande)

PubMed Central

Yang, Xian-Ming; Sun, Jing-Tao; Xue, Xiao-Feng; Zhu, Wen-Chao; Hong, Xiao-Yue

2012-01-01

The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. For a better understanding of the genetic makeup and migration patterns of F. occidentalis throughout the world, we characterized 18 novel polymorphic EST-derived microsatellites. The mutational mechanism of these EST-SSRs was also investigated to facilitate the selection of appropriate combinations of markers for population genetic studies. Genetic diversity of these novel markers was assessed in 96 individuals from three populations in China (Harbin, Dali, and Guiyang). The results showed that all these 18 loci were highly polymorphic; the number of alleles ranged from 2 to 15, with an average of 5.50 alleles per locus. The observed (HO) and expected (HE) heterozygosities ranged from 0.072 to 0.707 and 0.089 to 0.851, respectively. Furthermore, only two locus/population combinations (WFT144 in Dali and WFT50 in Guiyang) significantly deviated from Hardy–Weinberg equilibrium (HWE). Pairwise FST analysis showed a low but significant differentiation (0.026 < FST < 0.032) among all three pairwise population comparisons. Sequence analysis of alleles per locus revealed a complex mutational pattern of these EST-SSRs. Thus, these EST-SSRs are useful markers but greater attention should be paid to the mutational characteristics of these microsatellites when they are used in population genetic studies. PMID:22489130

Development and characterization of 18 novel EST-SSRs from the western flower Thrips, Frankliniella occidentalis (Pergande).

PubMed

Yang, Xian-Ming; Sun, Jing-Tao; Xue, Xiao-Feng; Zhu, Wen-Chao; Hong, Xiao-Yue

2012-01-01

The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. For a better understanding of the genetic makeup and migration patterns of F. occidentalis throughout the world, we characterized 18 novel polymorphic EST-derived microsatellites. The mutational mechanism of these EST-SSRs was also investigated to facilitate the selection of appropriate combinations of markers for population genetic studies. Genetic diversity of these novel markers was assessed in 96 individuals from three populations in China (Harbin, Dali, and Guiyang). The results showed that all these 18 loci were highly polymorphic; the number of alleles ranged from 2 to 15, with an average of 5.50 alleles per locus. The observed (H(O)) and expected (H(E)) heterozygosities ranged from 0.072 to 0.707 and 0.089 to 0.851, respectively. Furthermore, only two locus/population combinations (WFT144 in Dali and WFT50 in Guiyang) significantly deviated from Hardy-Weinberg equilibrium (HWE). Pairwise F(ST) analysis showed a low but significant differentiation (0.026 < F(ST) < 0.032) among all three pairwise population comparisons. Sequence analysis of alleles per locus revealed a complex mutational pattern of these EST-SSRs. Thus, these EST-SSRs are useful markers but greater attention should be paid to the mutational characteristics of these microsatellites when they are used in population genetic studies.

MultiSETTER: web server for multiple RNA structure comparison.

PubMed

Čech, Petr; Hoksza, David; Svozil, Daniel

2015-08-12

Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

Comparing the Effects of Different Body Armor Systems on the Occupational Performance of Police Officers.

PubMed

Schram, Ben; Orr, Robin; Pope, Rodney; Hinton, Ben; Norris, Geoff

2018-05-01

Policing duties may inherently be dangerous due to stab, blunt trauma and ballistic threats. The addition of individual light armor vests (ILAVs) has been suggested as a means to protect officers. However, the addition of the extra load of the ILAV may affect officer ability to conduct occupational tasks. The purpose of this study was to determine if wearing any of three different ILAVs made by different companies with their preferred materials and designs (ILAV A, 4.68 percent body weight, ILAV B, 4.05 percent body weight, & ILAV C, 3.71 percent body weight) affected occupational task performance when compared to that in normal station wear. A prospective, within-subjects repeated measures design was employed, using a counterbalanced randomization in which each ILAV was worn for an entire day while officers completed a variety of occupationally relevant tasks. These tasks included a victim drag, car exit and 5-meter sprint, step down and marksmanship task. To compare the effects of the ILAVs on these tasks, a multivariate repeated measures analysis of variance (ANOVA) was conducted, with post hoc pairwise comparisons using a Bonferroni adjustment. Results showed that performance in each task did not vary between any of the ILAV or normal station wear conditions. There was less variability in the marksmanship task with ILAV B, however. The results suggest that none of the ILAVs used in this study were heavy enough to significantly affect task performance in the assessed tasks when compared to wearing normal station wear.

Video-based training to improve perceptual-cognitive decision-making performance of Australian football umpires.

PubMed

Larkin, Paul; Mesagno, Christopher; Berry, Jason; Spittle, Michael; Harvey, Jack

2018-02-01

Decision-making is a central component of the in-game performance of Australian football umpires; however, current umpire training focuses largely on physiological development with decision-making skills development conducted via explicit lecture-style meetings with limited practice devoted to making actual decisions. Therefore, this study investigated the efficacy of a video-based training programme, aimed to provide a greater amount of contextualised visual experiences without explicit instruction, to improve decision-making skills of umpires. Australian football umpires (n = 52) were recruited from metropolitan and regional Division 1 competitions. Participants were randomly assigned to an intervention or control group and classified according to previous umpire game experience (i.e., experienced; less experienced). The intervention group completed a 12-week video-based decision-making training programme, with decision-making performance assessed at pre-training, and 1-week retention and 3-week retention periods. The control group did not complete any video-based training. Results indicated a significant Group (intervention; Control) × Test interaction (F(1, 100) = 3.98; P = 0.02, partial ῆ 2  = 0.074), with follow-up pairwise comparisons indicating significant within-group differences over time for the intervention group. In addition, decision-making performance of the less experienced umpires in the intervention group significantly improved (F(2, 40) = 5.03, P = 0.01, partial ῆ 2  = 0.201). Thus, video-based training programmes may be a viable adjunct to current training programmes to hasten decision-making development, especially for less experienced umpires.

Work-related stress is associated with impaired neuropsychological test performance: a clinical cross-sectional study.

PubMed

Eskildsen, Anita; Andersen, Lars Peter; Pedersen, Anders Degn; Vandborg, Sanne Kjær; Andersen, Johan Hviid

2015-01-01

Patients on sick leave due to work-related stress often complain about impaired concentration and memory. However, it is undetermined how widespread these impairments are, and which cognitive domains are most long-term stress sensitive. Previous studies show inconsistent results and are difficult to synthesize. The primary aim of this study was to examine whether patients with work-related stress complaints have cognitive impairments compared to a matched control group without stress. Our secondary aim was to examine whether the level of self-reported perceived stress is associated with neuropsychological test performance. We used a broad neuropsychological test battery to assess 59 outpatients with work-related stress complaints (without major depression) and 59 healthy controls. We matched the patients and controls pairwise by sex, age and educational level. Compared to controls, patients generally showed mildly reduced performance across all the measured domains of the neuropsychological test battery. However, only three comparisons reached statistical significance (p < 0.05). Effect sizes (Cohen's d) were generally small to medium. The most pronounced differences between patients and controls were seen on tests of prospective memory, speed and complex working memory. There were no statistical significant associations between self-reported perceived stress level and neuropsychological test performance. In conclusion, we recommend that cognitive functions should be considered when evaluating patients with work-related stress complaints, especially when given advice regarding return to work. Since this study had a cross-sectional design, it is still uncertain whether the impairments are permanent. Further study is required to establish causal links between work-related stress and cognitive deficits.

Comparing the Effects of Different Body Armor Systems on the Occupational Performance of Police Officers

PubMed Central

Orr, Robin; Hinton, Ben; Norris, Geoff

2018-01-01

Policing duties may inherently be dangerous due to stab, blunt trauma and ballistic threats. The addition of individual light armor vests (ILAVs) has been suggested as a means to protect officers. However, the addition of the extra load of the ILAV may affect officer ability to conduct occupational tasks. The purpose of this study was to determine if wearing any of three different ILAVs made by different companies with their preferred materials and designs (ILAV A, 4.68 percent body weight, ILAV B, 4.05 percent body weight, & ILAV C, 3.71 percent body weight) affected occupational task performance when compared to that in normal station wear. A prospective, within-subjects repeated measures design was employed, using a counterbalanced randomization in which each ILAV was worn for an entire day while officers completed a variety of occupationally relevant tasks. These tasks included a victim drag, car exit and 5-meter sprint, step down and marksmanship task. To compare the effects of the ILAVs on these tasks, a multivariate repeated measures analysis of variance (ANOVA) was conducted, with post hoc pairwise comparisons using a Bonferroni adjustment. Results showed that performance in each task did not vary between any of the ILAV or normal station wear conditions. There was less variability in the marksmanship task with ILAV B, however. The results suggest that none of the ILAVs used in this study were heavy enough to significantly affect task performance in the assessed tasks when compared to wearing normal station wear. PMID:29723995

Design, Implementation and Deployment of PAIRwise

ERIC Educational Resources Information Center

Knight, Allan; Almeroth, Kevin; Bimber, Bruce

2008-01-01

Increased access to the Internet has dramatically increased the sources from which students can deliberately or accidentally copy information. This article discusses our motivation to design, implement, and deploy an Internet based plagiarism detection system, called PAIRwise, to address this growing problem. We give details as to how we detect…

Sparse Contextual Activation for Efficient Visual Re-Ranking.

PubMed

Bai, Song; Bai, Xiang

2016-03-01

In this paper, we propose an extremely efficient algorithm for visual re-ranking. By considering the original pairwise distance in the contextual space, we develop a feature vector called sparse contextual activation (SCA) that encodes the local distribution of an image. Hence, re-ranking task can be simply accomplished by vector comparison under the generalized Jaccard metric, which has its theoretical meaning in the fuzzy set theory. In order to improve the time efficiency of re-ranking procedure, inverted index is successfully introduced to speed up the computation of generalized Jaccard metric. As a result, the average time cost of re-ranking for a certain query can be controlled within 1 ms. Furthermore, inspired by query expansion, we also develop an additional method called local consistency enhancement on the proposed SCA to improve the retrieval performance in an unsupervised manner. On the other hand, the retrieval performance using a single feature may not be satisfactory enough, which inspires us to fuse multiple complementary features for accurate retrieval. Based on SCA, a robust feature fusion algorithm is exploited that also preserves the characteristic of high time efficiency. We assess our proposed method in various visual re-ranking tasks. Experimental results on Princeton shape benchmark (3D object), WM-SRHEC07 (3D competition), YAEL data set B (face), MPEG-7 data set (shape), and Ukbench data set (image) manifest the effectiveness and efficiency of SCA.

Sensitivity of Chemical Shift-Encoded Fat Quantification to Calibration of Fat MR Spectrum

PubMed Central

Wang, Xiaoke; Hernando, Diego; Reeder, Scott B.

2015-01-01

Purpose To evaluate the impact of different fat spectral models on proton density fat-fraction (PDFF) quantification using chemical shift-encoded (CSE) MRI. Material and Methods Simulations and in vivo imaging were performed. In a simulation study, spectral models of fat were compared pairwise. Comparison of magnitude fitting and mixed fitting was performed over a range of echo times and fat fractions. In vivo acquisitions from 41 patients were reconstructed using 7 published spectral models of fat. T2-corrected STEAM-MRS was used as reference. Results Simulations demonstrate that imperfectly calibrated spectral models of fat result in biases that depend on echo times and fat fraction. Mixed fitting is more robust against this bias than magnitude fitting. Multi-peak spectral models showed much smaller differences among themselves than when compared to the single-peak spectral model. In vivo studies show all multi-peak models agree better (for mixed fitting, slope ranged from 0.967–1.045 using linear regression) with reference standard than the single-peak model (for mixed fitting, slope=0.76). Conclusion It is essential to use a multi-peak fat model for accurate quantification of fat with CSE-MRI. Further, fat quantification techniques using multi-peak fat models are comparable and no specific choice of spectral model is shown to be superior to the rest. PMID:25845713

A Computational Framework for Quantitative Evaluation of Movement during Rehabilitation

NASA Astrophysics Data System (ADS)

Chen, Yinpeng; Duff, Margaret; Lehrer, Nicole; Sundaram, Hari; He, Jiping; Wolf, Steven L.; Rikakis, Thanassis

2011-06-01

This paper presents a novel generalized computational framework for quantitative kinematic evaluation of movement in a rehabilitation clinic setting. The framework integrates clinical knowledge and computational data-driven analysis together in a systematic manner. The framework provides three key benefits to rehabilitation: (a) the resulting continuous normalized measure allows the clinician to monitor movement quality on a fine scale and easily compare impairments across participants, (b) the framework reveals the effect of individual movement components on the composite movement performance helping the clinician decide the training foci, and (c) the evaluation runs in real-time, which allows the clinician to constantly track a patient's progress and make appropriate adaptations to the therapy protocol. The creation of such an evaluation is difficult because of the sparse amount of recorded clinical observations, the high dimensionality of movement and high variations in subject's performance. We address these issues by modeling the evaluation function as linear combination of multiple normalized kinematic attributes y = Σwiφi(xi) and estimating the attribute normalization function φi(ṡ) by integrating distributions of idealized movement and deviated movement. The weights wi are derived from a therapist's pair-wise comparison using a modified RankSVM algorithm. We have applied this framework to evaluate upper limb movement for stroke survivors with excellent results—the evaluation results are highly correlated to the therapist's observations.

Academic burnout and eating disorder among students in Monash University Malaysia.

PubMed

Kristanto, Tommy; Chen, Won Sun; Thoo, Yin Yin

2016-08-01

This study examined the prevalence of academic burnout and the relationship between academic burnout and eating disorder among Monash university students for a period of one year. One hundred and thirty-two participants were recruited for the study via advertisement. They were invited to complete three instruments, namely Demographic Questionnaire, Maslach Burnout Inventory - Student Survey (MBI-SS) and Three Factor Eating Questionnaire-Revised 18-item (TFEQ-18). In addition, anthropometric measurements such as weight, height, body mass index (BMI), body fat percentage and waist circumference were taken. All data were collected at baseline and after 6-8weeks. Analysis of Variance (ANOVA), Kruskal-Wallis and Bonferroni pairwise comparison tests were performed using Stata version 13. The prevalence of academic burnout after 6-8weeks was revealed to be 17.4% and 73.5% respectively for moderate and high level of academic burnout respectively. Emotional eating (EEat) scores were significantly different over levels of academic burnout after 6-8weeks (p=0.0103) while no significant differences was observed in other subscales such as cognitive restraint (CR) and uncontrolled eating (UE). These findings evidenced partial associations between academic burnout and eating disorder. Copyright © 2016 Elsevier Ltd. All rights reserved.

Patch forest: a hybrid framework of random forest and patch-based segmentation

NASA Astrophysics Data System (ADS)

Xie, Zhongliu; Gillies, Duncan

2016-03-01

The development of an accurate, robust and fast segmentation algorithm has long been a research focus in medical computer vision. State-of-the-art practices often involve non-rigidly registering a target image with a set of training atlases for label propagation over the target space to perform segmentation, a.k.a. multi-atlas label propagation (MALP). In recent years, the patch-based segmentation (PBS) framework has gained wide attention due to its advantage of relaxing the strict voxel-to-voxel correspondence to a series of pair-wise patch comparisons for contextual pattern matching. Despite a high accuracy reported in many scenarios, computational efficiency has consistently been a major obstacle for both approaches. Inspired by recent work on random forest, in this paper we propose a patch forest approach, which by equipping the conventional PBS with a fast patch search engine, is able to boost segmentation speed significantly while retaining an equal level of accuracy. In addition, a fast forest training mechanism is also proposed, with the use of a dynamic grid framework to efficiently approximate data compactness computation and a 3D integral image technique for fast box feature retrieval.

Further Improvements to Linear Mixed Models for Genome-Wide Association Studies

PubMed Central

Widmer, Christian; Lippert, Christoph; Weissbrod, Omer; Fusi, Nicolo; Kadie, Carl; Davidson, Robert; Listgarten, Jennifer; Heckerman, David

2014-01-01

We examine improvements to the linear mixed model (LMM) that better correct for population structure and family relatedness in genome-wide association studies (GWAS). LMMs rely on the estimation of a genetic similarity matrix (GSM), which encodes the pairwise similarity between every two individuals in a cohort. These similarities are estimated from single nucleotide polymorphisms (SNPs) or other genetic variants. Traditionally, all available SNPs are used to estimate the GSM. In empirical studies across a wide range of synthetic and real data, we find that modifications to this approach improve GWAS performance as measured by type I error control and power. Specifically, when only population structure is present, a GSM constructed from SNPs that well predict the phenotype in combination with principal components as covariates controls type I error and yields more power than the traditional LMM. In any setting, with or without population structure or family relatedness, a GSM consisting of a mixture of two component GSMs, one constructed from all SNPs and another constructed from SNPs that well predict the phenotype again controls type I error and yields more power than the traditional LMM. Software implementing these improvements and the experimental comparisons are available at http://microsoft.com/science. PMID:25387525

Population-genetic properties of differentiated copy number variations in cattle.

PubMed

Xu, Lingyang; Hou, Yali; Bickhart, Derek M; Zhou, Yang; Hay, El Hamidi Abdel; Song, Jiuzhou; Sonstegard, Tad S; Van Tassell, Curtis P; Liu, George E

2016-03-23

While single nucleotide polymorphism (SNP) is typically the variant of choice for population genetics, copy number variation (CNV) which comprises insertion, deletion and duplication of genomic sequence, is an informative type of genetic variation. CNVs have been shown to be both common in mammals and important for understanding the relationship between genotype and phenotype. However, CNV differentiation, selection and its population genetic properties are not well understood across diverse populations. We performed a population genetics survey based on CNVs derived from the BovineHD SNP array data of eight distinct cattle breeds. We generated high resolution results that show geographical patterns of variations and genome-wide admixture proportions within and among breeds. Similar to the previous SNP-based studies, our CNV-based results displayed a strong correlation of population structure and geographical location. By conducting three pairwise comparisons among European taurine, African taurine, and indicine groups, we further identified 78 unique CNV regions that were highly differentiated, some of which might be due to selection. These CNV regions overlapped with genes involved in traits related to parasite resistance, immunity response, body size, fertility, and milk production. Our results characterize CNV diversity among cattle populations and provide a list of lineage-differentiated CNVs.

Sockeye: A 3D Environment for Comparative Genomics

PubMed Central

Montgomery, Stephen B.; Astakhova, Tamara; Bilenky, Mikhail; Birney, Ewan; Fu, Tony; Hassel, Maik; Melsopp, Craig; Rak, Marcin; Robertson, A. Gordon; Sleumer, Monica; Siddiqui, Asim S.; Jones, Steven J.M.

2004-01-01

Comparative genomics techniques are used in bioinformatics analyses to identify the structural and functional properties of DNA sequences. As the amount of available sequence data steadily increases, the ability to perform large-scale comparative analyses has become increasingly relevant. In addition, the growing complexity of genomic feature annotation means that new approaches to genomic visualization need to be explored. We have developed a Java-based application called Sockeye that uses three-dimensional (3D) graphics technology to facilitate the visualization of annotation and conservation across multiple sequences. This software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization. PMID:15123592

GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU.

PubMed

Su, Xiaoquan; Wang, Xuetao; Jing, Gongchao; Ning, Kang

2014-04-01

The number of microbial community samples is increasing with exponential speed. Data-mining among microbial community samples could facilitate the discovery of valuable biological information that is still hidden in the massive data. However, current methods for the comparison among microbial communities are limited by their ability to process large amount of samples each with complex community structure. We have developed an optimized GPU-based software, GPU-Meta-Storms, to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. Our results have shown that GPU-Meta-Storms would be able to compute the pair-wise similarity scores for 10 240 samples within 20 min, which gained a speed-up of >17 000 times compared with single-core CPU, and >2600 times compared with 16-core CPU. Therefore, the high-performance of GPU-Meta-Storms could facilitate in-depth data mining among massive microbial community samples, and make the real-time analysis and monitoring of temporal or conditional changes for microbial communities possible. GPU-Meta-Storms is implemented by CUDA (Compute Unified Device Architecture) and C++. Source code is available at http://www.computationalbioenergy.org/meta-storms.html.

Identifying the Source of Misfit in Item Response Theory Models.

PubMed

Liu, Yang; Maydeu-Olivares, Alberto

2014-01-01

When an item response theory model fails to fit adequately, the items for which the model provides a good fit and those for which it does not must be determined. To this end, we compare the performance of several fit statistics for item pairs with known asymptotic distributions under maximum likelihood estimation of the item parameters: (a) a mean and variance adjustment to bivariate Pearson's X(2), (b) a bivariate subtable analog to Reiser's (1996) overall goodness-of-fit test, (c) a z statistic for the bivariate residual cross product, and (d) Maydeu-Olivares and Joe's (2006) M2 statistic applied to bivariate subtables. The unadjusted Pearson's X(2) with heuristically determined degrees of freedom is also included in the comparison. For binary and ordinal data, our simulation results suggest that the z statistic has the best Type I error and power behavior among all the statistics under investigation when the observed information matrix is used in its computation. However, if one has to use the cross-product information, the mean and variance adjusted X(2) is recommended. We illustrate the use of pairwise fit statistics in 2 real-data examples and discuss possible extensions of the current research in various directions.

Visualizing and enhancing a deep learning framework using patients age and gender for chest x-ray image retrieval

NASA Astrophysics Data System (ADS)

Anavi, Yaron; Kogan, Ilya; Gelbart, Elad; Geva, Ofer; Greenspan, Hayit

2016-03-01

We explore the combination of text metadata, such as patients' age and gender, with image-based features, for X-ray chest pathology image retrieval. We focus on a feature set extracted from a pre-trained deep convolutional network shown in earlier work to achieve state-of-the-art results. Two distance measures are explored: a descriptor-based measure, which computes the distance between image descriptors, and a classification-based measure, which performed by a comparison of the corresponding SVM classification probabilities. We show that retrieval results increase once the age and gender information combined with the features extracted from the last layers of the network, with best results using the classification-based scheme. Visualization of the X-ray data is presented by embedding the high dimensional deep learning features in a 2-D dimensional space while preserving the pairwise distances using the t-SNE algorithm. The 2-D visualization gives the unique ability to find groups of X-ray images that are similar to the query image and among themselves, which is a characteristic we do not see in a 1-D traditional ranking.

Further Improvements to Linear Mixed Models for Genome-Wide Association Studies

NASA Astrophysics Data System (ADS)

Widmer, Christian; Lippert, Christoph; Weissbrod, Omer; Fusi, Nicolo; Kadie, Carl; Davidson, Robert; Listgarten, Jennifer; Heckerman, David

2014-11-01

We examine improvements to the linear mixed model (LMM) that better correct for population structure and family relatedness in genome-wide association studies (GWAS). LMMs rely on the estimation of a genetic similarity matrix (GSM), which encodes the pairwise similarity between every two individuals in a cohort. These similarities are estimated from single nucleotide polymorphisms (SNPs) or other genetic variants. Traditionally, all available SNPs are used to estimate the GSM. In empirical studies across a wide range of synthetic and real data, we find that modifications to this approach improve GWAS performance as measured by type I error control and power. Specifically, when only population structure is present, a GSM constructed from SNPs that well predict the phenotype in combination with principal components as covariates controls type I error and yields more power than the traditional LMM. In any setting, with or without population structure or family relatedness, a GSM consisting of a mixture of two component GSMs, one constructed from all SNPs and another constructed from SNPs that well predict the phenotype again controls type I error and yields more power than the traditional LMM. Software implementing these improvements and the experimental comparisons are available at http://microsoft.com/science.

Further improvements to linear mixed models for genome-wide association studies.

PubMed

Widmer, Christian; Lippert, Christoph; Weissbrod, Omer; Fusi, Nicolo; Kadie, Carl; Davidson, Robert; Listgarten, Jennifer; Heckerman, David

2014-11-12

We examine improvements to the linear mixed model (LMM) that better correct for population structure and family relatedness in genome-wide association studies (GWAS). LMMs rely on the estimation of a genetic similarity matrix (GSM), which encodes the pairwise similarity between every two individuals in a cohort. These similarities are estimated from single nucleotide polymorphisms (SNPs) or other genetic variants. Traditionally, all available SNPs are used to estimate the GSM. In empirical studies across a wide range of synthetic and real data, we find that modifications to this approach improve GWAS performance as measured by type I error control and power. Specifically, when only population structure is present, a GSM constructed from SNPs that well predict the phenotype in combination with principal components as covariates controls type I error and yields more power than the traditional LMM. In any setting, with or without population structure or family relatedness, a GSM consisting of a mixture of two component GSMs, one constructed from all SNPs and another constructed from SNPs that well predict the phenotype again controls type I error and yields more power than the traditional LMM. Software implementing these improvements and the experimental comparisons are available at http://microsoft.com/science.

Arterial input function derived from pairwise correlations between PET-image voxels.

PubMed

Schain, Martin; Benjaminsson, Simon; Varnäs, Katarina; Forsberg, Anton; Halldin, Christer; Lansner, Anders; Farde, Lars; Varrone, Andrea

2013-07-01

A metabolite corrected arterial input function is a prerequisite for quantification of positron emission tomography (PET) data by compartmental analysis. This quantitative approach is also necessary for radioligands without suitable reference regions in brain. The measurement is laborious and requires cannulation of a peripheral artery, a procedure that can be associated with patient discomfort and potential adverse events. A non invasive procedure for obtaining the arterial input function is thus preferable. In this study, we present a novel method to obtain image-derived input functions (IDIFs). The method is based on calculation of the Pearson correlation coefficient between the time-activity curves of voxel pairs in the PET image to localize voxels displaying blood-like behavior. The method was evaluated using data obtained in human studies with the radioligands [(11)C]flumazenil and [(11)C]AZ10419369, and its performance was compared with three previously published methods. The distribution volumes (VT) obtained using IDIFs were compared with those obtained using traditional arterial measurements. Overall, the agreement in VT was good (∼3% difference) for input functions obtained using the pairwise correlation approach. This approach performed similarly or even better than the other methods, and could be considered in applied clinical studies. Applications to other radioligands are needed for further verification.

Feature Grouping and Selection Over an Undirected Graph.

PubMed

Yang, Sen; Yuan, Lei; Lai, Ying-Cheng; Shen, Xiaotong; Wonka, Peter; Ye, Jieping

2012-01-01

High-dimensional regression/classification continues to be an important and challenging problem, especially when features are highly correlated. Feature selection, combined with additional structure information on the features has been considered to be promising in promoting regression/classification performance. Graph-guided fused lasso (GFlasso) has recently been proposed to facilitate feature selection and graph structure exploitation, when features exhibit certain graph structures. However, the formulation in GFlasso relies on pairwise sample correlations to perform feature grouping, which could introduce additional estimation bias. In this paper, we propose three new feature grouping and selection methods to resolve this issue. The first method employs a convex function to penalize the pairwise l ∞ norm of connected regression/classification coefficients, achieving simultaneous feature grouping and selection. The second method improves the first one by utilizing a non-convex function to reduce the estimation bias. The third one is the extension of the second method using a truncated l 1 regularization to further reduce the estimation bias. The proposed methods combine feature grouping and feature selection to enhance estimation accuracy. We employ the alternating direction method of multipliers (ADMM) and difference of convex functions (DC) programming to solve the proposed formulations. Our experimental results on synthetic data and two real datasets demonstrate the effectiveness of the proposed methods.

DNorm: disease name normalization with pairwise learning to rank.

PubMed

Leaman, Robert; Islamaj Dogan, Rezarta; Lu, Zhiyong

2013-11-15

Despite the central role of diseases in biomedical research, there have been much fewer attempts to automatically determine which diseases are mentioned in a text-the task of disease name normalization (DNorm)-compared with other normalization tasks in biomedical text mining research. In this article we introduce the first machine learning approach for DNorm, using the NCBI disease corpus and the MEDIC vocabulary, which combines MeSH® and OMIM. Our method is a high-performing and mathematically principled framework for learning similarities between mentions and concept names directly from training data. The technique is based on pairwise learning to rank, which has not previously been applied to the normalization task but has proven successful in large optimization problems for information retrieval. We compare our method with several techniques based on lexical normalization and matching, MetaMap and Lucene. Our algorithm achieves 0.782 micro-averaged F-measure and 0.809 macro-averaged F-measure, an increase over the highest performing baseline method of 0.121 and 0.098, respectively. The source code for DNorm is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/DNorm, along with a web-based demonstration and links to the NCBI disease corpus. Results on PubMed abstracts are available in PubTator: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator .

Generation of Synthetic Spike Trains with Defined Pairwise Correlations

PubMed Central

Niebur, Ernst

2008-01-01

Recent technological advances as well as progress in theoretical understanding of neural systems have created a need for synthetic spike trains with controlled mean rate and pairwise cross-correlation. This report introduces and analyzes a novel algorithm for the generation of discretized spike trains with arbitrary mean rates and controlled cross correlation. Pairs of spike trains with any pairwise correlation can be generated, and higher-order correlations are compatible with common synaptic input. Relations between allowable mean rates and correlations within a population are discussed. The algorithm is highly efficient, its complexity increasing linearly with the number of spike trains generated and therefore inversely with the number of cross-correlated pairs. PMID:17521277

Pembrolizumab versus the standard of care for relapsed and refractory classical Hodgkin's lymphoma progressing after brentuximab vedotin: an indirect treatment comparison.

PubMed

Keeping, Sam; Wu, Elise; Chan, Keith; Mojebi, Ali; Ferrante, Shannon Allen; Balakumaran, Arun

2018-05-15

There is significant unmet need among patients with relapsed and refractory classical Hodgkin's lymphoma (RRcHL) who have failed multiple lines of therapy, including brentuximab vedotin (BV). Pembrolizumab, an immune checkpoint inhibitor, is one possible treatment solution for this population. The objective of this study was to compare progression-free survival (PFS) with standard of care (SOC) versus pembrolizumab in previously BV treated RRcHL patients. A systematic literature review identified one observational study (Cheah et al., 2016) of SOC that was suitable for comparison with KEYNOTE-087, the principal trial of pembrolizumab in this population. Both naïve and population-adjusted (using outcomes regression) pairwise indirect comparisons were conducted. The primary analysis included all patients who had failed BV, with a secondary analysis conducted including only those known to have failed BV that was part of definitive treatment. In the primary analysis, SOC was inferior to pembrolizumab in both the unadjusted comparison (HR 5.00 [95% confidence interval (CI) 3.56-7.01]) and the adjusted comparison (HR 6.35 [95% CI 4.04-9.98]). These HRs increased to 5.16 (95% CI 3.61-7.38) and 6.56 (95% CI 4.01-10.72), respectively, in the secondary analysis. Pembrolizumab offers a significant improvement in PFS compared to SOC in this population.

Prospects for inferring pairwise relationships with single nucleotide polymorphisms

Treesearch

Jeffery C. Glaubitz; O. Eugene, Jr. Rhodes; J. Andrew DeWoody

2003-01-01

An extraordinarily large number of single nucleotide polymorphisms (SNPs) are now available in humans as well as in other model organisms. Technological advancements may soon make it feasible to assay hundreds of SNPs in virtually any organism of interest. One potential application of SNPs is the determination of pairwise genetic relationships in populations without...

Hierarchical semi-numeric method for pairwise fuzzy group decision making.

PubMed

Marimin, M; Umano, M; Hatono, I; Tamura, H

2002-01-01

Gradual improvements to a single-level semi-numeric method, i.e., linguistic labels preference representation by fuzzy sets computation for pairwise fuzzy group decision making are summarized. The method is extended to solve multiple criteria hierarchical structure pairwise fuzzy group decision-making problems. The problems are hierarchically structured into focus, criteria, and alternatives. Decision makers express their evaluations of criteria and alternatives based on each criterion by using linguistic labels. The labels are converted into and processed in triangular fuzzy numbers (TFNs). Evaluations of criteria yield relative criteria weights. Evaluations of the alternatives, based on each criterion, yield a degree of preference for each alternative or a degree of satisfaction for each preference value. By using a neat ordered weighted average (OWA) or a fuzzy weighted average operator, solutions obtained based on each criterion are aggregated into final solutions. The hierarchical semi-numeric method is suitable for solving a larger and more complex pairwise fuzzy group decision-making problem. The proposed method has been verified and applied to solve some real cases and is compared to Saaty's (1996) analytic hierarchy process (AHP) method.

Performance analysis of a dual-tree algorithm for computing spatial distance histograms

PubMed Central

Chen, Shaoping; Tu, Yi-Cheng; Xia, Yuni

2011-01-01

Many scientific and engineering fields produce large volume of spatiotemporal data. The storage, retrieval, and analysis of such data impose great challenges to database systems design. Analysis of scientific spatiotemporal data often involves computing functions of all point-to-point interactions. One such analytics, the Spatial Distance Histogram (SDH), is of vital importance to scientific discovery. Recently, algorithms for efficient SDH processing in large-scale scientific databases have been proposed. These algorithms adopt a recursive tree-traversing strategy to process point-to-point distances in the visited tree nodes in batches, thus require less time when compared to the brute-force approach where all pairwise distances have to be computed. Despite the promising experimental results, the complexity of such algorithms has not been thoroughly studied. In this paper, we present an analysis of such algorithms based on a geometric modeling approach. The main technique is to transform the analysis of point counts into a problem of quantifying the area of regions where pairwise distances can be processed in batches by the algorithm. From the analysis, we conclude that the number of pairwise distances that are left to be processed decreases exponentially with more levels of the tree visited. This leads to the proof of a time complexity lower than the quadratic time needed for a brute-force algorithm and builds the foundation for a constant-time approximate algorithm. Our model is also general in that it works for a wide range of point spatial distributions, histogram types, and space-partitioning options in building the tree. PMID:21804753

Evaluation of satellite rainfall estimates for drought and flood monitoring in Mozambique

USGS Publications Warehouse

Tote, Carolien; Patricio, Domingos; Boogaard, Hendrik; van der Wijngaart, Raymond; Tarnavsky, Elena; Funk, Christopher C.

2015-01-01

Satellite derived rainfall products are useful for drought and flood early warning and overcome the problem of sparse, unevenly distributed and erratic rain gauge observations, provided their accuracy is well known. Mozambique is highly vulnerable to extreme weather events such as major droughts and floods and thus, an understanding of the strengths and weaknesses of different rainfall products is valuable. Three dekadal (10-day) gridded satellite rainfall products (TAMSAT African Rainfall Climatology And Time-series (TARCAT) v2.0, Famine Early Warning System NETwork (FEWS NET) Rainfall Estimate (RFE) v2.0, and Climate Hazards Group InfraRed Precipitation with Stations (CHIRPS)) are compared to independent gauge data (2001–2012). This is done using pairwise comparison statistics to evaluate the performance in estimating rainfall amounts and categorical statistics to assess rain-detection capabilities. The analysis was performed for different rainfall categories, over the seasonal cycle and for regions dominated by different weather systems. Overall, satellite products overestimate low and underestimate high dekadal rainfall values. The RFE and CHIRPS products perform as good, generally outperforming TARCAT on the majority of statistical measures of skill. TARCAT detects best the relative frequency of rainfall events, while RFE underestimates and CHIRPS overestimates the rainfall events frequency. Differences in products performance disappear with higher rainfall and all products achieve better results during the wet season. During the cyclone season, CHIRPS shows the best results, while RFE outperforms the other products for lower dekadal rainfall. Products blending thermal infrared and passive microwave imagery perform better than infrared only products and particularly when meteorological patterns are more complex, such as over the coastal, central and south regions of Mozambique, where precipitation is influenced by frontal systems.

Effects of non-neuronal components for functional connectivity analysis from resting-state functional MRI toward automated diagnosis of schizophrenia

NASA Astrophysics Data System (ADS)

Kim, Junghoe; Lee, Jong-Hwan

2014-03-01

A functional connectivity (FC) analysis from resting-state functional MRI (rsfMRI) is gaining its popularity toward the clinical application such as diagnosis of neuropsychiatric disease. To delineate the brain networks from rsfMRI data, non-neuronal components including head motions and physiological artifacts mainly observed in cerebrospinal fluid (CSF), white matter (WM) along with a global brain signal have been regarded as nuisance variables in calculating the FC level. However, it is still unclear how the non-neuronal components can affect the performance toward diagnosis of neuropsychiatric disease. In this study, a systematic comparison of classification performance of schizophrenia patients was provided employing the partial correlation coefficients (CCs) as feature elements. Pair-wise partial CCs were calculated between brain regions, in which six combinatorial sets of nuisance variables were considered. The partial CCs were used as candidate feature elements followed by feature selection based on the statistical significance test between two groups in the training set. Once a linear support vector machine was trained using the selected features from the training set, the classification performance was evaluated using the features from the test set (i.e. leaveone- out cross validation scheme). From the results, the error rate using all non-neuronal components as nuisance variables (12.4%) was significantly lower than those using remaining combination of non-neuronal components as nuisance variables (13.8 ~ 20.0%). In conclusion, the non-neuronal components substantially degraded the automated diagnosis performance, which supports our hypothesis that the non-neuronal components are crucial in controlling the automated diagnosis performance of the neuropsychiatric disease using an fMRI modality.

No added diagnostic value of non-phosphorylated tau fraction (p-taurel) in CSF as a biomarker for differential dementia diagnosis.

PubMed

Goossens, Joery; Bjerke, Maria; Struyfs, Hanne; Niemantsverdriet, Ellis; Somers, Charisse; Van den Bossche, Tobi; Van Mossevelde, Sara; De Vil, Bart; Sieben, Anne; Martin, Jean-Jacques; Cras, Patrick; Goeman, Johan; De Deyn, Peter Paul; Van Broeckhoven, Christine; van der Zee, Julie; Engelborghs, Sebastiaan

2017-07-14

The Alzheimer's disease (AD) cerebrospinal fluid (CSF) biomarkers Aβ 1-42 , t-tau, and p-tau 181 overlap with other diseases. New tau modifications or epitopes, such as the non-phosphorylated tau fraction (p-tau rel ), may improve differential dementia diagnosis. The goal of this study is to investigate if p-tau rel can improve the diagnostic performance of the AD CSF biomarker panel for differential dementia diagnosis. The study population consisted of 45 AD, 45 frontotemporal lobar degeneration (FTLD), 45 dementia with Lewy bodies (DLB), and 21 Creutzfeldt-Jakob disease (CJD) patients, and 20 cognitively healthy controls. A substantial subset of the patients was pathology-confirmed. CSF levels of Aβ 1-42 , t-tau, p-tau 181 , and p-tau rel were determined with commercially available single-analyte enzyme-linked immunosorbent assay (ELISA) kits. Diagnostic performance was evaluated by receiver operating characteristic (ROC) curve analyses, and area under the curve (AUC) values were compared using DeLong tests. The diagnostic performance of single markers as well as biomarker ratios was determined for each pairwise comparison of different dementia groups and controls. The addition of p-tau rel to the AD biomarker panel decreased its diagnostic performance when discriminating non-AD, FTLD, and DLB from AD. As a single marker, p-tau rel increased the diagnostic performance for CJD. No significant difference was found in AUC values with the addition of p-tau rel when differentiating between AD or non-AD dementias and controls. The addition of p-tau rel to the AD CSF biomarker panel failed to improve differentiation between AD and non-AD dementias.

The acute effect of a plyometric stimulus on jump performance in professional rugby players.

PubMed

Tobin, Daniel P; Delahunt, Eamonn

2014-02-01

Post-activation potentiation (PAP) is the elevation of motor performance to a higher level in response to a conditioning stimulus. Extensive research exists examining the PAP effect after a heavy resistance exercise. However, there is limited research examining the PAP effect after a plyometric stimulus. This study was designed to examine whether a plyometric stimulus could produce a PAP effect comparable to that typically reported with a heavy resistance protocol. Importantly, it was hypothesized that the PAP effect would exist without the same levels of acute fatigue resulting from a heavy stimulus, thus allowing improvement in performance within a short rest interval range. Twenty professional rugby players were recruited for the study. Subjects performed 2 countermovement jumps (CMJs) at baseline and at 1, 3, and 5 minutes after a plyometric stimulus consisting of 40 jumps. Two separate 1-way repeated-measures analyses of variance were conducted to compare the dependent variables CMJ height and peak force at the 4 time points. Results of the Bonferroni adjusted pairwise comparisons indicated that jump height and peak force before plyometric exercises were significantly lower than all other time points (p < 0.01). The main finding of this study indicates that a series of plyometric exercises causes a significant acute enhancement in CMJ height (p < 0.01) and peak force (p < 0.01) throughout the rest interval range of 1-5 minutes. The plyometric series induced an improvement in CMJ height comparable to that reported elsewhere after a heavy lifting stimulus but without the need for a prolonged rest interval. Performing repeated series of plyometric jumps appears to be an efficient method of taking advantage of the PAP phenomenon, thus possibly eliminating the need for a complex training protocol.

Adjusting protein graphs based on graph entropy.

PubMed

Peng, Sheng-Lung; Tsay, Yu-Wei

2014-01-01

Measuring protein structural similarity attempts to establish a relationship of equivalence between polymer structures based on their conformations. In several recent studies, researchers have explored protein-graph remodeling, instead of looking a minimum superimposition for pairwise proteins. When graphs are used to represent structured objects, the problem of measuring object similarity become one of computing the similarity between graphs. Graph theory provides an alternative perspective as well as efficiency. Once a protein graph has been created, its structural stability must be verified. Therefore, a criterion is needed to determine if a protein graph can be used for structural comparison. In this paper, we propose a measurement for protein graph remodeling based on graph entropy. We extend the concept of graph entropy to determine whether a graph is suitable for representing a protein. The experimental results suggest that when applied, graph entropy helps a conformational on protein graph modeling. Furthermore, it indirectly contributes to protein structural comparison if a protein graph is solid.

First-principles anharmonic quantum calculations for peptide spectroscopy: VSCF calculations and comparison with experiments.

PubMed

Roy, Tapta Kanchan; Sharma, Rahul; Gerber, R Benny

2016-01-21

First-principles quantum calculations for anharmonic vibrational spectroscopy of three protected dipeptides are carried out and compared with experimental data. Using hybrid HF/MP2 potentials, the Vibrational Self-Consistent Field with Second-Order Perturbation Correction (VSCF-PT2) algorithm is used to compute the spectra without any ad hoc scaling or fitting. All of the vibrational modes (135 for the largest system) are treated quantum mechanically and anharmonically using full pair-wise coupling potentials to represent the interaction between different modes. In the hybrid potential scheme the MP2 method is used for the harmonic part of the potential and a modified HF method is used for the anharmonic part. The overall agreement between computed spectra and experiment is very good and reveals different signatures for different conformers. This study shows that first-principles spectroscopic calculations of good accuracy are possible for dipeptides hence it opens possibilities for determination of dipeptide conformer structures by comparison of spectroscopic calculations with experiment.

Geographic profiling to assess the risk of rare plant poaching in natural areas

USGS Publications Warehouse

Young, J.A.; Van Manen, F.T.; Thatcher, C.A.

2011-01-01

We demonstrate the use of an expert-assisted spatial model to examine geographic factors influencing the poaching risk of a rare plant (American ginseng, Panax quinquefolius L.) in Shenandoah National Park, Virginia, USA. Following principles of the analytic hierarchy process (AHP), we identified a hierarchy of 11 geographic factors deemed important to poaching risk and requested law enforcement personnel of the National Park Service to rank those factors in a series of pair-wise comparisons. We used those comparisons to determine statistical weightings of each factor and combined them into a spatial model predicting poaching risk. We tested the model using 69 locations of previous poaching incidents recorded by law enforcement personnel. These locations occurred more frequently in areas predicted by the model to have a higher risk of poaching than random locations. The results of our study can be used to evaluate resource protection strategies and to target law enforcement activities. ?? Springer Science+Business Media, LLC (outside the USA) 2011.