Optimal random Lévy-loop searching: New insights into the searching behaviours of central-place foragers

NASA Astrophysics Data System (ADS)

Reynolds, A. M.

2008-04-01

A random Lévy-looping model of searching is devised and optimal random Lévy-looping searching strategies are identified for the location of a single target whose position is uncertain. An inverse-square power law distribution of loop lengths is shown to be optimal when the distance between the centre of the search and the target is much shorter than the size of the longest possible loop in the searching pattern. Optimal random Lévy-looping searching patterns have recently been observed in the flight patterns of honeybees (Apis mellifera) when attempting to locate their hive and when searching after a known food source becomes depleted. It is suggested that the searching patterns of desert ants (Cataglyphis) are consistent with the adoption of an optimal Lévy-looping searching strategy.

Expected Fitness Gains of Randomized Search Heuristics for the Traveling Salesperson Problem.

PubMed

Nallaperuma, Samadhi; Neumann, Frank; Sudholt, Dirk

2017-01-01

Randomized search heuristics are frequently applied to NP-hard combinatorial optimization problems. The runtime analysis of randomized search heuristics has contributed tremendously to our theoretical understanding. Recently, randomized search heuristics have been examined regarding their achievable progress within a fixed-time budget. We follow this approach and present a fixed-budget analysis for an NP-hard combinatorial optimization problem. We consider the well-known Traveling Salesperson Problem (TSP) and analyze the fitness increase that randomized search heuristics are able to achieve within a given fixed-time budget. In particular, we analyze Manhattan and Euclidean TSP instances and Randomized Local Search (RLS), (1+1) EA and (1+[Formula: see text]) EA algorithms for the TSP in a smoothed complexity setting, and derive the lower bounds of the expected fitness gain for a specified number of generations.

Structural Relations among Spirituality, Religiosity, and Thriving in Adolescence

ERIC Educational Resources Information Center

Dowling, Elizabeth M.; Gestsdottir, Steinunn; Anderson, Pamela M.; Von Eye, Alexander; Almerigi, Jason; Lerner, Richard M.

2004-01-01

Using the randomly selected subsample of 1,000 youth (472 boys, M age = 12.2 years, SD = 1.5; 528 girls, M age = 12.1 years, SD = 1.4) drawn by Dowling, Getsdottir, Anderson, von Eye, and Lerner (in press) from a Search Institute (1984) archival data set, Young Adolescents and Their Parents (YAP), this research employed structural equation…

Knowledge Representation for Decision Making Agents

DTIC Science & Technology

2013-07-15

knowledge map. This knowledge map is a dictionary data structure called tmap in the code. It represents a network of locations with a number [0,1...fillRandom(): Informed initial tmap distribution (randomly generated per node) with belief one. • initialBelief = 3 uses fillCenter(): normal...triggered on AllMyFMsHaveBeenInitialized. 2. Executes main.py • Initializes knowledge map labeled tmap . • Calls initialize search() – resets distanceTot and

An energy-based perturbation and a taboo strategy for improving the searching ability of stochastic structural optimization methods

NASA Astrophysics Data System (ADS)

Cheng, Longjiu; Cai, Wensheng; Shao, Xueguang

2005-03-01

An energy-based perturbation and a new idea of taboo strategy are proposed for structural optimization and applied in a benchmark problem, i.e., the optimization of Lennard-Jones (LJ) clusters. It is proved that the energy-based perturbation is much better than the traditional random perturbation both in convergence speed and searching ability when it is combined with a simple greedy method. By tabooing the most wide-spread funnel instead of the visited solutions, the hit rate of other funnels can be significantly improved. Global minima of (LJ) clusters up to 200 atoms are found with high efficiency.

Decision making in family medicine: randomized trial of the effects of the InfoClinique and Trip database search engines.

PubMed

Labrecque, Michel; Ratté, Stéphane; Frémont, Pierre; Cauchon, Michel; Ouellet, Jérôme; Hogg, William; McGowan, Jessie; Gagnon, Marie-Pierre; Njoya, Merlin; Légaré, France

2013-10-01

To compare the ability of users of 2 medical search engines, InfoClinique and the Trip database, to provide correct answers to clinical questions and to explore the perceived effects of the tools on the clinical decision-making process. Randomized trial. Three family medicine units of the family medicine program of the Faculty of Medicine at Laval University in Quebec city, Que. Fifteen second-year family medicine residents. Residents generated 30 structured questions about therapy or preventive treatment (2 questions per resident) based on clinical encounters. Using an Internet platform designed for the trial, each resident answered 20 of these questions (their own 2, plus 18 of the questions formulated by other residents, selected randomly) before and after searching for information with 1 of the 2 search engines. For each question, 5 residents were randomly assigned to begin their search with InfoClinique and 5 with the Trip database. The ability of residents to provide correct answers to clinical questions using the search engines, as determined by third-party evaluation. After answering each question, participants completed a questionnaire to assess their perception of the engine's effect on the decision-making process in clinical practice. Of 300 possible pairs of answers (1 answer before and 1 after the initial search), 254 (85%) were produced by 14 residents. Of these, 132 (52%) and 122 (48%) pairs of answers concerned questions that had been assigned an initial search with InfoClinique and the Trip database, respectively. Both engines produced an important and similar absolute increase in the proportion of correct answers after searching (26% to 62% for InfoClinique, for an increase of 36%; 24% to 63% for the Trip database, for an increase of 39%; P = .68). For all 30 clinical questions, at least 1 resident produced the correct answer after searching with either search engine. The mean (SD) time of the initial search for each question was 23.5 (7.6) minutes with InfoClinique and 22.3 (7.8) minutes with the Trip database (P = .30). Participants' perceptions of each engine's effect on the decision-making process were very positive and similar for both search engines. Family medicine residents' ability to provide correct answers to clinical questions increased dramatically and similarly with the use of both InfoClinique and the Trip database. These tools have strong potential to increase the quality of medical care.

Stochastic generation of complex crystal structures combining group and graph theory with application to carbon

NASA Astrophysics Data System (ADS)

Shi, Xizhi; He, Chaoyu; Pickard, Chris J.; Tang, Chao; Zhong, Jianxin

2018-01-01

A method is introduced to stochastically generate crystal structures with defined structural characteristics. Reasonable quotient graphs for symmetric crystals are constructed using a random strategy combined with space group and graph theory. Our algorithm enables the search for large-size and complex crystal structures with a specified connectivity, such as threefold sp2 carbons, fourfold sp3 carbons, as well as mixed sp2-sp3 carbons. To demonstrate the method, we randomly construct initial structures adhering to space groups from 75 to 230 and a range of lattice constants, and we identify 281 new sp3 carbon crystals. First-principles optimization of these structures show that most of them are dynamically and mechanically stable and are energetically comparable to those previously proposed. Some of the new structures can be considered as candidates to explain the experimental cold compression of graphite.

Bridging the Gap Between Theory and Practice: Structure and Randomization in Large Scale Combinatorial Search

DTIC Science & Technology

2012-01-17

PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION...world problems. Our work brings together techniques from constraint programming, mathematical programming, and satisfiability in a symbiotic way to...power-­‐law  search  tree  model  for  complete  or  exact  methods     (See [9] for a detailed description of this work and

Advanced fitness landscape analysis and the performance of memetic algorithms.

PubMed

Merz, Peter

2004-01-01

Memetic algorithms (MAs) have demonstrated very effective in combinatorial optimization. This paper offers explanations as to why this is so by investigating the performance of MAs in terms of efficiency and effectiveness. A special class of MAs is used to discuss efficiency and effectiveness for local search and evolutionary meta-search. It is shown that the efficiency of MAs can be increased drastically with the use of domain knowledge. However, effectiveness highly depends on the structure of the problem. As is well-known, identifying this structure is made easier with the notion of fitness landscapes: the local properties of the fitness landscape strongly influence the effectiveness of the local search while the global properties strongly influence the effectiveness of the evolutionary meta-search. This paper also introduces new techniques for analyzing the fitness landscapes of combinatorial problems; these techniques focus on the investigation of random walks in the fitness landscape starting at locally optimal solutions as well as on the escape from the basins of attractions of current local optima. It is shown for NK-landscapes and landscapes of the unconstrained binary quadratic programming problem (BQP) that a random walk to another local optimum can be used to explain the efficiency of recombination in comparison to mutation. Moreover, the paper shows that other aspects like the size of the basins of attractions of local optima are important for the efficiency of MAs and a local search escape analysis is proposed. These simple analysis techniques have several advantages over previously proposed statistical measures and provide valuable insight into the behaviour of MAs on different kinds of landscapes.

Ab initio structure prediction of silicon and germanium sulfides for lithium-ion battery materials

NASA Astrophysics Data System (ADS)

Hsueh, Connie; Mayo, Martin; Morris, Andrew J.

Conventional experimental-based approaches to materials discovery, which can rely heavily on trial and error, are time-intensive and costly. We discuss approaches to coupling experimental and computational techniques in order to systematize, automate, and accelerate the process of materials discovery, which is of particular relevance to developing new battery materials. We use the ab initio random structure searching (AIRSS) method to conduct a systematic investigation of Si-S and Ge-S binary compounds in order to search for novel materials for lithium-ion battery (LIB) anodes. AIRSS is a high-throughput, density functional theory-based approach to structure prediction which has been successful at predicting the structures of LIBs containing sulfur and silicon and germanium. We propose a lithiation mechanism for Li-GeS2 anodes as well as report new, theoretically stable, layered and porous structures in the Si-S and Ge-S systems that pique experimental interest.

The effects of prey patchiness, predator aggregation, and mutual interference on the functional response of Phytoseiulus persimilis feeding on Tetranychus urticae (Acari: Phytoseiidae, Tetranychidae).

PubMed

Nachman, Gösta

2006-01-01

The spatial distributions of two-spotted spider mites Tetranychus urticae and their natural enemy, the phytoseiid predator Phytoseiulus persimilis, were studied on six full-grown cucumber plants. Both mite species were very patchily distributed and P. persimilis tended to aggregate on leaves with abundant prey. The effects of non-homogenous distributions and degree of spatial overlap between prey and predators on the per capita predation rate were studied by means of a stage-specific predation model that averages the predation rates over all the local populations inhabiting the individual leaves. The empirical predation rates were compared with predictions assuming random predator search and/or an even distribution of prey. The analysis clearly shows that the ability of the predators to search non-randomly increases their predation rate. On the other hand, the prey may gain if it adopts a more even distribution when its density is low and a more patchy distribution when density increases. Mutual interference between searching predators reduces the predation rate, but the effect is negligible. The stage-specific functional response model was compared with two simpler models without explicit stage structure. Both unstructured models yielded predictions that were quite similar to those of the stage-structured model.

An adaptive random search for short term generation scheduling with network constraints.

PubMed

Marmolejo, J A; Velasco, Jonás; Selley, Héctor J

2017-01-01

This paper presents an adaptive random search approach to address a short term generation scheduling with network constraints, which determines the startup and shutdown schedules of thermal units over a given planning horizon. In this model, we consider the transmission network through capacity limits and line losses. The mathematical model is stated in the form of a Mixed Integer Non Linear Problem with binary variables. The proposed heuristic is a population-based method that generates a set of new potential solutions via a random search strategy. The random search is based on the Markov Chain Monte Carlo method. The main key of the proposed method is that the noise level of the random search is adaptively controlled in order to exploring and exploiting the entire search space. In order to improve the solutions, we consider coupling a local search into random search process. Several test systems are presented to evaluate the performance of the proposed heuristic. We use a commercial optimizer to compare the quality of the solutions provided by the proposed method. The solution of the proposed algorithm showed a significant reduction in computational effort with respect to the full-scale outer approximation commercial solver. Numerical results show the potential and robustness of our approach.

Mechanistic analysis of the search behaviour of Caenorhabditis elegans

PubMed Central

Salvador, Liliana C. M.; Bartumeus, Frederic; Levin, Simon A.; Ryu, William S.

2014-01-01

A central question in movement research is how animals use information and movement to promote encounter success. Current random search theory identifies reorientation patterns as key to the compromise between optimizing encounters for both nearby and faraway targets, but how the balance between intrinsic motor programmes and previous environmental experience determines the occurrence of these reorientation behaviours remains unknown. We used high-resolution tracking and imaging data to describe the complete motor behaviour of Caenorhabditis elegans when placed in a novel environment (one in which food is absent). Movement in C. elegans is structured around different reorientation behaviours, and we measured how these contributed to changing search strategies as worms became familiar with their new environment. This behavioural transition shows that different reorientation behaviours are governed by two processes: (i) an environmentally informed ‘extrinsic’ strategy that is influenced by recent experience and that controls for area-restricted search behaviour, and (ii) a time-independent, ‘intrinsic’ strategy that reduces spatial oversampling and improves random encounter success. Our results show how movement strategies arise from a balance between intrinsic and extrinsic mechanisms, that search behaviour in C. elegans is initially determined by expectations developed from previous environmental experiences, and which reorientation behaviours are modified as information is acquired from new environments. PMID:24430127

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.

PubMed

Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme

2013-07-01

The design of RNA sequences folding into predefined secondary structures is a milestone for many synthetic biology and gene therapy studies. Most of the current software uses similar local search strategies (i.e. a random seed is progressively adapted to acquire the desired folding properties) and more importantly do not allow the user to control explicitly the nucleotide distribution such as the GC-content in their sequences. However, the latter is an important criterion for large-scale applications as it could presumably be used to design sequences with better transcription rates and/or structural plasticity. In this article, we introduce IncaRNAtion, a novel algorithm to design RNA sequences folding into target secondary structures with a predefined nucleotide distribution. IncaRNAtion uses a global sampling approach and weighted sampling techniques. We show that our approach is fast (i.e. running time comparable or better than local search methods), seedless (we remove the bias of the seed in local search heuristics) and successfully generates high-quality sequences (i.e. thermodynamically stable) for any GC-content. To complete this study, we develop a hybrid method combining our global sampling approach with local search strategies. Remarkably, our glocal methodology overcomes both local and global approaches for sampling sequences with a specific GC-content and target structure. IncaRNAtion is available at csb.cs.mcgill.ca/incarnation/. Supplementary data are available at Bioinformatics online.

Phase diagram of germanium telluride encapsulated in carbon nanotubes from first-principles searches

NASA Astrophysics Data System (ADS)

Wynn, Jamie M.; Medeiros, Paulo V. C.; Vasylenko, Andrij; Sloan, Jeremy; Quigley, David; Morris, Andrew J.

2017-12-01

Germanium telluride has attracted great research interest, primarily because of its phase-change properties. We have developed a general scheme, based on the ab initio random structure searching (AIRSS) method, for predicting the structures of encapsulated nanowires, and using this we predict a number of thermodynamically stable structures of GeTe nanowires encapsulated inside carbon nanotubes of radii under 9 Å . We construct the phase diagram of encapsulated GeTe, which provides quantitative predictions about the energetic favorability of different filling structures as a function of the nanotube radius, such as the formation of a quasi-one-dimensional rock-salt-like phase inside nanotubes of radii between 5.4 and 7.9 Å . Simulated TEM images of our structures show excellent agreement between our results and experimental TEM imagery. We show that, for some nanotubes, the nanowires undergo temperature-induced phase transitions from one crystalline structure to another due to vibrational contributions to the free energy, which is a first step toward nano-phase-change memory devices.

Data-Driven Learning of Total and Local Energies in Elemental Boron

NASA Astrophysics Data System (ADS)

Deringer, Volker L.; Pickard, Chris J.; Csányi, Gábor

2018-04-01

The allotropes of boron continue to challenge structural elucidation and solid-state theory. Here we use machine learning combined with random structure searching (RSS) algorithms to systematically construct an interatomic potential for boron. Starting from ensembles of randomized atomic configurations, we use alternating single-point quantum-mechanical energy and force computations, Gaussian approximation potential (GAP) fitting, and GAP-driven RSS to iteratively generate a representation of the element's potential-energy surface. Beyond the total energies of the very different boron allotropes, our model readily provides atom-resolved, local energies and thus deepened insight into the frustrated β -rhombohedral boron structure. Our results open the door for the efficient and automated generation of GAPs, and other machine-learning-based interatomic potentials, and suggest their usefulness as a tool for materials discovery.

Data-Driven Learning of Total and Local Energies in Elemental Boron.

PubMed

Deringer, Volker L; Pickard, Chris J; Csányi, Gábor

2018-04-13

The allotropes of boron continue to challenge structural elucidation and solid-state theory. Here we use machine learning combined with random structure searching (RSS) algorithms to systematically construct an interatomic potential for boron. Starting from ensembles of randomized atomic configurations, we use alternating single-point quantum-mechanical energy and force computations, Gaussian approximation potential (GAP) fitting, and GAP-driven RSS to iteratively generate a representation of the element's potential-energy surface. Beyond the total energies of the very different boron allotropes, our model readily provides atom-resolved, local energies and thus deepened insight into the frustrated β-rhombohedral boron structure. Our results open the door for the efficient and automated generation of GAPs, and other machine-learning-based interatomic potentials, and suggest their usefulness as a tool for materials discovery.

Truss Optimization for a Manned Nuclear Electric Space Vehicle using Genetic Algorithms

NASA Technical Reports Server (NTRS)

Benford, Andrew; Tinker, Michael L.

2004-01-01

The purpose of this paper is to utilize the genetic algorithm (GA) optimization method for structural design of a nuclear propulsion vehicle. Genetic algorithms provide a guided, random search technique that mirrors biological adaptation. To verify the GA capabilities, other traditional optimization methods were used to generate results for comparison to the GA results, first for simple two-dimensional structures, and then for full-scale three-dimensional truss designs.

Study on Multi-stage Logistics System Design Problem with Inventory Considering Demand Change by Hybrid Genetic Algorithm

NASA Astrophysics Data System (ADS)

Inoue, Hisaki; Gen, Mitsuo

The logistics model used in this study is 3-stage model employed by an automobile company, which aims to solve traffic problems at a total minimum cost. Recently, research on the metaheuristics method has advanced as an approximate means for solving optimization problems like this model. These problems can be solved using various methods such as the genetic algorithm (GA), simulated annealing, and tabu search. GA is superior in robustness and adjustability toward a change in the structure of these problems. However, GA has a disadvantage in that it has a slightly inefficient search performance because it carries out a multi-point search. A hybrid GA that combines another method is attracting considerable attention since it can compensate for a fault to a partial solution that early convergence gives a bad influence on a result. In this study, we propose a novel hybrid random key-based GA(h-rkGA) that combines local search and parameter tuning of crossover rate and mutation rate; h-rkGA is an improved version of the random key-based GA (rk-GA). We attempted comparative experiments with spanning tree-based GA, priority based GA and random key-based GA. Further, we attempted comparative experiments with “h-GA by only local search” and “h-GA by only parameter tuning”. We reported the effectiveness of the proposed method on the basis of the results of these experiments.

Improved hybrid optimization algorithm for 3D protein structure prediction.

PubMed

Zhou, Changjun; Hou, Caixia; Wei, Xiaopeng; Zhang, Qiang

2014-07-01

A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins.

Determination of Slope Safety Factor with Analytical Solution and Searching Critical Slip Surface with Genetic-Traversal Random Method

PubMed Central

2014-01-01

In the current practice, to determine the safety factor of a slope with two-dimensional circular potential failure surface, one of the searching methods for the critical slip surface is Genetic Algorithm (GA), while the method to calculate the slope safety factor is Fellenius' slices method. However GA needs to be validated with more numeric tests, while Fellenius' slices method is just an approximate method like finite element method. This paper proposed a new method to determine the minimum slope safety factor which is the determination of slope safety factor with analytical solution and searching critical slip surface with Genetic-Traversal Random Method. The analytical solution is more accurate than Fellenius' slices method. The Genetic-Traversal Random Method uses random pick to utilize mutation. A computer automatic search program is developed for the Genetic-Traversal Random Method. After comparison with other methods like slope/w software, results indicate that the Genetic-Traversal Random Search Method can give very low safety factor which is about half of the other methods. However the obtained minimum safety factor with Genetic-Traversal Random Search Method is very close to the lower bound solutions of slope safety factor given by the Ansys software. PMID:24782679

Structured sedation programs in the emergency department, hospital and other acute settings: protocol for systematic review of effects and events.

PubMed

McCoy, Siobhán; Wakai, Abel; Blackburn, Carol; Barrett, Michael; Murphy, Adrian; Brenner, Maria; Larkin, Philip; Crispino-O'Connell, Gloria; Ratnapalan, Savithiri; O'Sullivan, Ronan

2013-10-01

The use of procedural sedation outside the operating theatre has increased in hospital settings and has gained popularity among non-anesthesiologists. Sedative agents used for procedural pain, although effective, also pose significant risks to the patient if used incorrectly. There is currently no universally accepted program of education for practitioners using or introducing procedural sedation into their practice. There is emerging literature identifying structured procedural sedation programs (PSPs) as a method of ensuring a standardized level of competency among staff and reducing risks to the patient. We hypothesize that programs of education for healthcare professionals using procedural sedation outside the operating theatre are beneficial in improving patient care, safety, practitioner competence and reducing adverse event rates. Electronic databases will be systematically searched for studies (randomized and non-randomized) examining the effectiveness of structured PSPs from 1966 to present. Database searches will be supplemented by contact with experts, reference and citation checking, and a grey literature search. No language restriction will be imposed. Screening of titles and abstracts, and data extraction will be performed by two independent reviewers. All disagreements will be resolved by discussion with an independent third party. Data analysis will be completed adhering to procedures outlined in the Cochrane Handbook of Systematic Reviews of Interventions. If the data allows, a meta-analysis will be performed. This review will cohere evidence on the effectiveness of structured PSPs on sedation events and patient outcomes within the hospital and other acute care settings. In addition, it will examine key components identified within a PSP associated with patient safety and improved patient outcomes. PROSPERO registration number: CRD42013003851.

Is Internet search better than structured instruction for web-based health education?

PubMed

Finkelstein, Joseph; Bedra, McKenzie

2013-01-01

Internet provides access to vast amounts of comprehensive information regarding any health-related subject. Patients increasingly use this information for health education using a search engine to identify education materials. An alternative approach of health education via Internet is based on utilizing a verified web site which provides structured interactive education guided by adult learning theories. Comparison of these two approaches in older patients was not performed systematically. The aim of this study was to compare the efficacy of a web-based computer-assisted education (CO-ED) system versus searching the Internet for learning about hypertension. Sixty hypertensive older adults (age 45+) were randomized into control or intervention groups. The control patients spent 30 to 40 minutes searching the Internet using a search engine for information about hypertension. The intervention patients spent 30 to 40 minutes using the CO-ED system, which provided computer-assisted instruction about major hypertension topics. Analysis of pre- and post- knowledge scores indicated a significant improvement among CO-ED users (14.6%) as opposed to Internet users (2%). Additionally, patients using the CO-ED program rated their learning experience more positively than those using the Internet.

Emergence of Lévy Walks from Second-Order Stochastic Optimization

NASA Astrophysics Data System (ADS)

Kuśmierz, Łukasz; Toyoizumi, Taro

2017-12-01

In natural foraging, many organisms seem to perform two different types of motile search: directed search (taxis) and random search. The former is observed when the environment provides cues to guide motion towards a target. The latter involves no apparent memory or information processing and can be mathematically modeled by random walks. We show that both types of search can be generated by a common mechanism in which Lévy flights or Lévy walks emerge from a second-order gradient-based search with noisy observations. No explicit switching mechanism is required—instead, continuous transitions between the directed and random motions emerge depending on the Hessian matrix of the cost function. For a wide range of scenarios, the Lévy tail index is α =1 , consistent with previous observations in foraging organisms. These results suggest that adopting a second-order optimization method can be a useful strategy to combine efficient features of directed and random search.

Evolutionary optimization of biopolymers and sequence structure maps

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

Reidys, C.M.; Kopp, S.; Schuster, P.

1996-06-01

Searching for biopolymers having a predefined function is a core problem of biotechnology, biochemistry and pharmacy. On the level of RNA sequences and their corresponding secondary structures we show that this problem can be analyzed mathematically. The strategy will be to study the properties of the RNA sequence to secondary structure mapping that is essential for the understanding of the search process. We show that to each secondary structure s there exists a neutral network consisting of all sequences folding into s. This network can be modeled as a random graph and has the following generic properties: it is densemore » and has a giant component within the graph of compatible sequences. The neutral network percolates sequence space and any two neutral nets come close in terms of Hamming distance. We investigate the distribution of the orders of neutral nets and show that above a certain threshold the topology of neutral nets allows to find practically all frequent secondary structures.« less

School Locker Searches and the Fourth Amendment.

ERIC Educational Resources Information Center

Bjorklun, Eugene C.

1995-01-01

Because school lockers are potential hiding places for weapons and drugs, some schools are eliminating them. Searching student lockers on a random basis raises legal questions. Examines the legality of random locker searches based upon the guidelines for student searches set forth by the Supreme Court in "New Jersey v. T.L.O." and lower…

Recursive Branching Simulated Annealing Algorithm

NASA Technical Reports Server (NTRS)

Bolcar, Matthew; Smith, J. Scott; Aronstein, David

2012-01-01

This innovation is a variation of a simulated-annealing optimization algorithm that uses a recursive-branching structure to parallelize the search of a parameter space for the globally optimal solution to an objective. The algorithm has been demonstrated to be more effective at searching a parameter space than traditional simulated-annealing methods for a particular problem of interest, and it can readily be applied to a wide variety of optimization problems, including those with a parameter space having both discrete-value parameters (combinatorial) and continuous-variable parameters. It can take the place of a conventional simulated- annealing, Monte-Carlo, or random- walk algorithm. In a conventional simulated-annealing (SA) algorithm, a starting configuration is randomly selected within the parameter space. The algorithm randomly selects another configuration from the parameter space and evaluates the objective function for that configuration. If the objective function value is better than the previous value, the new configuration is adopted as the new point of interest in the parameter space. If the objective function value is worse than the previous value, the new configuration may be adopted, with a probability determined by a temperature parameter, used in analogy to annealing in metals. As the optimization continues, the region of the parameter space from which new configurations can be selected shrinks, and in conjunction with lowering the annealing temperature (and thus lowering the probability for adopting configurations in parameter space with worse objective functions), the algorithm can converge on the globally optimal configuration. The Recursive Branching Simulated Annealing (RBSA) algorithm shares some features with the SA algorithm, notably including the basic principles that a starting configuration is randomly selected from within the parameter space, the algorithm tests other configurations with the goal of finding the globally optimal solution, and the region from which new configurations can be selected shrinks as the search continues. The key difference between these algorithms is that in the SA algorithm, a single path, or trajectory, is taken in parameter space, from the starting point to the globally optimal solution, while in the RBSA algorithm, many trajectories are taken; by exploring multiple regions of the parameter space simultaneously, the algorithm has been shown to converge on the globally optimal solution about an order of magnitude faster than when using conventional algorithms. Novel features of the RBSA algorithm include: 1. More efficient searching of the parameter space due to the branching structure, in which multiple random configurations are generated and multiple promising regions of the parameter space are explored; 2. The implementation of a trust region for each parameter in the parameter space, which provides a natural way of enforcing upper- and lower-bound constraints on the parameters; and 3. The optional use of a constrained gradient- search optimization, performed on the continuous variables around each branch s configuration in parameter space to improve search efficiency by allowing for fast fine-tuning of the continuous variables within the trust region at that configuration point.

A global sampling approach to designing and reengineering RNA secondary structures.

PubMed

Levin, Alex; Lis, Mieszko; Ponty, Yann; O'Donnell, Charles W; Devadas, Srinivas; Berger, Bonnie; Waldispühl, Jérôme

2012-11-01

The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed sequence is generated; next, this seed is progressively modified (i.e. mutated) to adopt the desired folding properties. Although computationally inexpensive, this approach raises several questions such as (i) the influence of the seed; and (ii) the efficiency of single-path directed searches that may be affected by energy barriers in the mutational landscape. In this article, we present RNA-ensign, a novel paradigm for RNA design. Instead of taking a progressive adaptive walk driven by local search criteria, we use an efficient global sampling algorithm to examine large regions of the mutational landscape under structural and thermodynamical constraints until a solution is found. When considering the influence of the seeds and the target secondary structures, our results show that, compared to single-path directed searches, our approach is more robust, succeeds more often and generates more thermodynamically stable sequences. An ensemble approach to RNA design is thus well worth pursuing as a complement to existing approaches. RNA-ensign is available at http://csb.cs.mcgill.ca/RNAensign.

A global sampling approach to designing and reengineering RNA secondary structures

PubMed Central

Levin, Alex; Lis, Mieszko; Ponty, Yann; O’Donnell, Charles W.; Devadas, Srinivas; Berger, Bonnie; Waldispühl, Jérôme

2012-01-01

The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed sequence is generated; next, this seed is progressively modified (i.e. mutated) to adopt the desired folding properties. Although computationally inexpensive, this approach raises several questions such as (i) the influence of the seed; and (ii) the efficiency of single-path directed searches that may be affected by energy barriers in the mutational landscape. In this article, we present RNA-ensign, a novel paradigm for RNA design. Instead of taking a progressive adaptive walk driven by local search criteria, we use an efficient global sampling algorithm to examine large regions of the mutational landscape under structural and thermodynamical constraints until a solution is found. When considering the influence of the seeds and the target secondary structures, our results show that, compared to single-path directed searches, our approach is more robust, succeeds more often and generates more thermodynamically stable sequences. An ensemble approach to RNA design is thus well worth pursuing as a complement to existing approaches. RNA-ensign is available at http://csb.cs.mcgill.ca/RNAensign. PMID:22941632

Introducing the Levinthal's Protein Folding Paradox and Its Solution

ERIC Educational Resources Information Center

Martínez, Leandro

2014-01-01

The protein folding (Levinthal's) paradox states that it would not be possible in a physically meaningful time to a protein to reach the native (functional) conformation by a random search of the enormously large number of possible structures. This paradox has been solved: it was shown that small biases toward the native conformation result…

Optimizing random searches on three-dimensional lattices

NASA Astrophysics Data System (ADS)

Yang, Benhao; Yang, Shunkun; Zhang, Jiaquan; Li, Daqing

2018-07-01

Search is a universal behavior related to many types of intelligent individuals. While most studies have focused on search in two or infinite-dimensional space, it is still missing how search can be optimized in three-dimensional space. Here we study random searches on three-dimensional (3d) square lattices with periodic boundary conditions, and explore the optimal search strategy with a power-law step length distribution, p(l) ∼l-μ, known as Lévy flights. We find that compared to random searches on two-dimensional (2d) lattices, the optimal exponent μopt on 3d lattices is relatively smaller in non-destructive case and remains similar in destructive case. We also find μopt decreases as the lattice length in z direction increases under high target density. Our findings may help us to understand the role of spatial dimension in search behaviors.

A search for anisotrophy in the cosmic microwave background on intermediate angular scales

NASA Technical Reports Server (NTRS)

Alsop, D. C.; Cheng, E. S.; Clapp, A. C.; Cottingham, D. A.; Fischer, M. L.; Gundersen, J. O.; Kreysa, E.; Lange, A. E.; Lubin, P. M.; Meinhold, P. R.

1992-01-01

The results of a search for anisotropy in the cosmic microwave background on angular scales near 1 deg are presented. Observations were simultaneously performed in bands centered at frequencies of 6, 9, and 12 per cm with a multifrequency bolometric receiver mounted on a balloon-borne telescope. The statistical sensitivity of the data is the highest reported to date at this angular scale, which is of critical importance for understanding the formation of structure in the universe. Signals in excess of random were observed in the data. The experiment, data analysis, and interpretation are described.

Randomized trial for answers to clinical questions: evaluating a pre-appraised versus a MEDLINE search protocol.

PubMed

Patel, Manesh R; Schardt, Connie M; Sanders, Linda L; Keitz, Sheri A

2006-10-01

The paper compares the speed, validity, and applicability of two different protocols for searching the primary medical literature. A randomized trial involving medicine residents was performed. An inpatient general medicine rotation was used. Thirty-two internal medicine residents were block randomized into four groups of eight. Success rate of each search protocol was measured by perceived search time, number of questions answered, and proportion of articles that were applicable and valid. Residents randomized to the MEDLINE-first (protocol A) group searched 120 questions, and residents randomized to the MEDLINE-last (protocol B) searched 133 questions. In protocol A, 104 answers (86.7%) and, in protocol B, 117 answers (88%) were found to clinical questions. In protocol A, residents reported that 26 (25.2%) of the answers were obtained quickly or rated as "fast" (<5 minutes) as opposed to 55 (51.9%) in protocol B, (P = 0.0004). A subset of questions and articles (n = 79) were reviewed by faculty who found that both protocols identified similar numbers of answer articles that addressed the questions and were felt to be valid using critical appraisal criteria. For resident-generated clinical questions, both protocols produced a similarly high percentage of applicable and valid articles. The MEDLINE-last search protocol was perceived to be faster. However, in the MEDLINE-last protocol, a significant portion of questions (23%) still required searching MEDLINE to find an answer.

A protein-dependent side-chain rotamer library.

PubMed

Bhuyan, Md Shariful Islam; Gao, Xin

2011-12-14

Protein side-chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein side-chain prediction methods are a rotamer library, an energy function and a search algorithm. Rotamer libraries summarize the existing knowledge of the experimentally determined structures quantitatively. Depending on how much contextual information is encoded, there are backbone-independent rotamer libraries and backbone-dependent rotamer libraries. Backbone-independent libraries only encode sequential information, whereas backbone-dependent libraries encode both sequential and locally structural information. However, side-chain conformations are determined by spatially local information, rather than sequentially local information. Since in the side-chain prediction problem, the backbone structure is given, spatially local information should ideally be encoded into the rotamer libraries. In this paper, we propose a new type of backbone-dependent rotamer library, which encodes structural information of all the spatially neighboring residues. We call it protein-dependent rotamer libraries. Given any rotamer library and a protein backbone structure, we first model the protein structure as a Markov random field. Then the marginal distributions are estimated by the inference algorithms, without doing global optimization or search. The rotamers from the given library are then re-ranked and associated with the updated probabilities. Experimental results demonstrate that the proposed protein-dependent libraries significantly outperform the widely used backbone-dependent libraries in terms of the side-chain prediction accuracy and the rotamer ranking ability. Furthermore, without global optimization/search, the side-chain prediction power of the protein-dependent library is still comparable to the global-search-based side-chain prediction methods.

Synthesis of sodium polyhydrides at high pressures

NASA Astrophysics Data System (ADS)

Struzhkin, Viktor V.; Kim, Duck Young; Stavrou, Elissaios; Muramatsu, Takaki; Mao, Ho-Kwang; Pickard, Chris J.; Needs, Richard J.; Prakapenka, Vitali B.; Goncharov, Alexander F.

2016-07-01

The only known compound of sodium and hydrogen is archetypal ionic NaH. Application of high pressure is known to promote states with higher atomic coordination, but extensive searches for polyhydrides with unusual stoichiometry have had only limited success in spite of several theoretical predictions. Here we report the first observation of the formation of polyhydrides of Na (NaH3 and NaH7) above 40 GPa and 2,000 K. We combine synchrotron X-ray diffraction and Raman spectroscopy in a laser-heated diamond anvil cell and theoretical random structure searching, which both agree on the stable structures and compositions. Our results support the formation of multicenter bonding in a material with unusual stoichiometry. These results are applicable to the design of new energetic solids and high-temperature superconductors based on hydrogen-rich materials.

Comparison of Structural Optimization Techniques for a Nuclear Electric Space Vehicle

NASA Technical Reports Server (NTRS)

Benford, Andrew

2003-01-01

The purpose of this paper is to utilize the optimization method of genetic algorithms (GA) for truss design on a nuclear propulsion vehicle. Genetic Algorithms are a guided, random search that mirrors Darwin s theory of natural selection and survival of the fittest. To verify the GA s capabilities, other traditional optimization methods were used to compare the results obtained by the GA's, first on simple 2-D structures, and eventually on full-scale 3-D truss designs.

Decision making in family medicine

PubMed Central

Labrecque, Michel; Ratté, Stéphane; Frémont, Pierre; Cauchon, Michel; Ouellet, Jérôme; Hogg, William; McGowan, Jessie; Gagnon, Marie-Pierre; Njoya, Merlin; Légaré, France

2013-01-01

Abstract Objective To compare the ability of users of 2 medical search engines, InfoClinique and the Trip database, to provide correct answers to clinical questions and to explore the perceived effects of the tools on the clinical decision-making process. Design Randomized trial. Setting Three family medicine units of the family medicine program of the Faculty of Medicine at Laval University in Quebec city, Que. Participants Fifteen second-year family medicine residents. Intervention Residents generated 30 structured questions about therapy or preventive treatment (2 questions per resident) based on clinical encounters. Using an Internet platform designed for the trial, each resident answered 20 of these questions (their own 2, plus 18 of the questions formulated by other residents, selected randomly) before and after searching for information with 1 of the 2 search engines. For each question, 5 residents were randomly assigned to begin their search with InfoClinique and 5 with the Trip database. Main outcome measures The ability of residents to provide correct answers to clinical questions using the search engines, as determined by third-party evaluation. After answering each question, participants completed a questionnaire to assess their perception of the engine’s effect on the decision-making process in clinical practice. Results Of 300 possible pairs of answers (1 answer before and 1 after the initial search), 254 (85%) were produced by 14 residents. Of these, 132 (52%) and 122 (48%) pairs of answers concerned questions that had been assigned an initial search with InfoClinique and the Trip database, respectively. Both engines produced an important and similar absolute increase in the proportion of correct answers after searching (26% to 62% for InfoClinique, for an increase of 36%; 24% to 63% for the Trip database, for an increase of 39%; P = .68). For all 30 clinical questions, at least 1 resident produced the correct answer after searching with either search engine. The mean (SD) time of the initial search for each question was 23.5 (7.6) minutes with InfoClinique and 22.3 (7.8) minutes with the Trip database (P = .30). Participants’ perceptions of each engine’s effect on the decision-making process were very positive and similar for both search engines. Conclusion Family medicine residents’ ability to provide correct answers to clinical questions increased dramatically and similarly with the use of both InfoClinique and the Trip database. These tools have strong potential to increase the quality of medical care. PMID:24130286

Silvabase: A flexible data file management system

NASA Technical Reports Server (NTRS)

Lambing, Steven J.; Reynolds, Sandra J.

1991-01-01

The need for a more flexible and efficient data file management system for mission planning in the Mission Operations Laboratory (EO) at MSFC has spawned the development of Silvabase. Silvabase is a new data file structure based on a B+ tree data structure. This data organization allows for efficient forward and backward sequential reads, random searches, and appends to existing data. It also provides random insertions and deletions with reasonable efficiency, utilization of storage space well but not at the expense of speed, and performance of these functions on a large volume of data. Mission planners required that some data be keyed and manipulated in ways not found in a commercial product. Mission planning software is currently being converted to use Silvabase in the Spacelab and Space Station Mission Planning Systems. Silvabase runs on a Digital Equipment Corporation's popular VAX/VMS computers in VAX Fortran. Silvabase has unique features involving time histories and intervals such as in operations research. Because of its flexibility and unique capabilities, Silvabase could be used in almost any government or commercial application that requires efficient reads, searches, and appends in medium to large amounts of almost any kind of data.

Symptom and structure modification in osteoarthritis with pharmaceutical-grade chondroitin sulfate: what's the evidence?

PubMed

Hochberg, M; Chevalier, X; Henrotin, Y; Hunter, D J; Uebelhart, D

2013-03-01

Osteoarthritis is a chronic disease characterized by irreversible damage to joint structures, including loss of articular cartilage, osteophyte formation, alterations in the subchondral bone and synovial inflammation. It has been shown that chondroitin sulfate interferes with the progression of structural changes in joint tissues and is used in the management of patients with osteoarthritis. This review summarizes data from relevant reports describing the mechanisms of action of chondroitin sulfate that may explain the beneficial effects of the drug and examines the evidence for clinical efficacy of oral chondroitin sulfate in osteoarthritis. Data included in the review were derived from a literature search in PubMed. Literature searches were performed in PubMed using the search terms 'chondroitin sulfate', 'pharmaceutical-grade', 'osteoarthritis', 'randomized clinical trials', 'humans'. The MEDLINE database was searched from January 1996 through August 2012 for all randomized controlled trials, meta-analyses, systematic reviews, and review articles of chondroitin sulfate in osteoarthritis. Chondroitin sulfate exerts in vitro a beneficial effect on the metabolism of different cell lines: chondrocytes, synoviocytes and cells from subchondral bone, all involved in osteoarthritis. It increases type II collagen and proteoglycan synthesis in human articular chondrocytes and is able to reduce the production of some pro-inflammatory factors and proteases, to reduce the cellular death process, and improve the anabolic/catabolic balance of the extracellular cartilage matrix (ECM). Clinical trials have reported a beneficial effect of chondroitin sulfate on pain and function. The structure-modifying effects of chondroitin sulfate have been reported and analyzed in recent meta-analyses. The results in knee osteoarthritis demonstrate a small but significant reduction in the rate of decline in joint space width. Because chondroitin sulfate quality of several nutraceuticals has been found to be poor, it is recommended that pharmaceutical-grade chondroitin sulfate is used rather than food supplements in the treatment of OA. Chondroitin sulfate is recommended by several guidelines from international societies in the management of knee and hip OA. Furthermore, its safety profile is favorable when compared with many other therapies used in OA. Chondroitin sulfate is an effective and safe treatment option for patients with osteoarthritis.

Construction of a filamentous phage display peptide library.

PubMed

Fagerlund, Annette; Myrset, Astrid Hilde; Kulseth, Mari Ann

2014-01-01

The concept of phage display is based on insertion of random oligonucleotides at an appropriate location within a structural gene of a bacteriophage. The resulting phage will constitute a library of random peptides displayed on the surface of the bacteriophages, with the encoding genotype packaged within each phage particle. Using a phagemid/helper phage system, the random peptides are interspersed between wild-type coat proteins. Libraries of phage-expressed peptides may be used to search for novel peptide ligands to target proteins. The success of finding a peptide with a desired property in a given library is highly dependent on the diversity and quality of the library. The protocols in this chapter describe the construction of a high-diversity library of phagemid vector encoding fusions of the phage coat protein pVIII with random peptides, from which a phage library displaying random peptides can be prepared.

How evolutionary crystal structure prediction works--and why.

PubMed

Oganov, Artem R; Lyakhov, Andriy O; Valle, Mario

2011-03-15

Once the crystal structure of a chemical substance is known, many properties can be predicted reliably and routinely. Therefore if researchers could predict the crystal structure of a material before it is synthesized, they could significantly accelerate the discovery of new materials. In addition, the ability to predict crystal structures at arbitrary conditions of pressure and temperature is invaluable for the study of matter at extreme conditions, where experiments are difficult. Crystal structure prediction (CSP), the problem of finding the most stable arrangement of atoms given only the chemical composition, has long remained a major unsolved scientific problem. Two problems are entangled here: search, the efficient exploration of the multidimensional energy landscape, and ranking, the correct calculation of relative energies. For organic crystals, which contain a few molecules in the unit cell, search can be quite simple as long as a researcher does not need to include many possible isomers or conformations of the molecules; therefore ranking becomes the main challenge. For inorganic crystals, quantum mechanical methods often provide correct relative energies, making search the most critical problem. Recent developments provide useful practical methods for solving the search problem to a considerable extent. One can use simulated annealing, metadynamics, random sampling, basin hopping, minima hopping, and data mining. Genetic algorithms have been applied to crystals since 1995, but with limited success, which necessitated the development of a very different evolutionary algorithm. This Account reviews CSP using one of the major techniques, the hybrid evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary Xtallography). Using recent developments in the theory of energy landscapes, we unravel the reasons evolutionary techniques work for CSP and point out their limitations. We demonstrate that the energy landscapes of chemical systems have an overall shape and explore their intrinsic dimensionalities. Because of the inverse relationships between order and energy and between the dimensionality and diversity of an ensemble of crystal structures, the chances that a random search will find the ground state decrease exponentially with increasing system size. A well-designed evolutionary algorithm allows for much greater computational efficiency. We illustrate the power of evolutionary CSP through applications that examine matter at high pressure, where new, unexpected phenomena take place. Evolutionary CSP has allowed researchers to make unexpected discoveries such as a transparent phase of sodium, a partially ionic form of boron, complex superconducting forms of calcium, a novel superhard allotrope of carbon, polymeric modifications of nitrogen, and a new class of compounds, perhydrides. These methods have also led to the discovery of novel hydride superconductors including the "impossible" LiH(n) (n=2, 6, 8) compounds, and CaLi(2). We discuss extensions of the method to molecular crystals, systems of variable composition, and the targeted optimization of specific physical properties. © 2011 American Chemical Society

The optimal number of menu options per panel

NASA Technical Reports Server (NTRS)

Paap, Kenneth R.; Roske-Hofstrand, Renate J.

1986-01-01

An evaluation is made of the effects of the 'funneling' phenomenon, in an analysis of hierarchical menu structures' optimal search times which builds on the work of Lee and MacGregor (1985). Funneling is a reduction in the total number of options processed through the design of a system of greater choice 'depth' and correspondingly restricted choice 'breadth'. Both random and ordered menus are treated. The available evidence is found to support the general conclusion that randomly ordered menu panels should have only a few (4-8) options, while organized menus should contain as many options as 64.

Validating the random search model for two targets of different difficulty.

PubMed

Chan, Alan H S; Yu, Ruifeng

2010-02-01

A random visual search model was fitted to 1,788 search times obtained from a nonidentical double-target search task. 30 Hong Kong Chinese (13 men, 17 women) ages 18 to 33 years (M = 23, SD = 6.8) took part in the experiment voluntarily. The overall adequacy and prediction accuracy of the model for various search time parameters (mean and median search times and response times) for both individual and pooled data show that search strategy may reasonably be inferred from search time distributions. The results also suggested the general applicability of the random search model for describing the search behavior of a large number of participants performing the type of search used here, as well as the practical feasibility of its application for determination of stopping policy for optimization of an inspection system design. Although the data generally conformed to the model the search for the more difficult target was faster than expected. The more difficult target was usually detected after the easier target and it is suggested that some degree of memory-guided searching may have been used for the second target. Some abnormally long search times were observed and it is possible that these might have been due to the characteristics of visual lobes, nonoptimum interfixation distances and inappropriate overlapping of lobes, as has been previously reported.

A novel ternary content addressable memory design based on resistive random access memory with high intensity and low search energy

NASA Astrophysics Data System (ADS)

Han, Runze; Shen, Wensheng; Huang, Peng; Zhou, Zheng; Liu, Lifeng; Liu, Xiaoyan; Kang, Jinfeng

2018-04-01

A novel ternary content addressable memory (TCAM) design based on resistive random access memory (RRAM) is presented. Each TCAM cell consists of two parallel RRAM to both store and search for ternary data. The cell size of the proposed design is 8F2, enable a ∼60× cell area reduction compared with the conventional static random access memory (SRAM) based implementation. Simulation results also show that the search delay and energy consumption of the proposed design at the 64-bit word search are 2 ps and 0.18 fJ/bit/search respectively at 22 nm technology node, where significant improvements are achieved compared to previous works. The desired characteristics of RRAM for implementation of the high performance TCAM search chip are also discussed.

Quantity and quality assessment of randomized controlled trials on orthodontic practice in PubMed.

PubMed

Shimada, Tatsuo; Takayama, Hisako; Nakamura, Yoshiki

2010-07-01

To find current high-quality evidence for orthodontic practice within a reasonable time, we tested the performance of a PubMed search. PubMed was searched using publication type randomized controlled trial and medical subject heading term "orthodontics" for articles published between 2003 and 2007. The PubMed search results were compared with those from a hand search of four orthodontic journals to determine the sensitivity of PubMed search. We evaluated the precision of the PubMed search result and assessed the quality of individual randomized controlled trials using the Jadad scale. Sensitivity and precision were 97.46% and 58.12%, respectively. In PubMed, of the 277 articles retrieved, 161 (58.12%) were randomized controlled trials on orthodontic practice, and 115 of the 161 articles (71.42%) were published in four orthodontic journals: American Journal of Orthodontics and Dentofacial Orthopedics, The Angle Orthodontist, the European Journal of Orthodontics, and the Journal of Orthodontics. Assessment by the Jadad scale revealed 60 high-quality randomized controlled trials on orthodontic practice, of which 45 (75%) were published in these four journals. PubMed is a highly desirable search engine for evidence-based orthodontic practice. To stay current and get high-quality evidence, it is reasonable to look through four orthodontic journals: American Journal of Orthodontics and Dentofacial Orthopedics, The Angle Orthodontist, the European Journal of Orthodontics, and the Journal of Orthodontics.

Surface shape affects the three-dimensional exploratory movements of nocturnal arboreal snakes.

PubMed

Jayne, Bruce C; Olberding, Jeffrey P; Athreya, Dilip; Riley, Michael A

2012-12-01

Movement and searching behaviors at diverse spatial scales are important for understanding how animals interact with their environment. Although the shapes of branches and the voids in arboreal habitats seem likely to affect searching behaviors, their influence is poorly understood. To gain insights into how both environmental structure and the attributes of an animal may affect movement and searching, we compared the three-dimensional exploratory movements of snakes in the dark on two simulated arboreal surfaces (disc and horizontal cylinder). Most of the exploratory movements of snakes in the dark were a small fraction of the distances they could reach while bridging gaps in the light. The snakes extended farther away from the edge of the supporting surface at the ends of the cylinder than from the sides of the cylinder or from any direction from the surface of the disc. The exploratory movements were not random, and the surface shape and three-dimensional directions had significant interactive effects on how the movements were structured in time. Thus, the physical capacity for reaching did not limit the area that was explored, but the shape of the supporting surface and the orientation relative to gravity did create biased searching patterns.

Searches for Randomized Controlled Trials of Drugs in MEDLINE and EMBASE Using Only Generic Drug Names Compared with Searches Applied in Current Practice in Systematic Reviews

ERIC Educational Resources Information Center

Waffenschmidt, Siw; Guddat, Charlotte

2015-01-01

Background: It is unclear which terms should be included in bibliographic searches for randomized controlled trials (RCTs) of drugs, and identifying relevant drug terms can be extremely laborious. The aim of our analysis was to determine whether a bibliographic search using only the generic drug name produces sufficient results for the generation…

Robustness of optimal random searches in fragmented environments

NASA Astrophysics Data System (ADS)

Wosniack, M. E.; Santos, M. C.; Raposo, E. P.; Viswanathan, G. M.; da Luz, M. G. E.

2015-05-01

The random search problem is a challenging and interdisciplinary topic of research in statistical physics. Realistic searches usually take place in nonuniform heterogeneous distributions of targets, e.g., patchy environments and fragmented habitats in ecological systems. Here we present a comprehensive numerical study of search efficiency in arbitrarily fragmented landscapes with unlimited visits to targets that can only be found within patches. We assume a random walker selecting uniformly distributed turning angles and step lengths from an inverse power-law tailed distribution with exponent μ . Our main finding is that for a large class of fragmented environments the optimal strategy corresponds approximately to the same value μopt≈2 . Moreover, this exponent is indistinguishable from the well-known exact optimal value μopt=2 for the low-density limit of homogeneously distributed revisitable targets. Surprisingly, the best search strategies do not depend (or depend only weakly) on the specific details of the fragmentation. Finally, we discuss the mechanisms behind this observed robustness and comment on the relevance of our results to both the random search theory in general, as well as specifically to the foraging problem in the biological context.

Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.

PubMed

He, Yi; Xiao, Yi; Liwo, Adam; Scheraga, Harold A

2009-10-01

We explored the energy-parameter space of our coarse-grained UNRES force field for large-scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual-bond-angle bending and side-chain-rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy-term weights were generated randomly, and good sets were selected by carrying out replica-exchange molecular dynamics simulations of two peptides with a minimal alpha-helical and a minimal beta-hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native-like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native-like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with alpha or alpha + beta structure and found to locate native-like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. Copyright 2009 Wiley Periodicals, Inc.

Boosting the FM-Index on the GPU: Effective Techniques to Mitigate Random Memory Access.

PubMed

Chacón, Alejandro; Marco-Sola, Santiago; Espinosa, Antonio; Ribeca, Paolo; Moure, Juan Carlos

2015-01-01

The recent advent of high-throughput sequencing machines producing big amounts of short reads has boosted the interest in efficient string searching techniques. As of today, many mainstream sequence alignment software tools rely on a special data structure, called the FM-index, which allows for fast exact searches in large genomic references. However, such searches translate into a pseudo-random memory access pattern, thus making memory access the limiting factor of all computation-efficient implementations, both on CPUs and GPUs. Here, we show that several strategies can be put in place to remove the memory bottleneck on the GPU: more compact indexes can be implemented by having more threads work cooperatively on larger memory blocks, and a k-step FM-index can be used to further reduce the number of memory accesses. The combination of those and other optimisations yields an implementation that is able to process about two Gbases of queries per second on our test platform, being about 8 × faster than a comparable multi-core CPU version, and about 3 × to 5 × faster than the FM-index implementation on the GPU provided by the recently announced Nvidia NVBIO bioinformatics library.

Synthesis of sodium polyhydrides at high pressures

DOE PAGES

Struzhkin, Viktor V.; Kim, Duck Young; Stavrou, Elissaios; ...

2016-07-28

Archetypal ionic NaH is the only known compound of sodium and hydrogen. Application of high pressure is known to promote states with higher atomic coordination, but extensive searches for polyhydrides with unusual stoichiometry have had only limited success in spite of several theoretical predictions. Here we report the first observation of the formation of polyhydrides of Na (NaH 3 and NaH 7) above 40 GPa and 2,000 K. Moreover, we combine synchrotron X-ray diffraction and Raman spectroscopy in a laser-heated diamond anvil cell and theoretical random structure searching, which both agree on the stable structures and compositions. Our results supportmore » the formation of multicenter bonding in a material with unusual stoichiometry. These results are applicable to the design of new energetic solids and high-temperature superconductors based on hydrogen-rich materials.« less

A Hybrid Search Algorithm for Swarm Robots Searching in an Unknown Environment

PubMed Central

Li, Shoutao; Li, Lina; Lee, Gordon; Zhang, Hao

2014-01-01

This paper proposes a novel method to improve the efficiency of a swarm of robots searching in an unknown environment. The approach focuses on the process of feeding and individual coordination characteristics inspired by the foraging behavior in nature. A predatory strategy was used for searching; hence, this hybrid approach integrated a random search technique with a dynamic particle swarm optimization (DPSO) search algorithm. If a search robot could not find any target information, it used a random search algorithm for a global search. If the robot found any target information in a region, the DPSO search algorithm was used for a local search. This particle swarm optimization search algorithm is dynamic as all the parameters in the algorithm are refreshed synchronously through a communication mechanism until the robots find the target position, after which, the robots fall back to a random searching mode. Thus, in this searching strategy, the robots alternated between two searching algorithms until the whole area was covered. During the searching process, the robots used a local communication mechanism to share map information and DPSO parameters to reduce the communication burden and overcome hardware limitations. If the search area is very large, search efficiency may be greatly reduced if only one robot searches an entire region given the limited resources available and time constraints. In this research we divided the entire search area into several subregions, selected a target utility function to determine which subregion should be initially searched and thereby reduced the residence time of the target to improve search efficiency. PMID:25386855

A hybrid search algorithm for swarm robots searching in an unknown environment.

PubMed

Li, Shoutao; Li, Lina; Lee, Gordon; Zhang, Hao

2014-01-01

This paper proposes a novel method to improve the efficiency of a swarm of robots searching in an unknown environment. The approach focuses on the process of feeding and individual coordination characteristics inspired by the foraging behavior in nature. A predatory strategy was used for searching; hence, this hybrid approach integrated a random search technique with a dynamic particle swarm optimization (DPSO) search algorithm. If a search robot could not find any target information, it used a random search algorithm for a global search. If the robot found any target information in a region, the DPSO search algorithm was used for a local search. This particle swarm optimization search algorithm is dynamic as all the parameters in the algorithm are refreshed synchronously through a communication mechanism until the robots find the target position, after which, the robots fall back to a random searching mode. Thus, in this searching strategy, the robots alternated between two searching algorithms until the whole area was covered. During the searching process, the robots used a local communication mechanism to share map information and DPSO parameters to reduce the communication burden and overcome hardware limitations. If the search area is very large, search efficiency may be greatly reduced if only one robot searches an entire region given the limited resources available and time constraints. In this research we divided the entire search area into several subregions, selected a target utility function to determine which subregion should be initially searched and thereby reduced the residence time of the target to improve search efficiency.

Emergence of an optimal search strategy from a simple random walk

PubMed Central

Sakiyama, Tomoko; Gunji, Yukio-Pegio

2013-01-01

In reports addressing animal foraging strategies, it has been stated that Lévy-like algorithms represent an optimal search strategy in an unknown environment, because of their super-diffusion properties and power-law-distributed step lengths. Here, starting with a simple random walk algorithm, which offers the agent a randomly determined direction at each time step with a fixed move length, we investigated how flexible exploration is achieved if an agent alters its randomly determined next step forward and the rule that controls its random movement based on its own directional moving experiences. We showed that our algorithm led to an effective food-searching performance compared with a simple random walk algorithm and exhibited super-diffusion properties, despite the uniform step lengths. Moreover, our algorithm exhibited a power-law distribution independent of uniform step lengths. PMID:23804445

Emergence of an optimal search strategy from a simple random walk.

PubMed

Sakiyama, Tomoko; Gunji, Yukio-Pegio

2013-09-06

In reports addressing animal foraging strategies, it has been stated that Lévy-like algorithms represent an optimal search strategy in an unknown environment, because of their super-diffusion properties and power-law-distributed step lengths. Here, starting with a simple random walk algorithm, which offers the agent a randomly determined direction at each time step with a fixed move length, we investigated how flexible exploration is achieved if an agent alters its randomly determined next step forward and the rule that controls its random movement based on its own directional moving experiences. We showed that our algorithm led to an effective food-searching performance compared with a simple random walk algorithm and exhibited super-diffusion properties, despite the uniform step lengths. Moreover, our algorithm exhibited a power-law distribution independent of uniform step lengths.

Parameter identification using a creeping-random-search algorithm

NASA Technical Reports Server (NTRS)

Parrish, R. V.

1971-01-01

A creeping-random-search algorithm is applied to different types of problems in the field of parameter identification. The studies are intended to demonstrate that a random-search algorithm can be applied successfully to these various problems, which often cannot be handled by conventional deterministic methods, and, also, to introduce methods that speed convergence to an extremal of the problem under investigation. Six two-parameter identification problems with analytic solutions are solved, and two application problems are discussed in some detail. Results of the study show that a modified version of the basic creeping-random-search algorithm chosen does speed convergence in comparison with the unmodified version. The results also show that the algorithm can successfully solve problems that contain limits on state or control variables, inequality constraints (both independent and dependent, and linear and nonlinear), or stochastic models.

PREFACE: The random search problem: trends and perspectives The random search problem: trends and perspectives

NASA Astrophysics Data System (ADS)

da Luz, Marcos G. E.; Grosberg, Alexander; Raposo, Ernesto P.; Viswanathan, Gandhi M.

2009-10-01

`I can't find my keys!' Who hasn't gone through this experience when leaving, in a hurry, to attend to some urgent matter? The keys could be in many different places. Unless one remembers where he or she has left the keys, the only solution is to look around, more or less randomly. Random searches are common because in many cases the locations of the specific targets are not known a priori. Indeed, such problems have been discussed in diverse contexts, attracting the interest of scientists from many fields, for example: the dynamical or stochastic search for a stable minimum in a complex energy landscape, relevant to systems such as glasses, protein (folding), and others; oil recovery from mature reservoirs; proteins searching for their specific target sites on DNA; animal foraging; survival at the edge of extinction due to low availability of energetic resources; automated searches of registers in high-capacity databases, search engine (e.g., `crawlers') that explore the internet; and even pizza delivery in a jammed traffic system of a medium-size town. In this way, the subject is interesting, challenging and has recently become an important scientific area of investigation. Although the applications are diverse, the underlying physical mechanisms are the same which will become clear in this special issue. Moreover, the inherent complexity of the problem, the abundance of ideas and methods found in this growing interdisciplinary field of research is studied in many areas of physics. In particular, the concepts and methods of statistical mechanics are particularly useful to the study of random searches. On one hand, it centres on how to find the global or local maxima of search efficiency functions with incomplete information. This is, of course, related to the long tradition in physics of using different conceptual and mathematical tools, such as variational methods, to extremize relevant quantities, e.g., energy, entropy and action. Such ideas and approaches are very important to solve computationally complex problems (e.g., protein folding), which involve optimizations in very high dimensional energy landscapes. On the other hand, random searches can also be studied from the perspective of diffusion and transport properties which is an important topic in condensed matter and statistical physics. For instance, the features of light scattered in a media, where the scatterers have a power-law distribution of sizes in many aspects, may resemble the patterns generated by a searcher performing Lévy walks. There are many questions related to random searches: how the searcher moves or should move, what are the patterns generated during the locomotion, how do the encounter rates depend on parameters of the search, etc. But perhaps, the most well known issue is how to optimize the search for specific target scenarios. The optimization can be in either continuous or discrete environments, when the information available is limited. The answer to this question determines specific strategies of movement that would maximize some properly defined search efficiency measure. The relevance of the question stems from the fact that the strategy-dynamics represents one of the most important factors that modulate the rate of encounters (e.g., the encounter rate between predator and prey). In the general context, strategy choices can be essential in determining the outcome and thus the success of a given search. For instance, realistic searches—and locomotion in general—require the expenditure of energy. Thus, inefficient search could deplete energy reserves (e.g., fat) and lead to rates of encounters below a minimum acceptable threshold (resulting in extinction of a species, for example). The framework of the random search `game' distinguishes between the two interacting players in a context of pursuit and chance. They are either a `searcher' (e.g., predator, protein, radar, `crawler') or a `target' (e.g., prey, DNA sequence, a missing aircraft, a given web site). Regarding the nature of the searching drive, in certain instances, it can be guided almost entirely by external cues, either by the cognitive (memory) or detective (olfaction, vision, etc) skills of the searcher. However, in many situations the movement is non-oriented, being in essence a stochastic process. Therefore, in such cases (and even when a small deterministic component in the locomotion exists) a random search effectively defines the final rates of encounters. Hence, one reason underlying the richness of the random search problem relates just to the `ignorance' of the locations of the randomly located targets. Contrary to conventional wisdom, the lack of complete information does not necessarily lead to greater complexity. As an illustrative example, let us consider the case of complete information. If the positions of all target sites are known in advance, then the question of what sequential order to visit the sites so to reduce the energy costs of locomotion itself becomes a rather challenging problem: the famous `travelling salesman' optimization query, belonging to the NP-complete class of problems. The ignorance of the target site locations, however, considerably modifies the problem and renders it not amenable to be treated by purely deterministic computational methods. In fact, as expected, the random search problem is not particularly suited to search algorithms that do not use elements of randomness. So, only a statistical approach to the search problem can adequately deal with the element of ignorance. In other words, the incomplete information renders the search under-determined, i.e., it is not possible to find the `best' solution to the problem because all the information is not given. Instead, one must guess and probabilistic or stochastic strategies become unavoidable. Also, the random search problem bears a relation to reaction-diffusion processes, because the search involves a diffusive aspect, movement, as well as a reactive component, e.g., eating, mating, etc. From the comments above, it is clear that the subject can be treated from the perspective of different fields and subfields of physics and mathematics: statistical mechanics, stochastic processes, Lévy walks and flights, complex systems, fractal geometry, and non-linear phenomena. Some important questions in random searches, especially in the case of discrete landscapes, are also associated with graph theory, random lattices, and complex networks. The aim of this special issue is to bring together, in a single publication, all or most of the relevant theoretical concepts-ideas together with discussions of recent findings that are important for understanding the main elements of random searches. In addition, we will address the types of problems which are characteristic of random searching. Thus, we sincerely hope that this collection of works will provide a good overview for anyone interested in this field. Finally, we should thank the editors and staff of Journal of Physics A: Mathematical and Theoretical for opining that random searches are an interesting topic of research deserving a topical publication. Furthermore, we are very grateful to Rebecca Gillan for helping us at all stages of the preparation and organization of this special issue. Finally, we would like to thank the contributing authors who share with the guest editors the enthusiasm and interest for this fascinating field of research.

The fast algorithm of spark in compressive sensing

NASA Astrophysics Data System (ADS)

Xie, Meihua; Yan, Fengxia

2017-01-01

Compressed Sensing (CS) is an advanced theory on signal sampling and reconstruction. In CS theory, the reconstruction condition of signal is an important theory problem, and spark is a good index to study this problem. But the computation of spark is NP hard. In this paper, we study the problem of computing spark. For some special matrixes, for example, the Gaussian random matrix and 0-1 random matrix, we obtain some conclusions. Furthermore, for Gaussian random matrix with fewer rows than columns, we prove that its spark equals to the number of its rows plus one with probability 1. For general matrix, two methods are given to compute its spark. One is the method of directly searching and the other is the method of dual-tree searching. By simulating 24 Gaussian random matrixes and 18 0-1 random matrixes, we tested the computation time of these two methods. Numerical results showed that the dual-tree searching method had higher efficiency than directly searching, especially for those matrixes which has as much as rows and columns.

Robust hashing with local models for approximate similarity search.

PubMed

Song, Jingkuan; Yang, Yi; Li, Xuelong; Huang, Zi; Yang, Yang

2014-07-01

Similarity search plays an important role in many applications involving high-dimensional data. Due to the known dimensionality curse, the performance of most existing indexing structures degrades quickly as the feature dimensionality increases. Hashing methods, such as locality sensitive hashing (LSH) and its variants, have been widely used to achieve fast approximate similarity search by trading search quality for efficiency. However, most existing hashing methods make use of randomized algorithms to generate hash codes without considering the specific structural information in the data. In this paper, we propose a novel hashing method, namely, robust hashing with local models (RHLM), which learns a set of robust hash functions to map the high-dimensional data points into binary hash codes by effectively utilizing local structural information. In RHLM, for each individual data point in the training dataset, a local hashing model is learned and used to predict the hash codes of its neighboring data points. The local models from all the data points are globally aligned so that an optimal hash code can be assigned to each data point. After obtaining the hash codes of all the training data points, we design a robust method by employing l2,1 -norm minimization on the loss function to learn effective hash functions, which are then used to map each database point into its hash code. Given a query data point, the search process first maps it into the query hash code by the hash functions and then explores the buckets, which have similar hash codes to the query hash code. Extensive experimental results conducted on real-life datasets show that the proposed RHLM outperforms the state-of-the-art methods in terms of search quality and efficiency.

Randomized Approaches for Nearest Neighbor Search in Metric Space When Computing the Pairwise Distance Is Extremely Expensive

NASA Astrophysics Data System (ADS)

Wang, Lusheng; Yang, Yong; Lin, Guohui

Finding the closest object for a query in a database is a classical problem in computer science. For some modern biological applications, computing the similarity between two objects might be very time consuming. For example, it takes a long time to compute the edit distance between two whole chromosomes and the alignment cost of two 3D protein structures. In this paper, we study the nearest neighbor search problem in metric space, where the pair-wise distance between two objects in the database is known and we want to minimize the number of distances computed on-line between the query and objects in the database in order to find the closest object. We have designed two randomized approaches for indexing metric space databases, where objects are purely described by their distances with each other. Analysis and experiments show that our approaches only need to compute O(logn) objects in order to find the closest object, where n is the total number of objects in the database.

Application of multivariable search techniques to structural design optimization

NASA Technical Reports Server (NTRS)

Jones, R. T.; Hague, D. S.

1972-01-01

Multivariable optimization techniques are applied to a particular class of minimum weight structural design problems: the design of an axially loaded, pressurized, stiffened cylinder. Minimum weight designs are obtained by a variety of search algorithms: first- and second-order, elemental perturbation, and randomized techniques. An exterior penalty function approach to constrained minimization is employed. Some comparisons are made with solutions obtained by an interior penalty function procedure. In general, it would appear that an interior penalty function approach may not be as well suited to the class of design problems considered as the exterior penalty function approach. It is also shown that a combination of search algorithms will tend to arrive at an extremal design in a more reliable manner than a single algorithm. The effect of incorporating realistic geometrical constraints on stiffener cross-sections is investigated. A limited comparison is made between minimum weight cylinders designed on the basis of a linear stability analysis and cylinders designed on the basis of empirical buckling data. Finally, a technique for locating more than one extremal is demonstrated.

Ternary alloy material prediction using genetic algorithm and cluster expansion

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

Chen, Chong

2015-12-01

This thesis summarizes our study on the crystal structures prediction of Fe-V-Si system using genetic algorithm and cluster expansion. Our goal is to explore and look for new stable compounds. We started from the current ten known experimental phases, and calculated formation energies of those compounds using density functional theory (DFT) package, namely, VASP. The convex hull was generated based on the DFT calculations of the experimental known phases. Then we did random search on some metal rich (Fe and V) compositions and found that the lowest energy structures were body centered cube (bcc) underlying lattice, under which we didmore » our computational systematic searches using genetic algorithm and cluster expansion. Among hundreds of the searched compositions, thirteen were selected and DFT formation energies were obtained by VASP. The stability checking of those thirteen compounds was done in reference to the experimental convex hull. We found that the composition, 24-8-16, i.e., Fe 3VSi 2 is a new stable phase and it can be very inspiring to the future experiments.« less

Restricted random search method based on taboo search in the multiple minima problem

NASA Astrophysics Data System (ADS)

Hong, Seung Do; Jhon, Mu Shik

1997-03-01

The restricted random search method is proposed as a simple Monte Carlo sampling method to search minima fast in the multiple minima problem. This method is based on taboo search applied recently to continuous test functions. The concept of the taboo region instead of the taboo list is used and therefore the sampling of a region near an old configuration is restricted in this method. This method is applied to 2-dimensional test functions and the argon clusters. This method is found to be a practical and efficient method to search near-global configurations of test functions and the argon clusters.

3D statistical shape models incorporating 3D random forest regression voting for robust CT liver segmentation

NASA Astrophysics Data System (ADS)

Norajitra, Tobias; Meinzer, Hans-Peter; Maier-Hein, Klaus H.

2015-03-01

During image segmentation, 3D Statistical Shape Models (SSM) usually conduct a limited search for target landmarks within one-dimensional search profiles perpendicular to the model surface. In addition, landmark appearance is modeled only locally based on linear profiles and weak learners, altogether leading to segmentation errors from landmark ambiguities and limited search coverage. We present a new method for 3D SSM segmentation based on 3D Random Forest Regression Voting. For each surface landmark, a Random Regression Forest is trained that learns a 3D spatial displacement function between the according reference landmark and a set of surrounding sample points, based on an infinite set of non-local randomized 3D Haar-like features. Landmark search is then conducted omni-directionally within 3D search spaces, where voxelwise forest predictions on landmark position contribute to a common voting map which reflects the overall position estimate. Segmentation experiments were conducted on a set of 45 CT volumes of the human liver, of which 40 images were randomly chosen for training and 5 for testing. Without parameter optimization, using a simple candidate selection and a single resolution approach, excellent results were achieved, while faster convergence and better concavity segmentation were observed, altogether underlining the potential of our approach in terms of increased robustness from distinct landmark detection and from better search coverage.

Sample size determination for bibliographic retrieval studies

PubMed Central

Yao, Xiaomei; Wilczynski, Nancy L; Walter, Stephen D; Haynes, R Brian

2008-01-01

Background Research for developing search strategies to retrieve high-quality clinical journal articles from MEDLINE is expensive and time-consuming. The objective of this study was to determine the minimal number of high-quality articles in a journal subset that would need to be hand-searched to update or create new MEDLINE search strategies for treatment, diagnosis, and prognosis studies. Methods The desired width of the 95% confidence intervals (W) for the lowest sensitivity among existing search strategies was used to calculate the number of high-quality articles needed to reliably update search strategies. New search strategies were derived in journal subsets formed by 2 approaches: random sampling of journals and top journals (having the most high-quality articles). The new strategies were tested in both the original large journal database and in a low-yielding journal (having few high-quality articles) subset. Results For treatment studies, if W was 10% or less for the lowest sensitivity among our existing search strategies, a subset of 15 randomly selected journals or 2 top journals were adequate for updating search strategies, based on each approach having at least 99 high-quality articles. The new strategies derived in 15 randomly selected journals or 2 top journals performed well in the original large journal database. Nevertheless, the new search strategies developed using the random sampling approach performed better than those developed using the top journal approach in a low-yielding journal subset. For studies of diagnosis and prognosis, no journal subset had enough high-quality articles to achieve the expected W (10%). Conclusion The approach of randomly sampling a small subset of journals that includes sufficient high-quality articles is an efficient way to update or create search strategies for high-quality articles on therapy in MEDLINE. The concentrations of diagnosis and prognosis articles are too low for this approach. PMID:18823538

A Darwinian approach to control-structure design

NASA Technical Reports Server (NTRS)

Zimmerman, David C.

1993-01-01

Genetic algorithms (GA's), as introduced by Holland (1975), are one form of directed random search. The form of direction is based on Darwin's 'survival of the fittest' theories. GA's are radically different from the more traditional design optimization techniques. GA's work with a coding of the design variables, as opposed to working with the design variables directly. The search is conducted from a population of designs (i.e., from a large number of points in the design space), unlike the traditional algorithms which search from a single design point. The GA requires only objective function information, as opposed to gradient or other auxiliary information. Finally, the GA is based on probabilistic transition rules, as opposed to deterministic rules. These features allow the GA to attack problems with local-global minima, discontinuous design spaces and mixed variable problems, all in a single, consistent framework.

Using a Genetic Algorithm to Model Broadband Regional Waveforms for Crustal Structure in the Western United States

NASA Technical Reports Server (NTRS)

Bhattacharyya, Joydeep; Sheehan, Anne F.; Tiampo, Kristy; Rundle, John

1999-01-01

In this study, we analyze regional seismograms to obtain the crustal structure in the eastern Great Basin and western Colorado plateau. Adopting a for- ward-modeling approach, we develop a genetic algorithm (GA) based parameter search technique to constrain the one-dimensional crustal structure in these regions. The data are broadband three-component seismograms recorded at the 1994-95 IRIS PASSCAL Colorado Plateau to Great Basin experiment (CPGB) stations and supplemented by data from U.S. National Seismic Network (USNSN) stations in Utah and Nevada. We use the southwestern Wyoming mine collapse event (M(sub b) = 5.2) that occurred on 3 February 1995 as the seismic source. We model the regional seismograms using a four-layer crustal model with constant layer parameters. Timing of teleseismic receiver functions at CPGB stations are added as an additional constraint in the modeling. GA allows us to efficiently search the model space. A carefully chosen fitness function and a windowing scheme are added to the algorithm to prevent search stagnation. The technique is tested with synthetic data, both with and without random Gaussian noise added to it. Several separate model searches are carried out to estimate the variability of the model parameters. The average Colorado plateau crustal structure is characterized by a 40-km-thick crust with velocity increases at depths of about 10 and 25 km and a fast lower crust while the Great Basin has approximately 35- km-thick crust and a 2.9-km-thick sedimentary layer.

Application of firefly algorithm to the dynamic model updating problem

NASA Astrophysics Data System (ADS)

Shabbir, Faisal; Omenzetter, Piotr

2015-04-01

Model updating can be considered as a branch of optimization problems in which calibration of the finite element (FE) model is undertaken by comparing the modal properties of the actual structure with these of the FE predictions. The attainment of a global solution in a multi dimensional search space is a challenging problem. The nature-inspired algorithms have gained increasing attention in the previous decade for solving such complex optimization problems. This study applies the novel Firefly Algorithm (FA), a global optimization search technique, to a dynamic model updating problem. This is to the authors' best knowledge the first time FA is applied to model updating. The working of FA is inspired by the flashing characteristics of fireflies. Each firefly represents a randomly generated solution which is assigned brightness according to the value of the objective function. The physical structure under consideration is a full scale cable stayed pedestrian bridge with composite bridge deck. Data from dynamic testing of the bridge was used to correlate and update the initial model by using FA. The algorithm aimed at minimizing the difference between the natural frequencies and mode shapes of the structure. The performance of the algorithm is analyzed in finding the optimal solution in a multi dimensional search space. The paper concludes with an investigation of the efficacy of the algorithm in obtaining a reference finite element model which correctly represents the as-built original structure.

Hierarchical random walks in trace fossils and the origin of optimal search behavior

PubMed Central

Sims, David W.; Reynolds, Andrew M.; Humphries, Nicolas E.; Southall, Emily J.; Wearmouth, Victoria J.; Metcalfe, Brett; Twitchett, Richard J.

2014-01-01

Efficient searching is crucial for timely location of food and other resources. Recent studies show that diverse living animals use a theoretically optimal scale-free random search for sparse resources known as a Lévy walk, but little is known of the origins and evolution of foraging behavior and the search strategies of extinct organisms. Here, using simulations of self-avoiding trace fossil trails, we show that randomly introduced strophotaxis (U-turns)—initiated by obstructions such as self-trail avoidance or innate cueing—leads to random looping patterns with clustering across increasing scales that is consistent with the presence of Lévy walks. This predicts that optimal Lévy searches may emerge from simple behaviors observed in fossil trails. We then analyzed fossilized trails of benthic marine organisms by using a novel path analysis technique and find the first evidence, to our knowledge, of Lévy-like search strategies in extinct animals. Our results show that simple search behaviors of extinct animals in heterogeneous environments give rise to hierarchically nested Brownian walk clusters that converge to optimal Lévy patterns. Primary productivity collapse and large-scale food scarcity characterizing mass extinctions evident in the fossil record may have triggered adaptation of optimal Lévy-like searches. The findings suggest that Lévy-like behavior has been used by foragers since at least the Eocene but may have a more ancient origin, which might explain recent widespread observations of such patterns among modern taxa. PMID:25024221

Ab initio random structure searching of organic molecular solids: assessment and validation against experimental data† †Electronic supplementary information (ESI) available: Results of similarity analysis between the 11 structures of lowest energy obtained in the AIRSS calculations and the reported structures of form III and form IV of m-ABA; unit cell parameters and volumes for all structures considered; comparison of 2θ values derived from the unit cell parameters of different structural models representing form III of m-ABA; Le Bail fitting of the experimental powder XRD pattern of form IV of m-ABA recorded at 70 K using, as the initial structural model, the reported crystal structure following geometry optimization; table of calculated (GIPAW) absolute isotropic NMR shieldings; simulated powder XRD data for the considered structures after precise geometry optimization; experimental 1H MAS NMR spectra of forms III and IV. (pdf) The calculated and experimental data for this study are provided as a supporting dataset from WRAP, the Warwick Research Archive Portal at http://wrap.warwick.ac.uk/91884. See DOI: 10.1039/c7cp04186a

PubMed Central

Zilka, Miri; Dudenko, Dmytro V.; Hughes, Colan E.; Williams, P. Andrew; Sturniolo, Simone; Franks, W. Trent; Pickard, Chris J.

2017-01-01

This paper explores the capability of using the DFT-D ab initio random structure searching (AIRSS) method to generate crystal structures of organic molecular materials, focusing on a system (m-aminobenzoic acid; m-ABA) that is known from experimental studies to exhibit abundant polymorphism. Within the structural constraints selected for the AIRSS calculations (specifically, centrosymmetric structures with Z = 4 for zwitterionic m-ABA molecules), the method is shown to successfully generate the two known polymorphs of m-ABA (form III and form IV) that have these structural features. We highlight various issues that are encountered in comparing crystal structures generated by AIRSS to experimental powder X-ray diffraction (XRD) data and solid-state magic-angle spinning (MAS) NMR data, demonstrating successful fitting for some of the lowest energy structures from the AIRSS calculations against experimental low-temperature powder XRD data for known polymorphs of m-ABA, and showing that comparison of computed and experimental solid-state NMR parameters allows different hydrogen-bonding motifs to be discriminated. PMID:28944393

Exhaustive Versus Randomized Searchers for Nonlinear Optimization in 21st Century Computing: Solar Application

NASA Technical Reports Server (NTRS)

Sen, Syamal K.; AliShaykhian, Gholam

2010-01-01

We present a simple multi-dimensional exhaustive search method to obtain, in a reasonable time, the optimal solution of a nonlinear programming problem. It is more relevant in the present day non-mainframe computing scenario where an estimated 95% computing resources remains unutilized and computing speed touches petaflops. While the processor speed is doubling every 18 months, the band width is doubling every 12 months, and the hard disk space is doubling every 9 months. A randomized search algorithm or, equivalently, an evolutionary search method is often used instead of an exhaustive search algorithm. The reason is that a randomized approach is usually polynomial-time, i.e., fast while an exhaustive search method is exponential-time i.e., slow. We discuss the increasing importance of exhaustive search in optimization with the steady increase of computing power for solving many real-world problems of reasonable size. We also discuss the computational error and complexity of the search algorithm focusing on the fact that no measuring device can usually measure a quantity with an accuracy greater than 0.005%. We stress the fact that the quality of solution of the exhaustive search - a deterministic method - is better than that of randomized search. In 21 st century computing environment, exhaustive search cannot be left aside as an untouchable and it is not always exponential. We also describe a possible application of these algorithms in improving the efficiency of solar cells - a real hot topic - in the current energy crisis. These algorithms could be excellent tools in the hands of experimentalists and could save not only large amount of time needed for experiments but also could validate the theory against experimental results fast.

VES/TEM 1D joint inversion by using Controlled Random Search (CRS) algorithm

NASA Astrophysics Data System (ADS)

Bortolozo, Cassiano Antonio; Porsani, Jorge Luís; Santos, Fernando Acácio Monteiro dos; Almeida, Emerson Rodrigo

2015-01-01

Electrical (DC) and Transient Electromagnetic (TEM) soundings are used in a great number of environmental, hydrological, and mining exploration studies. Usually, data interpretation is accomplished by individual 1D models resulting often in ambiguous models. This fact can be explained by the way as the two different methodologies sample the medium beneath surface. Vertical Electrical Sounding (VES) is good in marking resistive structures, while Transient Electromagnetic sounding (TEM) is very sensitive to conductive structures. Another difference is VES is better to detect shallow structures, while TEM soundings can reach deeper layers. A Matlab program for 1D joint inversion of VES and TEM soundings was developed aiming at exploring the best of both methods. The program uses CRS - Controlled Random Search - algorithm for both single and 1D joint inversions. Usually inversion programs use Marquadt type algorithms but for electrical and electromagnetic methods, these algorithms may find a local minimum or not converge. Initially, the algorithm was tested with synthetic data, and then it was used to invert experimental data from two places in Paraná sedimentary basin (Bebedouro and Pirassununga cities), both located in São Paulo State, Brazil. Geoelectric model obtained from VES and TEM data 1D joint inversion is similar to the real geological condition, and ambiguities were minimized. Results with synthetic and real data show that 1D VES/TEM joint inversion better recovers simulated models and shows a great potential in geological studies, especially in hydrogeological studies.

Evidence Synthesis in Harm Assessment of Medicines Using the Example of Rosiglitazone and Myocardial Infarction.

PubMed

Rietbergen, Charlotte; Stefansdottir, Gudrun; Leufkens, Hubert G; Knol, Mirjam J; De Bruin, Marie L; Klugkist, Irene

2017-01-01

The current system of harm assessment of medicines has been criticized for relying on intuitive expert judgment. There is a call for more quantitative approaches and transparency in decision-making. Illustrated with the case of cardiovascular safety concerns for rosiglitazone, we aimed to explore a structured procedure for the collection, quality assessment, and statistical modeling of safety data from observational and randomized studies. We distinguished five stages in the synthesis process. In Stage I, the general research question, population and outcome, and general inclusion and exclusion criteria are defined and a systematic search is performed. Stage II focusses on the identification of sub-questions examined in the included studies and the classification of the studies into the different categories of sub-questions. In Stage III, the quality of the identified studies is assessed. Coding and data extraction are performed in Stage IV. Finally, meta-analyses on the study results per sub-question are performed in Stage V. A Pubmed search identified 30 randomized and 14 observational studies meeting our search criteria. From these studies, we identified 4 higher level sub-questions and 4 lower level sub-questions. We were able to categorize 29 individual treatment comparisons into one or more of the sub-question categories, and selected study duration as an important covariate. We extracted covariate, outcome, and sample size information at the treatment arm level of the studies. We extracted absolute numbers of myocardial infarctions from the randomized study, and adjusted risk estimates with 95% confidence intervals from the observational studies. Overall, few events were observed in the randomized studies that were frequently of relatively short duration. The large observational studies provided more information since these were often of longer duration. A Bayesian random effects meta-analysis on these data showed no significant increase in risk of rosiglitazone for any of the sub-questions. The proposed procedure can be of additional value for drug safety assessment because it provides a stepwise approach that guides the decision-making in increasing process transparency. The procedure allows for the inclusion of results from both randomized an observational studies, which is especially relevant for this type of research.

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

Zhu, Li; Fuhrer, Tobias; Schaefer, Bastian

Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not directly suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell, we introduce crystal fingerprints that can be calculated easily and define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures.more » The new method can be a useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms, and high-throughput screenings.« less

Fitness landscapes, heuristics and technological paradigms: A critique on random search models in evolutionary economics

NASA Astrophysics Data System (ADS)

Frenken, Koen

2001-06-01

The biological evolution of complex organisms, in which the functioning of genes is interdependent, has been analyzed as "hill-climbing" on NK fitness landscapes through random mutation and natural selection. In evolutionary economics, NK fitness landscapes have been used to simulate the evolution of complex technological systems containing elements that are interdependent in their functioning. In these models, economic agents randomly search for new technological design by trial-and-error and run the risk of ending up in sub-optimal solutions due to interdependencies between the elements in a complex system. These models of random search are legitimate for reasons of modeling simplicity, but remain limited as these models ignore the fact that agents can apply heuristics. A specific heuristic is one that sequentially optimises functions according to their ranking by users of the system. To model this heuristic, a generalized NK-model is developed. In this model, core elements that influence many functions can be distinguished from peripheral elements that affect few functions. The concept of paradigmatic search can then be analytically defined as search that leaves core elements in tact while concentrating on improving functions by mutation of peripheral elements.

NOBAI: a web server for character coding of geometrical and statistical features in RNA structure

PubMed Central

Knudsen, Vegeir; Caetano-Anollés, Gustavo

2008-01-01

The Numeration of Objects in Biology: Alignment Inferences (NOBAI) web server provides a web interface to the applications in the NOBAI software package. This software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly in NEXUS format and provides sequence randomization options. The web server is an effective tool that facilitates the search for evolutionary history embedded in the structure of functional RNA molecules. The NOBAI web server is accessible at ‘http://www.manet.uiuc.edu/nobai/nobai.php’. This web site is free and open to all users and there is no login requirement. PMID:18448469

Efficient search of multiple types of targets

NASA Astrophysics Data System (ADS)

Wosniack, M. E.; Raposo, E. P.; Viswanathan, G. M.; da Luz, M. G. E.

2015-12-01

Random searches often take place in fragmented landscapes. Also, in many instances like animal foraging, significant benefits to the searcher arise from visits to a large diversity of patches with a well-balanced distribution of targets found. Up to date, such aspects have been widely ignored in the usual single-objective analysis of search efficiency, in which one seeks to maximize just the number of targets found per distance traversed. Here we address the problem of determining the best strategies for the random search when these multiple-objective factors play a key role in the process. We consider a figure of merit (efficiency function), which properly "scores" the mentioned tasks. By considering random walk searchers with a power-law asymptotic Lévy distribution of step lengths, p (ℓ ) ˜ℓ-μ , with 1 <μ ≤3 , we show that the standard optimal strategy with μopt≈2 no longer holds universally. Instead, optimal searches with enhanced superdiffusivity emerge, including values as low as μopt≈1.3 (i.e., tending to the ballistic limit). For the general theory of random search optimization, our findings emphasize the necessity to correctly characterize the multitude of aims in any concrete metric to compare among possible candidates to efficient strategies. In the context of animal foraging, our results might explain some empirical data pointing to stronger superdiffusion (μ <2 ) in the search behavior of different animal species, conceivably associated to multiple goals to be achieved in fragmented landscapes.

Enhancing access to reports of randomized trials published world-wide – the contribution of EMBASE records to the Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library

PubMed Central

Lefebvre, Carol; Eisinga, Anne; McDonald, Steve; Paul, Nina

2008-01-01

Background Randomized trials are essential in assessing the effects of healthcare interventions and are a key component in systematic reviews of effectiveness. Searching for reports of randomized trials in databases is problematic due to the absence of appropriate indexing terms until the 1990s and inconsistent application of these indexing terms thereafter. Objectives The objectives of this study are to devise a search strategy for identifying reports of randomized trials in EMBASE which are not already indexed as trials in MEDLINE and to make these reports easily accessible by including them in the Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library, with the permission of Elsevier, the publishers of EMBASE. Methods A highly sensitive search strategy was designed for EMBASE based on free-text and thesaurus terms which occurred frequently in the titles, abstracts, EMTREE terms (or some combination of these) of reports of trials indexed in EMBASE. This search strategy was run against EMBASE from 1980 to 2005 (1974 to 2005 for four of the terms) and records retrieved by the search, which were not already indexed as randomized trials in MEDLINE, were downloaded from EMBASE, printed and read. An analysis of the language of publication was conducted for the reports of trials published in 2005 (the most recent year completed at the time of this study). Results Twenty-two search terms were used (including nine which were later rejected due to poor cumulative precision). More than a third of a million records were downloaded and scanned and approximately 80,000 reports of trials were identified which were not already indexed as randomized trials in MEDLINE. These are now easily identifiable in CENTRAL, in The Cochrane Library. Cumulative sensitivity ranged from 0.1% to 60% and cumulative precision ranged from 8% to 61%. The truncated term 'random$' identified 60% of the total number of reports of trials but only 35% of the more than 130,000 records retrieved by this term were reports of trials. The language analysis for the sample year 2005 indicated that of the 18,427 reports indexed as randomized trials in MEDLINE, 959 (5%) were in languages other than English. The EMBASE search identified an additional 658 reports in languages other than English, of which the highest number were in Chinese (320). Conclusion The results of the search to date have greatly increased access to reports of trials in EMBASE, especially in some languages other than English. The search strategy used was subjectively derived from a small 'gold standard' set of test records and was not validated in an independent test set. We intend to design an objectively-derived validated search strategy using logistic regression based on the frequency of occurrence of terms in the approximately 80,000 reports of randomized trials identified compared with the frequency of these terms across the entire EMBASE database. PMID:18826567

MAP: an iterative experimental design methodology for the optimization of catalytic search space structure modeling.

PubMed

Baumes, Laurent A

2006-01-01

One of the main problems in high-throughput research for materials is still the design of experiments. At early stages of discovery programs, purely exploratory methodologies coupled with fast screening tools should be employed. This should lead to opportunities to find unexpected catalytic results and identify the "groups" of catalyst outputs, providing well-defined boundaries for future optimizations. However, very few new papers deal with strategies that guide exploratory studies. Mostly, traditional designs, homogeneous covering, or simple random samplings are exploited. Typical catalytic output distributions exhibit unbalanced datasets for which an efficient learning is hardly carried out, and interesting but rare classes are usually unrecognized. Here is suggested a new iterative algorithm for the characterization of the search space structure, working independently of learning processes. It enhances recognition rates by transferring catalysts to be screened from "performance-stable" space zones to "unsteady" ones which necessitate more experiments to be well-modeled. The evaluation of new algorithm attempts through benchmarks is compulsory due to the lack of past proofs about their efficiency. The method is detailed and thoroughly tested with mathematical functions exhibiting different levels of complexity. The strategy is not only empirically evaluated, the effect or efficiency of sampling on future Machine Learning performances is also quantified. The minimum sample size required by the algorithm for being statistically discriminated from simple random sampling is investigated.

Hybrid Self-Adaptive Evolution Strategies Guided by Neighborhood Structures for Combinatorial Optimization Problems.

PubMed

Coelho, V N; Coelho, I M; Souza, M J F; Oliveira, T A; Cota, L P; Haddad, M N; Mladenovic, N; Silva, R C P; Guimarães, F G

2016-01-01

This article presents an Evolution Strategy (ES)--based algorithm, designed to self-adapt its mutation operators, guiding the search into the solution space using a Self-Adaptive Reduced Variable Neighborhood Search procedure. In view of the specific local search operators for each individual, the proposed population-based approach also fits into the context of the Memetic Algorithms. The proposed variant uses the Greedy Randomized Adaptive Search Procedure with different greedy parameters for generating its initial population, providing an interesting exploration-exploitation balance. To validate the proposal, this framework is applied to solve three different [Formula: see text]-Hard combinatorial optimization problems: an Open-Pit-Mining Operational Planning Problem with dynamic allocation of trucks, an Unrelated Parallel Machine Scheduling Problem with Setup Times, and the calibration of a hybrid fuzzy model for Short-Term Load Forecasting. Computational results point out the convergence of the proposed model and highlight its ability in combining the application of move operations from distinct neighborhood structures along the optimization. The results gathered and reported in this article represent a collective evidence of the performance of the method in challenging combinatorial optimization problems from different application domains. The proposed evolution strategy demonstrates an ability of adapting the strength of the mutation disturbance during the generations of its evolution process. The effectiveness of the proposal motivates the application of this novel evolutionary framework for solving other combinatorial optimization problems.

Effects of programmed exercise on depressive symptoms in midlife and older women: A meta-analysis of randomized controlled trials.

PubMed

Pérez-López, Faustino R; Martínez-Domínguez, Samuel J; Lajusticia, Héctor; Chedraui, Peter

2017-12-01

To perform a systematic review and meta-analysis to clarify the effect of programmed exercise on depressive symptoms (DSs) in midlife and older women. We carried out a structured search of PubMed-Medline, Web of Science, Scopus, Embase, Cochrane Library and Scielo, from database inception through June 29, 2017, without language restriction. The search included the following terms: "depression", "depressive symptoms", "exercise", "physical activity", "menopause", and "randomized controlled trial" (RCTs) in midlife and older women. The US, UK and Australian Clinical Trials databases were also searched. We assessed randomized controlled trials (RCTs) that compared the effect of exercise for at least 6 weeks versus no intervention on DSs as the outcome (as defined by trial authors). Exercise was classified according to duration as "mid-term exercise intervention" (MTEI; lasting for 12 weeks to 4 months), and "long-term exercise intervention" (LTEI; lasting for 6-12 months). Mean changes (±standard deviations) in DSs, as assessed with different questionnaires, were extracted to calculate Hedges' g and then used as the effect size for meta-analysis. Standardized mean differences (SMDs) of DSs after intervention were pooled using a random-effects model. Eleven publications were included for analysis related to 1943 midlife and older women (age range 44-55 years minimum to 65.5±4.0 maximum), none of whom was using a hormone therapy. Seven MTEIs were associated with a significant reduction in DSs (SMD=-0.44; 95% CI -0.69, -0.18; p=0.0008) compared with controls. The reduction in DSs was also significant in six LTEIs (SMD=- 0.29; 95% CI -0.49; -0.09; p=0.005). Heterogeneity of effects among studies was moderate to high. Less perceived stress and insomnia (after exercise) were also found as secondary outcomes. Exercise of low to moderate intensity reduces depressive symptoms in midlife and older women. Copyright © 2017. Published by Elsevier B.V.

A New Framework for Analysis of Coevolutionary Systems-Directed Graph Representation and Random Walks.

PubMed

Chong, Siang Yew; Tiňo, Peter; He, Jun; Yao, Xin

2017-11-20

Studying coevolutionary systems in the context of simplified models (i.e., games with pairwise interactions between coevolving solutions modeled as self plays) remains an open challenge since the rich underlying structures associated with pairwise-comparison-based fitness measures are often not taken fully into account. Although cyclic dynamics have been demonstrated in several contexts (such as intransitivity in coevolutionary problems), there is no complete characterization of cycle structures and their effects on coevolutionary search. We develop a new framework to address this issue. At the core of our approach is the directed graph (digraph) representation of coevolutionary problems that fully captures structures in the relations between candidate solutions. Coevolutionary processes are modeled as a specific type of Markov chains-random walks on digraphs. Using this framework, we show that coevolutionary problems admit a qualitative characterization: a coevolutionary problem is either solvable (there is a subset of solutions that dominates the remaining candidate solutions) or not. This has an implication on coevolutionary search. We further develop our framework that provides the means to construct quantitative tools for analysis of coevolutionary processes and demonstrate their applications through case studies. We show that coevolution of solvable problems corresponds to an absorbing Markov chain for which we can compute the expected hitting time of the absorbing class. Otherwise, coevolution will cycle indefinitely and the quantity of interest will be the limiting invariant distribution of the Markov chain. We also provide an index for characterizing complexity in coevolutionary problems and show how they can be generated in a controlled manner.

Optimal random search for a single hidden target.

PubMed

Snider, Joseph

2011-01-01

A single target is hidden at a location chosen from a predetermined probability distribution. Then, a searcher must find a second probability distribution from which random search points are sampled such that the target is found in the minimum number of trials. Here it will be shown that if the searcher must get very close to the target to find it, then the best search distribution is proportional to the square root of the target distribution regardless of dimension. For a Gaussian target distribution, the optimum search distribution is approximately a Gaussian with a standard deviation that varies inversely with how close the searcher must be to the target to find it. For a network where the searcher randomly samples nodes and looks for the fixed target along edges, the optimum is either to sample a node with probability proportional to the square root of the out-degree plus 1 or not to do so at all.

Hide and seek: How do DNA glycosylases locate oxidatively damaged DNA bases amidst a sea of undamaged bases?

PubMed

Lee, Andrea J; Wallace, Susan S

2017-06-01

The first step of the base excision repair (BER) pathway responsible for removing oxidative DNA damage utilizes DNA glycosylases to find and remove the damaged DNA base. How glycosylases find the damaged base amidst a sea of undamaged bases has long been a question in the BER field. Single molecule total internal reflection fluorescence microscopy (SM TIRFM) experiments have allowed for an exciting look into this search mechanism and have found that DNA glycosylases scan along the DNA backbone in a bidirectional and random fashion. By comparing the search behavior of bacterial glycosylases from different structural families and with varying substrate specificities, it was found that glycosylases search for damage by periodically inserting a wedge residue into the DNA stack as they redundantly search tracks of DNA that are 450-600bp in length. These studies open up a wealth of possibilities for further study in real time of the interactions of DNA glycosylases and other BER enzymes with various DNA substrates. Copyright © 2016 Elsevier Inc. All rights reserved.

Collinear masking effect in visual search is independent of perceptual salience.

PubMed

Jingling, Li; Lu, Yi-Hui; Cheng, Miao; Tseng, Chia-Huei

2017-07-01

Searching for a target in a salient region should be easier than looking for one in a nonsalient region. However, we previously discovered a contradictory phenomenon in which a local target in a salient structure was more difficult to find than one in the background. The salient structure was constructed of orientation singletons aligned to each other to form a collinear structure. In the present study, we undertake to determine whether such a masking effect was a result of salience competition between a global structure and the local target. In the first 3 experiments, we increased the salience value of the local target with the hope of adding to its competitive advantage and eventually eliminating the masking effect; nevertheless, the masking effect persisted. In an additional 2 experiments, we reduced salience of the global collinear structure by altering the orientation of the background bars and the masking effect still emerged. Our salience manipulations were validated by a controlled condition in which the global structure was grouped noncollinearly. In this case, local target salience increase (e.g., onset) or global distractor salience reduction (e.g., randomized flanking orientations) effectively removed the facilitation effect of the noncollinear structure. Our data suggest that salience competition is unlikely to explain the collinear masking effect, and other mechanisms such as contour integration, border formation, or the crowding effect may be prospective candidates for further investigation.

A computational method for the identification of new candidate carcinogenic and non-carcinogenic chemicals.

PubMed

Chen, Lei; Chu, Chen; Lu, Jing; Kong, Xiangyin; Huang, Tao; Cai, Yu-Dong

2015-09-01

Cancer is one of the leading causes of human death. Based on current knowledge, one of the causes of cancer is exposure to toxic chemical compounds, including radioactive compounds, dioxin, and arsenic. The identification of new carcinogenic chemicals may warn us of potential danger and help to identify new ways to prevent cancer. In this study, a computational method was proposed to identify potential carcinogenic chemicals, as well as non-carcinogenic chemicals. According to the current validated carcinogenic and non-carcinogenic chemicals from the CPDB (Carcinogenic Potency Database), the candidate chemicals were searched in a weighted chemical network constructed according to chemical-chemical interactions. Then, the obtained candidate chemicals were further selected by a randomization test and information on chemical interactions and structures. The analyses identified several candidate carcinogenic chemicals, while those candidates identified as non-carcinogenic were supported by a literature search. In addition, several candidate carcinogenic/non-carcinogenic chemicals exhibit structural dissimilarity with validated carcinogenic/non-carcinogenic chemicals.

Text Mining Metal-Organic Framework Papers.

PubMed

Park, Sanghoon; Kim, Baekjun; Choi, Sihoon; Boyd, Peter G; Smit, Berend; Kim, Jihan

2018-02-26

We have developed a simple text mining algorithm that allows us to identify surface area and pore volumes of metal-organic frameworks (MOFs) using manuscript html files as inputs. The algorithm searches for common units (e.g., m 2 /g, cm 3 /g) associated with these two quantities to facilitate the search. From the sample set data of over 200 MOFs, the algorithm managed to identify 90% and 88.8% of the correct surface area and pore volume values. Further application to a test set of randomly chosen MOF html files yielded 73.2% and 85.1% accuracies for the two respective quantities. Most of the errors stem from unorthodox sentence structures that made it difficult to identify the correct data as well as bolded notations of MOFs (e.g., 1a) that made it difficult identify its real name. These types of tools will become useful when it comes to discovering structure-property relationships among MOFs as well as collecting a large set of data for references.

Two-dimensional materials from high-throughput computational exfoliation of experimentally known compounds.

PubMed

Mounet, Nicolas; Gibertini, Marco; Schwaller, Philippe; Campi, Davide; Merkys, Andrius; Marrazzo, Antimo; Sohier, Thibault; Castelli, Ivano Eligio; Cepellotti, Andrea; Pizzi, Giovanni; Marzari, Nicola

2018-03-01

Two-dimensional (2D) materials have emerged as promising candidates for next-generation electronic and optoelectronic applications. Yet, only a few dozen 2D materials have been successfully synthesized or exfoliated. Here, we search for 2D materials that can be easily exfoliated from their parent compounds. Starting from 108,423 unique, experimentally known 3D compounds, we identify a subset of 5,619 compounds that appear layered according to robust geometric and bonding criteria. High-throughput calculations using van der Waals density functional theory, validated against experimental structural data and calculated random phase approximation binding energies, further allowed the identification of 1,825 compounds that are either easily or potentially exfoliable. In particular, the subset of 1,036 easily exfoliable cases provides novel structural prototypes and simple ternary compounds as well as a large portfolio of materials to search from for optimal properties. For a subset of 258 compounds, we explore vibrational, electronic, magnetic and topological properties, identifying 56 ferromagnetic and antiferromagnetic systems, including half-metals and half-semiconductors.

Two-dimensional materials from high-throughput computational exfoliation of experimentally known compounds

NASA Astrophysics Data System (ADS)

Mounet, Nicolas; Gibertini, Marco; Schwaller, Philippe; Campi, Davide; Merkys, Andrius; Marrazzo, Antimo; Sohier, Thibault; Castelli, Ivano Eligio; Cepellotti, Andrea; Pizzi, Giovanni; Marzari, Nicola

2018-02-01

Two-dimensional (2D) materials have emerged as promising candidates for next-generation electronic and optoelectronic applications. Yet, only a few dozen 2D materials have been successfully synthesized or exfoliated. Here, we search for 2D materials that can be easily exfoliated from their parent compounds. Starting from 108,423 unique, experimentally known 3D compounds, we identify a subset of 5,619 compounds that appear layered according to robust geometric and bonding criteria. High-throughput calculations using van der Waals density functional theory, validated against experimental structural data and calculated random phase approximation binding energies, further allowed the identification of 1,825 compounds that are either easily or potentially exfoliable. In particular, the subset of 1,036 easily exfoliable cases provides novel structural prototypes and simple ternary compounds as well as a large portfolio of materials to search from for optimal properties. For a subset of 258 compounds, we explore vibrational, electronic, magnetic and topological properties, identifying 56 ferromagnetic and antiferromagnetic systems, including half-metals and half-semiconductors.

Optimizing event selection with the random grid search

NASA Astrophysics Data System (ADS)

Bhat, Pushpalatha C.; Prosper, Harrison B.; Sekmen, Sezen; Stewart, Chip

2018-07-01

The random grid search (RGS) is a simple, but efficient, stochastic algorithm to find optimal cuts that was developed in the context of the search for the top quark at Fermilab in the mid-1990s. The algorithm, and associated code, have been enhanced recently with the introduction of two new cut types, one of which has been successfully used in searches for supersymmetry at the Large Hadron Collider. The RGS optimization algorithm is described along with the recent developments, which are illustrated with two examples from particle physics. One explores the optimization of the selection of vector boson fusion events in the four-lepton decay mode of the Higgs boson and the other optimizes SUSY searches using boosted objects and the razor variables.

[A Decade of Online Physician-Rating Websites in Germany: an Assessment of the Current Level of Development].

PubMed

Emmert, Martin; Meszmer, Nina

2017-07-31

Objective On physician-rating websites (PRW), patients have the opportunity to search for physicians and also evaluate their performance. PRW in Germany has been in existence for a decade; this study aims to provide an overview of the current level of their significance for both patients and the health care system. Methods (1) A systematic internet search was carried out to identify German PRW. (2) Online-derived cross-sectional data (N=1,044 respondents) were analyzed with respect to awareness, usage, and impact of PRW as well as patient preferences when searching online for physicians. (3) An analysis of the structure of online ratings for a random sample of 11% of German dermatologists was conducted. Results In total, we identified 29 PRWs. Slightly more than half of all respondents (54%) were aware of German PRW and every fourth respondent has already used PRW to search for a physician. Approximately 70% of all users stated they had already made a decision for or against a particular physician based on the quality ratings shown on PRW. Almost all dermatologists could be identified on PRW and 93% have already been rated on any PRW (mean number of ratings: 24.55). More than half of all ratings (55%) were positive. Conclusion After one decade of development, PRWs seem to have gained significant importance in the German health care sector. However, high-quality and adequately powered randomized controlled trials are required to determine the impact of PRWs on patient steerage. © Georg Thieme Verlag KG Stuttgart · New York.

Pushing the glass transition towards random close packing using self-propelled hard spheres

NASA Astrophysics Data System (ADS)

Ni, Ran; Stuart, Martien A. Cohen; Dijkstra, Marjolein

2013-10-01

Although the concept of random close packing with an almost universal packing fraction of approximately 0.64 for hard spheres was introduced more than half a century ago, there are still ongoing debates. The main difficulty in searching the densest packing is that states with packing fractions beyond the glass transition at approximately 0.58 are inherently non-equilibrium systems, where the dynamics slows down with a structural relaxation time diverging with density; hence, the random close packing is inaccessible. Here we perform simulations of self-propelled hard spheres, and we find that with increasing activity the relaxation dynamics can be sped up by orders of magnitude. The glass transition shifts to higher packing fractions upon increasing the activity, allowing the study of sphere packings with fluid-like dynamics at packing fractions close to RCP. Our study opens new possibilities of investigating dense packings and the glass transition in systems of hard particles.

Robust local search for spacecraft operations using adaptive noise

NASA Technical Reports Server (NTRS)

Fukunaga, Alex S.; Rabideau, Gregg; Chien, Steve

2004-01-01

Randomization is a standard technique for improving the performance of local search algorithms for constraint satisfaction. However, it is well-known that local search algorithms are constraints satisfaction. However, it is well-known that local search algorithms are to the noise values selected. We investigate the use of an adaptive noise mechanism in an iterative repair-based planner/scheduler for spacecraft operations. Preliminary results indicate that adaptive noise makes the use of randomized repair moves safe and robust; that is, using adaptive noise makes it possible to consistently achieve, performance comparable with the best tuned noise setting without the need for manually tuning the noise parameter.

Particle swarm optimization-based automatic parameter selection for deep neural networks and its applications in large-scale and high-dimensional data

PubMed Central

2017-01-01

In this paper, we propose a new automatic hyperparameter selection approach for determining the optimal network configuration (network structure and hyperparameters) for deep neural networks using particle swarm optimization (PSO) in combination with a steepest gradient descent algorithm. In the proposed approach, network configurations were coded as a set of real-number m-dimensional vectors as the individuals of the PSO algorithm in the search procedure. During the search procedure, the PSO algorithm is employed to search for optimal network configurations via the particles moving in a finite search space, and the steepest gradient descent algorithm is used to train the DNN classifier with a few training epochs (to find a local optimal solution) during the population evaluation of PSO. After the optimization scheme, the steepest gradient descent algorithm is performed with more epochs and the final solutions (pbest and gbest) of the PSO algorithm to train a final ensemble model and individual DNN classifiers, respectively. The local search ability of the steepest gradient descent algorithm and the global search capabilities of the PSO algorithm are exploited to determine an optimal solution that is close to the global optimum. We constructed several experiments on hand-written characters and biological activity prediction datasets to show that the DNN classifiers trained by the network configurations expressed by the final solutions of the PSO algorithm, employed to construct an ensemble model and individual classifier, outperform the random approach in terms of the generalization performance. Therefore, the proposed approach can be regarded an alternative tool for automatic network structure and parameter selection for deep neural networks. PMID:29236718

The Impact of Random Metal Detector Searches on Contraband Possession and Feelings of Safety at School

ERIC Educational Resources Information Center

Bhatt, Rachana; Davis, Tomeka

2018-01-01

Weapons at school pose a danger to students as well as faculty. Educational administrators have attempted to reduce their prevalence by implementing random weapons searches in schools. This article examines the effectiveness of this approach using data from two geographically adjacent school districts in Florida (Miami-Dade and Broward). In the…

The Lévy flight paradigm: random search patterns and mechanisms.

PubMed

Reynolds, A M; Rhodes, C J

2009-04-01

Over recent years there has been an accumulation of evidence from a variety of experimental, theoretical, and field studies that many organisms use a movement strategy approximated by Lévy flights when they are searching for resources. Lévy flights are random movements that can maximize the efficiency of resource searches in uncertain environments. This is a highly significant finding because it suggests that Lévy flights provide a rigorous mathematical basis for separating out evolved, innate behaviors from environmental influences. We discuss recent developments in random-search theory, as well as the many different experimental and data collection initiatives that have investigated search strategies. Methods for trajectory construction and robust data analysis procedures are presented. The key to prediction and understanding does, however, lie in the elucidation of mechanisms underlying the observed patterns. We discuss candidate neurological, olfactory, and learning mechanisms for the emergence of Lévy flight patterns in some organisms, and note that convergence of behaviors along such different evolutionary pathways is not surprising given the energetic efficiencies that Lévy flight movement patterns confer.

Surgery for congenital choanal atresia.

PubMed

Cedin, Antonio C; Atallah, Alvaro N; Andriolo, Régis B; Cruz, Oswaldo L; Pignatari, Shirley N

2012-02-15

Congenital choanal atresia is a rare abnormality characterized by unilateral or bilateral lack of patency of the posterior end of the nasal cavity. With an incidence of 1:5000 to 1:8000 births, it is twice as prevalent in females as it is in males. Surgical procedures aim to provide adequate functional choanal patency and a low rate of restenosis, avoid harm to any structure in development, enable shorter surgery and hospitalization times, and minimize morbidity and mortality. To evaluate the effectiveness and safety of the available surgical techniques for the treatment of congenital choanal atresia in patients with unilateral and bilateral atresia. We searched the Cochrane Ear, Nose and Throat Disorders Group Trials Register; the Cochrane Central Register of Controlled Trials (CENTRAL); PubMed; EMBASE; CINAHL; Web of Science; BIOSIS Previews; Cambridge Scientific Abstracts; ISRCTN and additional sources for published and unpublished trials. The date of the search was 31 January 2011. We planned to include parallel randomized or quasi-randomized controlled trials testing surgical approaches for the treatment of congenital atresia (irrespective of gender and age) that evaluated normal/adequate respiratory function (self reported or preserved nasal airway) and restenosis as the main primary outcomes. We did not consider reoperation and non-congenital atresia (e.g. traumatic, iatrogenic atresias) for inclusion. Three review authors independently assessed the titles and abstracts of the identified articles to determine potential relevance. For dichotomous and continuous variables, we planned to calculate risk ratios (relative risks; RR) and mean differences (MD) with 95% confidence intervals (CI), respectively. We planned to use the random-effects model since we were expecting substantial clinical and methodological heterogeneity. No randomized controlled trials were identified. From the 120 reports retrieved using our search strategy, 46 primary studies had the potential to be included since they had tested surgical approaches for choanal atresia. However, we excluded all of them during the final selection process because their study designs did not meet our inclusion criteria. There is no definitive evidence, based on randomized controlled trials, to demonstrate the potential advantages and disadvantages of any specific surgical technique for patients with choanal atresia. Specialists should unify their efforts in multicenter randomized controlled trials that test the effectiveness and safety of different surgical techniques in patients with choanal atresia.

Current role of cryotherapy in retinopathy of prematurity: a report by the American Academy of Ophthalmology.

PubMed

Simpson, Jennifer L; Melia, Michele; Yang, Michael B; Buffenn, Angela N; Chiang, Michael F; Lambert, Scott R

2012-04-01

To evaluate the role of cryotherapy in the current treatment of retinopathy of prematurity (ROP). Literature searches of PubMed and the Cochrane Library were conducted on December 2, 2009, for articles published after 1984. The searches included all languages and retrieved 187 relevant citations. Thirteen articles were deemed relevant to the assessment question and were rated according to the strength of evidence. Four articles reported results from 2 large multicenter randomized clinical trials, and the remaining 9 articles reported results of 3 small randomized trials that directly compared cryotherapy and laser. Neither of the multicenter randomized clinical trials was a direct comparison of cryotherapy with laser. These studies were used to evaluate the comparative trials based on treatment criteria, study populations, and clinical results. Higher percentages of poor structural and functional outcomes generally were seen in eyes treated with cryotherapy compared with eyes undergoing laser treatment. Higher rates of systemic complications and myopia also were identified after treatment with cryotherapy. Despite a relative paucity of level I evidence directly comparing cryotherapy and laser treatment for threshold ROP, the literature suggests that neonatal facilities should gain access to laser technology and laser-trained ophthalmic staff to achieve better outcomes for treatment of the disease. Copyright © 2012 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Optimizing event selection with the random grid search

DOE PAGES

Bhat, Pushpalatha C.; Prosper, Harrison B.; Sekmen, Sezen; ...

2018-02-27

In this paper, the random grid search (RGS) is a simple, but efficient, stochastic algorithm to find optimal cuts that was developed in the context of the search for the top quark at Fermilab in the mid-1990s. The algorithm, and associated code, have been enhanced recently with the introduction of two new cut types, one of which has been successfully used in searches for supersymmetry at the Large Hadron Collider. The RGS optimization algorithm is described along with the recent developments, which are illustrated with two examples from particle physics. One explores the optimization of the selection of vector bosonmore » fusion events in the four-lepton decay mode of the Higgs boson and the other optimizes SUSY searches using boosted objects and the razor variables.« less

Optimizing Event Selection with the Random Grid Search

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

Bhat, Pushpalatha C.; Prosper, Harrison B.; Sekmen, Sezen

2017-06-29

The random grid search (RGS) is a simple, but efficient, stochastic algorithm to find optimal cuts that was developed in the context of the search for the top quark at Fermilab in the mid-1990s. The algorithm, and associated code, have been enhanced recently with the introduction of two new cut types, one of which has been successfully used in searches for supersymmetry at the Large Hadron Collider. The RGS optimization algorithm is described along with the recent developments, which are illustrated with two examples from particle physics. One explores the optimization of the selection of vector boson fusion events inmore » the four-lepton decay mode of the Higgs boson and the other optimizes SUSY searches using boosted objects and the razor variables.« less

Optimizing event selection with the random grid search

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

Bhat, Pushpalatha C.; Prosper, Harrison B.; Sekmen, Sezen

In this paper, the random grid search (RGS) is a simple, but efficient, stochastic algorithm to find optimal cuts that was developed in the context of the search for the top quark at Fermilab in the mid-1990s. The algorithm, and associated code, have been enhanced recently with the introduction of two new cut types, one of which has been successfully used in searches for supersymmetry at the Large Hadron Collider. The RGS optimization algorithm is described along with the recent developments, which are illustrated with two examples from particle physics. One explores the optimization of the selection of vector bosonmore » fusion events in the four-lepton decay mode of the Higgs boson and the other optimizes SUSY searches using boosted objects and the razor variables.« less

Online games: a novel approach to explore how partial information influences human random searches

NASA Astrophysics Data System (ADS)

Martínez-García, Ricardo; Calabrese, Justin M.; López, Cristóbal

2017-01-01

Many natural processes rely on optimizing the success ratio of a search process. We use an experimental setup consisting of a simple online game in which players have to find a target hidden on a board, to investigate how the rounds are influenced by the detection of cues. We focus on the search duration and the statistics of the trajectories traced on the board. The experimental data are explained by a family of random-walk-based models and probabilistic analytical approximations. If no initial information is given to the players, the search is optimized for cues that cover an intermediate spatial scale. In addition, initial information about the extension of the cues results, in general, in faster searches. Finally, strategies used by informed players turn into non-stationary processes in which the length of e ach displacement evolves to show a well-defined characteristic scale that is not found in non-informed searches.

Online games: a novel approach to explore how partial information influences human random searches.

PubMed

Martínez-García, Ricardo; Calabrese, Justin M; López, Cristóbal

2017-01-06

Many natural processes rely on optimizing the success ratio of a search process. We use an experimental setup consisting of a simple online game in which players have to find a target hidden on a board, to investigate how the rounds are influenced by the detection of cues. We focus on the search duration and the statistics of the trajectories traced on the board. The experimental data are explained by a family of random-walk-based models and probabilistic analytical approximations. If no initial information is given to the players, the search is optimized for cues that cover an intermediate spatial scale. In addition, initial information about the extension of the cues results, in general, in faster searches. Finally, strategies used by informed players turn into non-stationary processes in which the length of e ach displacement evolves to show a well-defined characteristic scale that is not found in non-informed searches.

Benefits and Harms of Sick Leave: Lack of Randomized, Controlled Trials

ERIC Educational Resources Information Center

Axelsson, Inge; Marnetoft, Sven-Uno

2010-01-01

The aim of this study was to try to identify those randomized controlled trials that compare sick leave with no sick leave or a different duration or degree of sick leave. A comprehensive, systematic, electronic search of Clinical Evidence, the Cochrane Library and PubMed, and a manual search of the Campbell Library and a journal supplement was…

Contingency and statistical laws in replicate microbial closed ecosystems.

PubMed

Hekstra, Doeke R; Leibler, Stanislas

2012-05-25

Contingency, the persistent influence of past random events, pervades biology. To what extent, then, is each course of ecological or evolutionary dynamics unique, and to what extent are these dynamics subject to a common statistical structure? Addressing this question requires replicate measurements to search for emergent statistical laws. We establish a readily replicated microbial closed ecosystem (CES), sustaining its three species for years. We precisely measure the local population density of each species in many CES replicates, started from the same initial conditions and kept under constant light and temperature. The covariation among replicates of the three species densities acquires a stable structure, which could be decomposed into discrete eigenvectors, or "ecomodes." The largest ecomode dominates population density fluctuations around the replicate-average dynamics. These fluctuations follow simple power laws consistent with a geometric random walk. Thus, variability in ecological dynamics can be studied with CES replicates and described by simple statistical laws. Copyright © 2012 Elsevier Inc. All rights reserved.

Optimal Quantum Spatial Search on Random Temporal Networks

NASA Astrophysics Data System (ADS)

Chakraborty, Shantanav; Novo, Leonardo; Di Giorgio, Serena; Omar, Yasser

2017-12-01

To investigate the performance of quantum information tasks on networks whose topology changes in time, we study the spatial search algorithm by continuous time quantum walk to find a marked node on a random temporal network. We consider a network of n nodes constituted by a time-ordered sequence of Erdös-Rényi random graphs G (n ,p ), where p is the probability that any two given nodes are connected: After every time interval τ , a new graph G (n ,p ) replaces the previous one. We prove analytically that, for any given p , there is always a range of values of τ for which the running time of the algorithm is optimal, i.e., O (√{n }), even when search on the individual static graphs constituting the temporal network is suboptimal. On the other hand, there are regimes of τ where the algorithm is suboptimal even when each of the underlying static graphs are sufficiently connected to perform optimal search on them. From this first study of quantum spatial search on a time-dependent network, it emerges that the nontrivial interplay between temporality and connectivity is key to the algorithmic performance. Moreover, our work can be extended to establish high-fidelity qubit transfer between any two nodes of the network. Overall, our findings show that one can exploit temporality to achieve optimal quantum information tasks on dynamical random networks.

Failure rate of single-unit restorations on posterior vital teeth: A systematic review.

PubMed

Afrashtehfar, Kelvin I; Emami, Elham; Ahmadi, Motahareh; Eilayyan, Owis; Abi-Nader, Samer; Tamimi, Faleh

2017-03-01

No knowledge synthesis exists concerning when to use a direct restoration versus a complete-coverage indirect restoration in posterior vital teeth. The purpose of this systematic review was to identify the failure rate of conventional single-unit tooth-supported restorations in posterior permanent vital teeth as a function of remaining tooth structure. Four databases were searched electronically, and 8 selected journals were searched manually up to February 2015. Clinical studies of tooth-supported single-unit restorative treatments with a mean follow-up period of at least 3 years were selected. The outcome measured was the restorations' clinical or radiological failure. Following the Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines, the Cochrane Collaboration procedures for randomized control trials, the Strengthening the Reporting of Observational Studies in Epidemiology criteria for observational studies, 2 reviewers independently applied eligibility criteria, extracted data, and assessed the quality of the evidence of the included studies using the American Association of Critical Care Nurses' system. The weighted-mean group 5-year failure rates of the restorations were reported according to the type of treatment and remaining tooth structure. A metaregression model was used to assess the correlation between the number of remaining tooth walls and the weighted-mean 5-year failure rates. Five randomized controlled trials and 9 observational studies were included and their quality ranged from low to moderate. These studies included a total of 358 crowns, 4804 composite resins, and 303582 amalgams. Data obtained from the randomized controlled trials showed that, regardless of the amount of remaining tooth structure, amalgams presented better outcomes than composite resins. Furthermore, in teeth with fewer than 2 remaining walls, high-quality observational studies demonstrated that crowns were better than amalgams. A clear inverse correlation was found between the amount of remaining tooth structure and restoration failure. Insufficient high-quality data are available to support one restorative treatment or material over another for the restoration of vital posterior teeth. However, the current evidence suggests that the failure rates of treatments may depend on the amount of remaining tooth structure and types of treatment. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.

PubMed

de Oliveira, Saulo H P; Law, Eleanor C; Shi, Jiye; Deane, Charlotte M

2018-04-01

Most current de novo structure prediction methods randomly sample protein conformations and thus require large amounts of computational resource. Here, we consider a sequential sampling strategy, building on ideas from recent experimental work which shows that many proteins fold cotranslationally. We have investigated whether a pseudo-greedy search approach, which begins sequentially from one of the termini, can improve the performance and accuracy of de novo protein structure prediction. We observed that our sequential approach converges when fewer than 20 000 decoys have been produced, fewer than commonly expected. Using our software, SAINT2, we also compared the run time and quality of models produced in a sequential fashion against a standard, non-sequential approach. Sequential prediction produces an individual decoy 1.5-2.5 times faster than non-sequential prediction. When considering the quality of the best model, sequential prediction led to a better model being produced for 31 out of 41 soluble protein validation cases and for 18 out of 24 transmembrane protein cases. Correct models (TM-Score > 0.5) were produced for 29 of these cases by the sequential mode and for only 22 by the non-sequential mode. Our comparison reveals that a sequential search strategy can be used to drastically reduce computational time of de novo protein structure prediction and improve accuracy. Data are available for download from: http://opig.stats.ox.ac.uk/resources. SAINT2 is available for download from: https://github.com/sauloho/SAINT2. saulo.deoliveira@dtc.ox.ac.uk. Supplementary data are available at Bioinformatics online.

CALL FOR PAPERS: Special issue on the random search problem: trends and perspectives

NASA Astrophysics Data System (ADS)

da Luz, Marcos G. E.; Grosberg, Alexander Y.; Raposo, Ernesto P.; Viswanathan, Gandhi M.

2008-11-01

This is a call for contributions to a special issue of Journal of Physics A: Mathematical and Theoretical dedicated to the subject of the random search problem. The motivation behind this special issue is to summarize in a single comprehensive publication, the main aspects (past and present), latest developments, different viewpoints and the directions being followed in this multidisciplinary field. We hope that such a special issue could become a particularly valuable reference for the broad scientific community working with the general random search problem. The Editorial Board has invited Marcos G E da Luz, Alexander Y Grosberg, Ernesto P Raposo and Gandhi M Viswanathan to serve as Guest Editors for the special issue. The general question of how to optimize the search for specific target objects in either continuous or discrete environments when the information available is limited is of significant importance in a broad range of fields. Representative examples include ecology (animal foraging, dispersion of populations), geology (oil recovery from mature reservoirs), information theory (automated researchers of registers in high-capacity database), molecular biology (proteins searching for their sites, e.g., on DNA ), etc. One reason underlying the richness of the random search problem relates to the `ignorance' of the locations of the randomly located `targets'. A statistical approach to the search problem can deal adequately with incomplete information and so stochastic strategies become advantageous. The general problem of how to search efficiently for randomly located target sites can thus be quantitatively described using the concepts and methods of statistical physics and stochastic processes. Scope Thus far, to the best of our knowledge, no recent textbook or review article in a physics journal has appeared on this topic. This makes a special issue with review and research articles attractive to those interested in acquiring a general introduction to the field. The subject can be approached from the perspective of different fields: ecology, networks, transport problems, molecular biology, etc. The study of the problem is particularly suited to the concepts and methods of statistical physics and stochastic processes; for example, fractals, random walks, anomalous diffusion. Discrete landscapes can be approached via graph theory, random lattices and complex networks. Such topics are regularly discussed in Journal of Physics A: Mathematical and Theoretical. All such aspects of the problem fall within the scope and focus of this special issue on the random search problem: trends and perspectives. Editorial policy All contributions to the special issue will be refereed in accordance with the refereeing policy of the journal. In particular, all research papers will be expected to be original work reporting substantial new results. The issue will also contain a number of review articles by invitation only. The Guest Editors reserve the right to judge whether a contribution fits the scope of the special issue. Guidelines for preparation of contributions We aim to publish the special issue in August 2009. To realize this, the DEADLINE for contributed papers is 15 January 2009. There is a page limit of 15 printed pages (approximately 9000 words) per contribution. For papers exceeding this limit, the Guest Editors reserve the right to request a reduction in length. Further advice on document preparation can be found at www.iop.org/Journals/jphysa. Contributions to the special issue should if possible be submitted electronically by web upload at www.iop.org/Journals/jphysa, or by email to jphysa@iop.org, quoting 'J. Phys. A Special Issue— Random Search Problem'. Please state whether the paper has been invited or is contributed. Submissions should ideally be in standard LaTeX form. Please see the website for further information on electronic submissions. Authors unable to submit electronically may send hard-copy contributions to: Publishing Administrators, Journal of Physics A, Institute of Physics Publishing, Dirac House, Temple Back, Bristol BS1 6BE, UK, enclosing electronic code on CD if available and quoting 'J. Phys. A Special Issue—Random Search Problem'. All contributions should be accompanied by a read-me file or covering letter giving the postal and e-mail addresses for correspondence. The Publishing Office should be notified of any subsequent change of address. This special issue will be published in the paper and online version of the journal. The corresponding author of each contribution will receive a complimentary copy of the issue.

Ringed Seal Search for Global Optimization via a Sensitive Search Model.

PubMed

Saadi, Younes; Yanto, Iwan Tri Riyadi; Herawan, Tutut; Balakrishnan, Vimala; Chiroma, Haruna; Risnumawan, Anhar

2016-01-01

The efficiency of a metaheuristic algorithm for global optimization is based on its ability to search and find the global optimum. However, a good search often requires to be balanced between exploration and exploitation of the search space. In this paper, a new metaheuristic algorithm called Ringed Seal Search (RSS) is introduced. It is inspired by the natural behavior of the seal pup. This algorithm mimics the seal pup movement behavior and its ability to search and choose the best lair to escape predators. The scenario starts once the seal mother gives birth to a new pup in a birthing lair that is constructed for this purpose. The seal pup strategy consists of searching and selecting the best lair by performing a random walk to find a new lair. Affected by the sensitive nature of seals against external noise emitted by predators, the random walk of the seal pup takes two different search states, normal state and urgent state. In the normal state, the pup performs an intensive search between closely adjacent lairs; this movement is modeled via a Brownian walk. In an urgent state, the pup leaves the proximity area and performs an extensive search to find a new lair from sparse targets; this movement is modeled via a Levy walk. The switch between these two states is realized by the random noise emitted by predators. The algorithm keeps switching between normal and urgent states until the global optimum is reached. Tests and validations were performed using fifteen benchmark test functions to compare the performance of RSS with other baseline algorithms. The results show that RSS is more efficient than Genetic Algorithm, Particles Swarm Optimization and Cuckoo Search in terms of convergence rate to the global optimum. The RSS shows an improvement in terms of balance between exploration (extensive) and exploitation (intensive) of the search space. The RSS can efficiently mimic seal pups behavior to find best lair and provide a new algorithm to be used in global optimization problems.

An e-mail survey identified unpublished studies for systematic reviews.

PubMed

Reveiz, Ludovic; Cardona, Andres Felipe; Ospina, Edgar Guillermo; de Agular, Sylvia

2006-07-01

A large number of trials remain difficult to locate or unpublished for systematic reviews. The objective of this article was to determine the usefulness of making e-mail contact with authors of clinical trials and literature reviews found in MEDLINE to identify unpublished or difficult to locate Randomized Controlled Trials (RCTs). A structured search for detecting RCTs in MEDLINE was made from January 1999 to June 2003; a questionnaire was sent to a random sample of 525 author's mails. Those RCTs obtained were sought in MEDLINE, EMBASE, the Cochrane Controlled Trials Register, LILACS, and ongoing registers. 40 (7.6%) replies were received; 10 previously undescribed and unpublished RCTs and 21 unregistered ongoing RCTs were found. The most frequently given reasons for not publishing were: lack of time for finalizing the statistical analysis and preparing the manuscript, contractual obligations with the pharmaceutical industry, methodologic errors in designing, and editorial rejection. Using the e-mails of authors detected by the search in electronic databases could contribute toward detecting potentially relevant ongoing or unpublished RCTs enabling rapid, straightforward, low-cost systematic review; in addition, the results of this study support the need of universal registration of all studies at their inception.

Surgery for post-vitrectomy cataract

PubMed Central

Do, Diana V; Gichuhi, Stephen; Vedula, Satyanarayana S; Hawkins, Barbara S

2014-01-01

Background Cataract formation or acceleration can occur after intraocular surgery, especially following vitrectomy, a surgical technique for removing the vitreous which is used in the treatment of disorders that affect the posterior segment of the eye. The underlying problem that led to vitrectomy may limit the benefit from cataract surgery. Objectives The objective of this review was to evaluate the effectiveness and safety of surgery for post-vitrectomy cataract with respect to visual acuity, quality of life, and other outcomes. Search methods We searched CENTRAL (which contains the Cochrane Eyes and Vision Group Trials Register) (The Cochrane Library 2013, Issue 4), Ovid MEDLINE, Ovid MEDLINE in-Process and Other Non-Indexed Citations, Ovid MEDLINE Daily Update, Ovid OLDMED-LINE (January 1946 to May 2013), EMBASE (January 1980 to May 2013, Latin American and Caribbean Health Sciences Literature Database (LILACS) (January 1982 to May 2013), PubMed (January 1946 to May 2013), the metaRegister of Controlled Trials (mRCT) (www.controlled-trials.com), ClinicalTrials.gov (www.clinicaltrial.gov) and the WHO International Clinical Trials Registry Platform (ICTRP) (www.who.int/ictrp/search/en). We did not use any date or language restrictions in the electronic searches for trials. We last searched the electronic databases on 22 May 2013. Selection criteria We planned to include randomized and quasi-randomized controlled trials comparing cataract surgery with no surgery in adult patients who developed cataract following vitrectomy. Data collection and analysis Two authors screened the search results independently according to the standard methodological procedures expected by The Cochrane Collaboration. Main results We found no randomized or quasi-randomized controlled trials comparing cataract surgery with no cataract surgery for patients who developed cataracts following vitrectomy surgery. Authors' conclusions There is no evidence from randomized or quasi-randomized controlled trials on which to base clinical recommendations for surgery for post-vitrectomy cataract. There is a clear need for randomized controlled trials to address this evidence gap. Such trials should stratify participants by their age, the retinal disorder leading to vitrectomy, and the status of the underlying disease process in the contralateral eye. Outcomes assessed in such trials may include gain of vision on the Early Treatment Diabetic Retinopathy Study (ETDRS) scale, quality of life, and adverse events such as posterior capsular rupture. Both short-term (six-month) and long-term (one-year or two-year) outcomes should be examined. PMID:24357418

Superionic Phases of the 1:1 Water–Ammonia Mixture

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

Bethkenhagen, Mandy; Cebulla, Daniel; Redmer, Ronald

We report four structures for the 1:1 water–ammonia mixture showing superionic behavior at high temperature with the space groups P4/ nmm, Ima2, Pma2, and Pm, which have been identified from evolutionary random structure search calculations at 0 K. Analyzing the respective pair distribution functions and diffusive properties the superionic phase is found to be stable in a temperature range between 1000 and 6000 K for pressures up to 800 GPa. We propose a high-pressure phase diagram of the water–ammonia mixture for the first time and compare the self-diffusion coefficients in the mixture to the ones found in water and ammonia.more » Lastly, possible implications on the interior structure of the giant planets Uranus and Neptune are discussed.« less

Superionic Phases of the 1:1 Water–Ammonia Mixture

DOE PAGES

Bethkenhagen, Mandy; Cebulla, Daniel; Redmer, Ronald; ...

2015-09-21

We report four structures for the 1:1 water–ammonia mixture showing superionic behavior at high temperature with the space groups P4/ nmm, Ima2, Pma2, and Pm, which have been identified from evolutionary random structure search calculations at 0 K. Analyzing the respective pair distribution functions and diffusive properties the superionic phase is found to be stable in a temperature range between 1000 and 6000 K for pressures up to 800 GPa. We propose a high-pressure phase diagram of the water–ammonia mixture for the first time and compare the self-diffusion coefficients in the mixture to the ones found in water and ammonia.more » Lastly, possible implications on the interior structure of the giant planets Uranus and Neptune are discussed.« less

Effective search for stable segregation configurations at grain boundaries with data-mining techniques

NASA Astrophysics Data System (ADS)

Kiyohara, Shin; Mizoguchi, Teruyasu

2018-03-01

Grain boundary segregation of dopants plays a crucial role in materials properties. To investigate the dopant segregation behavior at the grain boundary, an enormous number of combinations have to be considered in the segregation of multiple dopants at the complex grain boundary structures. Here, two data mining techniques, the random-forests regression and the genetic algorithm, were applied to determine stable segregation sites at grain boundaries efficiently. Using the random-forests method, a predictive model was constructed from 2% of the segregation configurations and it has been shown that this model could determine the stable segregation configurations. Furthermore, the genetic algorithm also successfully determined the most stable segregation configuration with great efficiency. We demonstrate that these approaches are quite effective to investigate the dopant segregation behaviors at grain boundaries.

Random search optimization based on genetic algorithm and discriminant function

NASA Technical Reports Server (NTRS)

Kiciman, M. O.; Akgul, M.; Erarslanoglu, G.

1990-01-01

The general problem of optimization with arbitrary merit and constraint functions, which could be convex, concave, monotonic, or non-monotonic, is treated using stochastic methods. To improve the efficiency of the random search methods, a genetic algorithm for the search phase and a discriminant function for the constraint-control phase were utilized. The validity of the technique is demonstrated by comparing the results to published test problem results. Numerical experimentation indicated that for cases where a quick near optimum solution is desired, a general, user-friendly optimization code can be developed without serious penalties in both total computer time and accuracy.

Chondroprotection and the prevention of osteoarthritis progression of the knee: a systematic review of treatment agents.

PubMed

Gallagher, Brian; Tjoumakaris, Fotios P; Harwood, Marc I; Good, Robert P; Ciccotti, Michael G; Freedman, Kevin B

2015-03-01

Structure-modifying medications or nutraceuticals may be an effective treatment for osteoarthritis. This study identified 12 treatments that may possess chondroprotective properties: oral glucosamine; chondroitin; nonsteroidal anti-inflammatory drugs (NSAIDs); polyunsaturated fatty acids; S-adenosylmethionine; avocado and soybean unsaponifiable fractions; methylsulfonylmethane; vitamins C, D, and E; intra-articular injections of hyaluronic acid; and platelet-rich plasma (PRP). To perform a systematic review of randomized controlled trials for the effectiveness of each agent in preserving articular cartilage of the knee and delaying the progression of osteoarthritis. Systematic review; Level of evidence, 2. A literature search was performed using PubMed, EMBASE, and the Cochrane Central Register of Controlled Trials. Searches were performed using "treatment," "osteoarthritis," and "knee" as keywords. Selection criteria included randomized controlled trials of ≥12 months, with a placebo control, measuring radiographic changes in joint space width, cartilage volume, or radiographic progression of osteoarthritis. The primary outcome was changes in joint integrity measures. A total of 3514 studies were identified from the initial search, 13 of which met inclusion criteria. Treatment with chondroitin sulfate showed a significant reduction in cartilage loss in 3 of 4 studies identified compared with placebo. Two of 3 trials identified for glucosamine also reported significant structural effects relative to placebo. Intra-articular hyaluronic acid was effective in lowering the rate of cartilage loss in only 1 of 3 studies identified versus placebo. Of the 6 studies identified for NSAIDs, vitamin E, and vitamin D, none showed any structural effect compared with placebo. No studies were found that met the inclusion criteria for polyunsaturated fatty acids, S-adenosylmethionine, avocado and soybean unsaponifiable fractions, methylsulfonylmethane, vitamin C, or PRP. For patients with or at risk for osteoarthritis, the use of glucosamine and chondroitin sulfate may serve as a nonoperative means to protect joint cartilage and delay osteoarthritis progression. Hyaluronic acid injections showed variable efficacy, while NSAIDs and vitamins E and D showed no effect on osteoarthritis progression. The other agents evaluated had no evidence in the literature to support or refute their use for chondroprotection. © 2014 The Author(s).

The effect of supervised prenatal exercise on fetal growth: a meta-analysis.

PubMed

Wiebe, Henry W; Boulé, Normand G; Chari, Radha; Davenport, Margie H

2015-05-01

To estimate the influence of structured prenatal exercise on newborn birth weight, macrosomia, and growth restriction. A structured search of MEDLINE, EMBASE, CINAHL, Sport Discus, Ovid's All EBM Reviews, and ClinicalTrials.gov databases up to January 13, 2015. The search combined keywords and MeSH-like terms including, but not limited, to "physical activity," "exercise," "pregnancy," "gestation," "neonatal," and "randomized controlled trial." Articles reporting randomized controlled trials comparing standard care with standard care plus supervised prenatal exercise for which birth size was available were included. Supervision was defined as at least one exercise session performed with study personnel every 2 weeks throughout the program. Interventions consisting solely of pelvic floor exercises, stretching, or relaxation were excluded. Our search yielded 1,036 publications of which 79 were assessed for eligibility. Twenty-eight studies reporting on 5,322 pregnancies were subsequently included in the analysis. Our meta-analysis demonstrated that prenatal exercise reduced the odds of having a large newborn (birth weight greater than 4,000 g or greater than the 90th percentile for gestational age and sex) by 31% (odds ratio [OR] 0.69, 95% confidence interval [CI] 0.55-0.86; I 25%) without altering the risk of having a small newborn (birth weight less than 2,500 g or less than the 10th percentile for gestational age and sex) (OR 1.02, 95% CI 0.72-1.46; I 0%) or gestational age at delivery (weighted mean difference -0.00 weeks, 95% CI -0.09 to 0.09; I 0%). Newborns of mothers assigned to exercise were lighter than those of nonexercising controls (weighted mean difference -31 g, 95% CI -57 to -4; I 0%). Maternal gestational weight gain (weighted mean difference -1.1 kg, 95% CI -1.5 to -0.6; I 53%) and odds of cesarean delivery (OR 0.80, 95% CI 0.69-0.94; I 0%) were also reduced. These data demonstrate that structured prenatal exercise reduces the risk of having a large newborn without a change in the risk of having a small newborn.

Searching the Polish Medical Bibliography (Polska Bibliografia Lekarska) for trials.

PubMed

Almerie, Muhammad Qutayba; Matar, Hosam El-Din; Jones, Vicki; Kumar, Ajit; Wright, Judith; Wlostowska, Ewa; Adams, Clive E

2007-12-01

The Polish Medical Bibliography (Polska Bibliografia Lekarska) contains 350 000 records dating from 1979. These records from the fields of medicine, nursing, dentistry, health care systems and preclinical sciences are from nearly 300 biomedical journals published in Poland. We systematically searched the Polish Medical Bibliography Part II (1996-2006) CD-ROM (July 2006) using both English and Polish phrases for randomized trials, manually checked results and, for the trials identified in this way, sought these on medline and embase. Systematic searching identified records of 680 randomized trials from all areas of health care. Nearly 40% of these were not found on either medline or embase. The Polish Medical Bibliography should be of interest to health care information specialists concerned with comprehensive searches for trials.

Evaluating random search strategies in three mammals from distinct feeding guilds.

PubMed

Auger-Méthé, Marie; Derocher, Andrew E; DeMars, Craig A; Plank, Michael J; Codling, Edward A; Lewis, Mark A

2016-09-01

Searching allows animals to find food, mates, shelter and other resources essential for survival and reproduction and is thus among the most important activities performed by animals. Theory predicts that animals will use random search strategies in highly variable and unpredictable environments. Two prominent models have been suggested for animals searching in sparse and heterogeneous environments: (i) the Lévy walk and (ii) the composite correlated random walk (CCRW) and its associated area-restricted search behaviour. Until recently, it was difficult to differentiate between the movement patterns of these two strategies. Using a new method that assesses whether movement patterns are consistent with these two strategies and two other common random search strategies, we investigated the movement behaviour of three species inhabiting sparse northern environments: woodland caribou (Rangifer tarandus caribou), barren-ground grizzly bear (Ursus arctos) and polar bear (Ursus maritimus). These three species vary widely in their diets and thus allow us to contrast the movement patterns of animals from different feeding guilds. Our results showed that although more traditional methods would have found evidence for the Lévy walk for some individuals, a comparison of the Lévy walk to CCRWs showed stronger support for the latter. While a CCRW was the best model for most individuals, there was a range of support for its absolute fit. A CCRW was sufficient to explain the movement of nearly half of herbivorous caribou and a quarter of omnivorous grizzly bears, but was insufficient to explain the movement of all carnivorous polar bears. Strong evidence for CCRW movement patterns suggests that many individuals may use a multiphasic movement strategy rather than one-behaviour strategies such as the Lévy walk. The fact that the best model was insufficient to describe the movement paths of many individuals suggests that some animals living in sparse environments may use strategies that are more complicated than those described by the standard random search models. Thus, our results indicate a need to develop movement models that incorporate factors such as the perceptual and cognitive capacities of animals. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

When Gravity Fails: Local Search Topology

NASA Technical Reports Server (NTRS)

Frank, Jeremy; Cheeseman, Peter; Stutz, John; Lau, Sonie (Technical Monitor)

1997-01-01

Local search algorithms for combinatorial search problems frequently encounter a sequence of states in which it is impossible to improve the value of the objective function; moves through these regions, called {\\em plateau moves), dominate the time spent in local search. We analyze and characterize {\\em plateaus) for three different classes of randomly generated Boolean Satisfiability problems. We identify several interesting features of plateaus that impact the performance of local search algorithms. We show that local minima tend to be small but occasionally may be very large. We also show that local minima can be escaped without unsatisfying a large number of clauses, but that systematically searching for an escape route may be computationally expensive if the local minimum is large. We show that plateaus with exits, called benches, tend to be much larger than minima, and that some benches have very few exit states which local search can use to escape. We show that the solutions (i.e. global minima) of randomly generated problem instances form clusters, which behave similarly to local minima. We revisit several enhancements of local search algorithms and explain their performance in light of our results. Finally we discuss strategies for creating the next generation of local search algorithms.

Improve homology search sensitivity of PacBio data by correcting frameshifts.

PubMed

Du, Nan; Sun, Yanni

2016-09-01

Single-molecule, real-time sequencing (SMRT) developed by Pacific BioSciences produces longer reads than secondary generation sequencing technologies such as Illumina. The long read length enables PacBio sequencing to close gaps in genome assembly, reveal structural variations, and identify gene isoforms with higher accuracy in transcriptomic sequencing. However, PacBio data has high sequencing error rate and most of the errors are insertion or deletion errors. During alignment-based homology search, insertion or deletion errors in genes will cause frameshifts and may only lead to marginal alignment scores and short alignments. As a result, it is hard to distinguish true alignments from random alignments and the ambiguity will incur errors in structural and functional annotation. Existing frameshift correction tools are designed for data with much lower error rate and are not optimized for PacBio data. As an increasing number of groups are using SMRT, there is an urgent need for dedicated homology search tools for PacBio data. In this work, we introduce Frame-Pro, a profile homology search tool for PacBio reads. Our tool corrects sequencing errors and also outputs the profile alignments of the corrected sequences against characterized protein families. We applied our tool to both simulated and real PacBio data. The results showed that our method enables more sensitive homology search, especially for PacBio data sets of low sequencing coverage. In addition, we can correct more errors when comparing with a popular error correction tool that does not rely on hybrid sequencing. The source code is freely available at https://sourceforge.net/projects/frame-pro/ yannisun@msu.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Multivariate classification with random forests for gravitational wave searches of black hole binary coalescence

NASA Astrophysics Data System (ADS)

Baker, Paul T.; Caudill, Sarah; Hodge, Kari A.; Talukder, Dipongkar; Capano, Collin; Cornish, Neil J.

2015-03-01

Searches for gravitational waves produced by coalescing black hole binaries with total masses ≳25 M⊙ use matched filtering with templates of short duration. Non-Gaussian noise bursts in gravitational wave detector data can mimic short signals and limit the sensitivity of these searches. Previous searches have relied on empirically designed statistics incorporating signal-to-noise ratio and signal-based vetoes to separate gravitational wave candidates from noise candidates. We report on sensitivity improvements achieved using a multivariate candidate ranking statistic derived from a supervised machine learning algorithm. We apply the random forest of bagged decision trees technique to two separate searches in the high mass (≳25 M⊙ ) parameter space. For a search which is sensitive to gravitational waves from the inspiral, merger, and ringdown of binary black holes with total mass between 25 M⊙ and 100 M⊙ , we find sensitive volume improvements as high as 70±13%-109±11% when compared to the previously used ranking statistic. For a ringdown-only search which is sensitive to gravitational waves from the resultant perturbed intermediate mass black hole with mass roughly between 10 M⊙ and 600 M⊙ , we find sensitive volume improvements as high as 61±4%-241±12% when compared to the previously used ranking statistic. We also report how sensitivity improvements can differ depending on mass regime, mass ratio, and available data quality information. Finally, we describe the techniques used to tune and train the random forest classifier that can be generalized to its use in other searches for gravitational waves.

Searching for Survivors through Random Human-Body Movement Outdoors by Continuous-Wave Radar Array

PubMed Central

Liu, Miao; Li, Zhao; Liang, Fulai; Jing, Xijing; Lu, Guohua; Wang, Jianqi

2016-01-01

It is a major challenge to search for survivors after chemical or nuclear leakage or explosions. At present, biological radar can be used to achieve this goal by detecting the survivor’s respiration signal. However, owing to the random posture of an injured person at a rescue site, the radar wave may directly irradiate the person’s head or feet, in which it is difficult to detect the respiration signal. This paper describes a multichannel-based antenna array technology, which forms an omnidirectional detection system via 24-GHz Doppler biological radar, to address the random positioning relative to the antenna of an object to be detected. Furthermore, since the survivors often have random body movement such as struggling and twitching, the slight movements of the body caused by breathing are obscured by these movements. Therefore, a method is proposed to identify random human-body movement by utilizing multichannel information to calculate the background variance of the environment in combination with a constant-false-alarm-rate detector. The conducted outdoor experiments indicate that the system can realize the omnidirectional detection of random human-body movement and distinguish body movement from environmental interference such as movement of leaves and grass. The methods proposed in this paper will be a promising way to search for survivors outdoors. PMID:27073860

Searching for Survivors through Random Human-Body Movement Outdoors by Continuous-Wave Radar Array.

PubMed

Li, Chuantao; Chen, Fuming; Qi, Fugui; Liu, Miao; Li, Zhao; Liang, Fulai; Jing, Xijing; Lu, Guohua; Wang, Jianqi

2016-01-01

It is a major challenge to search for survivors after chemical or nuclear leakage or explosions. At present, biological radar can be used to achieve this goal by detecting the survivor's respiration signal. However, owing to the random posture of an injured person at a rescue site, the radar wave may directly irradiate the person's head or feet, in which it is difficult to detect the respiration signal. This paper describes a multichannel-based antenna array technology, which forms an omnidirectional detection system via 24-GHz Doppler biological radar, to address the random positioning relative to the antenna of an object to be detected. Furthermore, since the survivors often have random body movement such as struggling and twitching, the slight movements of the body caused by breathing are obscured by these movements. Therefore, a method is proposed to identify random human-body movement by utilizing multichannel information to calculate the background variance of the environment in combination with a constant-false-alarm-rate detector. The conducted outdoor experiments indicate that the system can realize the omnidirectional detection of random human-body movement and distinguish body movement from environmental interference such as movement of leaves and grass. The methods proposed in this paper will be a promising way to search for survivors outdoors.

A Boltzmann machine for the organization of intelligent machines

NASA Technical Reports Server (NTRS)

Moed, Michael C.; Saridis, George N.

1990-01-01

A three-tier structure consisting of organization, coordination, and execution levels forms the architecture of an intelligent machine using the principle of increasing precision with decreasing intelligence from a hierarchically intelligent control. This system has been formulated as a probabilistic model, where uncertainty and imprecision can be expressed in terms of entropies. The optimal strategy for decision planning and task execution can be found by minimizing the total entropy in the system. The focus is on the design of the organization level as a Boltzmann machine. Since this level is responsible for planning the actions of the machine, the Boltzmann machine is reformulated to use entropy as the cost function to be minimized. Simulated annealing, expanding subinterval random search, and the genetic algorithm are presented as search techniques to efficiently find the desired action sequence and illustrated with numerical examples.

Attributing intentions to random motion engages the posterior superior temporal sulcus.

PubMed

Lee, Su Mei; Gao, Tao; McCarthy, Gregory

2014-01-01

The right posterior superior temporal sulcus (pSTS) is a neural region involved in assessing the goals and intentions underlying the motion of social agents. Recent research has identified visual cues, such as chasing, that trigger animacy detection and intention attribution. When readily available in a visual display, these cues reliably activate the pSTS. Here, using functional magnetic resonance imaging, we examined if attributing intentions to random motion would likewise engage the pSTS. Participants viewed displays of four moving circles and were instructed to search for chasing or mirror-correlated motion. On chasing trials, one circle chased another circle, invoking the percept of an intentional agent; while on correlated motion trials, one circle's motion was mirror reflected by another. On the remaining trials, all circles moved randomly. As expected, pSTS activation was greater when participants searched for chasing vs correlated motion when these cues were present in the displays. Of critical importance, pSTS activation was also greater when participants searched for chasing compared to mirror-correlated motion when the displays in both search conditions were statistically identical random motion. We conclude that pSTS activity associated with intention attribution can be invoked by top-down processes in the absence of reliable visual cues for intentionality.

Application of multivariable search techniques to the optimization of airfoils in a low speed nonlinear inviscid flow field

NASA Technical Reports Server (NTRS)

Hague, D. S.; Merz, A. W.

1975-01-01

Multivariable search techniques are applied to a particular class of airfoil optimization problems. These are the maximization of lift and the minimization of disturbance pressure magnitude in an inviscid nonlinear flow field. A variety of multivariable search techniques contained in an existing nonlinear optimization code, AESOP, are applied to this design problem. These techniques include elementary single parameter perturbation methods, organized search such as steepest-descent, quadratic, and Davidon methods, randomized procedures, and a generalized search acceleration technique. Airfoil design variables are seven in number and define perturbations to the profile of an existing NACA airfoil. The relative efficiency of the techniques are compared. It is shown that elementary one parameter at a time and random techniques compare favorably with organized searches in the class of problems considered. It is also shown that significant reductions in disturbance pressure magnitude can be made while retaining reasonable lift coefficient values at low free stream Mach numbers.

Parallel coding of conjunctions in visual search.

PubMed

Found, A

1998-10-01

Two experiments investigated whether the conjunctive nature of nontarget items influenced search for a conjunction target. Each experiment consisted of two conditions. In both conditions, the target item was a red bar tilted to the right, among white tilted bars and vertical red bars. As well as color and orientation, display items also differed in terms of size. Size was irrelevant to search in that the size of the target varied randomly from trial to trial. In one condition, the size of items correlated with the other attributes of display items (e.g., all red items were big and all white items were small). In the other condition, the size of items varied randomly (i.e., some red items were small and some were big, and some white items were big and some were small). Search was more efficient in the size-correlated condition, consistent with the parallel coding of conjunctions in visual search.

A method for generating reliable atomistic models of amorphous polymers based on a random search of energy minima

NASA Astrophysics Data System (ADS)

Curcó, David; Casanovas, Jordi; Roca, Marc; Alemán, Carlos

2005-07-01

A method for generating atomistic models of dense amorphous polymers is presented. The method is organized in a two-steps procedure. First, structures are generated using an algorithm that minimizes the torsional strain. After this, a relaxation algorithm is applied to minimize the non-bonding interactions. Two alternative relaxation methods, which are based simple minimization and Concerted Rotation techniques, have been implemented. The performance of the method has been checked by simulating polyethylene, polypropylene, nylon 6, poly(L,D-lactic acid) and polyglycolic acid.

Stochastic optimization of broadband reflecting photonic structures.

PubMed

Estrada-Wiese, D; Del Río-Chanona, E A; Del Río, J A

2018-01-19

Photonic crystals (PCs) are built to control the propagation of light within their structure. These can be used for an assortment of applications where custom designed devices are of interest. Among them, one-dimensional PCs can be produced to achieve the reflection of specific and broad wavelength ranges. However, their design and fabrication are challenging due to the diversity of periodic arrangement and layer configuration that each different PC needs. In this study, we present a framework to design high reflecting PCs for any desired wavelength range. Our method combines three stochastic optimization algorithms (Random Search, Particle Swarm Optimization and Simulated Annealing) along with a reduced space-search methodology to obtain a custom and optimized PC configuration. The optimization procedure is evaluated through theoretical reflectance spectra calculated by using the Equispaced Thickness Method, which improves the simulations due to the consideration of incoherent light transmission. We prove the viability of our procedure by fabricating different reflecting PCs made of porous silicon and obtain good agreement between experiment and theory using a merit function. With this methodology, diverse reflecting PCs can be designed for any applications and fabricated with different materials.

Evolutionary Strategies for Protein Folding

NASA Astrophysics Data System (ADS)

Murthy Gopal, Srinivasa; Wenzel, Wolfgang

2006-03-01

The free energy approach for predicting the protein tertiary structure describes the native state of a protein as the global minimum of an appropriate free-energy forcefield. The low-energy region of the free-energy landscape of a protein is extremely rugged. Efficient optimization methods must therefore speed up the search for the global optimum by avoiding high energy transition states, adapt large scale moves or accept unphysical intermediates. Here we investigate an evolutionary strategies(ES) for optimizing a protein conformation in our all-atom free-energy force field([1],[2]). A set of random conformations is evolved using an ES to get a diverse population containing low energy structure. The ES is shown to balance energy improvement and yet maintain diversity in structures. The ES is implemented as a master-client model for distributed computing. Starting from random structures and by using this optimization technique, we were able to fold a 20 amino-acid helical protein and 16 amino-acid beta hairpin[3]. We compare ES to basin hopping method. [1]T. Herges and W. Wenzel,Biophys.J. 87,3100(2004) [2] A. Verma and W. Wenzel Stabilization and folding of beta-sheet and alpha-helical proteins in an all-atom free energy model(submitted)(2005) [3] S. M. Gopal and W. Wenzel Evolutionary Strategies for Protein Folding (in preparation)

77 FR 37713 - Comment Request for Information Collection for ETA 9162, Random Audit of EUC 2008 Claimants...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-22

... Collection for ETA 9162, Random Audit of EUC 2008 Claimants, Comment Request for Extension Without Change... assessed. Currently, ETA is soliciting comments concerning the collection of data about Random Audit of... describing random audits of the work search provision of Public Law 112-96 (see Section 2141(b)). Random...

An analysis of iterated local search for job-shop scheduling.

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

Whitley, L. Darrell; Howe, Adele E.; Watson, Jean-Paul

2003-08-01

Iterated local search, or ILS, is among the most straightforward meta-heuristics for local search. ILS employs both small-step and large-step move operators. Search proceeds via iterative modifications to a single solution, in distinct alternating phases. In the first phase, local neighborhood search (typically greedy descent) is used in conjunction with the small-step operator to transform solutions into local optima. In the second phase, the large-step operator is applied to generate perturbations to the local optima obtained in the first phase. Ideally, when local neighborhood search is applied to the resulting solution, search will terminate at a different local optimum, i.e.,more » the large-step perturbations should be sufficiently large to enable escape from the attractor basins of local optima. ILS has proven capable of delivering excellent performance on numerous N P-Hard optimization problems. [LMS03]. However, despite its implicity, very little is known about why ILS can be so effective, and under what conditions. The goal of this paper is to advance the state-of-the-art in the analysis of meta-heuristics, by providing answers to this research question. They focus on characterizing both the relationship between the structure of the underlying search space and ILS performance, and the dynamic behavior of ILS. The analysis proceeds in the context of the job-shop scheduling problem (JSP) [Tai94]. They begin by demonstrating that the attractor basins of local optima in the JSP are surprisingly weak, and can be escaped with high probaiblity by accepting a short random sequence of less-fit neighbors. this result is used to develop a new ILS algorithms for the JSP, I-JAR, whose performance is competitive with tabu search on difficult benchmark instances. They conclude by developing a very accurate behavioral model of I-JAR, which yields significant insights into the dynamics of search. The analysis is based on a set of 100 random 10 x 10 problem instances, in addition to some widely used benchmark instances. Both I-JAR and the tabu search algorithm they consider are based on the N1 move operator introduced by van Laarhoven et al. [vLAL92]. The N1 operator induces a connected search space, such that it is always possible to move from an arbitrary solution to an optimal solution; this property is integral to the development of a behavioral model of I-JAR. However, much of the analysis generalizes to other move operators, including that of Nowicki and Smutnick [NS96]. Finally the models are based on the distance between two solutions, which they take as the well-known disjunctive graph distance [MBK99].« less

Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations.

PubMed

Suratanee, Apichat; Plaimas, Kitiporn

2017-01-01

The associations between proteins and diseases are crucial information for investigating pathological mechanisms. However, the number of known and reliable protein-disease associations is quite small. In this study, an analysis framework to infer associations between proteins and diseases was developed based on a large data set of a human protein-protein interaction network integrating an effective network search, namely, the reverse k -nearest neighbor (R k NN) search. The R k NN search was used to identify an impact of a protein on other proteins. Then, associations between proteins and diseases were inferred statistically. The method using the R k NN search yielded a much higher precision than a random selection, standard nearest neighbor search, or when applying the method to a random protein-protein interaction network. All protein-disease pair candidates were verified by a literature search. Supporting evidence for 596 pairs was identified. In addition, cluster analysis of these candidates revealed 10 promising groups of diseases to be further investigated experimentally. This method can be used to identify novel associations to better understand complex relationships between proteins and diseases.

Escalated convergent artificial bee colony

NASA Astrophysics Data System (ADS)

Jadon, Shimpi Singh; Bansal, Jagdish Chand; Tiwari, Ritu

2016-03-01

Artificial bee colony (ABC) optimisation algorithm is a recent, fast and easy-to-implement population-based meta heuristic for optimisation. ABC has been proved a rival algorithm with some popular swarm intelligence-based algorithms such as particle swarm optimisation, firefly algorithm and ant colony optimisation. The solution search equation of ABC is influenced by a random quantity which helps its search process in exploration at the cost of exploitation. In order to find a fast convergent behaviour of ABC while exploitation capability is maintained, in this paper basic ABC is modified in two ways. First, to improve exploitation capability, two local search strategies, namely classical unidimensional local search and levy flight random walk-based local search are incorporated with ABC. Furthermore, a new solution search strategy, namely stochastic diffusion scout search is proposed and incorporated into the scout bee phase to provide more chance to abandon solution to improve itself. Efficiency of the proposed algorithm is tested on 20 benchmark test functions of different complexities and characteristics. Results are very promising and they prove it to be a competitive algorithm in the field of swarm intelligence-based algorithms.

Perceptions of randomized security schedules.

PubMed

Scurich, Nicholas; John, Richard S

2014-04-01

Security of infrastructure is a major concern. Traditional security schedules are unable to provide omnipresent coverage; consequently, adversaries can exploit predictable vulnerabilities to their advantage. Randomized security schedules, which randomly deploy security measures, overcome these limitations, but public perceptions of such schedules have not been examined. In this experiment, participants were asked to make a choice between attending a venue that employed a traditional (i.e., search everyone) or a random (i.e., a probability of being searched) security schedule. The absolute probability of detecting contraband was manipulated (i.e., 1/10, 1/4, 1/2) but equivalent between the two schedule types. In general, participants were indifferent to either security schedule, regardless of the probability of detection. The randomized schedule was deemed more convenient, but the traditional schedule was considered fairer and safer. There were no differences between traditional and random schedule in terms of perceived effectiveness or deterrence. Policy implications for the implementation and utilization of randomized schedules are discussed. © 2013 Society for Risk Analysis.

DNA damage may drive nucleosomal reorganization to facilitate damage detection

NASA Astrophysics Data System (ADS)

LeGresley, Sarah E.; Wilt, Jamie; Antonik, Matthew

2014-03-01

One issue in genome maintenance is how DNA repair proteins find lesions at rates that seem to exceed diffusion-limited search rates. We propose a phenomenon where DNA damage induces nucleosomal rearrangements which move lesions to potential rendezvous points in the chromatin structure. These rendezvous points are the dyad and the linker DNA between histones, positions in the chromatin which are more likely to be accessible by repair proteins engaged in a random search. The feasibility of this mechanism is tested by considering the statistical mechanics of DNA containing a single lesion wrapped onto the nucleosome. We consider lesions which make the DNA either more flexible or more rigid by modeling the lesion as either a decrease or an increase in the bending energy. We include this energy in a partition function model of nucleosome breathing. Our results indicate that the steady state for a breathing nucleosome will most likely position the lesion at the dyad or in the linker, depending on the energy of the lesion. A role for DNA binding proteins and chromatin remodelers is suggested based on their ability to alter the mechanical properties of the DNA and DNA-histone binding, respectively. We speculate that these positions around the nucleosome potentially serve as rendezvous points where DNA lesions may be encountered by repair proteins which may be sterically hindered from searching the rest of the nucleosomal DNA. The strength of the repositioning is strongly dependent on the structural details of the DNA lesion and the wrapping and breathing of the nucleosome. A more sophisticated evaluation of this proposed mechanism will require detailed information about breathing dynamics, the structure of partially wrapped nucleosomes, and the structural properties of damaged DNA.

Meta-analysis of structured triglyceride versus other lipid emulsions for parenteral nutrition.

PubMed

Zhu, Mengbai; Li, Xueliang

2013-06-01

Structured triglyceride (STG) is a new emulsion synthesized from long-chain fatty acids and medium-chain fatty acids bound to the same glycerol backbone. We performed a meta-analysis to examine the safety, efficacy, and tolerability of STG for parenteral nutrition. We searched MEDLINE, EMBASE, and the Chinese Biomedicine Database, with the last search done in May 2012. Only randomized controlled trials in humans published in Chinese or English were included. Search terms included structured triglyceride and structural lipid. Methodologic quality was evaluated using the Jadad Scale. Meta-analysis was conducted using Review Manager 5.0.24 to calculate the weighted mean difference (WMD) and standardized mean difference (SMD) with 95% confidence intervals. Twenty-one studies (833 participants) published in English or Chinese were included in the analysis. STG significantly affected plasma triglycerides (WMD = -0.15; 95% confidence interval [CI], -0.29 to -0.01; P = 0.04), plasma glycerol (WMD = 0.21; 95% CI, 0.01-0.41; P = 0.04), free fatty acids (WMD = 0.21; 95% CI, 0.03-0.39; P = 0.02), nitrogen balance (SMD = 1.13; 95% CI, 0.26-1.99; P = 0.01), AST (WMD = -5.97; 95% CI, -7.17 to -4.76; P < 0.00001), and glucose (WMD = -0.18; 95% CI, -0.30 to -0.06; P = 004), but not respiratory quotient, resting energy expenditure, alanine aminotransferase, alkaline phosphatase, gamma-glutamyl transpeptidase, bilirubin, cholesterol, serum creatinine, or vital signs. STG is rapidly metabolized without harming the liver, and positively affects nitrogen balance. STG is at least as safe and effective for parenteral nutrition as other triglycerides. Copyright © 2013 Elsevier Inc. All rights reserved.

Adding statistical regularity results in a global slowdown in visual search.

PubMed

Vaskevich, Anna; Luria, Roy

2018-05-01

Current statistical learning theories predict that embedding implicit regularities within a task should further improve online performance, beyond general practice. We challenged this assumption by contrasting performance in a visual search task containing either a consistent-mapping (regularity) condition, a random-mapping condition, or both conditions, mixed. Surprisingly, performance in a random visual search, without any regularity, was better than performance in a mixed design search that contained a beneficial regularity. This result was replicated using different stimuli and different regularities, suggesting that mixing consistent and random conditions leads to an overall slowing down of performance. Relying on the predictive-processing framework, we suggest that this global detrimental effect depends on the validity of the regularity: when its predictive value is low, as it is in the case of a mixed design, reliance on all prior information is reduced, resulting in a general slowdown. Our results suggest that our cognitive system does not maximize speed, but rather continues to gather and implement statistical information at the expense of a possible slowdown in performance. Copyright © 2018 Elsevier B.V. All rights reserved.

Ringed Seal Search for Global Optimization via a Sensitive Search Model

PubMed Central

Saadi, Younes; Yanto, Iwan Tri Riyadi; Herawan, Tutut; Balakrishnan, Vimala; Chiroma, Haruna; Risnumawan, Anhar

2016-01-01

The efficiency of a metaheuristic algorithm for global optimization is based on its ability to search and find the global optimum. However, a good search often requires to be balanced between exploration and exploitation of the search space. In this paper, a new metaheuristic algorithm called Ringed Seal Search (RSS) is introduced. It is inspired by the natural behavior of the seal pup. This algorithm mimics the seal pup movement behavior and its ability to search and choose the best lair to escape predators. The scenario starts once the seal mother gives birth to a new pup in a birthing lair that is constructed for this purpose. The seal pup strategy consists of searching and selecting the best lair by performing a random walk to find a new lair. Affected by the sensitive nature of seals against external noise emitted by predators, the random walk of the seal pup takes two different search states, normal state and urgent state. In the normal state, the pup performs an intensive search between closely adjacent lairs; this movement is modeled via a Brownian walk. In an urgent state, the pup leaves the proximity area and performs an extensive search to find a new lair from sparse targets; this movement is modeled via a Levy walk. The switch between these two states is realized by the random noise emitted by predators. The algorithm keeps switching between normal and urgent states until the global optimum is reached. Tests and validations were performed using fifteen benchmark test functions to compare the performance of RSS with other baseline algorithms. The results show that RSS is more efficient than Genetic Algorithm, Particles Swarm Optimization and Cuckoo Search in terms of convergence rate to the global optimum. The RSS shows an improvement in terms of balance between exploration (extensive) and exploitation (intensive) of the search space. The RSS can efficiently mimic seal pups behavior to find best lair and provide a new algorithm to be used in global optimization problems. PMID:26790131

Assessing Performance Tradeoffs in Undersea Distributed Sensor Networks

DTIC Science & Technology

2006-09-01

time. We refer to this process as track - before - detect (see [5] for a description), since the final determination of a target presence is not made until...expressions for probability of successful search and probability of false search for modeling the track - before - detect process. We then describe a numerical...random manner (randomly sampled from a uniform distribution). II. SENSOR NETWORK PERFORMANCE MODELS We model the process of track - before - detect by

Stochastic Leader Gravitational Search Algorithm for Enhanced Adaptive Beamforming Technique

PubMed Central

Darzi, Soodabeh; Islam, Mohammad Tariqul; Tiong, Sieh Kiong; Kibria, Salehin; Singh, Mandeep

2015-01-01

In this paper, stochastic leader gravitational search algorithm (SL-GSA) based on randomized k is proposed. Standard GSA (SGSA) utilizes the best agents without any randomization, thus it is more prone to converge at suboptimal results. Initially, the new approach randomly choses k agents from the set of all agents to improve the global search ability. Gradually, the set of agents is reduced by eliminating the agents with the poorest performances to allow rapid convergence. The performance of the SL-GSA was analyzed for six well-known benchmark functions, and the results are compared with SGSA and some of its variants. Furthermore, the SL-GSA is applied to minimum variance distortionless response (MVDR) beamforming technique to ensure compatibility with real world optimization problems. The proposed algorithm demonstrates superior convergence rate and quality of solution for both real world problems and benchmark functions compared to original algorithm and other recent variants of SGSA. PMID:26552032

Directional Bias and Pheromone for Discovery and Coverage on Networks

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

Fink, Glenn A.; Berenhaut, Kenneth S.; Oehmen, Christopher S.

2012-09-11

Natural multi-agent systems often rely on “correlated random walks” (random walks that are biased toward a current heading) to distribute their agents over a space (e.g., for foraging, search, etc.). Our contribution involves creation of a new movement and pheromone model that applies the concept of heading bias in random walks to a multi-agent, digital-ants system designed for cyber-security monitoring. We examine the relative performance effects of both pheromone and heading bias on speed of discovery of a target and search-area coverage in a two-dimensional network layout. We found that heading bias was unexpectedly helpful in reducing search time andmore » that it was more influential than pheromone for improving coverage. We conclude that while pheromone is very important for rapid discovery, heading bias can also greatly improve both performance metrics.« less

Multi-INT Complex Event Processing using Approximate, Incremental Graph Pattern Search

DTIC Science & Technology

2012-06-01

graph pattern search and SPARQL queries . Total execution time for 10 executions each of 5 random pattern searches in synthetic data sets...01/11 1000 10000 100000 RDF triples Time (secs) 10 20 Graph pattern algorithm SPARQL queries Initial Performance Comparisons 09/18/11 2011 Thrust Area

Search and Seizure in the Schools

ERIC Educational Resources Information Center

Staros, Kari; Williams, Charles F.

2007-01-01

The Fourth Amendment to the U.S. Constitution protects the people of the United States from unreasonable searches and seizures. On first reading, these protections seem clearly defined. The amendment was meant to protect Americans from the kinds of random searches and seizures that the colonists experienced under British colonial rule. Under…

Effects of Exercise on Mild-to-Moderate Depressive Symptoms in the Postpartum Period: A Meta-analysis.

PubMed

McCurdy, Ashley P; Boulé, Normand G; Sivak, Allison; Davenport, Margie H

2017-06-01

To examine the influence of exercise on depressive symptoms and the prevalence of depression in the postpartum period. A structured search of MEDLINE, EMBASE, CINAHL, Sport Discus, Ovid's All EBM Reviews, and ClinicalTrials.gov databases was performed with dates from the beginning of the databases until June 16, 2016. The search combined keywords and MeSH-like terms including, but not limited to, "exercise," "postpartum," "depression," and "randomized controlled trial." Randomized controlled trials comparing postpartum exercise (structured, planned, repetitive physical activity) with the standard care for which outcomes assessing depressive symptoms or depressive episodes (as defined by trial authors) were assessed. Trials were identified as prevention trials (women from the general postpartum population) or treatment trials (women were classified as having depression by the trial authors). Effect sizes with 95% confidence intervals (CIs) were calculated using Hedges' g method and standardized mean differences in postintervention depression outcomes were pooled using a random-effects model. Across all 16 trials (1,327 women), the pooled standardized mean difference was -0.34 (95% CI -0.50 to -0.19, I=37%), suggesting a small effect of exercise among all postpartum women on depressive symptoms. Among the 10 treatment trials, a moderate effect size of exercise on depressive symptoms was found (standardized mean difference-0.48, 95% CI -0.73 to -0.22, I=42%). In six prevention trials, a small effect (standardized mean difference-0.22, 95% CI -0.36 to -0.08, I=2%) was found. In women with depression preintervention, exercise increased the odds of resolving depression postintervention by 54% (odds ratio 0.46, Mantel-Haenszel method, 95% CI 0.25-0.84, I=0%). The trials included in this meta-analysis were small and some had methodologic limitations. Light-to-moderate intensity aerobic exercise improves mild-to-moderate depressive symptoms and increases the likelihood that mild-to-moderate depression will resolve.

Search Algorithms as a Framework for the Optimization of Drug Combinations

PubMed Central

Coquin, Laurence; Schofield, Jennifer; Feala, Jacob D.; Reed, John C.; McCulloch, Andrew D.; Paternostro, Giovanni

2008-01-01

Combination therapies are often needed for effective clinical outcomes in the management of complex diseases, but presently they are generally based on empirical clinical experience. Here we suggest a novel application of search algorithms—originally developed for digital communication—modified to optimize combinations of therapeutic interventions. In biological experiments measuring the restoration of the decline with age in heart function and exercise capacity in Drosophila melanogaster, we found that search algorithms correctly identified optimal combinations of four drugs using only one-third of the tests performed in a fully factorial search. In experiments identifying combinations of three doses of up to six drugs for selective killing of human cancer cells, search algorithms resulted in a highly significant enrichment of selective combinations compared with random searches. In simulations using a network model of cell death, we found that the search algorithms identified the optimal combinations of 6–9 interventions in 80–90% of tests, compared with 15–30% for an equivalent random search. These findings suggest that modified search algorithms from information theory have the potential to enhance the discovery of novel therapeutic drug combinations. This report also helps to frame a biomedical problem that will benefit from an interdisciplinary effort and suggests a general strategy for its solution. PMID:19112483

Pressure-Stabilized Cubic Perovskite Oxyhydride BaScO2H.

PubMed

Goto, Yoshihiro; Tassel, Cédric; Noda, Yasuto; Hernandez, Olivier; Pickard, Chris J; Green, Mark A; Sakaebe, Hikari; Taguchi, Noboru; Uchimoto, Yoshiharu; Kobayashi, Yoji; Kageyama, Hiroshi

2017-05-01

We report a scandium oxyhydride BaScO 2 H prepared by solid state reaction under high pressure. Rietveld refinements against powder synchrotron X-ray and neutron diffraction data revealed that BaScO 2 H adopts the ideal cubic perovskite structure (Pm3̅m), where oxide (O 2- ) and hydride (H - ) anions are disordered. 1 H nuclear magnetic resonance (NMR) spectroscopy provides a positive chemical shift of about +4.4 ppm, which can be understood by the distance to the nearest (and possibly the next nearest) cation from the H nucleus. A further analysis of the NMR data and calculations based on ab initio random structure searches suggest a partial cis preference in ScO 4 H 2 octahedra. The present oxyhydride, if compositionally or structurally tuned, may become a candidate for H - conductors.

Spacer conformation in biologically active molecules. Part 2. Structure and conformation of 4-[2-(diphenylmethylamino)ethyl]-1-(2-methoxyphenyl) piperazine and its diphenylmethoxy analog—potential 5-HT 1A receptor ligands

NASA Astrophysics Data System (ADS)

Karolak-Wojciechowska, J.; Fruziński, A.; Czylkowski, R.; Paluchowska, M. H.; Mokrosz, M. J.

2003-09-01

As a part of studies on biologically active molecule structures with aliphatic linking chain, the structures of 4-[2-diphenylmethylamino)ethyl]-1-(2-methoxyphenyl)piperazine dihydrochloride ( 1) and 4-[2-diphenylmethoxy)ethyl]-1-(2-methoxyphenyl)piperazine fumarate ( 2) have been reported. In both compounds, four atomic non-all-carbons linking chains (N)C-C-X-C are present. The conformation of that linking spacer depends on the nature of the X-atom. The preferred conformation for chain with XNH has been found to be fully extended while for that with XO—the bend one. It was confirmed by conformational calculations (strain energy distribution and random search) and crystallographic data, including statistics from CCDC.

Comparison of Decisions Quality of Heuristic Methods with Limited Depth-First Search Techniques in the Graph Shortest Path Problem

NASA Astrophysics Data System (ADS)

Vatutin, Eduard

2017-12-01

The article deals with the problem of analysis of effectiveness of the heuristic methods with limited depth-first search techniques of decision obtaining in the test problem of getting the shortest path in graph. The article briefly describes the group of methods based on the limit of branches number of the combinatorial search tree and limit of analyzed subtree depth used to solve the problem. The methodology of comparing experimental data for the estimation of the quality of solutions based on the performing of computational experiments with samples of graphs with pseudo-random structure and selected vertices and arcs number using the BOINC platform is considered. It also shows description of obtained experimental results which allow to identify the areas of the preferable usage of selected subset of heuristic methods depending on the size of the problem and power of constraints. It is shown that the considered pair of methods is ineffective in the selected problem and significantly inferior to the quality of solutions that are provided by ant colony optimization method and its modification with combinatorial returns.

Exploring MEDLINE Space with Random Indexing and Pathfinder Networks

PubMed Central

Cohen, Trevor

2008-01-01

The integration of disparate research domains is a prerequisite for the success of the translational science initiative. MEDLINE abstracts contain content from a broad range of disciplines, presenting an opportunity for the development of methods able to integrate the knowledge they contain. Latent Semantic Analysis (LSA) and related methods learn human-like associations between terms from unannotated text. However, their computational and memory demands limits their ability to address a corpus of this size. Furthermore, visualization methods previously used in conjunction with LSA have limited ability to define the local structure of the associative networks LSA learns. This paper explores these issues by (1) processing the entire MEDLINE corpus using Random Indexing, a variant of LSA, and (2) exploring learned associations using Pathfinder Networks. Meaningful associations are inferred from MEDLINE, including a drug-disease association undetected by PUBMED search. PMID:18999236

Exploring MEDLINE space with random indexing and pathfinder networks.

PubMed

Cohen, Trevor

2008-11-06

The integration of disparate research domains is a prerequisite for the success of the translational science initiative. MEDLINE abstracts contain content from a broad range of disciplines, presenting an opportunity for the development of methods able to integrate the knowledge they contain. Latent Semantic Analysis (LSA) and related methods learn human-like associations between terms from unannotated text. However, their computational and memory demands limits their ability to address a corpus of this size. Furthermore, visualization methods previously used in conjunction with LSA have limited ability to define the local structure of the associative networks LSA learns. This paper explores these issues by (1) processing the entire MEDLINE corpus using Random Indexing, a variant of LSA, and (2) exploring learned associations using Pathfinder Networks. Meaningful associations are inferred from MEDLINE, including a drug-disease association undetected by PUBMED search.

Gray level co-occurrence and random forest algorithm-based gender determination with maxillary tooth plaster images.

PubMed

Akkoç, Betül; Arslan, Ahmet; Kök, Hatice

2016-06-01

Gender is one of the intrinsic properties of identity, with performance enhancement reducing the cluster when a search is performed. Teeth have durable and resistant structure, and as such are important sources of identification in disasters (accident, fire, etc.). In this study, gender determination is accomplished by maxillary tooth plaster models of 40 people (20 males and 20 females). The images of tooth plaster models are taken with a lighting mechanism set-up. A gray level co-occurrence matrix of the image with segmentation is formed and classified via a Random Forest (RF) algorithm by extracting pertinent features of the matrix. Automatic gender determination has a 90% success rate, with an applicable system to determine gender from maxillary tooth plaster images. Copyright © 2016 Elsevier Ltd. All rights reserved.

Combining structured and unstructured data to identify a cohort of ICU patients who received dialysis

PubMed Central

Abhyankar, Swapna; Demner-Fushman, Dina; Callaghan, Fiona M; McDonald, Clement J

2014-01-01

Objective To develop a generalizable method for identifying patient cohorts from electronic health record (EHR) data—in this case, patients having dialysis—that uses simple information retrieval (IR) tools. Methods We used the coded data and clinical notes from the 24 506 adult patients in the Multiparameter Intelligent Monitoring in Intensive Care database to identify patients who had dialysis. We used SQL queries to search the procedure, diagnosis, and coded nursing observations tables based on ICD-9 and local codes. We used a domain-specific search engine to find clinical notes containing terms related to dialysis. We manually validated the available records for a 10% random sample of patients who potentially had dialysis and a random sample of 200 patients who were not identified as having dialysis based on any of the sources. Results We identified 1844 patients that potentially had dialysis: 1481 from the three coded sources and 1624 from the clinical notes. Precision for identifying dialysis patients based on available data was estimated to be 78.4% (95% CI 71.9% to 84.2%) and recall was 100% (95% CI 86% to 100%). Conclusions Combining structured EHR data with information from clinical notes using simple queries increases the utility of both types of data for cohort identification. Patients identified by more than one source are more likely to meet the inclusion criteria; however, including patients found in any of the sources increases recall. This method is attractive because it is available to researchers with access to EHR data and off-the-shelf IR tools. PMID:24384230

Hyperparameterization of soil moisture statistical models for North America with Ensemble Learning Models (Elm)

NASA Astrophysics Data System (ADS)

Steinberg, P. D.; Brener, G.; Duffy, D.; Nearing, G. S.; Pelissier, C.

2017-12-01

Hyperparameterization, of statistical models, i.e. automated model scoring and selection, such as evolutionary algorithms, grid searches, and randomized searches, can improve forecast model skill by reducing errors associated with model parameterization, model structure, and statistical properties of training data. Ensemble Learning Models (Elm), and the related Earthio package, provide a flexible interface for automating the selection of parameters and model structure for machine learning models common in climate science and land cover classification, offering convenient tools for loading NetCDF, HDF, Grib, or GeoTiff files, decomposition methods like PCA and manifold learning, and parallel training and prediction with unsupervised and supervised classification, clustering, and regression estimators. Continuum Analytics is using Elm to experiment with statistical soil moisture forecasting based on meteorological forcing data from NASA's North American Land Data Assimilation System (NLDAS). There Elm is using the NSGA-2 multiobjective optimization algorithm for optimizing statistical preprocessing of forcing data to improve goodness-of-fit for statistical models (i.e. feature engineering). This presentation will discuss Elm and its components, including dask (distributed task scheduling), xarray (data structures for n-dimensional arrays), and scikit-learn (statistical preprocessing, clustering, classification, regression), and it will show how NSGA-2 is being used for automate selection of soil moisture forecast statistical models for North America.

Comparison of genetic algorithm methods for fuel management optimization

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

DeChaine, M.D.; Feltus, M.A.

1995-12-31

The CIGARO system was developed for genetic algorithm fuel management optimization. Tests are performed to find the best fuel location swap mutation operator probability and to compare genetic algorithm to a truly random search method. Tests showed the fuel swap probability should be between 0% and 10%, and a 50% definitely hampered the optimization. The genetic algorithm performed significantly better than the random search method, which did not even satisfy the peak normalized power constraint.

Model Checking with Multi-Threaded IC3 Portfolios

DTIC Science & Technology

2015-01-15

different runs varies randomly depending on the thread interleaving. The use of a portfolio of solvers to maximize the likelihood of a quick solution is...empirically show (cf. Sec. 5.2) that the predictions based on this formula have high accuracy. Note that each solver in the portfolio potentially searches...speedup of over 300. We also show that widening the proof search of ic3 by randomizing its SAT solver is not as effective as paral- lelization

Protein structural similarity search by Ramachandran codes

PubMed Central

Lo, Wei-Cheng; Huang, Po-Jung; Chang, Chih-Hung; Lyu, Ping-Chiang

2007-01-01

Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation). SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE) and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era. PMID:17716377

In Search of Speedier Searches.

ERIC Educational Resources Information Center

Peterson, Ivars

1984-01-01

Methods to make computer searching as simple and efficient as possible have led to the development of various data structures. Data structures specify the items involved in searching and what can be done to them. The nature and advantages of using "self-adjusting" data structures (self-adjusting binary search trees) are discussed. (JN)

Contextual Cueing in Multiconjunction Visual Search Is Dependent on Color- and Configuration-Based Intertrial Contingencies

ERIC Educational Resources Information Center

Geyer, Thomas; Shi, Zhuanghua; Muller, Hermann J.

2010-01-01

Three experiments examined memory-based guidance of visual search using a modified version of the contextual-cueing paradigm (Jiang & Chun, 2001). The target, if present, was a conjunction of color and orientation, with target (and distractor) features randomly varying across trials (multiconjunction search). Under these conditions, reaction times…

Central and Peripheral Vision Loss Differentially Affects Contextual Cueing in Visual Search

ERIC Educational Resources Information Center

Geringswald, Franziska; Pollmann, Stefan

2015-01-01

Visual search for targets in repeated displays is more efficient than search for the same targets in random distractor layouts. Previous work has shown that this contextual cueing is severely impaired under central vision loss. Here, we investigated whether central vision loss, simulated with gaze-contingent displays, prevents the incidental…

Inference-Based Similarity Search in Randomized Montgomery Domains for Privacy-Preserving Biometric Identification.

PubMed

Wang, Yi; Wan, Jianwu; Guo, Jun; Cheung, Yiu-Ming; Yuen, Pong C; Yi Wang; Jianwu Wan; Jun Guo; Yiu-Ming Cheung; Yuen, Pong C; Cheung, Yiu-Ming; Guo, Jun; Yuen, Pong C; Wan, Jianwu; Wang, Yi

2018-07-01

Similarity search is essential to many important applications and often involves searching at scale on high-dimensional data based on their similarity to a query. In biometric applications, recent vulnerability studies have shown that adversarial machine learning can compromise biometric recognition systems by exploiting the biometric similarity information. Existing methods for biometric privacy protection are in general based on pairwise matching of secured biometric templates and have inherent limitations in search efficiency and scalability. In this paper, we propose an inference-based framework for privacy-preserving similarity search in Hamming space. Our approach builds on an obfuscated distance measure that can conceal Hamming distance in a dynamic interval. Such a mechanism enables us to systematically design statistically reliable methods for retrieving most likely candidates without knowing the exact distance values. We further propose to apply Montgomery multiplication for generating search indexes that can withstand adversarial similarity analysis, and show that information leakage in randomized Montgomery domains can be made negligibly small. Our experiments on public biometric datasets demonstrate that the inference-based approach can achieve a search accuracy close to the best performance possible with secure computation methods, but the associated cost is reduced by orders of magnitude compared to cryptographic primitives.

Hybrid foraging search: Searching for multiple instances of multiple types of target.

PubMed

Wolfe, Jeremy M; Aizenman, Avigael M; Boettcher, Sage E P; Cain, Matthew S

2016-02-01

This paper introduces the "hybrid foraging" paradigm. In typical visual search tasks, observers search for one instance of one target among distractors. In hybrid search, observers search through visual displays for one instance of any of several types of target held in memory. In foraging search, observers collect multiple instances of a single target type from visual displays. Combining these paradigms, in hybrid foraging tasks observers search visual displays for multiple instances of any of several types of target (as might be the case in searching the kitchen for dinner ingredients or an X-ray for different pathologies). In the present experiment, observers held 8-64 target objects in memory. They viewed displays of 60-105 randomly moving photographs of objects and used the computer mouse to collect multiple targets before choosing to move to the next display. Rather than selecting at random among available targets, observers tended to collect items in runs of one target type. Reaction time (RT) data indicate searching again for the same item is more efficient than searching for any other targets, held in memory. Observers were trying to maximize collection rate. As a result, and consistent with optimal foraging theory, they tended to leave 25-33% of targets uncollected when moving to the next screen/patch. The pattern of RTs shows that while observers were collecting a target item, they had already begun searching memory and the visual display for additional targets, making the hybrid foraging task a useful way to investigate the interaction of visual and memory search. Copyright © 2015 Elsevier Ltd. All rights reserved.

Hybrid foraging search: Searching for multiple instances of multiple types of target

PubMed Central

Wolfe, Jeremy M.; Aizenman, Avigael M.; Boettcher, Sage E.P.; Cain, Matthew S.

2016-01-01

This paper introduces the “hybrid foraging” paradigm. In typical visual search tasks, observers search for one instance of one target among distractors. In hybrid search, observers search through visual displays for one instance of any of several types of target held in memory. In foraging search, observers collect multiple instances of a single target type from visual displays. Combining these paradigms, in hybrid foraging tasks observers search visual displays for multiple instances of any of several types of target (as might be the case in searching the kitchen for dinner ingredients or an X-ray for different pathologies). In the present experiment, observers held 8–64 targets objects in memory. They viewed displays of 60–105 randomly moving photographs of objects and used the computer mouse to collect multiple targets before choosing to move to the next display. Rather than selecting at random among available targets, observers tended to collect items in runs of one target type. Reaction time (RT) data indicate searching again for the same item is more efficient than searching for any other targets, held in memory. Observers were trying to maximize collection rate. As a result, and consistent with optimal foraging theory, they tended to leave 25–33% of targets uncollected when moving to the next screen/patch. The pattern of RTs shows that while observers were collecting a target item, they had already begun searching memory and the visual display for additional targets, making the hybrid foraging task a useful way to investigate the interaction of visual and memory search. PMID:26731644

Corticosteroids for ocular toxoplasmosis

PubMed Central

Jasper, Smitha; Vedula, Satyanarayana S; John, Sheeja S; Horo, Saban; Sepah, Yasir J; Nguyen, Quan Dong

2014-01-01

Background Ocular infestation with Toxoplasma gondii, a parasite, may result in inflammation in the retina, choroid, and uvea and consequently lead to complications such as glaucoma, cataract, and posterior synechiae. Objectives The objective of this systematic review was to assess the effects of adjunctive use of corticosteroids for ocular toxoplasmosis. Search methods We searched CENTRAL (which contains the Cochrane Eyes and Vision Group Trials Register) (The Cochrane Library 2012, Issue 9), Ovid MEDLINE, Ovid MEDLINE In-Process and Other Non-Indexed Citations, Ovid MEDLINE Daily, Ovid OLDMEDLINE, (January 1950 to October 2012), EMBASE (January 1980 to October 2012), Latin American and Caribbean Literature on Health Sciences (LILACS) (January 1982 to October 2012), the metaRegister of Controlled Trials (mRCT) (www.controlled-trials.com), ClinicalTrials.gov (www.clinicaltrials.gov) and the WHO International Clinical Trials Registry Platform (ICTRP) (www.who.int/ictrp/search/en). We searched the reference lists of included studies for any additional studies not identified by the electronic searches. We did not use any date or language restrictions in the electronic searches for trials. We last searched the electronic databases on 11 October 2012. Selection criteria We planned to include randomized and quasi-randomized controlled trials. Eligible trials would have enrolled participants of any age who were immunocompetent and were diagnosed with active ocular toxoplasmosis. Included trials would have compared anti-parasitic therapy plus corticosteroids versus anti-parasitic therapy alone, or different doses or times of initiation of corticosteroids. Data collection and analysis Two authors independently screened titles and abstracts retrieved from the electronic searches. We retrieved full-text articles of studies categorized as ‘unsure’ or ‘include’ after review of the abstracts. Two authors independently reviewed each full-text article. Discrepancies were resolved through discussion. Main results The electronic searches retrieved 368 titles and abstracts. We reviewed 20 full-text articles. We identified no trials eligible for inclusion in this systematic review. Authors' conclusions Although research has identified wide variation in practices regarding use of corticosteroids, our systematic review did not identify evidence from randomized controlled trials for the role of corticosteroids in the management of ocular toxoplasmosis. Several questions remain unanswered by well-conducted randomized trials in this context, including whether use of corticosteroids is more effective than use of anti-parasitic therapy alone, when corticosteroids should be initiated in the treatment regimen (early versus late course of treatment), and which dosage and duration of steroid use is best. These questions are easily amenable to research using a randomized controlled design and they are ethical due to the absence of evidence to support or discourage use of corticosteroids for this condition. The question of foremost importance, however, is whether they should be used as adjunct therapy (that is, additional) to anti-parasitic agents. PMID:23633342

Visual search for arbitrary objects in real scenes

PubMed Central

Alvarez, George A.; Rosenholtz, Ruth; Kuzmova, Yoana I.; Sherman, Ashley M.

2011-01-01

How efficient is visual search in real scenes? In searches for targets among arrays of randomly placed distractors, efficiency is often indexed by the slope of the reaction time (RT) × Set Size function. However, it may be impossible to define set size for real scenes. As an approximation, we hand-labeled 100 indoor scenes and used the number of labeled regions as a surrogate for set size. In Experiment 1, observers searched for named objects (a chair, bowl, etc.). With set size defined as the number of labeled regions, search was very efficient (~5 ms/item). When we controlled for a possible guessing strategy in Experiment 2, slopes increased somewhat (~15 ms/item), but they were much shallower than search for a random object among other distinctive objects outside of a scene setting (Exp. 3: ~40 ms/item). In Experiments 4–6, observers searched repeatedly through the same scene for different objects. Increased familiarity with scenes had modest effects on RTs, while repetition of target items had large effects (>500 ms). We propose that visual search in scenes is efficient because scene-specific forms of attentional guidance can eliminate most regions from the “functional set size” of items that could possibly be the target. PMID:21671156

Visual search for arbitrary objects in real scenes.

PubMed

Wolfe, Jeremy M; Alvarez, George A; Rosenholtz, Ruth; Kuzmova, Yoana I; Sherman, Ashley M

2011-08-01

How efficient is visual search in real scenes? In searches for targets among arrays of randomly placed distractors, efficiency is often indexed by the slope of the reaction time (RT) × Set Size function. However, it may be impossible to define set size for real scenes. As an approximation, we hand-labeled 100 indoor scenes and used the number of labeled regions as a surrogate for set size. In Experiment 1, observers searched for named objects (a chair, bowl, etc.). With set size defined as the number of labeled regions, search was very efficient (~5 ms/item). When we controlled for a possible guessing strategy in Experiment 2, slopes increased somewhat (~15 ms/item), but they were much shallower than search for a random object among other distinctive objects outside of a scene setting (Exp. 3: ~40 ms/item). In Experiments 4-6, observers searched repeatedly through the same scene for different objects. Increased familiarity with scenes had modest effects on RTs, while repetition of target items had large effects (>500 ms). We propose that visual search in scenes is efficient because scene-specific forms of attentional guidance can eliminate most regions from the "functional set size" of items that could possibly be the target.

Systematic harmonic power laws inter-relating multiple fundamental constants

NASA Astrophysics Data System (ADS)

Chakeres, Donald; Buckhanan, Wayne; Andrianarijaona, Vola

2017-01-01

Power laws and harmonic systems are ubiquitous in physics. We hypothesize that 2, π, the electron, Bohr radius, Rydberg constant, neutron, fine structure constant, Higgs boson, top quark, kaons, pions, muon, Tau, W, and Z when scaled in a common single unit are all inter-related by systematic harmonic powers laws. This implies that if the power law is known it is possible to derive a fundamental constant's scale in the absence of any direct experimental data of that constant. This is true for the case of the hydrogen constants. We created a power law search engine computer program that randomly generated possible positive or negative powers searching when the product of logical groups of constants equals 1, confirming they are physically valid. For 2, π, and the hydrogen constants the search engine found Planck's constant, Coulomb's energy law, and the kinetic energy law. The product of ratios defined by two constants each was the standard general format. The search engine found systematic resonant power laws based on partial harmonic fraction powers of the neutron for all of the constants with products near 1, within their known experimental precision, when utilized with appropriate hydrogen constants. We conclude that multiple fundamental constants are inter-related within a harmonic power law system.

Coordinated Search for a Random Walk Target Motion

NASA Astrophysics Data System (ADS)

El-Hadidy, Mohamed Abd Allah; Abou-Gabal, Hamdy M.

This paper presents the cooperation between two searchers at the origin to find a Random Walk moving target on the real line. No information is not available about the target’s position all the time. Rather than finding the conditions that make the expected value of the first meeting time between one of the searchers and the target is finite, we show the existence of the optimal search strategy which minimizes this first meeting time. The effectiveness of this model is illustrated using a numerical example.

Finding paths in tree graphs with a quantum walk

NASA Astrophysics Data System (ADS)

Koch, Daniel; Hillery, Mark

2018-01-01

We analyze the potential for different types of searches using the formalism of scattering random walks on quantum computers. Given a particular type of graph consisting of nodes and connections, a "tree maze," we would like to find a selected final node as quickly as possible, faster than any classical search algorithm. We show that this can be done using a quantum random walk, both through numerical calculations as well as by using the eigenvectors and eigenvalues of the quantum system.

Clinical effectiveness of garlic (Allium sativum).

PubMed

Pittler, Max H; Ernst, Edzard

2007-11-01

The objective of this review is to update and assess the clinical evidence based on rigorous trials of the effectiveness of garlic (A. sativum). Systematic searches were carried out in Medline, Embase, Amed, the Cochrane Database of Systematic Reviews, Natural Standard, and the Natural Medicines Comprehensive Database (search date December 2006). Our own files, the bibliographies of relevant papers and the contents pages of all issues of the review journal FACT were searched for further studies. No language restrictions were imposed. To be included, trials were required to state that they were randomized and double blind. Systematic reviews and meta-analyses of garlic were included if based on the results of randomized, double-blind trials. The literature searches identified six relevant systematic reviews and meta-analysis and double-blind randomized trials (RCT) that were published subsequently. These relate to cancer, common cold, hypercholesterolemia, hypertension, peripheral arterial disease and pre-eclampsia. The evidence based on rigorous clinical trials of garlic is not convincing. For hypercholesterolemia, the reported effects are small and may therefore not be of clinical relevance. For reducing blood pressure, few studies are available and the reported effects are too small to be clinically meaningful. For all other conditions not enough data are available for clinical recommendations.

Effect of Delay on Search Decisions in a Task-Oriented Reading Environment

ERIC Educational Resources Information Center

Mañá, Amelia; Vidal-Abarca, Eduardo; Salmerón, Ladislao

2017-01-01

The goal of this study was to determine the effect of setting a delay between reading a text and answering comprehension questions on "when"-to-search and "what"-to-search decisions in a task-oriented reading environment. Fifty-five eighth-grade students were randomly divided into two groups. One group read one text, answered…

The Validity of Warrantless Searches under the Occupational Safety and Health Act of 1970

ERIC Educational Resources Information Center

Shanks, Michael D.

1975-01-01

One of the most controversial federal acts providing for random administrative searches is the Occupational Safety and Health Act of 1970 (OSHA). The author reviews the search and seizure law and concludes that abandonment of Fourth Amendment rights should not be predicated on the mere convenience of even a justifiable regulatory scheme. (JT)

Boosting association rule mining in large datasets via Gibbs sampling.

PubMed

Qian, Guoqi; Rao, Calyampudi Radhakrishna; Sun, Xiaoying; Wu, Yuehua

2016-05-03

Current algorithms for association rule mining from transaction data are mostly deterministic and enumerative. They can be computationally intractable even for mining a dataset containing just a few hundred transaction items, if no action is taken to constrain the search space. In this paper, we develop a Gibbs-sampling-induced stochastic search procedure to randomly sample association rules from the itemset space, and perform rule mining from the reduced transaction dataset generated by the sample. Also a general rule importance measure is proposed to direct the stochastic search so that, as a result of the randomly generated association rules constituting an ergodic Markov chain, the overall most important rules in the itemset space can be uncovered from the reduced dataset with probability 1 in the limit. In the simulation study and a real genomic data example, we show how to boost association rule mining by an integrated use of the stochastic search and the Apriori algorithm.

Threat captures attention but does not affect learning of contextual regularities.

PubMed

Yamaguchi, Motonori; Harwood, Sarah L

2017-04-01

Some of the stimulus features that guide visual attention are abstract properties of objects such as potential threat to one's survival, whereas others are complex configurations such as visual contexts that are learned through past experiences. The present study investigated the two functions that guide visual attention, threat detection and learning of contextual regularities, in visual search. Search arrays contained images of threat and non-threat objects, and their locations were fixed on some trials but random on other trials. Although they were irrelevant to the visual search task, threat objects facilitated attention capture and impaired attention disengagement. Search time improved for fixed configurations more than for random configurations, reflecting learning of visual contexts. Nevertheless, threat detection had little influence on learning of the contextual regularities. The results suggest that factors guiding visual attention are different from factors that influence learning to guide visual attention.

Efficiency improvement by navigated safety inspection involving visual clutter based on the random search model.

PubMed

Sun, Xinlu; Chong, Heap-Yih; Liao, Pin-Chao

2018-06-25

Navigated inspection seeks to improve hazard identification (HI) accuracy. With tight inspection schedule, HI also requires efficiency. However, lacking quantification of HI efficiency, navigated inspection strategies cannot be comprehensively assessed. This work aims to determine inspection efficiency in navigated safety inspection, controlling for the HI accuracy. Based on a cognitive method of the random search model (RSM), an experiment was conducted to observe the HI efficiency in navigation, for a variety of visual clutter (VC) scenarios, while using eye-tracking devices to record the search process and analyze the search performance. The results show that the RSM is an appropriate instrument, and VC serves as a hazard classifier for navigation inspection in improving inspection efficiency. This suggests a new and effective solution for addressing the low accuracy and efficiency of manual inspection through navigated inspection involving VC and the RSM. It also provides insights into the inspectors' safety inspection ability.

mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

PubMed

Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

2018-05-21

With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

Formation of superconducting platinum hydride under pressure: an ab initio approach

NASA Astrophysics Data System (ADS)

Kim, Duck Young; Scheicher, Ralph; Pickard, Chris; Needs, Richard; Ahuja, Rajeev

2012-02-01

Noble metals such as Pt, Au, or Re are commonly used for electrodes and gaskets in diamond anvil cells for high-pressure research because they are expected to rarely undergo structural transformation and possess simple equation of states. Specifically Pt has been used widely for high-pressure experiments and has been considered to resist hydride formation under pressure. Pressure-induced reactions of metals with hydrogen are in fact quite likely because hydrogen atoms can occupy interstitial positions in the metal lattice, which can lead to unexpected effects in experiments. In our study, PRL 107 117002 (2011), we investigated crystal structures using ab initio random structure searching (AIRSS) and predicted the formation of platinum mono-hydride above 22 GPa and superconductivity Tc was estimated to be 10 -- 25 K above around 80 GPa. Furthermore, we showed that the formation of fcc noble metal hydrides under pressure is common and examined the possibility of superconductivity in these materials.

Model fitting for small skin permeability data sets: hyperparameter optimisation in Gaussian Process Regression.

PubMed

Ashrafi, Parivash; Sun, Yi; Davey, Neil; Adams, Roderick G; Wilkinson, Simon C; Moss, Gary Patrick

2018-03-01

The aim of this study was to investigate how to improve predictions from Gaussian Process models by optimising the model hyperparameters. Optimisation methods, including Grid Search, Conjugate Gradient, Random Search, Evolutionary Algorithm and Hyper-prior, were evaluated and applied to previously published data. Data sets were also altered in a structured manner to reduce their size, which retained the range, or 'chemical space' of the key descriptors to assess the effect of the data range on model quality. The Hyper-prior Smoothbox kernel results in the best models for the majority of data sets, and they exhibited significantly better performance than benchmark quantitative structure-permeability relationship (QSPR) models. When the data sets were systematically reduced in size, the different optimisation methods generally retained their statistical quality, whereas benchmark QSPR models performed poorly. The design of the data set, and possibly also the approach to validation of the model, is critical in the development of improved models. The size of the data set, if carefully controlled, was not generally a significant factor for these models and that models of excellent statistical quality could be produced from substantially smaller data sets. © 2018 Royal Pharmaceutical Society.

SA-Search: a web tool for protein structure mining based on a Structural Alphabet

PubMed Central

Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre

2004-01-01

SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search. PMID:15215446

SA-Search: a web tool for protein structure mining based on a Structural Alphabet.

PubMed

Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre

2004-07-01

SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search.

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.

PubMed

Suzuki, Hirofumi; Kawabata, Takeshi; Nakamura, Haruki

2016-02-15

Omokage search is a service to search the global shape similarity of biological macromolecules and their assemblies, in both the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB). The server compares global shapes of assemblies independent of sequence order and number of subunits. As a search query, the user inputs a structure ID (PDB ID or EMDB ID) or uploads an atomic model or 3D density map to the server. The search is performed usually within 1 min, using one-dimensional profiles (incremental distance rank profiles) to characterize the shapes. Using the gmfit (Gaussian mixture model fitting) program, the found structures are fitted onto the query structure and their superimposed structures are displayed on the Web browser. Our service provides new structural perspectives to life science researchers. Omokage search is freely accessible at http://pdbj.org/omokage/. © The Author 2015. Published by Oxford University Press.

Data Mining of Web-Based Documents on Social Networking Sites That Included Suicide-Related Words Among Korean Adolescents.

PubMed

Song, Juyoung; Song, Tae Min; Seo, Dong-Chul; Jin, Jae Hyun

2016-12-01

To investigate online search activity of suicide-related words in South Korean adolescents through data mining of social media Web sites as the suicide rate in South Korea is one of the highest in the world. Out of more than 2.35 billion posts for 2 years from January 1, 2011 to December 31, 2012 on 163 social media Web sites in South Korea, 99,693 suicide-related documents were retrieved by Crawler and analyzed using text mining and opinion mining. These data were further combined with monthly employment rate, monthly rental prices index, monthly youth suicide rate, and monthly number of reported bully victims to fit multilevel models as well as structural equation models. The link from grade pressure to suicide risk showed the largest standardized path coefficient (beta = .357, p < .001) in structural models and a significant random effect (p < .01) in multilevel models. Depression was a partial mediator between suicide risk and grade pressure, low body image, victims of bullying, and concerns about disease. The largest total effect was observed in the grade pressure to depression to suicide risk. The multilevel models indicate about 27% of the variance in the daily suicide-related word search activity is explained by month-to-month variations. A lower employment rate, a higher rental prices index, and more bullying were associated with an increased suicide-related word search activity. Academic pressure appears to be the biggest contributor to Korean adolescents' suicide risk. Real-time suicide-related word search activity monitoring and response system needs to be developed. Copyright © 2016 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Localization Transition Induced by Learning in Random Searches

NASA Astrophysics Data System (ADS)

Falcón-Cortés, Andrea; Boyer, Denis; Giuggioli, Luca; Majumdar, Satya N.

2017-10-01

We solve an adaptive search model where a random walker or Lévy flight stochastically resets to previously visited sites on a d -dimensional lattice containing one trapping site. Because of reinforcement, a phase transition occurs when the resetting rate crosses a threshold above which nondiffusive stationary states emerge, localized around the inhomogeneity. The threshold depends on the trapping strength and on the walker's return probability in the memoryless case. The transition belongs to the same class as the self-consistent theory of Anderson localization. These results show that similarly to many living organisms and unlike the well-studied Markovian walks, non-Markov movement processes can allow agents to learn about their environment and promise to bring adaptive solutions in search tasks.

Expertise and processing distorted structure in chess.

PubMed

Bartlett, James C; Boggan, Amy L; Krawczyk, Daniel C

2013-01-01

A classic finding in research on human expertise and knowledge is that of enhanced memory for stimuli in a domain of expertise as compared to either stimuli outside that domain, or within-domain stimuli that have been degraded or distorted in some way. However, we do not understand how experts process degradation or distortion of stimuli within the expert domain (e.g., a face with the eyes, nose, and mouth in the wrong positions, or a chessboard with pieces placed randomly). Focusing on the domain of chess, we present new fMRI evidence that when experts view such distorted/within-domain stimuli, they engage an active search for structure-a kind of exploratory chunking-that involves a component of a prefrontal-parietal network linked to consciousness, attention and working memory.

"Simulated molecular evolution" or computer-generated artifacts?

PubMed

Darius, F; Rojas, R

1994-11-01

1. The authors define a function with value 1 for the positive examples and 0 for the negative ones. They fit a continuous function but do not deal at all with the error margin of the fit, which is almost as large as the function values they compute. 2. The term "quality" for the value of the fitted function gives the impression that some biological significance is associated with values of the fitted function strictly between 0 and 1, but there is no justification for this kind of interpretation and finding the point where the fit achieves its maximum does not make sense. 3. By neglecting the error margin the authors try to optimize the fitted function using differences in the second, third, fourth, and even fifth decimal place which have no statistical significance. 4. Even if such a fit could profit from more data points, the authors should first prove that the region of interest has some kind of smoothness, that is, that a continuous fit makes any sense at all. 5. "Simulated molecular evolution" is a misnomer. We are dealing here with random search. Since the margin of error is so large, the fitted function does not provide statistically significant information about the points in search space where strings with cleavage sites could be found. This implies that the method is a highly unreliable stochastic search in the space of strings, even if the neural network is capable of learning some simple correlations. 6. Classical statistical methods are for these kind of problems with so few data points clearly superior to the neural networks used as a "black box" by the authors, which in the way they are structured provide a model with an error margin as large as the numbers being computed.7. And finally, even if someone would provide us with a function which separates strings with cleavage sites from strings without them perfectly, so-called simulated molecular evolution would not be better than random selection.Since a perfect fit would only produce exactly ones or zeros,starting a search in a region of space where all strings in the neighborhood get the value zero would not provide any kind of directional information for new iterations. We would just skip from one point to the other in a typical random walk manner.

Metal-backed versus all-polyethylene tibial components in primary total knee arthroplasty

PubMed Central

2011-01-01

Background and purpose The choice of either all-polyethylene (AP) tibial components or metal-backed (MB) tibial components in total knee arthroplasty (TKA) remains controversial. We therefore performed a meta-analysis and systematic review of randomized controlled trials that have evaluated MB and AP tibial components in primary TKA. Methods The search strategy included a computerized literature search (Medline, EMBASE, Scopus, and the Cochrane Central Register of Controlled Trials) and a manual search of major orthopedic journals. A meta-analysis and systematic review of randomized or quasi-randomized trials that compared the performance of tibial components in primary TKA was performed using a fixed or random effects model. We assessed the methodological quality of studies using Detsky quality scale. Results 9 randomized controlled trials (RCTs) published between 2000 and 2009 met the inclusion quality standards for the systematic review. The mean standardized Detsky score was 14 (SD 3). We found that the frequency of radiolucent lines in the MB group was significantly higher than that in the AP group. There were no statistically significant differences between the MB and AP tibial components regarding component positioning, knee score, knee range of motion, quality of life, and postoperative complications. Interpretation Based on evidence obtained from this study, the AP tibial component was comparable with or better than the MB tibial component in TKA. However, high-quality RCTs are required to validate the results. PMID:21895503

Tuning Monotonic Basin Hopping: Improving the Efficiency of Stochastic Search as Applied to Low-Thrust Trajectory Optimization

NASA Technical Reports Server (NTRS)

Englander, Jacob A.; Englander, Arnold C.

2014-01-01

Trajectory optimization methods using monotonic basin hopping (MBH) have become well developed during the past decade [1, 2, 3, 4, 5, 6]. An essential component of MBH is a controlled random search through the multi-dimensional space of possible solutions. Historically, the randomness has been generated by drawing random variable (RV)s from a uniform probability distribution. Here, we investigate the generating the randomness by drawing the RVs from Cauchy and Pareto distributions, chosen because of their characteristic long tails. We demonstrate that using Cauchy distributions (as first suggested by J. Englander [3, 6]) significantly improves monotonic basin hopping (MBH) performance, and that Pareto distributions provide even greater improvements. Improved performance is defined in terms of efficiency and robustness. Efficiency is finding better solutions in less time. Robustness is efficiency that is undiminished by (a) the boundary conditions and internal constraints of the optimization problem being solved, and (b) by variations in the parameters of the probability distribution. Robustness is important for achieving performance improvements that are not problem specific. In this work we show that the performance improvements are the result of how these long-tailed distributions enable MBH to search the solution space faster and more thoroughly. In developing this explanation, we use the concepts of sub-diffusive, normally-diffusive, and super-diffusive random walks (RWs) originally developed in the field of statistical physics.

Sundanese ancient manuscripts search engine using probability approach

NASA Astrophysics Data System (ADS)

Suryani, Mira; Hadi, Setiawan; Paulus, Erick; Nurma Yulita, Intan; Supriatna, Asep K.

2017-10-01

Today, Information and Communication Technology (ICT) has become a regular thing for every aspect of live include cultural and heritage aspect. Sundanese ancient manuscripts as Sundanese heritage are in damage condition and also the information that containing on it. So in order to preserve the information in Sundanese ancient manuscripts and make them easier to search, a search engine has been developed. The search engine must has good computing ability. In order to get the best computation in developed search engine, three types of probabilistic approaches: Bayesian Networks Model, Divergence from Randomness with PL2 distribution, and DFR-PL2F as derivative form DFR-PL2 have been compared in this study. The three probabilistic approaches supported by index of documents and three different weighting methods: term occurrence, term frequency, and TF-IDF. The experiment involved 12 Sundanese ancient manuscripts. From 12 manuscripts there are 474 distinct terms. The developed search engine tested by 50 random queries for three types of query. The experiment results showed that for the single query and multiple query, the best searching performance given by the combination of PL2F approach and TF-IDF weighting method. The performance has been evaluated using average time responds with value about 0.08 second and Mean Average Precision (MAP) about 0.33.

Technology and Teaching: Searching under Cups for Clues about Memory--An Online Demonstration

ERIC Educational Resources Information Center

Kahan, Todd A.; Mathis, Katherine M.

2007-01-01

An online demonstration, designed to enhance comprehension of Sternberg's (1966) short-term memory scanning task, involved rapidly searching under virtual cups for a ball. We randomly assigned students to 1 of 3 groups, all of whom read the same textbook description of Sternberg's work: A demonstration group used 3 search methods to look for balls…

Quality of the written radiology report: a review of the literature.

PubMed

Pool, Felicity; Goergen, Stacy

2010-08-01

A literature review was carried out, guided by the question, What are the important elements of a high-quality radiology written report? Two papers known to the authors were used as a basis for 5 PubMed search strategies. Exclusion criteria were applied to retrieved citations. Reference lists of retrieved citations were scanned for additional relevant papers and exclusion criteria applied to these. Web sites of professional radiology organizations were scanned for guidelines relating to the written radiology report. Retrieved guidelines were appraised using the Appraisal of Guidelines for Research & Evaluation instrument. Methodologies of retrieved papers were not suitable for conventional appraisal, and an evidence table was constructed. The search strategy identified 25 published papers and 4 guidelines. Published study methodologies included 1 randomized controlled trial; 1 before-and-after study of interventions; 10 observational studies, audits, or analyses; 12 surveys; and 1 narrative review of the literature. Existing guidelines have a number of weaknesses with regard to scope and purpose, methods of development, stakeholder consultation, and editorial independence and applicability. There is a major gap in published studies relating to testing of interventions to improve report quality using conventional randomized controlled trial methods. Published studies and guidelines generally support report content, including clinical history, examination quality, description of findings, comparison, and diagnosis. Important report attributes include accuracy, clarity, and certainty. There is wide variation in the language used to describe imaging findings and diagnostic certainty. Survey participants strongly preferred reports with structured or itemized formats, but few studies exist regarding the effect of report structure on quality. Copyright 2010 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Exercise Therapy in Juvenile Idiopathic Arthritis: A Systematic Review and Meta-Analysis.

PubMed

Kuntze, Gregor; Nesbitt, Colleen; Whittaker, Jackie L; Nettel-Aguirre, Alberto; Toomey, Clodagh; Esau, Shane; Doyle-Baker, Patricia K; Shank, Jena; Brooks, Julia; Benseler, Susanne; Emery, Carolyn A

2018-01-01

To conduct a systematic review to evaluate the efficacy of exercise interventions in improving outcomes across domains of functioning and disability in children and adolescents with juvenile idiopathic arthritis (JIA). Seven electronic databases were systematically searched up to November 16, 2016. Original data, analytic prospective design, physical therapy-led exercise intervention evaluation, children and adolescents with JIA, and assessment of functional, structural, activity, participation, or quality of life outcomes. Two authors screened search results, and discrepancies were resolved by consensus. Of 5037 potentially relevant studies, 9 randomized controlled trials and 1 cohort study were included and scored. Study quality (Downs and Black quality assessment tool) and level of evidence (Oxford Centre of Evidence-Based Medicine model) were assessed and meta-analysis conducted where appropriate. Alternatively, a descriptive summary approach was chosen. All randomized controlled trials were moderate-quality intervention studies (level 2b evidence; median Downs and Black score, 20 out of 32; range, 15-27). Interventions included aquatic, strengthening, proprioceptive, aerobic, and Pilates exercises. Pediatric activity capacity (Child Health Assessment Questionnaire) improved with exercise (mean difference, .45; 95% confidence interval, .05-.76). Furthermore, descriptive summaries indicated improved activity capacity, body function and structure (pain and muscle strength), and quality of life outcomes. Exercise therapy appears to be well tolerated and beneficial across clinically relevant outcomes in patients with JIA. The paucity of high-quality evidence and study heterogeneity limited the ability to provide conclusive, generalizing evidence for the efficacy of exercise therapy and to provide specific recommendations for clinical practice at this time. Future research evaluating exercise program implementation using validated outcomes and detailed adherence and safety assessment is needed to optimize clinical decision pathways in patients with JIA. Copyright © 2016 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Fundamental resource-allocating model in colleges and universities based on Immune Clone Algorithms

NASA Astrophysics Data System (ADS)

Ye, Mengdie

2017-05-01

In this thesis we will seek the combination of antibodies and antigens converted from the optimal course arrangement and make an analogy with Immune Clone Algorithms. According to the character of the Algorithms, we apply clone, clone gene and clone selection to arrange courses. Clone operator can combine evolutionary search and random search, global search and local search. By cloning and clone mutating candidate solutions, we can find the global optimal solution quickly.

Quantum chemical calculations in the structural analysis of phloretin

NASA Astrophysics Data System (ADS)

Gómez-Zavaglia, Andrea

2009-07-01

In this work, a conformational search on the molecule of phloretin [2',4',6'-Trihydroxy-3-(4-hydroxyphenyl)-propiophenone] has been performed. The molecule of phloretin has eight dihedral angles, four of them taking part in the carbon backbone and the other four, related with the orientation of the hydroxyl groups. A systematic search involving a random variation of the dihedral angles has been used to generate input structures for the quantum chemical calculations. Calculations at the DFT(B3LYP)/6-311++G(d,p) level of theory permitted the identification of 58 local minima belonging to the C 1 symmetry point group. The molecular structures of the conformers have been analyzed using hierarchical cluster analysis. This method allowed us to group conformers according to their similarities, and thus, to correlate the conformers' stability with structural parameters. The dendrogram obtained from the hierarchical cluster analysis depicted two main clusters. Cluster I included all the conformers with relative energies lower than 25 kJ mol -1 and cluster II, the remaining conformers. The possibility of forming intramolecular hydrogen bonds resulted the main factor contributing for the stability. Accordingly, all conformers depicting intramolecular H-bonds belong to cluster I. These conformations are clearly favored when the carbon backbone is as planar as possible. The values of the νC dbnd O and νOH vibrational modes were compared among all the conformers of phloretin. The redshifts associated with intramolecular H-bonds were correlated with the H-bonds distances and energies.

Corticosteroids as adjuvant therapy for ocular toxoplasmosis.

PubMed

Jasper, Smitha; Vedula, Satyanarayana S; John, Sheeja S; Horo, Saban; Sepah, Yasir J; Nguyen, Quan Dong

2013-04-30

Ocular infestation with Toxoplasma gondii, a parasite, may result in inflammation in the retina, choroid, and uvea and consequently lead to complications such as glaucoma, cataract, and posterior synechiae. The objective of this systematic review was to assess the effects of adjunctive use of corticosteroids for ocular toxoplasmosis. We searched CENTRAL (which contains the Cochrane Eyes and Vision Group Trials Register) (The Cochrane Library 2012, Issue 9), Ovid MEDLINE, Ovid MEDLINE In-Process and Other Non-Indexed Citations, Ovid MEDLINE Daily, Ovid OLDMEDLINE, (January 1950 to October 2012), EMBASE (January 1980 to October 2012), Latin American and Caribbean Literature on Health Sciences (LILACS) (January 1982 to October 2012), the metaRegister of Controlled Trials (mRCT) (www.controlled-trials.com), ClinicalTrials.gov (www.clinicaltrials.gov) and the WHO International Clinical Trials Registry Platform (ICTRP) (www.who.int/ictrp/search/en). We searched the reference lists of included studies for any additional studies not identified by the electronic searches. We did not use any date or language restrictions in the electronic searches for trials. We last searched the electronic databases on 11 October 2012. We planned to include randomized and quasi-randomized controlled trials. Eligible trials would have enrolled participants of any age who were immunocompetent and were diagnosed with active ocular toxoplasmosis. Included trials would have compared anti-parasitic therapy plus corticosteroids versus anti-parasitic therapy alone, or different doses or times of initiation of corticosteroids. Two authors independently screened titles and abstracts retrieved from the electronic searches. We retrieved full-text articles of studies categorized as 'unsure' or 'include' after review of the abstracts. Two authors independently reviewed each full-text article. Discrepancies were resolved through discussion. The electronic searches retrieved 368 titles and abstracts. We reviewed 20 full-text articles. We identified no trials eligible for inclusion in this systematic review. Although research has identified wide variation in practices regarding use of corticosteroids, our systematic review did not identify evidence from randomized controlled trials for the role of corticosteroids in the management of ocular toxoplasmosis. Several questions remain unanswered by well-conducted randomized trials in this context, including whether use of corticosteroids is more effective than use of anti-parasitic therapy alone, when corticosteroids should be initiated in the treatment regimen (early versus late course of treatment), and which dosage and duration of steroid use is best. These questions are easily amenable to research using a randomized controlled design and they are ethical due to the absence of evidence to support or discourage use of corticosteroids for this condition. The question of foremost importance, however, is whether they should be used as adjunct therapy (that is, additional) to anti-parasitic agents.

Music education for improving reading skills in children and adolescents with dyslexia.

PubMed

Cogo-Moreira, Hugo; Andriolo, Régis B; Yazigi, Latife; Ploubidis, George B; Brandão de Ávila, Clara Regina; Mari, Jair J

2012-08-15

Dyslexia (or developmental dyslexia or specific reading disability) is a specific learning disorder that has a neurobiological origin. It is marked by difficulties with accurate or fluent recognition of words and poor spelling in people who have average or above average intelligence and these difficulties cannot be attributed to another cause, for example, poor vision, hearing difficulty, or lack of socio-environmental opportunities, motivation, or adequate instruction. Studies have correlated reading skills with musical abilities. It has been hypothesized that musical training may be able to remediate timing difficulties, improve pitch perception, or increase spatial awareness, thereby having a positive effect on skills needed in the development of language and literacy. To study the effectiveness of music education on reading skills (that is, oral reading skills, reading comprehension, reading fluency, phonological awareness, and spelling) in children and adolescents with dyslexia. We searched the following electronic databases in June 2012: CENTRAL (2012, Issue 5), MEDLINE (1948 to May Week 4 2012 ), EMBASE (1980 to 2012 Week 22), CINAHL (searched 7 June 2012), LILACS (searched 7 June 2012), PsycINFO (1887 to May Week 5 2012), ERIC (searched 7 June 2012), Arts and Humanities Citation Index (1970 to 6 June 2012), Conference Proceedings Citation Index - Social Sciences and Humanities (1990 to 6 June 2012), and WorldCat (searched 7 June 2012). We also searched the WHO International Clinical Trials Registry Platform (ICTRP) and reference lists of studies. We did not apply any date or language limits. We planned to include randomized controlled trials. We looked for studies that included at least one of our primary outcomes. The primary outcomes were related to the main domain of the reading: oral reading skills, reading comprehension, reading fluency, phonological awareness, and spelling, measured through validated instruments. The secondary outcomes were self esteem and academic achievement. Two authors (HCM and RBA) independently screened all titles and abstracts identified through the search strategy to determine their eligibility. For our analysis we had planned to use mean difference for continuous data, with 95% confidence intervals, and to use the random-effects statistical model when the effect estimates of two or more studies could be combined in a meta-analysis. We retrieved 851 references via the search strategy. No randomized controlled trials testing music education for the improvement of reading skills in children with dyslexia could be included in this review. There is no evidence available from randomized controlled trials on which to base a judgment about the effectiveness of music education for the improvement of reading skills in children and adolescents with dyslexia. This uncertainty warrants further research via randomized controlled trials, involving a interdisciplinary team: musicians, hearing and speech therapists, psychologists, and physicians.

The structure of tropical forests and sphere packings

PubMed Central

Jahn, Markus Wilhelm; Dobner, Hans-Jürgen; Wiegand, Thorsten; Huth, Andreas

2015-01-01

The search for simple principles underlying the complex architecture of ecological communities such as forests still challenges ecological theorists. We use tree diameter distributions—fundamental for deriving other forest attributes—to describe the structure of tropical forests. Here we argue that tree diameter distributions of natural tropical forests can be explained by stochastic packing of tree crowns representing a forest crown packing system: a method usually used in physics or chemistry. We demonstrate that tree diameter distributions emerge accurately from a surprisingly simple set of principles that include site-specific tree allometries, random placement of trees, competition for space, and mortality. The simple static model also successfully predicted the canopy structure, revealing that most trees in our two studied forests grow up to 30–50 m in height and that the highest packing density of about 60% is reached between the 25- and 40-m height layer. Our approach is an important step toward identifying a minimal set of processes responsible for generating the spatial structure of tropical forests. PMID:26598678

Efficient protein structure search using indexing methods

PubMed Central

2013-01-01

Understanding functions of proteins is one of the most important challenges in many studies of biological processes. The function of a protein can be predicted by analyzing the functions of structurally similar proteins, thus finding structurally similar proteins accurately and efficiently from a large set of proteins is crucial. A protein structure can be represented as a vector by 3D-Zernike Descriptor (3DZD) which compactly represents the surface shape of the protein tertiary structure. This simplified representation accelerates the searching process. However, computing the similarity of two protein structures is still computationally expensive, thus it is hard to efficiently process many simultaneous requests of structurally similar protein search. This paper proposes indexing techniques which substantially reduce the search time to find structurally similar proteins. In particular, we first exploit two indexing techniques, i.e., iDistance and iKernel, on the 3DZDs. After that, we extend the techniques to further improve the search speed for protein structures. The extended indexing techniques build and utilize an reduced index constructed from the first few attributes of 3DZDs of protein structures. To retrieve top-k similar structures, top-10 × k similar structures are first found using the reduced index, and top-k structures are selected among them. We also modify the indexing techniques to support θ-based nearest neighbor search, which returns data points less than θ to the query point. The results show that both iDistance and iKernel significantly enhance the searching speed. In top-k nearest neighbor search, the searching time is reduced 69.6%, 77%, 77.4% and 87.9%, respectively using iDistance, iKernel, the extended iDistance, and the extended iKernel. In θ-based nearest neighbor serach, the searching time is reduced 80%, 81%, 95.6% and 95.6% using iDistance, iKernel, the extended iDistance, and the extended iKernel, respectively. PMID:23691543

Efficient protein structure search using indexing methods.

PubMed

Kim, Sungchul; Sael, Lee; Yu, Hwanjo

2013-01-01

Understanding functions of proteins is one of the most important challenges in many studies of biological processes. The function of a protein can be predicted by analyzing the functions of structurally similar proteins, thus finding structurally similar proteins accurately and efficiently from a large set of proteins is crucial. A protein structure can be represented as a vector by 3D-Zernike Descriptor (3DZD) which compactly represents the surface shape of the protein tertiary structure. This simplified representation accelerates the searching process. However, computing the similarity of two protein structures is still computationally expensive, thus it is hard to efficiently process many simultaneous requests of structurally similar protein search. This paper proposes indexing techniques which substantially reduce the search time to find structurally similar proteins. In particular, we first exploit two indexing techniques, i.e., iDistance and iKernel, on the 3DZDs. After that, we extend the techniques to further improve the search speed for protein structures. The extended indexing techniques build and utilize an reduced index constructed from the first few attributes of 3DZDs of protein structures. To retrieve top-k similar structures, top-10 × k similar structures are first found using the reduced index, and top-k structures are selected among them. We also modify the indexing techniques to support θ-based nearest neighbor search, which returns data points less than θ to the query point. The results show that both iDistance and iKernel significantly enhance the searching speed. In top-k nearest neighbor search, the searching time is reduced 69.6%, 77%, 77.4% and 87.9%, respectively using iDistance, iKernel, the extended iDistance, and the extended iKernel. In θ-based nearest neighbor serach, the searching time is reduced 80%, 81%, 95.6% and 95.6% using iDistance, iKernel, the extended iDistance, and the extended iKernel, respectively.

Time-optimal trajectory planning for underactuated spacecraft using a hybrid particle swarm optimization algorithm

NASA Astrophysics Data System (ADS)

Zhuang, Yufei; Huang, Haibin

2014-02-01

A hybrid algorithm combining particle swarm optimization (PSO) algorithm with the Legendre pseudospectral method (LPM) is proposed for solving time-optimal trajectory planning problem of underactuated spacecrafts. At the beginning phase of the searching process, an initialization generator is constructed by the PSO algorithm due to its strong global searching ability and robustness to random initial values, however, PSO algorithm has a disadvantage that its convergence rate around the global optimum is slow. Then, when the change in fitness function is smaller than a predefined value, the searching algorithm is switched to the LPM to accelerate the searching process. Thus, with the obtained solutions by the PSO algorithm as a set of proper initial guesses, the hybrid algorithm can find a global optimum more quickly and accurately. 200 Monte Carlo simulations results demonstrate that the proposed hybrid PSO-LPM algorithm has greater advantages in terms of global searching capability and convergence rate than both single PSO algorithm and LPM algorithm. Moreover, the PSO-LPM algorithm is also robust to random initial values.

RAG-3D: A search tool for RNA 3D substructures

DOE PAGES

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; ...

2015-08-24

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

RAG-3D: a search tool for RNA 3D substructures

PubMed Central

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

2015-01-01

To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

RAG-3D: A search tool for RNA 3D substructures

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

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

An Overview of Meta-Analyses of Danhong Injection for Unstable Angina.

PubMed

Zhang, Xiaoxia; Wang, Hui; Chang, Yanxu; Wang, Yuefei; Lei, Xiang; Fu, Shufei; Zhang, Junhua

2015-01-01

Objective. To systematically collect evidence and evaluate the effects of Danhong injection (DHI) for unstable angina (UA). Methods. A comprehensive search was conducted in seven electronic databases up to January 2015. The methodological and reporting quality of included studies was assessed by using AMSTAR and PRISMA. Result. Five articles were included. The conclusions suggest that DHI plus conventional medicine treatment was effective for UA pectoris treatment, could alleviate symptoms of angina and ameliorate electrocardiograms. Flaws of the original studies and systematic reviews weaken the strength of evidence. Limitations of the methodology quality include performing an incomprehensive literature search, lacking detailed characteristics, ignoring clinical heterogeneity, and not assessing publication bias and other forms of bias. The flaws of reporting systematic reviews included the following: not providing a structured summary, no standardized search strategy. For the pooled findings, researchers took statistical heterogeneity into consideration, but clinical and methodology heterogeneity were ignored. Conclusion. DHI plus conventional medicine treatment generally appears to be effective for UA treatment. However, the evidence is not hard enough due to methodological flaws in original clinical trials and systematic reviews. Furthermore, rigorous designed randomized controlled trials are also needed. The methodology and reporting quality of systematic reviews should be improved.

An Overview of Meta-Analyses of Danhong Injection for Unstable Angina

PubMed Central

Zhang, Xiaoxia; Chang, Yanxu; Wang, Yuefei; Lei, Xiang; Fu, Shufei; Zhang, Junhua

2015-01-01

Objective. To systematically collect evidence and evaluate the effects of Danhong injection (DHI) for unstable angina (UA). Methods. A comprehensive search was conducted in seven electronic databases up to January 2015. The methodological and reporting quality of included studies was assessed by using AMSTAR and PRISMA. Result. Five articles were included. The conclusions suggest that DHI plus conventional medicine treatment was effective for UA pectoris treatment, could alleviate symptoms of angina and ameliorate electrocardiograms. Flaws of the original studies and systematic reviews weaken the strength of evidence. Limitations of the methodology quality include performing an incomprehensive literature search, lacking detailed characteristics, ignoring clinical heterogeneity, and not assessing publication bias and other forms of bias. The flaws of reporting systematic reviews included the following: not providing a structured summary, no standardized search strategy. For the pooled findings, researchers took statistical heterogeneity into consideration, but clinical and methodology heterogeneity were ignored. Conclusion. DHI plus conventional medicine treatment generally appears to be effective for UA treatment. However, the evidence is not hard enough due to methodological flaws in original clinical trials and systematic reviews. Furthermore, rigorous designed randomized controlled trials are also needed. The methodology and reporting quality of systematic reviews should be improved. PMID:26539221

LMSD: LIPID MAPS structure database

PubMed Central

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Brown, Alex; Dennis, Edward A.; Glass, Christopher K.; Merrill, Alfred H.; Murphy, Robert C.; Raetz, Christian R. H.; Russell, David W.; Subramaniam, Shankar

2007-01-01

The LIPID MAPS Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. Structures of lipids in the database come from four sources: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) computationally generated structures for appropriate lipid classes; (iv) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT and other public sources. All the lipid structures in LMSD are drawn in a consistent fashion. In addition to a classification-based retrieval of lipids, users can search LMSD using either text-based or structure-based search options. The text-based search implementation supports data retrieval by any combination of these data fields: LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass data fields. The structure-based search, in conjunction with optional data fields, provides the capability to perform a substructure search or exact match for the structure drawn by the user. Search results, in addition to structure and annotations, also include relevant links to external databases. The LMSD is publicly available at PMID:17098933

Biclustering of gene expression data using reactive greedy randomized adaptive search procedure.

PubMed

Dharan, Smitha; Nair, Achuthsankar S

2009-01-30

Biclustering algorithms belong to a distinct class of clustering algorithms that perform simultaneous clustering of both rows and columns of the gene expression matrix and can be a very useful analysis tool when some genes have multiple functions and experimental conditions are diverse. Cheng and Church have introduced a measure called mean squared residue score to evaluate the quality of a bicluster and has become one of the most popular measures to search for biclusters. In this paper, we review basic concepts of the metaheuristics Greedy Randomized Adaptive Search Procedure (GRASP)-construction and local search phases and propose a new method which is a variant of GRASP called Reactive Greedy Randomized Adaptive Search Procedure (Reactive GRASP) to detect significant biclusters from large microarray datasets. The method has two major steps. First, high quality bicluster seeds are generated by means of k-means clustering. In the second step, these seeds are grown using the Reactive GRASP, in which the basic parameter that defines the restrictiveness of the candidate list is self-adjusted, depending on the quality of the solutions found previously. We performed statistical and biological validations of the biclusters obtained and evaluated the method against the results of basic GRASP and as well as with the classic work of Cheng and Church. The experimental results indicate that the Reactive GRASP approach outperforms the basic GRASP algorithm and Cheng and Church approach. The Reactive GRASP approach for the detection of significant biclusters is robust and does not require calibration efforts.

Randomly iterated search and statistical competency as powerful inversion tools for deformation source modeling: Application to volcano interferometric synthetic aperture radar data

NASA Astrophysics Data System (ADS)

Shirzaei, M.; Walter, T. R.

2009-10-01

Modern geodetic techniques provide valuable and near real-time observations of volcanic activity. Characterizing the source of deformation based on these observations has become of major importance in related monitoring efforts. We investigate two random search approaches, simulated annealing (SA) and genetic algorithm (GA), and utilize them in an iterated manner. The iterated approach helps to prevent GA in general and SA in particular from getting trapped in local minima, and it also increases redundancy for exploring the search space. We apply a statistical competency test for estimating the confidence interval of the inversion source parameters, considering their internal interaction through the model, the effect of the model deficiency, and the observational error. Here, we present and test this new randomly iterated search and statistical competency (RISC) optimization method together with GA and SA for the modeling of data associated with volcanic deformations. Following synthetic and sensitivity tests, we apply the improved inversion techniques to two episodes of activity in the Campi Flegrei volcanic region in Italy, observed by the interferometric synthetic aperture radar technique. Inversion of these data allows derivation of deformation source parameters and their associated quality so that we can compare the two inversion methods. The RISC approach was found to be an efficient method in terms of computation time and search results and may be applied to other optimization problems in volcanic and tectonic environments.

Which components of heart failure programmes are effective? A systematic review and meta-analysis of the outcomes of structured telephone support or telemonitoring as the primary component of chronic heart failure management in 8323 patients: Abridged Cochrane Review.

PubMed

Inglis, Sally C; Clark, Robyn A; McAlister, Finlay A; Stewart, Simon; Cleland, John G F

2011-09-01

Telemonitoring (TM) and structured telephone support (STS) have the potential to deliver specialized management to more patients with chronic heart failure (CHF), but their efficacy is still to be proven. The aim of this meta-analysis was to review randomized controlled trials (RCTs) of TM or STS for all-cause mortality and all-cause and CHF-related hospitalizations in patients with CHF, as a non-invasive remote model of a specialized disease-management intervention. We searched all relevant electronic databases and search engines, hand-searched bibliographies of relevant studies, systematic reviews, and meeting abstracts. Two reviewers independently extracted all data. Randomized controlled trials comparing TM or STS to usual care in patients with CHF were included. Studies that included intensified management with additional home or clinic-visits were excluded. Primary outcomes (mortality and hospitalizations) were analysed; secondary outcomes (cost, length of stay, and quality of life) were tabulated. Thirty RCTs of STS and TM were identified (25 peer-reviewed publications (n= 8323) and five abstracts (n= 1482)). Of the 25 peer-reviewed studies, 11 evaluated TM (2710 participants), 16 evaluated STS (5613 participants) with two testing both STS and TM in separate intervention arms compared with usual care. Telemonitoring reduced all-cause mortality {risk ratio (RR) 0.66 [95% confidence interval (CI) 0.54-0.81], P< 0.0001 }and STS showed a similar, but non-significant trend [RR 0.88 (95% CI 0.76-1.01), P= 0.08]. Both TM [RR 0.79 (95% CI 0.67-0.94), P= 0.008], and STS [RR 0.77 (95% CI 0.68-0.87), P< 0.0001] reduced CHF-related hospitalizations. Both interventions improved quality of life, reduced costs, and were acceptable to patients. Improvements in prescribing, patient-knowledge and self-care, and functional class were observed. Telemonitoring and STS both appear effective interventions to improve outcomes in patients with CHF. Systematic Review Number: Cochrane Database of Systematic Reviews. 2008:Issue 3. Art. No.: CD007228. DOI: 10.1002/14651858.CD007228.

Catalog of Interstellar HI Shells Discovered in the SETHI Database

NASA Astrophysics Data System (ADS)

Sallmen, Shauna; Korpela, E. J.; Lo, C.; Tennyson, E.; Bellehumeur, B.; Douglas, K. A.

2013-01-01

The interstellar medium (ISM) plays a key role in the development and evolution of galaxies, including our own. The effects of supernovae and stellar winds from generations of stars produce a turbulent, multiphase medium filled with complex interacting structures. As hot gas expands outward, it sweeps up cold neutral material into a shell. Over time, the shells expand and cool, mixing with the ambient material. Shells and other features are therefore evidence of how energy and matter released by stars are redistributed, eventually resulting in the formation of new generations of stars. Several models have contributed to our broad understanding of the physical state and evolution of gas phases in our Galaxy, but a complete, detailed picture remains elusive. In general, random supernovae result in a turbulent ISM with hot, low-density gas surrounding warm & cool clouds. However, the extent to which supernovae disrupt the ambient medium is controversial, the energy inputs of shells are poorly understood, and the role of magnetic fields is unclear. Clearly, HI (neutral hydrogen) shells are central to our understanding of the ISM, so we need to study as many as possible, at all stages of evolution. Our census of Galactic HI shells ISM is incomplete because: (1) Many searches for shells use expansion as key criterion for shell identification, biasing against older, more evolved shells. (2) Shells with broken outlines are missed in most computer-based searches. The human eye is better at searching for such large, irregular features. (3) Most searches carried out in high-resolution data are restricted to the Galactic plane. We have visually examined the SETHI (Search for Extraterrestrial HI) database, searching for shell-like structures. This 21-cm radio survey has an angular resolution of 0.03° and a velocity resolution of 1.5 km/s. We present basic information (location, radial velocity, angular size, shape) for over 70 previously unidentified HI shells. We also discuss the kinematic distances and expansion velocities of shells in the catalog, and its completeness. This work has been supported by NSF grants AST/RUI-0507326, AST-0307596, and AST-0709347, Research Corporation award CC6476/6255, and a WSGC seed grant.

A Forensic Examination of Online Search Facility URL Record Structures.

PubMed

Horsman, Graeme

2018-05-29

The use of search engines and associated search functions to locate content online is now common practice. As a result, a forensic examination of a suspect's online search activity can be a critical aspect in establishing whether an offense has been committed in many investigations. This article offers an analysis of online search URL structures to support law enforcement and associated digital forensics practitioners interpret acts of online searching during an investigation. Google, Bing, Yahoo!, and DuckDuckGo searching functions are examined, and key URL attribute structures and metadata have been documented. In addition, an overview of social media searching covering Twitter, Facebook, Instagram, and YouTube is offered. Results show the ability to extract embedded metadata from search engine URLs which can establish online searching behaviors and the timing of searches. © 2018 American Academy of Forensic Sciences.

Iterative repair for scheduling and rescheduling

NASA Technical Reports Server (NTRS)

Zweben, Monte; Davis, Eugene; Deale, Michael

1991-01-01

An iterative repair search method is described called constraint based simulated annealing. Simulated annealing is a hill climbing search technique capable of escaping local minima. The utility of the constraint based framework is shown by comparing search performance with and without the constraint framework on a suite of randomly generated problems. Results are also shown of applying the technique to the NASA Space Shuttle ground processing problem. These experiments show that the search methods scales to complex, real world problems and reflects interesting anytime behavior.

Urineschool: A Study of the Impact of the Earls Decision on High School Random Drug Testing Policies.

ERIC Educational Resources Information Center

Conlon, Cynthia Kelly

2003-01-01

Examines impact of Supreme Court's 2002 decision in "Board of Education v. Earls" on high school random drug-testing policies and practices. Court held that random drug-testing policy at Tecumseh, Oklahoma, school district did not violate students' Fourth Amendment right against unreasonable searches. (Contains 46 references.) (PKP)

Encounter success of free-ranging marine predator movements across a dynamic prey landscape.

PubMed

Sims, David W; Witt, Matthew J; Richardson, Anthony J; Southall, Emily J; Metcalfe, Julian D

2006-05-22

Movements of wide-ranging top predators can now be studied effectively using satellite and archival telemetry. However, the motivations underlying movements remain difficult to determine because trajectories are seldom related to key biological gradients, such as changing prey distributions. Here, we use a dynamic prey landscape of zooplankton biomass in the north-east Atlantic Ocean to examine active habitat selection in the plankton-feeding basking shark Cetorhinus maximus. The relative success of shark searches across this landscape was examined by comparing prey biomass encountered by sharks with encounters by random-walk simulations of 'model' sharks. Movements of transmitter-tagged sharks monitored for 964 days (16754 km estimated minimum distance) were concentrated on the European continental shelf in areas characterized by high seasonal productivity and complex prey distributions. We show movements by adult and sub-adult sharks yielded consistently higher prey encounter rates than 90% of random-walk simulations. Behavioural patterns were consistent with basking sharks using search tactics structured across multiple scales to exploit the richest prey areas available in preferred habitats. Simple behavioural rules based on learned responses to previously encountered prey distributions may explain the high performances. This study highlights how dynamic prey landscapes enable active habitat selection in large predators to be investigated from a trophic perspective, an approach that may inform conservation by identifying critical habitat of vulnerable species.

Neural correlates of cognitive improvements following cognitive remediation in schizophrenia: a systematic review of randomized trials

PubMed Central

Isaac, Clémence; Januel, Dominique

2016-01-01

Background Cognitive impairments are a core feature in schizophrenia and are linked to poor social functioning. Numerous studies have shown that cognitive remediation can enhance cognitive and functional abilities in patients with this pathology. The underlying mechanism of these behavioral improvements seems to be related to structural and functional changes in the brain. However, studies on neural correlates of such enhancement remain scarce. Objectives We explored the neural correlates of cognitive enhancement following cognitive remediation interventions in schizophrenia and the differential effect between cognitive training and other therapeutic interventions or patients’ usual care. Method We searched MEDLINE, PsycInfo, and ScienceDirect databases for studies on cognitive remediation therapy in schizophrenia that used neuroimaging techniques and a randomized design. Search terms included randomized controlled trial, cognitive remediation, cognitive training, rehabilitation, magnetic resonance imaging, positron emission tomography, electroencephalography, magnetoencephalography, near infrared spectroscopy, and diffusion tensor imaging. We selected randomized controlled trials that proposed multiple sessions of cognitive training to adult patients with a schizophrenia spectrum disorder and assessed its efficacy with imaging techniques. Results In total, 15 reports involving 19 studies were included in the systematic review. They involved a total of 455 adult patients, 271 of whom received cognitive remediation. Cognitive remediation therapy seems to provide a neurobiological enhancing effect in schizophrenia. After therapy, increased activations are observed in various brain regions mainly in frontal – especially prefrontal – and also in occipital and anterior cingulate regions during working memory and executive tasks. Several studies provide evidence of an improved functional connectivity after cognitive training, suggesting a neuroplastic effect of therapy through mechanisms of functional reorganization. Neurocognitive and social-cognitive training may have a cumulative effect on neural networks involved in social cognition. The variety of proposed programs, imaging tasks, and techniques may explain the heterogeneity of observed neural improvements. Future studies would need to specify the effect of cognitive training depending on those variables. PMID:26993787

The effects of aquatic therapy on mobility of individuals with neurological diseases: a systematic review.

PubMed

Marinho-Buzelli, Andresa R; Bonnyman, Alison M; Verrier, Mary C

2015-08-01

To summarize evidence on the effects of aquatic therapy on mobility in individuals with neurological diseases. MEDLINE, EMBASE, PsycInfo, CENTRAL, CINAHL, SPORTDiscus, PEDro, PsycBITE and OT Seeker were searched from inception to 15 September 2014. Hand-searching of reference lists was performed in the selected studies. The search included randomized controlled trials and quasi-experimental studies that investigated the use of aquatic therapy and its effect on mobility of adults with neurological diseases. One reviewer screened titles and abstracts of retrieved studies from the search strategy. Two reviewers independently examined the full texts and conducted the study selection, data extraction and quality assessment. A narrative synthesis of data was applied to summarize information from included studies. The Downs and Black Scale was used to assess methodological quality. A total of 116 articles were obtained for full text eligibility. Twenty studies met the specified inclusion criteria: four Randomized Controlled Trials (RCTs), four non-randomized studies and 12 before-and-after tests. Two RCTs (30 patients with stroke in the aquatic therapy groups), three non-randomized studies and three before-and-after studies showed "fair" evidence that aquatic therapy increases dynamic balance in participants with some neurological disorders. One RCT (seven patients with stroke in the aquatic therapy group) and two before-and-after tests (20 patients with multiple sclerosis) demonstrated "fair" evidence on improvement of gait speed after aquatic therapy. Our synthesis showed "fair" evidence supporting the use of aquatic therapy to improve dynamic balance and gait speed in adults with certain neurological conditions. © The Author(s) 2014.

A lock-free priority queue design based on multi-dimensional linked lists

DOE PAGES

Dechev, Damian; Zhang, Deli

2015-04-03

The throughput of concurrent priority queues is pivotal to multiprocessor applications such as discrete event simulation, best-first search and task scheduling. Existing lock-free priority queues are mostly based on skiplists, which probabilistically create shortcuts in an ordered list for fast insertion of elements. The use of skiplists eliminates the need of global rebalancing in balanced search trees and ensures logarithmic sequential search time on average, but the worst-case performance is linear with respect to the input size. In this paper, we propose a quiescently consistent lock-free priority queue based on a multi-dimensional list that guarantees worst-case search time of O(logN)more » for key universe of size N. The novel multi-dimensional list (MDList) is composed of nodes that contain multiple links to child nodes arranged by their dimensionality. The insertion operation works by first injectively mapping the scalar key to a high-dimensional vector, then uniquely locating the target position by using the vector as coordinates. Nodes in MDList are ordered by their coordinate prefixes and the ordering property of the data structure is readily maintained during insertion without rebalancing nor randomization. Furthermore, in our experimental evaluation using a micro-benchmark, our priority queue achieves an average of 50% speedup over the state of the art approaches under high concurrency.« less

Searching for globally optimal functional forms for interatomic potentials using genetic programming with parallel tempering.

PubMed

Slepoy, A; Peters, M D; Thompson, A P

2007-11-30

Molecular dynamics and other molecular simulation methods rely on a potential energy function, based only on the relative coordinates of the atomic nuclei. Such a function, called a force field, approximately represents the electronic structure interactions of a condensed matter system. Developing such approximate functions and fitting their parameters remains an arduous, time-consuming process, relying on expert physical intuition. To address this problem, a functional programming methodology was developed that may enable automated discovery of entirely new force-field functional forms, while simultaneously fitting parameter values. The method uses a combination of genetic programming, Metropolis Monte Carlo importance sampling and parallel tempering, to efficiently search a large space of candidate functional forms and parameters. The methodology was tested using a nontrivial problem with a well-defined globally optimal solution: a small set of atomic configurations was generated and the energy of each configuration was calculated using the Lennard-Jones pair potential. Starting with a population of random functions, our fully automated, massively parallel implementation of the method reproducibly discovered the original Lennard-Jones pair potential by searching for several hours on 100 processors, sampling only a minuscule portion of the total search space. This result indicates that, with further improvement, the method may be suitable for unsupervised development of more accurate force fields with completely new functional forms. Copyright (c) 2007 Wiley Periodicals, Inc.

A lock-free priority queue design based on multi-dimensional linked lists

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

Dechev, Damian; Zhang, Deli

The throughput of concurrent priority queues is pivotal to multiprocessor applications such as discrete event simulation, best-first search and task scheduling. Existing lock-free priority queues are mostly based on skiplists, which probabilistically create shortcuts in an ordered list for fast insertion of elements. The use of skiplists eliminates the need of global rebalancing in balanced search trees and ensures logarithmic sequential search time on average, but the worst-case performance is linear with respect to the input size. In this paper, we propose a quiescently consistent lock-free priority queue based on a multi-dimensional list that guarantees worst-case search time of O(logN)more » for key universe of size N. The novel multi-dimensional list (MDList) is composed of nodes that contain multiple links to child nodes arranged by their dimensionality. The insertion operation works by first injectively mapping the scalar key to a high-dimensional vector, then uniquely locating the target position by using the vector as coordinates. Nodes in MDList are ordered by their coordinate prefixes and the ordering property of the data structure is readily maintained during insertion without rebalancing nor randomization. Furthermore, in our experimental evaluation using a micro-benchmark, our priority queue achieves an average of 50% speedup over the state of the art approaches under high concurrency.« less

Auto-biometric for M-mode echocardiography

NASA Astrophysics Data System (ADS)

Zhang, Wei; Park, Jinhyong; Zhou, S. Kevin

2010-03-01

In this paper we present a system for fast and accurate detection of anatomical structures (calipers) in M-mode images. The task is challenging because of dramatic variations in their appearances. We propose to solve the problem in a progressive manner, which ensures both robustness and efficiency. It first obtains rough caliper localization using the intensity profile image. Then run a constrained search for accurate caliper positions. Markov Random Field (MRF) and warping image detectors are used for jointly considering appearance information and the geometric relationship between calipers. Extensive experiments show that our system achieves more accurate results and uses less time in comparison with previously reported work.

[The study of M dwarf spectral classification].

PubMed

Yi, Zhen-Ping; Pan, Jing-Chang; Luo, A-Li

2013-08-01

As the most common stars in the galaxy, M dwarfs can be used to trace the structure and evolution of the Milky Way. Besides, investigating M dwarfs is important for searching for habitability of extrasolar planets orbiting M dwarfs. Spectral classification of M dwarfs is a fundamental work. The authors used DR7 M dwarf sample of SLOAN to extract important features from the range of 600-900 nm by random forest method. Compared to the features used in Hammer Code, the authors added three new indices. Our test showed that the improved Hammer with new indices is more accurate. Our method has been applied to classify M dwarf spectra of LAMOST.

Orthodontic treatment in periodontitis‐susceptible subjects: a systematic literature review

PubMed Central

Lindsten, Rune; Slotte, Christer; Bjerklin, Krister

2016-01-01

Abstract The aim is to evaluate the literature for clinical scientific data on possible effects of orthodontic treatment on periodontal status in periodontitis‐susceptible subjects. A systematic literature review was performed on studies in English using PubMed, MEDLINE, and Cochrane Library central databases (1965‐2014). By manually searching reference lists of selected studies, we identified additional articles; then we searched these publications: Journal of Periodontology, Periodontology 2000, Journal of Clinical Periodontology, American Journal of Orthodontics and Dentofacial Orthopedics, Angle Orthodontist, International Journal of Periodontics & Restorative Dentistry, and European Journal of Orthodontics. Search terms included randomized clinical trials, controlled clinical trials, prospective and retrospective clinical studies, case series >5 patients, periodontitis, orthodontics, alveolar bone loss, tooth migration, tooth movement, orthodontic extrusion, and orthodontic intrusion. Only studies on orthodontic treatment in periodontally compromised dentitions were included. One randomized controlled clinical trial, one controlled clinical trial, and 12 clinical studies were included. No evidence currently exists from controlled studies and randomized controlled clinical trials, which shows that orthodontic treatment improves or aggravates the status of periodontally compromised dentitions. PMID:29744163

Intervention randomized controlled trials involving wrist and shoulder arthroscopy: a systematic review

PubMed Central

2014-01-01

Background Although arthroscopy of upper extremity joints was initially a diagnostic tool, it is increasingly used for therapeutic interventions. Randomized controlled trials (RCTs) are considered the gold standard for assessing treatment efficacy. We aimed to review the literature for intervention RCTs involving wrist and shoulder arthroscopy. Methods We performed a systematic review for RCTs in which at least one arm was an intervention performed through wrist arthroscopy or shoulder arthroscopy. PubMed and Cochrane Library databases were searched up to December 2012. Two researchers reviewed each article and recorded the condition treated, randomization method, number of randomized participants, time of randomization, outcomes measures, blinding, and description of dropouts and withdrawals. We used the modified Jadad scale that considers the randomization method, blinding, and dropouts/withdrawals; score 0 (lowest quality) to 5 (highest quality). The scores for the wrist and shoulder RCTs were compared with the Mann–Whitney test. Results The first references to both wrist and shoulder arthroscopy appeared in the late 1970s. The search found 4 wrist arthroscopy intervention RCTs (Kienböck’s disease, dorsal wrist ganglia, volar wrist ganglia, and distal radius fracture; first 3 compared arthroscopic with open surgery). The median number of participants was 45. The search found 50 shoulder arthroscopy intervention RCTs (rotator cuff tears 22, instability 14, impingement 9, and other conditions 5). Of these, 31 compared different arthroscopic treatments, 12 compared arthroscopic with open treatment, and 7 compared arthroscopic with nonoperative treatment. The median number of participants was 60. The median modified Jadad score for the wrist RCTs was 0.5 (range 0–1) and for the shoulder RCTs 3.0 (range 0–5) (p = 0.012). Conclusion Despite the increasing use of wrist arthroscopy in the treatment of various wrist disorders the efficacy of arthroscopically performed wrist interventions has been studied in only 4 randomized studies compared to 50 randomized studies of significantly higher quality assessing interventions performed through shoulder arthroscopy. PMID:25059881

Vertical detachment energies of anionic thymidine: Microhydration effects.

PubMed

Kim, Sunghwan; Schaefer, Henry F

2010-10-14

Density functional theory has been employed to investigate microhydration effects on the vertical detachment energy (VDE) of the thymidine anion by considering the various structures of its monohydrates. Structures were located using a random searching procedure. Among 14 distinct structures of the anionic thymidine monohydrate, the low-energy structures, in general, have the water molecule bound to the thymine base unit. The negative charge developed on the thymine moiety increases the strength of the intermolecular hydrogen bonding between the water and base units. The computed VDE values of the thymidine monohydrate anions are predicted to range from 0.67 to 1.60 eV and the lowest-energy structure has a VDE of 1.32 eV. The VDEs of the monohydrates of the thymidine anion, where the N(1)[Single Bond]H hydrogen of thymine has been replaced by a 2(')-deoxyribose ring, are greater by ∼0.30 eV, compared to those of the monohydrates of the thymine anion. The results of the present study are in excellent agreement with the accompanying experimental results of Bowen and co-workers [J. Chem. Phys. 133, 144304 (2010)].

Hide and vanish: data sets where the most parsimonious tree is known but hard to find, and their implications for tree search methods.

PubMed

Goloboff, Pablo A

2014-10-01

Three different types of data sets, for which the uniquely most parsimonious tree can be known exactly but is hard to find with heuristic tree search methods, are studied. Tree searches are complicated more by the shape of the tree landscape (i.e. the distribution of homoplasy on different trees) than by the sheer abundance of homoplasy or character conflict. Data sets of Type 1 are those constructed by Radel et al. (2013). Data sets of Type 2 present a very rugged landscape, with narrow peaks and valleys, but relatively low amounts of homoplasy. For such a tree landscape, subjecting the trees to TBR and saving suboptimal trees produces much better results when the sequence of clipping for the tree branches is randomized instead of fixed. An unexpected finding for data sets of Types 1 and 2 is that starting a search from a random tree instead of a random addition sequence Wagner tree may increase the probability that the search finds the most parsimonious tree; a small artificial example where these probabilities can be calculated exactly is presented. Data sets of Type 3, the most difficult data sets studied here, comprise only congruent characters, and a single island with only one most parsimonious tree. Even if there is a single island, missing entries create a very flat landscape which is difficult to traverse with tree search algorithms because the number of equally parsimonious trees that need to be saved and swapped to effectively move around the plateaus is too large. Minor modifications of the parameters of tree drifting, ratchet, and sectorial searches allow travelling around these plateaus much more efficiently than saving and swapping large numbers of equally parsimonious trees with TBR. For these data sets, two new related criteria for selecting taxon addition sequences in Wagner trees (the "selected" and "informative" addition sequences) produce much better results than the standard random or closest addition sequences. These new methods for Wagner trees and for moving around plateaus can be useful when analyzing phylogenomic data sets formed by concatenation of genes with uneven taxon representation ("sparse" supermatrices), which are likely to present a tree landscape with extensive plateaus. Copyright © 2014 Elsevier Inc. All rights reserved.

Corticosteroids as adjuvant therapy for ocular toxoplasmosis

PubMed Central

Jasper, Smitha; Vedula, Satyanarayana S; John, Sheeja S; Horo, Saban; Sepah, Yasir J; Nguyen, Quan Dong

2017-01-01

Background Ocular infection caused by Toxoplasma gondii, a parasite, may result in inflammation in the retina, choroid, and uvea, and consequently lead to complications such as glaucoma, cataract, and posterior synechiae. Objectives The objective of this systematic review was to assess the effects of adjunctive use of corticosteroids to anti-parasitic therapy versus anti-parasitic therapy alone for ocular toxoplasmosis. Search methods We searched CENTRAL (which contains the Cochrane Eyes and Vision Trials Register (2016; Issue 11)), MEDLINE Ovid, Epub Ahead of Print, In-Process & Other Non-Indexed Citations, MEDLINE Ovid Daily (January 1946 to December 2016), Embase (January 1980 to December 2016), Latin American and Caribbean Literature on Health Sciences (LILACS (January 1982 to December 2016)), the ISRCTN registry (www.isrctn.com/editAdvancedSearch), ClinicalTrials.gov (www.clinicaltrials.gov), and the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP; www.who.int/ictrp/search/en). We used no date or language restrictions in the electronic searches for trials. We last searched the electronic databases on 7 December 2016. Selection criteria We had planned to include randomized and quasi-randomized controlled trials. Eligible trials would have enrolled participants of any age who were immunocompetent and were diagnosed with acute ocular toxoplasmosis. Included trials would have compared anti-parasitic therapy plus corticosteroids versus anti-parasitic therapy alone, different doses or times of initiation of corticosteroids. Data collection and analysis Two authors independently screened titles and abstracts retrieved through the electronic searches. We retrieved full-text reports of studies categorized as ’unsure’ or ’include’ after we reviewed the abstracts. Two authors independently reviewed each full-text report for eligibility. Discrepancies were resolved through discussion. Main results We identified no completed or ongoing trial that was eligible for this Cochrane review. Authors’ conclusions Although research has identified a wide variation in practice regarding the use of corticosteroids, our review did not identify any evidence from randomized controlled trials for or against the role of corticosteroids in the management of ocular toxoplasmosis. Several questions remain unanswered by well-conducted randomized trials in this context, including whether the use of corticosteroids as an adjunctive agent is more effective than the use of anti-parasitic therapy alone; if so, when corticosteroids should be initiated in the treatment regimen (early versus late course of treatment), and what would be the best dose and duration of steroid use. PMID:28125765

Origin of the computational hardness for learning with binary synapses.

PubMed

Huang, Haiping; Kabashima, Yoshiyuki

2014-11-01

Through supervised learning in a binary perceptron one is able to classify an extensive number of random patterns by a proper assignment of binary synaptic weights. However, to find such assignments in practice is quite a nontrivial task. The relation between the weight space structure and the algorithmic hardness has not yet been fully understood. To this end, we analytically derive the Franz-Parisi potential for the binary perceptron problem by starting from an equilibrium solution of weights and exploring the weight space structure around it. Our result reveals the geometrical organization of the weight space; the weight space is composed of isolated solutions, rather than clusters of exponentially many close-by solutions. The pointlike clusters far apart from each other in the weight space explain the previously observed glassy behavior of stochastic local search heuristics.

VAST PLANES OF SATELLITES IN A HIGH-RESOLUTION SIMULATION OF THE LOCAL GROUP: COMPARISON TO ANDROMEDA

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

Gillet, N.; Ocvirk, P.; Aubert, D.

2015-02-10

We search for vast planes of satellites (VPoS) in a high-resolution simulation of the Local Group performed by the CLUES project, which improves significantly the resolution of previous similar studies. We use a simple method for detecting planar configurations of satellites, and validate it on the known plane of M31. We implement a range of prescriptions for modeling the satellite populations, roughly reproducing the variety of recipes used in the literature, and investigate the occurrence and properties of planar structures in these populations. The structure of the simulated satellite systems is strongly non-random and contains planes of satellites, predominantly co-rotating,more » with, in some cases, sizes comparable to the plane observed in M31 by Ibata et al. However, the latter is slightly richer in satellites, slightly thinner, and has stronger co-rotation, which makes it stand out as overall more exceptional than the simulated planes, when compared to a random population. Although the simulated planes we find are generally dominated by one real structure forming its backbone, they are also partly fortuitous and are thus not kinematically coherent structures as a whole. Provided that the simulated and observed planes of satellites are indeed of the same nature, our results suggest that the VPoS of M31 is not a coherent disk and that one-third to one-half of its satellites must have large proper motions perpendicular to the plane.« less

How breast cancer patients want to search for and retrieve information from stories of other patients on the internet: an online randomized controlled experiment.

PubMed

Overberg, Regina; Otten, Wilma; de Man, Andries; Toussaint, Pieter; Westenbrink, Judith; Zwetsloot-Schonk, Bertie

2010-03-09

Other patients' stories on the Internet can give patients information, support, reassurance, and practical advice. We examined which search facility for online stories resulted in patients' satisfaction and search success. This study was a randomized controlled experiment with a 2x2 factorial design conducted online. We facilitated access to 170 stories of breast cancer patients in four ways based on two factors: (1) no versus yes search by story topic, and (2) no versus yes search by writer profile. Dutch speaking women with breast cancer were recruited. Women who gave informed consent were randomly assigned to one of four groups. After searching for stories, women were offered a questionnaire relating to satisfaction with the search facility, the stories retrieved, and impact of the stories on coping with breast cancer. Of 353 enrolled women, 182 (51.6%) completed the questionnaire: control group (n = 37), story topics group (n = 49), writer profile group (n = 51), and combination group (n = 45). Questionnaire completers were evenly distributed over the four groups (chi(2) (3) = 3.7, P = .30). Women who had access to the story topics search facility (yes vs no): were more positive about (mean scores 4.0 vs 3.6, P = .001) and more satisfied with the search facility (mean scores 7.3 vs 6.3, P < .001); were more positive about the number of search options (mean scores 2.3 vs 2.1, P = .04); were better enabled to find desired information (mean scores 3.3 vs 2.8, P = .001); were more likely to recommend the search facility to others or intend to use it themselves (mean scores 4.1 vs 3.5, P < .001); were more positive about how retrieved stories were displayed (mean scores 3.6 vs 3.2, P = .001); retrieved stories that better covered their information needs (mean scores 3.0 vs 2.6, P = .02); were more satisfied with the stories retrieved (mean scores 7.1 vs 6.4, P = .002); and were more likely to report an impact of the stories on coping with breast cancer (mean scores 3.2 vs 2.9, P =. 02). Three main effects were associated with use of the writer profile search (yes vs no): being more positive about (mean scores 3.9 vs 3.6, P = .005) and more satisfied with the search facility (mean scores 7.1 vs 6.5, P =. 01), and being more positive about how retrieved stories were displayed (mean scores 3.8 vs 2.9, P < .001). For satisfaction with the search facility, an interaction effect was found (P = .03): at least one of the two search facilities was needed for satisfaction. Having access to the story topics search facility clearly had the most positive effect on patient satisfaction and search success.

Summary of Meta-Analyses Dealing with Single-Row versus Double-Row Repair Techniques for Rotator Cuff Tears

PubMed Central

Spiegl, U.J.; Euler, S.A.; Millett, P.J.; Hepp, P.

2016-01-01

Background: Several meta-analyses of randomized clinical trials have been performed to analyze whether double-row (DR) rotator cuff repair (RCR) provides superior clinical outcomes and structural healing compared to single-row (SR) repair. The purpose of this study was to sum up the results of meta-analysis comparing SR and DR repair with respect on clinical outcomes and re-tear rates. Methods: A literature search was undertaken to identify all meta-analyses dealing with randomized controlled trials comparing clinical und structural outcomes after SR versus DR RCR. Results: Eight meta-analyses met the eligibility criteria: two including Level I studies only, five including both Level I and Level II studies, and one including additional Level III studies. Four meta-analyses found no differences between SR and DR RCR for patient outcomes, whereas four favored DR RCR for tears greater than 3 cm. Two meta-analyses found no structural healing differences between SR and DR RCR, whereas six found DR repair to be superior for tears greater than 3 cm tears. Conclusion: No clinical differences are seen between single-row and double-row repair for small and medium rotator cuff tears after a short-term follow-up period with a higher re-tear rate following single-row repairs. There seems to be a trend to superior results with double-row repair in large to massive tear sizes. PMID:27708735

Visual search in scenes involves selective and non-selective pathways

PubMed Central

Wolfe, Jeremy M; Vo, Melissa L-H; Evans, Karla K; Greene, Michelle R

2010-01-01

How do we find objects in scenes? For decades, visual search models have been built on experiments in which observers search for targets, presented among distractor items, isolated and randomly arranged on blank backgrounds. Are these models relevant to search in continuous scenes? This paper argues that the mechanisms that govern artificial, laboratory search tasks do play a role in visual search in scenes. However, scene-based information is used to guide search in ways that had no place in earlier models. Search in scenes may be best explained by a dual-path model: A “selective” path in which candidate objects must be individually selected for recognition and a “non-selective” path in which information can be extracted from global / statistical information. PMID:21227734

Structure Prediction and Analysis of DNA Transposon and LINE Retrotransposon Proteins*

PubMed Central

Abrusán, György; Zhang, Yang; Szilágyi, András

2013-01-01

Despite the considerable amount of research on transposable elements, no large-scale structural analyses of the TE proteome have been performed so far. We predicted the structures of hundreds of proteins from a representative set of DNA and LINE transposable elements and used the obtained structural data to provide the first general structural characterization of TE proteins and to estimate the frequency of TE domestication and horizontal transfer events. We show that 1) ORF1 and Gag proteins of retrotransposons contain high amounts of structural disorder; thus, despite their very low conservation, the presence of disordered regions and probably their chaperone function is conserved. 2) The distribution of SCOP classes in DNA transposons and LINEs indicates that the proteins of DNA transposons are more ancient, containing folds that already existed when the first cellular organisms appeared. 3) DNA transposon proteins have lower contact order than randomly selected reference proteins, indicating rapid folding, most likely to avoid protein aggregation. 4) Structure-based searches for TE homologs indicate that the overall frequency of TE domestication events is low, whereas we found a relatively high number of cases where horizontal transfer, frequently involving parasites, is the most likely explanation for the observed homology. PMID:23530042

The Effect of Teaching Search Strategies on Perceptual Performance.

PubMed

van der Gijp, Anouk; Vincken, Koen L; Boscardin, Christy; Webb, Emily M; Ten Cate, Olle Th J; Naeger, David M

2017-06-01

Radiology expertise is dependent on the use of efficient search strategies. The aim of this study is to investigate the effect of teaching search strategies on trainee's accuracy in detecting lung nodules at computed tomography. Two search strategies, "scanning" and "drilling," were tested with a randomized crossover design. Nineteen junior radiology residents were randomized into two groups. Both groups first completed a baseline lung nodule detection test allowing a free search strategy, followed by a test after scanning instruction and drilling instruction or vice versa. True positive (TP) and false positive (FP) scores and scroll behavior were registered. A mixed-design analysis of variance was applied to compare the three search conditions. Search strategy instruction had a significant effect on scroll behavior, F(1.3) = 54.2, P < 0.001; TP score, F(2) = 16.1, P < 0.001; and FP score, F(1.3) = 15.3, P < 0.001. Scanning instruction resulted in significantly lower TP scores than drilling instruction (M = 10.7, SD = 5.0 versus M = 16.3, SD = 5.3), t(18) = 4.78, P < 0.001; or free search (M = 15.3, SD = 4.6), t(18) = 4.44, P < 0.001. TP scores for drilling did not significantly differ from free search. FP scores for drilling (M = 7.3, SD = 5.6) were significantly lower than for free search (M = 12.5, SD = 7.8), t(18) = 4.86, P < 0.001. Teaching a drilling strategy is preferable to teaching a scanning strategy for finding lung nodules. Copyright © 2017 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

The relation between visualization size, grouping, and user performance.

PubMed

Gramazio, Connor C; Schloss, Karen B; Laidlaw, David H

2014-12-01

In this paper we make the following contributions: (1) we describe how the grouping, quantity, and size of visual marks affects search time based on the results from two experiments; (2) we report how search performance relates to self-reported difficulty in finding the target for different display types; and (3) we present design guidelines based on our findings to facilitate the design of effective visualizations. Both Experiment 1 and 2 asked participants to search for a unique target in colored visualizations to test how the grouping, quantity, and size of marks affects user performance. In Experiment 1, the target square was embedded in a grid of squares and in Experiment 2 the target was a point in a scatterplot. Search performance was faster when colors were spatially grouped than when they were randomly arranged. The quantity of marks had little effect on search time for grouped displays ("pop-out"), but increasing the quantity of marks slowed reaction time for random displays. Regardless of color layout (grouped vs. random), response times were slowest for the smallest mark size and decreased as mark size increased to a point, after which response times plateaued. In addition to these two experiments we also include potential application areas, as well as results from a small case study where we report preliminary findings that size may affect how users infer how visualizations should be used. We conclude with a list of design guidelines that focus on how to best create visualizations based on grouping, quantity, and size of visual marks.

Biclustering of gene expression data using reactive greedy randomized adaptive search procedure

PubMed Central

Dharan, Smitha; Nair, Achuthsankar S

2009-01-01

Background Biclustering algorithms belong to a distinct class of clustering algorithms that perform simultaneous clustering of both rows and columns of the gene expression matrix and can be a very useful analysis tool when some genes have multiple functions and experimental conditions are diverse. Cheng and Church have introduced a measure called mean squared residue score to evaluate the quality of a bicluster and has become one of the most popular measures to search for biclusters. In this paper, we review basic concepts of the metaheuristics Greedy Randomized Adaptive Search Procedure (GRASP)-construction and local search phases and propose a new method which is a variant of GRASP called Reactive Greedy Randomized Adaptive Search Procedure (Reactive GRASP) to detect significant biclusters from large microarray datasets. The method has two major steps. First, high quality bicluster seeds are generated by means of k-means clustering. In the second step, these seeds are grown using the Reactive GRASP, in which the basic parameter that defines the restrictiveness of the candidate list is self-adjusted, depending on the quality of the solutions found previously. Results We performed statistical and biological validations of the biclusters obtained and evaluated the method against the results of basic GRASP and as well as with the classic work of Cheng and Church. The experimental results indicate that the Reactive GRASP approach outperforms the basic GRASP algorithm and Cheng and Church approach. Conclusion The Reactive GRASP approach for the detection of significant biclusters is robust and does not require calibration efforts. PMID:19208127

CENTRAL, PEDro, PubMed, and EMBASE are the most comprehensive databases indexing randomized controlled trials of physical therapy interventions.

PubMed

Michaleff, Zoe A; Costa, Leonardo O P; Moseley, Anne M; Maher, Christopher G; Elkins, Mark R; Herbert, Robert D; Sherrington, Catherine

2011-02-01

Many bibliographic databases index research studies evaluating the effects of health care interventions. One study has concluded that the Physiotherapy Evidence Database (PEDro) has the most complete indexing of reports of randomized controlled trials of physical therapy interventions, but the design of that study may have exaggerated estimates of the completeness of indexing by PEDro. The purpose of this study was to compare the completeness of indexing of reports of randomized controlled trials of physical therapy interventions by 8 bibliographic databases. This study was an audit of bibliographic databases. Prespecified criteria were used to identify 400 reports of randomized controlled trials from the reference lists of systematic reviews published in 2008 that evaluated physical therapy interventions. Eight databases (AMED, CENTRAL, CINAHL, EMBASE, Hooked on Evidence, PEDro, PsycINFO, and PubMed) were searched for each trial report. The proportion of the 400 trial reports indexed by each database was calculated. The proportions of the 400 trial reports indexed by the databases were as follows: CENTRAL, 95%; PEDro, 92%; PubMed, 89%; EMBASE, 88%; CINAHL, 53%; AMED, 50%; Hooked on Evidence, 45%; and PsycINFO, 6%. Almost all of the trial reports (99%) were found in at least 1 database, and 88% were indexed by 4 or more databases. Four trial reports were uniquely indexed by a single database only (2 in CENTRAL and 1 each in PEDro and PubMed). The results are only applicable to searching for English-language published reports of randomized controlled trials evaluating physical therapy interventions. The 4 most comprehensive databases of trial reports evaluating physical therapy interventions were CENTRAL, PEDro, PubMed, and EMBASE. Clinicians seeking quick answers to clinical questions could search any of these databases knowing that all are reasonably comprehensive. PEDro, unlike the other 3 most complete databases, is specific to physical therapy, so studies not relevant to physical therapy are less likely to be retrieved. Researchers could use CENTRAL, PEDro, PubMed, and EMBASE in combination to conduct exhaustive searches for randomized trials in physical therapy.

Search of exploration opportunity for near earth objects based on analytical gradients

NASA Astrophysics Data System (ADS)

Ren, Y.; Cui, P. Y.; Luan, E. J.

2008-01-01

The problem of searching for exploration opportunity of near Earth objects is investigated. For rendezvous missions, the analytical gradients of performance index with respect to free parameters are derived by combining the calculus of variation with the theory of state-transition matrix. Then, some initial guesses are generated random in the search space, and the performance index is optimized with the guidance of analytical gradients from these initial guesses. This method not only keeps the property of global search in traditional method, but also avoids the blindness in the traditional exploration opportunity search; hence, the computing speed could be increased greatly. Furthermore, by using this method, the search precision could be controlled effectively.

The Pricing of Information--A Search-Based Approach to Pricing an Online Search Service.

ERIC Educational Resources Information Center

Boyle, Harry F.

1982-01-01

Describes innovative pricing structure consisting of low connect time fee, print fees, and search fees, offered by Chemical Abstracts Service (CAS) ONLINE--an online searching system used to locate chemical substances. Pricing options considered by CAS, the search-based pricing approach, and users' reactions to pricing structures are noted. (EJS)

Systematic Review of Integrative Health Care Research: Randomized Control Trials, Clinical Controlled Trials, and Meta-Analysis

PubMed Central

Khorsan, Raheleh; Coulter, Ian D.; Crawford, Cindy; Hsiao, An-Fu

2011-01-01

A systematic review was conducted to assess the level of evidence for integrative health care research. We searched PubMed, Allied and Complementary Medicine (AMED), BIOSIS Previews, EMBASE, the entire Cochrane Library, MANTIS, Social SciSearch, SciSearch Cited Ref Sci, PsychInfo, CINAHL, and NCCAM grantee publications listings, from database inception to May 2009, as well as searches of the “gray literature.” Available studies published in English language were included. Three independent reviewers rated each article and assessed the methodological quality of studies using the Scottish Intercollegiate Guidelines Network (SIGN 50). Our search yielded 11,891 total citations but 6 clinical studies, including 4 randomized, met our inclusion criteria. There are no available systematic reviews/meta-analyses published that met our inclusion criteria. The methodological quality of the included studies was assessed independently using quality checklists of the SIGN 50. Only a small number of RCTs and CCTs with a limited number of patients and lack of adequate control groups assessing integrative health care research are available. These studies provide limited evidence of effective integrative health care on some modalities. However, integrative health care regimen appears to be generally safe. PMID:20953383

Learning where to look: electrophysiological and behavioral indices of visual search in young and old subjects.

PubMed

Looren de Jong, H; Kok, A; Woestenburg, J C; Logman, C J; Van Rooy, J C

1988-06-01

The present investigation explores the way young and elderly subjects use regularities in target location in a visual display to guide search for targets. Although both young and old subjects show efficient use of search strategies, slight but reliable differences in reaction times suggest decreased ability in the elderly to use complex cues. Event-related potentials were very different for the young and the old. In the young, P3 amplitudes were larger on trials where the rule that governed the location of the target became evident; this was interpreted as an effect of memory updating. Enhanced positive Slow Wave amplitude indicated uncertainty in random search conditions. Elderly subjects' P3 and SW, however, seemed unrelated to behavioral performance, and they showed a large negative Slow Wave at central and parietal sites to randomly located targets. The latter finding was tentatively interpreted as a sign of increased effort in the elderly to allocate attention in visual space. This pattern of behavioral and ERP results suggests that age-related differences in search tasks can be understood in terms of changes in the strategy of allocating visual attention.

How happy is your web browsing? A model to quantify satisfaction of an Internet user searching for desired information

NASA Astrophysics Data System (ADS)

Banerji, Anirban; Magarkar, Aniket

2012-09-01

We feel happy when web browsing operations provide us with necessary information; otherwise, we feel bitter. How to measure this happiness (or bitterness)? How does the profile of happiness grow and decay during the course of web browsing? We propose a probabilistic framework that models the evolution of user satisfaction, on top of his/her continuous frustration at not finding the required information. It is found that the cumulative satisfaction profile of a web-searching individual can be modeled effectively as the sum of a random number of random terms, where each term is a mutually independent random variable, originating from ‘memoryless’ Poisson flow. Evolution of satisfaction over the entire time interval of a user’s browsing was modeled using auto-correlation analysis. A utilitarian marker, a magnitude of greater than unity of which describes happy web-searching operations, and an empirical limit that connects user’s satisfaction with his frustration level-are proposed too. The presence of pertinent information in the very first page of a website and magnitude of the decay parameter of user satisfaction (frustration, irritation etc.) are found to be two key aspects that dominate the web user’s psychology. The proposed model employed different combinations of decay parameter, searching time and number of helpful websites. The obtained results are found to match the results from three real-life case studies.

Mandibular single-implant overdentures: a review with surgical and prosthodontic perspectives of a novel approach.

PubMed

Alsabeeha, Nabeel; Payne, Alan G T; De Silva, Rohana K; Swain, Michael V

2009-04-01

To review the literature on mandibular single-implant overdentures (opposing complete maxillary dentures), and present surgical and prosthodontic perspectives of a novel approach for this treatment option. An electronic search through the databases of Pubmed, Embase and Medline using the linked key words 'mandibular single implant overdentures' was performed. The search was limited to English language articles published up to August 2008. Hand searches through articles retrieved from the electronic search, peer-reviewed journals and recent conference proceedings were also conducted. A limited number of reports were identified on mandibular single-implant overdentures (opposing maxillary complete dentures). They comprised of case-series reports, short-term prospective trials and current randomized-controlled clinical trials. Different loading protocols with different implant systems have been used, but always with regular diameter implants. Specific anatomical and vascular dangers of the mandibular midline symphysis are identified including a novel surgical approach using a currently available short, wide diameter tapered implant. In addition, the prosthodontic rationale for using a larger attachment system (incorporating a platform switch) for mandibular single-implant overdentures is described. The review reveals that there is a lack of published randomized clinical trials using mandibular single-implant overdentures, opposing maxillary complete dentures. Without the evidence from randomized clinical trials, routine use of this novel approach cannot be recommended, compared with using regular diameter implants and matching attachment systems.

The ecology of parasites of freshwater fishes: the search for patterns.

PubMed

Kennedy, C R

2009-10-01

Developments in the study of the ecology of helminth parasites of freshwater fishes over the last half century are reviewed. Most research has of necessity been field based and has involved the search for patterns in population and community dynamics that are repeatable in space and time. Mathematical models predict that under certain conditions host and parasite populations can attain equilibrial levels through operation of regulatory factors. Such factors have been identified in several host-parasite systems and some parasite populations have been shown to persist over long time-periods. However, there is no convincing evidence that fish parasite populations are stable and regulated since in all cases alternative explanations are equally acceptable and it appears that they are non-equilibrial systems. It has proved particularly difficult to detect replicable patterns in parasite communities. Inter-specific competition, evidenced by functional and numerical responses, has been detected in several communities but its occurrence is erratic and its significance unclear. Some studies have failed to find any nested patterns in parasite community structure and richness, whereas others have identified such patterns although they are seldom constant over space and time. Departures from randomness appear to be the exception and then only temporary. It appears that parasite communities are non-equilibrial, stochastic assemblages rather than structured and organized.

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

PubMed Central

Kurcinski, Mateusz; Jamroz, Michal; Blaszczyk, Maciej; Kolinski, Andrzej; Kmiecik, Sebastian

2015-01-01

Protein–peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein–peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein–peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock. PMID:25943545

Meta-analysis of laparoscopic versus open repair of perforated peptic ulcer.

PubMed

Antoniou, Stavros A; Antoniou, George A; Koch, Oliver O; Pointner, Rudolph; Granderath, Frank A

2013-01-01

Laparoscopic treatment of perforated peptic ulcer (PPU) has been introduced as an alternative procedure to open surgery. It has been postulated that the minimally invasive approach involves less operative stress and results in decreased morbidity and mortality. We conducted a meta-analysis of randomized trials to test this hypothesis. Medline, EMBASE, and the Cochrane Central Register of Randomized Trials databases were searched, with no date or language restrictions. Our literature search identified 4 randomized trials, with a cumulative number of 289 patients, that compared the laparoscopic approach with open sutured repair of perforated ulcer. Analysis of outcomes did not favor either approach in terms of morbidity, mortality, and reoperation rate, although odds ratios seemed to consistently support the laparoscopic approach. Results did not determine the comparative efficiency and safety of laparoscopic or open approach for PPU. In view of an increased interest in the laparoscopic approach, further randomized trials are considered essential to determine the relative effectiveness of laparoscopic and open repair of PPU.

Meta-analysis of Laparoscopic Versus Open Repair of Perforated Peptic Ulcer

PubMed Central

Antoniou, George A.; Koch, Oliver O.; Pointner, Rudolph; Granderath, Frank A.

2013-01-01

Background and Objectives: Laparoscopic treatment of perforated peptic ulcer (PPU) has been introduced as an alternative procedure to open surgery. It has been postulated that the minimally invasive approach involves less operative stress and results in decreased morbidity and mortality. Methods: We conducted a meta-analysis of randomized trials to test this hypothesis. Medline, EMBASE, and the Cochrane Central Register of Randomized Trials databases were searched, with no date or language restrictions. Results: Our literature search identified 4 randomized trials, with a cumulative number of 289 patients, that compared the laparoscopic approach with open sutured repair of perforated ulcer. Analysis of outcomes did not favor either approach in terms of morbidity, mortality, and reoperation rate, although odds ratios seemed to consistently support the laparoscopic approach. Results did not determine the comparative efficiency and safety of laparoscopic or open approach for PPU. Conclusion: In view of an increased interest in the laparoscopic approach, further randomized trials are considered essential to determine the relative effectiveness of laparoscopic and open repair of PPU. PMID:23743368

Genetic Testing Registry

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

Computer-aided diagnosis of lung nodule using gradient tree boosting and Bayesian optimization.

PubMed

Nishio, Mizuho; Nishizawa, Mitsuo; Sugiyama, Osamu; Kojima, Ryosuke; Yakami, Masahiro; Kuroda, Tomohiro; Togashi, Kaori

2018-01-01

We aimed to evaluate a computer-aided diagnosis (CADx) system for lung nodule classification focussing on (i) usefulness of the conventional CADx system (hand-crafted imaging feature + machine learning algorithm), (ii) comparison between support vector machine (SVM) and gradient tree boosting (XGBoost) as machine learning algorithms, and (iii) effectiveness of parameter optimization using Bayesian optimization and random search. Data on 99 lung nodules (62 lung cancers and 37 benign lung nodules) were included from public databases of CT images. A variant of the local binary pattern was used for calculating a feature vector. SVM or XGBoost was trained using the feature vector and its corresponding label. Tree Parzen Estimator (TPE) was used as Bayesian optimization for parameters of SVM and XGBoost. Random search was done for comparison with TPE. Leave-one-out cross-validation was used for optimizing and evaluating the performance of our CADx system. Performance was evaluated using area under the curve (AUC) of receiver operating characteristic analysis. AUC was calculated 10 times, and its average was obtained. The best averaged AUC of SVM and XGBoost was 0.850 and 0.896, respectively; both were obtained using TPE. XGBoost was generally superior to SVM. Optimal parameters for achieving high AUC were obtained with fewer numbers of trials when using TPE, compared with random search. Bayesian optimization of SVM and XGBoost parameters was more efficient than random search. Based on observer study, AUC values of two board-certified radiologists were 0.898 and 0.822. The results show that diagnostic accuracy of our CADx system was comparable to that of radiologists with respect to classifying lung nodules.

Dynamical analysis of Grover's search algorithm in arbitrarily high-dimensional search spaces

NASA Astrophysics Data System (ADS)

Jin, Wenliang

2016-01-01

We discuss at length the dynamical behavior of Grover's search algorithm for which all the Walsh-Hadamard transformations contained in this algorithm are exposed to their respective random perturbations inducing the augmentation of the dimension of the search space. We give the concise and general mathematical formulations for approximately characterizing the maximum success probabilities of finding a unique desired state in a large unsorted database and their corresponding numbers of Grover iterations, which are applicable to the search spaces of arbitrary dimension and are used to answer a salient open problem posed by Grover (Phys Rev Lett 80:4329-4332, 1998).

Effectiveness of Azadirachta indica (neem) mouthrinse in plaque and gingivitis control: a systematic review.

PubMed

Dhingra, K; Vandana, K L

2017-02-01

The aim of this systematic review was to evaluate the effectiveness of Azadirachta indica (neem)-based herbal mouthrinse in improving plaque control and gingival health. Literature search was accomplished using electronic databases (PubMed, Cochrane Central Register of Controlled Trials and EMBASE) and manual searching, up to February 2015, for randomized controlled trials (RCTs) presenting clinical data for efficacy of neem mouthrinses when used alone or as an adjunct to mechanical oral hygiene as compared to chlorhexidine mouthrinses for controlling plaque and gingival inflammation in patients with gingivitis. Of the total 206 articles searched, three randomized controlled trials evaluating neem-based herbal mouthrinses were included. Due to marked heterogeneity observed in study characteristics, meta-analysis was not performed. These studies reported that neem mouthrinse was as effective as chlorhexidine mouthrinse when used as an adjunct to toothbrushing in reducing plaque and gingival inflammation in gingivitis patients. However, the quality of reporting and evidence along with methods of studies was generally flawed with unclear risk of bias. Despite the promising results shown in existing randomized controlled trials, the evidence concerning the clinical use of neem mouthrinses is lacking and needs further reinforcement with high-quality randomized controlled trials based on the reporting guidelines of herbal CONSORT statement. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Puzzle of magnetic moments of Ni clusters revisited using quantum Monte Carlo method.

PubMed

Lee, Hung-Wen; Chang, Chun-Ming; Hsing, Cheng-Rong

2017-02-28

The puzzle of the magnetic moments of small nickel clusters arises from the discrepancy between values predicted using density functional theory (DFT) and experimental measurements. Traditional DFT approaches underestimate the magnetic moments of nickel clusters. Two fundamental problems are associated with this puzzle, namely, calculating the exchange-correlation interaction accurately and determining the global minimum structures of the clusters. Theoretically, the two problems can be solved using quantum Monte Carlo (QMC) calculations and the ab initio random structure searching (AIRSS) method correspondingly. Therefore, we combined the fixed-moment AIRSS and QMC methods to investigate the magnetic properties of Ni n (n = 5-9) clusters. The spin moments of the diffusion Monte Carlo (DMC) ground states are higher than those of the Perdew-Burke-Ernzerhof ground states and, in the case of Ni 8-9 , two new ground-state structures have been discovered using the DMC calculations. The predicted results are closer to the experimental findings, unlike the results predicted in previous standard DFT studies.

National Center for Biotechnology Information

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

Speckle lithography for fabricating Gaussian, quasi-random 2D structures and black silicon structures.

PubMed

Bingi, Jayachandra; Murukeshan, Vadakke Matham

2015-12-18

Laser speckle pattern is a granular structure formed due to random coherent wavelet interference and generally considered as noise in optical systems including photolithography. Contrary to this, in this paper, we use the speckle pattern to generate predictable and controlled Gaussian random structures and quasi-random structures photo-lithographically. The random structures made using this proposed speckle lithography technique are quantified based on speckle statistics, radial distribution function (RDF) and fast Fourier transform (FFT). The control over the speckle size, density and speckle clustering facilitates the successful fabrication of black silicon with different surface structures. The controllability and tunability of randomness makes this technique a robust method for fabricating predictable 2D Gaussian random structures and black silicon structures. These structures can enhance the light trapping significantly in solar cells and hence enable improved energy harvesting. Further, this technique can enable efficient fabrication of disordered photonic structures and random media based devices.

Protein Loop Structure Prediction Using Conformational Space Annealing.

PubMed

Heo, Seungryong; Lee, Juyong; Joo, Keehyoung; Shin, Hang-Cheol; Lee, Jooyoung

2017-05-22

We have developed a protein loop structure prediction method by combining a new energy function, which we call E PLM (energy for protein loop modeling), with the conformational space annealing (CSA) global optimization algorithm. The energy function includes stereochemistry, dynamic fragment assembly, distance-scaled finite ideal gas reference (DFIRE), and generalized orientation- and distance-dependent terms. For the conformational search of loop structures, we used the CSA algorithm, which has been quite successful in dealing with various hard global optimization problems. We assessed the performance of E PLM with two widely used loop-decoy sets, Jacobson and RAPPER, and compared the results against the DFIRE potential. The accuracy of model selection from a pool of loop decoys as well as de novo loop modeling starting from randomly generated structures was examined separately. For the selection of a nativelike structure from a decoy set, E PLM was more accurate than DFIRE in the case of the Jacobson set and had similar accuracy in the case of the RAPPER set. In terms of sampling more nativelike loop structures, E PLM outperformed E DFIRE for both decoy sets. This new approach equipped with E PLM and CSA can serve as the state-of-the-art de novo loop modeling method.

Model of myosin node aggregation into a contractile ring: the effect of local alignment

NASA Astrophysics Data System (ADS)

Ojkic, Nikola; Wu, Jian-Qiu; Vavylonis, Dimitrios

2011-09-01

Actomyosin bundles frequently form through aggregation of membrane-bound myosin clusters. One such example is the formation of the contractile ring in fission yeast from a broad band of cortical nodes. Nodes are macromolecular complexes containing several dozens of myosin-II molecules and a few formin dimers. The condensation of a broad band of nodes into the contractile ring has been previously described by a search, capture, pull and release (SCPR) model. In SCPR, a random search process mediated by actin filaments nucleated by formins leads to transient actomyosin connections among nodes that pull one another into a ring. The SCPR model reproduces the transport of nodes over long distances and predicts observed clump-formation instabilities in mutants. However, the model does not generate transient linear elements and meshwork structures as observed in some wild-type and mutant cells during ring assembly. As a minimal model of node alignment, we added short-range aligning forces to the SCPR model representing currently unresolved mechanisms that may involve structural components, cross-linking and bundling proteins. We studied the effect of the local node alignment mechanism on ring formation numerically. We varied the new parameters and found viable rings for a realistic range of values. Morphologically, transient structures that form during ring assembly resemble those observed in experiments with wild-type and cdc25-22 cells. Our work supports a hierarchical process of ring self-organization involving components drawn together from distant parts of the cell followed by progressive stabilization.

Guiding Conformation Space Search with an All-Atom Energy Potential

PubMed Central

Brunette, TJ; Brock, Oliver

2009-01-01

The most significant impediment for protein structure prediction is the inadequacy of conformation space search. Conformation space is too large and the energy landscape too rugged for existing search methods to consistently find near-optimal minima. To alleviate this problem, we present model-based search, a novel conformation space search method. Model-based search uses highly accurate information obtained during search to build an approximate, partial model of the energy landscape. Model-based search aggregates information in the model as it progresses, and in turn uses this information to guide exploration towards regions most likely to contain a near-optimal minimum. We validate our method by predicting the structure of 32 proteins, ranging in length from 49 to 213 amino acids. Our results demonstrate that model-based search is more effective at finding low-energy conformations in high-dimensional conformation spaces than existing search methods. The reduction in energy translates into structure predictions of increased accuracy. PMID:18536015

Practices that minimize trauma to the genital tract in childbirth: a systematic review of the literature.

PubMed

Renfrew, M J; Hannah, W; Albers, L; Floyd, E

1998-09-01

Trauma to the genital tract commonly occurs at birth, and can cause short- and long-term morbidity. Clinical measures to reduce its occurrence have not been fully identified. A systematic review of the English language literature was conducted to describe the current state of knowledge on reduction of genital tract trauma before planning a large randomized controlled trial of ways to prevent such trauma. Randomized trials and other published reports were identified from relevant databases and hand searches. Studies were reviewed and assessed using a structured format. A total of 77 papers and chapters were identified and placed into 5 categories after critical review: 25 randomized trials, 4 meta-analyses, 4 prospective studies, 36 retrospective studies, and 8 descriptions of practice from textbooks. The available evidence is conclusive in favor of restricted use of episiotomy. The contribution of maternal characteristics and attitudes to intact perineum has not been investigated. Several other topics warrant further study, including maternal position, style of pushing, and antenatal perineal massage. Strong opinions and sparse data exist regarding the role of hand maneuvers by the birth attendant for perineal management and birth of the baby. This became the topic of the planned randomized controlled trial, which was completed; results will be published soon. The case for restricting the use of episiotomy is conclusive. Several other clinical factors warrant investigation, including the role of hand maneuvers by the birth attendant in preventing birth trauma. A large randomized controlled trial will report on this topic.

Assessing quality of reports on randomized clinical trials in nursing journals.

PubMed

Parent, Nicole; Hanley, James A

2009-01-01

Several surveys have presented the quality of reports on randomized clinical trials (RCTs) published in general and specialty medical journals. The aim of these surveys was to raise scientific consciousness on methodological aspects pertaining to internal and external validity. These reviews have suggested that the methodological quality could be improved. We conducted a survey of reports on RCTs published in nursing journals to assess their methodological quality. The features we considered included sample size, flow of participants, assessment of baseline comparability, randomization, blinding, and statistical analysis. We collected data from all reports of RCTs published between January 1994 and December 1997 in Applied Nursing Research, Heart & Lung and Nursing Research. We hand-searched the journals and included all 54 articles in which authors reported that individuals have been randomly allocated to distinct groups. We collected data using a condensed form of the Consolidated Standards of Reporting Trials (CONSORT) statement for structured reporting of RCTs (Begg et al., 1996). Sample size calculations were included in only 22% of the reports. Only 48% of the reports provided information about the type of randomization, and a mere 22% described blinding strategies. Comparisons of baseline characteristics using hypothesis tests were abusively produced in more than 76% of the reports. Excessive use and unstructured reports of significance testing were common (59%), and all reports failed to provide magnitude of treatment differences with confidence intervals. Better methodological quality in reports of RCTs will contribute to increase the standards of nursing research.

SPIN or LURCH : a Comparative Assessment of Model Checking and Stochastic Search for Temporal Properties in Procedural Code

NASA Technical Reports Server (NTRS)

Powell, John D.; Owens, David; Menzies, Tim

2004-01-01

The difficulty of how to test large systems, such as the one on board a NASA robotic remote explorer (RRE) vehicle, is fundamentally a search issue: the global state space representing all possible has yet to be solved, even after many decades of work. Randomized algorithms have been known to outperform their deterministic counterparts for search problems representing a wide range of applications. In the case study presented here, the LURCH randomized algorithm proved to be adequate to the task of testing a NASA RRE vehicle. LURCH found all the errors found by an earlier analysis of a more complete method (SPIN). Our empirical results are that LURCH can scale to much larger models than standard model checkers like SMV and SPIN. Further, the LURCH analysis was simpler than the SPIN analysis. The simplicity and scalability of LURCH are two compelling reasons for experimenting further with this tool.

Modification Site Localization in Peptides.

PubMed

Chalkley, Robert J

2016-01-01

There are a large number of search engines designed to take mass spectrometry fragmentation spectra and match them to peptides from proteins in a database. These peptides could be unmodified, but they could also bear modifications that were added biologically or during sample preparation. As a measure of reliability for the peptide identification, software normally calculates how likely a given quality of match could have been achieved at random, most commonly through the use of target-decoy database searching (Elias and Gygi, Nat Methods 4(3): 207-214, 2007). Matching the correct peptide but with the wrong modification localization is not a random match, so results with this error will normally still be assessed as reliable identifications by the search engine. Hence, an extra step is required to determine site localization reliability, and the software approaches to measure this are the subject of this part of the chapter.

Encounter times of chromatin loci influenced by polymer decondensation

NASA Astrophysics Data System (ADS)

Amitai, A.; Holcman, D.

2018-03-01

The time for a DNA sequence to find its homologous counterpart depends on a long random search inside the cell nucleus. Using polymer models, we compute here the mean first encounter time (MFET) between two sites located on two different polymer chains and confined locally by potential wells. We find that reducing tethering forces acting on the polymers results in local decondensation, and numerical simulations of the polymer model show that these changes are associated with a reduction of the MFET by several orders of magnitude. We derive here new asymptotic formula for the MFET, confirmed by Brownian simulations. We conclude from the present modeling approach that the fast search for homology is mediated by a local chromatin decondensation due to the release of multiple chromatin tethering forces. The present scenario could explain how the homologous recombination pathway for double-stranded DNA repair is controlled by its random search step.

Crystal structure and genetic modifications of FI-CMCase from Aspergillus aculeatus F-50.

PubMed

Huang, Jian-Wen; Liu, Weidong; Lai, Hui-Lin; Cheng, Ya-Shan; Zheng, Yingying; Li, Qian; Sun, Hong; Kuo, Chih-Jung; Guo, Rey-Ting; Chen, Chun-Chi

2016-09-16

Cellulose is the major component of the plant cell wall and the most abundant renewable biomass on earth, and its decomposition has proven to be very useful in many commercial applications. Endo-1,4-β-d-glucanase (EC 3.2.1.4; endoglucanase), which catalyzes the random hydrolysis of 1,4-β-glycosidic bonds of the cellulose main chain to cleave cellulose into smaller fragments, is the key cellulolytic enzyme. An endoglucanase isolated from Aspergillus aculeatus F-50 (FI-CMCase), which is classified into the glycoside hydrolase (GH) family 12, was demonstrated to be effectively expressed in the industrial strain Pichia pastoris. Here, the crystal structure and complex structures of P. pastoris-expressed FI-CMCase were solved to high resolution. The overall structure is analyzed and compared to other GH12 members. In addition, the substrate-surrounding residues were engineered to search for variants with improved enzymatic activity. Among 14 mutants constructed, one with two-fold increase in protein expression was identified, which possesses a potential to be further developed as a commercial enzyme product. Copyright © 2016 Elsevier Inc. All rights reserved.

Notes on Search, Detection and Localization Modeling. Revision 4

DTIC Science & Technology

1990-10-01

2, --- , k where the subregions are relabeled so that the following order relation holds: pi/6 1 > p 2!6 2 > ... > pr65 and where k is chosen so... Interfaces ," Operations Research, Vol. 19, No.3, pp 559-586, 1971. 15. Coggins, P.B., "Detection Probability Computations for Random Search of an

Transtheoretical Model-Based Dietary Interventions in Primary Care: A Review of the Evidence in Diabetes

ERIC Educational Resources Information Center

Salmela, Sanna; Poskiparta, Marita; Kasila, Kirsti; Vahasarja, Kati; Vanhala, Mauno

2009-01-01

The objective of this study was to review the evidence concerning stage-based dietary interventions in primary care among persons with diabetes or an elevated diabetes risk. Search strategies were electronic databases and manual search. Selection criteria were randomized controlled studies with stage-based dietary intervention, conducted in…

Statistical signatures of a targeted search by bacteria

NASA Astrophysics Data System (ADS)

Jashnsaz, Hossein; Anderson, Gregory G.; Pressé, Steve

2017-12-01

Chemoattractant gradients are rarely well-controlled in nature and recent attention has turned to bacterial chemotaxis toward typical bacterial food sources such as food patches or even bacterial prey. In environments with localized food sources reminiscent of a bacterium’s natural habitat, striking phenomena—such as the volcano effect or banding—have been predicted or expected to emerge from chemotactic models. However, in practice, from limited bacterial trajectory data it is difficult to distinguish targeted searches from an untargeted search strategy for food sources. Here we use a theoretical model to identify statistical signatures of a targeted search toward point food sources, such as prey. Our model is constructed on the basis that bacteria use temporal comparisons to bias their random walk, exhibit finite memory and are subject to random (Brownian) motion as well as signaling noise. The advantage with using a stochastic model-based approach is that a stochastic model may be parametrized from individual stochastic bacterial trajectories but may then be used to generate a very large number of simulated trajectories to explore average behaviors obtained from stochastic search strategies. For example, our model predicts that a bacterium’s diffusion coefficient increases as it approaches the point source and that, in the presence of multiple sources, bacteria may take substantially longer to locate their first source giving the impression of an untargeted search strategy.

Identification of the ideal clutter metric to predict time dependence of human visual search

NASA Astrophysics Data System (ADS)

Cartier, Joan F.; Hsu, David H.

1995-05-01

The Army Night Vision and Electronic Sensors Directorate (NVESD) has recently performed a human perception experiment in which eye tracker measurements were made on trained military observers searching for targets in infrared images. This data offered an important opportunity to evaluate a new technique for search modeling. Following the approach taken by Jeff Nicoll, this model treats search as a random walk in which the observers are in one of two states until they quit: they are either searching, or they are wandering around looking for a point of interest. When wandering they skip rapidly from point to point. When examining they move more slowly, reflecting the fact that target discrimination requires additional thought processes. In this paper we simulate the random walk, using a clutter metric to assign relative attractiveness to points of interest within the image which are competing for the observer's attention. The NVESD data indicates that a number of standard clutter metrics are good estimators of the apportionment of observer's time between wandering and examining. Conversely, the apportionment of observer time spent wandering and examining could be used to reverse engineer the ideal clutter metric which would most perfectly describe the behavior of the group of observers. It may be possible to use this technique to design the optimal clutter metric to predict performance of visual search.

Optimum Parameters of a Tuned Liquid Column Damper in a Wind Turbine Subject to Stochastic Load

NASA Astrophysics Data System (ADS)

Alkmim, M. H.; de Morais, M. V. G.; Fabro, A. T.

2017-12-01

Parameter optimization for tuned liquid column dampers (TLCD), a class of passive structural control, have been previously proposed in the literature for reducing vibration in wind turbines, and several other applications. However, most of the available work consider the wind excitation as either a deterministic harmonic load or random load with white noise spectra. In this paper, a global direct search optimization algorithm to reduce vibration of a tuned liquid column damper (TLCD), a class of passive structural control device, is presented. The objective is to find optimized parameters for the TLCD under stochastic load from different wind power spectral density. A verification is made considering the analytical solution of undamped primary system under white noise excitation by comparing with result from the literature. Finally, it is shown that different wind profiles can significantly affect the optimum TLCD parameters.

Invariant spatial context is learned but not retrieved in gaze-contingent tunnel-view search.

PubMed

Zang, Xuelian; Jia, Lina; Müller, Hermann J; Shi, Zhuanghua

2015-05-01

Our visual brain is remarkable in extracting invariant properties from the noisy environment, guiding selection of where to look and what to identify. However, how the brain achieves this is still poorly understood. Here we explore interactions of local context and global structure in the long-term learning and retrieval of invariant display properties. Participants searched for a target among distractors, without knowing that some "old" configurations were presented repeatedly (randomly inserted among "new" configurations). We simulated tunnel vision, limiting the visible region around fixation. Robust facilitation of performance for old versus new contexts was observed when the visible region was large but not when it was small. However, once the display was made fully visible during the subsequent transfer phase, facilitation did become manifest. Furthermore, when participants were given a brief preview of the total display layout prior to tunnel view search with 2 items visible, facilitation was already obtained during the learning phase. The eye movement results revealed contextual facilitation to be coupled with changes of saccadic planning, characterized by slightly extended gaze durations but a reduced number of fixations and shortened scan paths for old displays. Taken together, our findings show that invariant spatial display properties can be acquired based on scarce, para-/foveal information, while their effective retrieval for search guidance requires the availability (even if brief) of a certain extent of peripheral information. (c) 2015 APA, all rights reserved).

Educational and Skills-Based Interventions to Prevent Relationship Violence in Young People

ERIC Educational Resources Information Center

Fellmeth, Gracia; Heffernan, Catherine; Nurse, Joanna; Habibula, Shakiba; Sethi, Dinesh

2015-01-01

Objectives: To assess the efficacy of educational and skills-based interventions to prevent relationship and dating violence in adolescents and young adults. Methods: We searched Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, CINAHL, PsycINFO, and other databases for randomized, cluster-randomized, and quasi-randomized…

Randomization Methods in Emergency Setting Trials: A Descriptive Review

ERIC Educational Resources Information Center

Corbett, Mark Stephen; Moe-Byrne, Thirimon; Oddie, Sam; McGuire, William

2016-01-01

Background: Quasi-randomization might expedite recruitment into trials in emergency care settings but may also introduce selection bias. Methods: We searched the Cochrane Library and other databases for systematic reviews of interventions in emergency medicine or urgent care settings. We assessed selection bias (baseline imbalances) in prognostic…

A study to enhance clinical end-user MEDLINE search skills: design and baseline findings.

PubMed

McKibbon, K A; Haynes, R B; Johnston, M E; Walker, C J

1991-01-01

To determine if a preceptor and timely, individualized feedback improves the performance of physicians in searching MEDLINE using GRATEFUL MED in clinical settings. Randomized controlled trial. A 300 bed primary to tertiary care teaching hospital. Computers were installed in wards and clinics of 6 major clinical services, and the emergency room, intensive care and neonatal intensive care units. All physicians and physicians-in-training from the departments of Medicine, Family Medicine, Surgery, Psychiatry, Pediatrics, and Obstetrics and Gynecology were included if they made patient care decisions for at least 8 weeks during the study period. All participants were given a 1-hour training class and 1 hour of individualized searching with 1 of the 2 study librarians. After training, participants were randomized to a control group who received no further intervention or to an intervention group in which each person chose a clinical preceptor experienced in MEDLINE searching and received individualized feedback by a study librarian on their first 10 searches, indicating search quality and providing suggestions for improvement. Feedback was mailed the first week day after the search was done. Baseline characteristics by study group, department and level of training, study participation rates, and searching rates. 308 of 392 eligible physicians joined the study. Participation was almost 80% with some variation by department and level of training. Excellent balance in the baseline characteristics was achieved for the 2 groups, as well as for the number who did first searches. Intervention group participants searched MEDLINE more often than did controls (3.5 searches per month vs 2.5 per month for controls, P = 0.046). The recall and precision for first searches for both groups was significantly less than that of librarians. The analysis of study data will be completed by September 1991. Clinicians are willing to do self-service searching of MEDLINE in clinical settings but their precision and recall are less than a trained librarian at baseline. Search skills enhancements are needed and the effect of feedback and preceptors is being tested. U.S. National Library of Medicine and Ontario Ministry of Health.

Mitral Valve Clip for Treatment of Mitral Regurgitation: An Evidence-Based Analysis

PubMed Central

Ansari, Mohammed T.; Ahmadzai, Nadera; Coyle, Kathryn; Coyle, Doug; Moher, David

2015-01-01

Background Many of the 500,000 North American patients with chronic mitral regurgitation may be poor candidates for mitral valve surgery. Objective The objective of this study was to investigate the comparative effectiveness, harms, and cost-effectiveness of percutaneous mitral valve repair using mitral valve clips in candidates at prohibitive risk for surgery. Data Sources We searched articles in MEDLINE, Embase, and the Cochrane Library published from 1994 to February 2014 for evidence of effectiveness and harms; for economic literature we also searched NHS EED and Tufts CEA registry. Grey literature was also searched. Review Methods Primary studies were sought from existing systematic reviews that had employed reliable search and screening methods. Newer studies were sought by searching the period subsequent to the last search date of the review. Two reviewers screened records and assessed study validity. We used the Cochrane risk of bias tool for randomized, generic assessment for non-randomized studies, and the Phillips checklist for economic studies. Results Ten studies including 1 randomized trial were included. The majority of the direct comparative evidence compared the mitral valve clip repair with surgery in patients not particularly at prohibitive surgical risk. Irrespective of degenerative or functional chronic mitral regurgitation etiology, evidence of effectiveness and harms is inconclusive and of very low quality. Very-low-quality evidence indicates that percutaneous mitral valve clip repair may provide a survival advantage, at least during the first 1 to 2 years, particularly in medically managed chronic functional mitral regurgitation. Because of limitations in the design of studies, the cost-effectiveness of mitral valve clips in patients at prohibitive risk for surgery also could not be established. Limitations Because of serious concerns of risk of bias, indirectness, and imprecision, evidence is of very low quality. Conclusions No meaningful conclusions can be drawn about the comparative effectiveness, harms, and cost-effectiveness of mitral valve clips in the population with chronic mitral regurgitation who are at prohibitive risk for surgery. PMID:26379810

Non-random dispersal in the butterfly Maniola jurtina: implications for metapopulation models.

PubMed Central

Conradt, L; Bodsworth, E J; Roper, T J; Thomas, C D

2000-01-01

The dispersal patterns of animals are important in metapopulation ecology because they affect the dynamics and survival of populations. Theoretical models assume random dispersal but little is known in practice about the dispersal behaviour of individual animals or the strategy by which dispersers locate distant habitat patches. In the present study, we released individual meadow brown butterflies (Maniola jurtina) in a non-habitat and investigated their ability to return to a suitable habitat. The results provided three reasons for supposing that meadow brown butterflies do not seek habitat by means of random flight. First, when released within the range of their normal dispersal distances, the butterflies orientated towards suitable habitat at a higher rate than expected at random. Second, when released at larger distances from their habitat, they used a non-random, systematic, search strategy in which they flew in loops around the release point and returned periodically to it. Third, butterflies returned to a familiar habitat patch rather than a non-familiar one when given a choice. If dispersers actively orientate towards or search systematically for distant habitat, this may be problematic for existing metapopulation models, including models of the evolution of dispersal rates in metapopulations. PMID:11007325

Speckle lithography for fabricating Gaussian, quasi-random 2D structures and black silicon structures

PubMed Central

Bingi, Jayachandra; Murukeshan, Vadakke Matham

2015-01-01

Laser speckle pattern is a granular structure formed due to random coherent wavelet interference and generally considered as noise in optical systems including photolithography. Contrary to this, in this paper, we use the speckle pattern to generate predictable and controlled Gaussian random structures and quasi-random structures photo-lithographically. The random structures made using this proposed speckle lithography technique are quantified based on speckle statistics, radial distribution function (RDF) and fast Fourier transform (FFT). The control over the speckle size, density and speckle clustering facilitates the successful fabrication of black silicon with different surface structures. The controllability and tunability of randomness makes this technique a robust method for fabricating predictable 2D Gaussian random structures and black silicon structures. These structures can enhance the light trapping significantly in solar cells and hence enable improved energy harvesting. Further, this technique can enable efficient fabrication of disordered photonic structures and random media based devices. PMID:26679513

Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia.

PubMed

Ertl, Peter; Patiny, Luc; Sander, Thomas; Rufener, Christian; Zasso, Michaël

2015-01-01

Wikipedia, the world's largest and most popular encyclopedia is an indispensable source of chemistry information. It contains among others also entries for over 15,000 chemicals including metabolites, drugs, agrochemicals and industrial chemicals. To provide an easy access to this wealth of information we decided to develop a substructure and similarity search tool for chemical structures referenced in Wikipedia. We extracted chemical structures from entries in Wikipedia and implemented a web system allowing structure and similarity searching on these data. The whole search as well as visualization system is written in JavaScript and therefore can run locally within a web page and does not require a central server. The Wikipedia Chemical Structure Explorer is accessible on-line at www.cheminfo.org/wikipedia and is available also as an open source project from GitHub for local installation. The web-based Wikipedia Chemical Structure Explorer provides a useful resource for research as well as for chemical education enabling both researchers and students easy and user friendly chemistry searching and identification of relevant information in Wikipedia. The tool can also help to improve quality of chemical entries in Wikipedia by providing potential contributors regularly updated list of entries with problematic structures. And last but not least this search system is a nice example of how the modern web technology can be applied in the field of cheminformatics. Graphical abstractWikipedia Chemical Structure Explorer allows substructure and similarity searches on molecules referenced in Wikipedia.

Corticosteroids as adjuvant therapy for ocular toxoplasmosis.

PubMed

Jasper, Smitha; Vedula, Satyanarayana S; John, Sheeja S; Horo, Saban; Sepah, Yasir J; Nguyen, Quan Dong

2017-01-26

Ocular infection caused by Toxoplasma gondii, a parasite, may result in inflammation in the retina, choroid, and uvea, and consequently lead to complications such as glaucoma, cataract, and posterior synechiae. The objective of this systematic review was to assess the effects of adjunctive use of corticosteroids to anti-parasitic therapy versus anti-parasitic therapy alone for ocular toxoplasmosis. We searched CENTRAL (which contains the Cochrane Eyes and Vision Trials Register (2016; Issue 11)), MEDLINE Ovid, Epub Ahead of Print, In-Process & Other Non-Indexed Citations, MEDLINE Ovid Daily (January 1946 to December 2016), Embase (January 1980 to December 2016), Latin American and Caribbean Literature on Health Sciences (LILACS (January 1982 to December 2016)), the ISRCTN registry (www.isrctn.com/editAdvancedSearch), ClinicalTrials.gov (www.clinicaltrials.gov), and the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP; www.who.int/ictrp/search/en). We used no date or language restrictions in the electronic searches for trials. We last searched the electronic databases on 7 December 2016. We had planned to include randomized and quasi-randomized controlled trials. Eligible trials would have enrolled participants of any age who were immunocompetent and were diagnosed with acute ocular toxoplasmosis. Included trials would have compared anti-parasitic therapy plus corticosteroids versus anti-parasitic therapy alone, different doses or times of initiation of corticosteroids. Two authors independently screened titles and abstracts retrieved through the electronic searches. We retrieved full-text reports of studies categorized as 'unsure' or 'include' after we reviewed the abstracts. Two authors independently reviewed each full-text report for eligibility. Discrepancies were resolved through discussion. We identified no completed or ongoing trial that was eligible for this Cochrane review. Although research has identified a wide variation in practice regarding the use of corticosteroids, our review did not identify any evidence from randomized controlled trials for or against the role of corticosteroids in the management of ocular toxoplasmosis. Several questions remain unanswered by well-conducted randomized trials in this context, including whether the use of corticosteroids as an adjunctive agent is more effective than the use of anti-parasitic therapy alone; if so, when corticosteroids should be initiated in the treatment regimen (early versus late course of treatment), and what would be the best dose and duration of steroid use.

Enhanced Recovery After Surgery (ERAS®) in Individuals with Diabetes: A Systematic Review.

PubMed

Albalawi, Zaina; Laffin, Michael; Gramlich, Leah; Senior, Peter; McAlister, Finlay A

2017-08-01

Prevalence of diabetes in surgical patients is 10-40%. It is well recognized that they have higher rates of complications, and longer stays in hospital compared to patients without diabetes. Enhanced recovery after surgery (ERAS) is an evidence-based multimodal surgical care pathway that improves postoperative complications and length of stay in patients without diabetes. This review evaluates the evidence on whether individuals with diabetes would benefit from ERAS implementation. MEDLINE, Cochrane Central Register of Controlled Trials (CENTRAL) and EMBASE searched with no language restrictions applied. Conference proceedings and bibliographies were reviewed. Experts in the field were contacted, and www.clinicaltrials.gov searched for ongoing trials. Randomized controlled trials (RCT) looking at individuals with diabetes undergoing surgery randomized to ERAS ® or conventional care. Non-randomized controlled trials, controlled before-after studies, interrupted time series, and cohort studies with concurrent controls were also considered. Two authors independently screened studies. The electronic search yielded 437 references. After removing duplicates, 376 were screened for eligibility. Conference proceedings and bibliographies identified additional references. Searching www.clinicaltrials.gov yielded 59 references. Contacting experts in the field identified no further studies. Fourteen full articles were assessed and subsequently excluded for the following reasons: used an intervention other than ERAS ® , did not include patients with diabetes, or used an uncontrolled observational design. To date, the effects of ERAS ® on patients with diabetes have not been rigorously evaluated. This review highlights the lack of evidence in this area and provides guidance on design for future studies.

Optimization and universality of Brownian search in a basic model of quenched heterogeneous media

NASA Astrophysics Data System (ADS)

Godec, Aljaž; Metzler, Ralf

2015-05-01

The kinetics of a variety of transport-controlled processes can be reduced to the problem of determining the mean time needed to arrive at a given location for the first time, the so-called mean first-passage time (MFPT) problem. The occurrence of occasional large jumps or intermittent patterns combining various types of motion are known to outperform the standard random walk with respect to the MFPT, by reducing oversampling of space. Here we show that a regular but spatially heterogeneous random walk can significantly and universally enhance the search in any spatial dimension. In a generic minimal model we consider a spherically symmetric system comprising two concentric regions with piecewise constant diffusivity. The MFPT is analyzed under the constraint of conserved average dynamics, that is, the spatially averaged diffusivity is kept constant. Our analytical calculations and extensive numerical simulations demonstrate the existence of an optimal heterogeneity minimizing the MFPT to the target. We prove that the MFPT for a random walk is completely dominated by what we term direct trajectories towards the target and reveal a remarkable universality of the spatially heterogeneous search with respect to target size and system dimensionality. In contrast to intermittent strategies, which are most profitable in low spatial dimensions, the spatially inhomogeneous search performs best in higher dimensions. Discussing our results alongside recent experiments on single-particle tracking in living cells, we argue that the observed spatial heterogeneity may be beneficial for cellular signaling processes.

Exploration Opportunity Search of Near-earth Objects Based on Analytical Gradients

NASA Astrophysics Data System (ADS)

Ren, Yuan; Cui, Ping-Yuan; Luan, En-Jie

2008-07-01

The problem of search of opportunity for the exploration of near-earth minor objects is investigated. For rendezvous missions, the analytical gradients of the performance index with respect to the free parameters are derived using the variational calculus and the theory of state-transition matrix. After generating randomly some initial guesses in the search space, the performance index is optimized, guided by the analytical gradients, leading to the local minimum points representing the potential launch opportunities. This method not only keeps the global-search property of the traditional method, but also avoids the blindness in the latter, thereby increasing greatly the computing speed. Furthermore, with this method, the searching precision could be controlled effectively.

The Role of Search Speed in the Contextual Cueing of Children's Attention.

PubMed

Darby, Kevin; Burling, Joseph; Yoshida, Hanako

2014-01-01

The contextual cueing effect is a robust phenomenon in which repeated exposure to the same arrangement of random elements guides attention to relevant information by constraining search. The effect is measured using an object search task in which a target (e.g., the letter T) is located within repeated or nonrepeated visual contexts (e.g., configurations of the letter L). Decreasing response times for the repeated configurations indicates that contextual information has facilitated search. Although the effect is robust among adult participants, recent attempts to document the effect in children have yielded mixed results. We examined the effect of search speed on contextual cueing with school-aged children, comparing three types of stimuli that promote different search times in order to observe how speed modulates this effect. Reliable effects of search time were found, suggesting that visual search speed uniquely constrains the role of attention toward contextually cued information.

The Role of Search Speed in the Contextual Cueing of Children’s Attention

PubMed Central

Darby, Kevin; Burling, Joseph; Yoshida, Hanako

2013-01-01

The contextual cueing effect is a robust phenomenon in which repeated exposure to the same arrangement of random elements guides attention to relevant information by constraining search. The effect is measured using an object search task in which a target (e.g., the letter T) is located within repeated or nonrepeated visual contexts (e.g., configurations of the letter L). Decreasing response times for the repeated configurations indicates that contextual information has facilitated search. Although the effect is robust among adult participants, recent attempts to document the effect in children have yielded mixed results. We examined the effect of search speed on contextual cueing with school-aged children, comparing three types of stimuli that promote different search times in order to observe how speed modulates this effect. Reliable effects of search time were found, suggesting that visual search speed uniquely constrains the role of attention toward contextually cued information. PMID:24505167

Effects of Physical Exercise Combined with Nutritional Supplements on Aging Brain Related Structures and Functions: A Systematic Review

PubMed Central

Schättin, Alexandra; Baur, Kilian; Stutz, Jan; Wolf, Peter; de Bruin, Eling D.

2016-01-01

Age-related decline in gray and white brain matter goes together with cognitive depletion. To influence cognitive functioning in elderly, several types of physical exercise and nutritional intervention have been performed. This paper systematically reviews the potential additive and complementary effects of nutrition/nutritional supplements and physical exercise on cognition. The search strategy was developed for EMBASE, Medline, PubMed, Cochrane, CINAHL, and PsycInfo databases and focused on the research question: “Is the combination of physical exercise with nutrition/nutritional supplementation more effective than nutrition/nutritional supplementation or physical exercise alone in effecting on brain structure, metabolism, and/or function?” Both mammalian and human studies were included. In humans, randomized controlled trials that evaluated the effects of nutrition/nutritional supplements and physical exercise on cognitive functioning and associated parameters in healthy elderly (>65 years) were included. The systematic search included English and German language literature without any limitation of publication date. The search strategy yielded a total of 3129 references of which 67 studies met the inclusion criteria; 43 human and 24 mammalian, mainly rodent, studies. Three out of 43 human studies investigated a nutrition/physical exercise combination and reported no additive effects. In rodent studies, additive effects were found for docosahexaenoic acid supplementation when combined with physical exercise. Although feasible combinations of physical exercise/nutritional supplements are available for influencing the brain, only a few studies evaluated which possible combinations of nutrition/nutritional supplementation and physical exercise might have an effect on brain structure, metabolism and/or function. The reason for no clear effects of combinatory approaches in humans might be explained by the misfit between the combinations of nutritional methods with the physical interventions in the sense that they were not selected on sharing of similar neuronal mechanisms. Based on the results from this systematic review, future human studies should focus on the combined effect of docosahexaenoic acid supplementation and physical exercise that contains elements of (motor) learning. PMID:27458371

Connectivity is a Poor Indicator of Fast Quantum Search

NASA Astrophysics Data System (ADS)

Meyer, David A.; Wong, Thomas G.

2015-03-01

A randomly walking quantum particle evolving by Schrödinger's equation searches on d -dimensional cubic lattices in O (√{N }) time when d ≥5 , and with progressively slower runtime as d decreases. This suggests that graph connectivity (including vertex, edge, algebraic, and normalized algebraic connectivities) is an indicator of fast quantum search, a belief supported by fast quantum search on complete graphs, strongly regular graphs, and hypercubes, all of which are highly connected. In this Letter, we show this intuition to be false by giving two examples of graphs for which the opposite holds true: one with low connectivity but fast search, and one with high connectivity but slow search. The second example is a novel two-stage quantum walk algorithm in which the walking rate must be adjusted to yield high search probability.

Development and Testing of a New Area Search Model with Partially Overlapping Target and Searcher Patrol Areas

DTIC Science & Technology

2008-12-01

1, /(2 ) T T VR A t A VR f t t F t VRt A t A VR t A VR ∈⎧ = ⎨ ⎩ <⎧ ⎪= ∈⎨ ⎪ >⎩ (2) The mean time to detection is given by...follows: Exhaustive Search (Black line): ( ) (2 ) /T sF t VRt A= . Random Search (Pink line): 2( ) 1 (1 / ) exp( 2 / )T s sF t R A RVt Aπ

Found and Missed: Failing to Recognize a Search Target despite Moving It

ERIC Educational Resources Information Center

Solman, Grayden J. F.; Cheyne, J. Allan; Smilek, Daniel

2012-01-01

We present results from five search experiments using a novel "unpacking" paradigm in which participants use a mouse to sort through random heaps of distractors to locate the target. We report that during this task participants often fail to recognize the target despite moving it, and despite having looked at the item. Additionally, the missed…

The Effect of Altering the Context Clues in Prose on Reading Rate in a Search Task

ERIC Educational Resources Information Center

Coke, Esther U.

1977-01-01

To determine whether the connectedness of prose passages had any effect on the behavior of readers who searched for information in the passages, the behavior of readers who saw the normal arrangement of a passage was contrasted with the behavior of readers who saw the random arrangement of the passage. (HOD)

Approaching the Affective Factors of Information Seeking: The Viewpoint of the Information Search Process Model

ERIC Educational Resources Information Center

Savolainen, Reijo

2015-01-01

Introduction: The article contributes to the conceptual studies of affective factors in information seeking by examining Kuhlthau's information search process model. Method: This random-digit dial telephone survey of 253 people (75% female) living in a rural, medically under-serviced area of Ontario, Canada, follows-up a previous interview study…

Efficient multifeature index structures for music data retrieval

NASA Astrophysics Data System (ADS)

Lee, Wegin; Chen, Arbee L. P.

1999-12-01

In this paper, we propose four index structures for music data retrieval. Based on suffix trees, we develop two index structures called combined suffix tree and independent suffix trees. These methods still show shortcomings for some search functions. Hence we develop another index, called Twin Suffix Trees, to overcome these problems. However, the Twin Suffix Trees lack of scalability when the amount of music data becomes large. Therefore we propose the fourth index, called Grid-Twin Suffix Trees, to provide scalability and flexibility for a large amount of music data. For each index, we can use different search functions, like exact search and approximate search, on different music features, like melody, rhythm or both. We compare the performance of the different search functions applied on each index structure by a series of experiments.

Stabilities and defect-mediated lithium-ion conduction in a ground state cubic Li 3 N structure

DOE PAGES

Nguyen, Manh Cuong; Hoang, Khang; Wang, Cai-Zhuang; ...

2016-01-07

A stable ground state structure with cubic symmetry of Li 3N (c-Li 3N) is found by ab initio initially symmetric random-generated crystal structure search method. Gibbs free energy, calculated within quasi-harmonic approximation, shows that c-Li 3N is the ground state structure for a wide range of temperature. The c-Li 3N structure has a negative thermal expansion coefficient at temperatures lower than room temperature, due mainly to two transverse acoustic phonon modes. This c-Li 3N phase is a semiconductor with an indirect band gap of 1.90 eV within hybrid density functional calculation. We also investigate the migration and energetics of nativemore » point defects in c-Li 3N, including lithium and nitrogen vacancies, interstitials, and anti-site defects. Lithium interstitials are found to have a very low migration barrier (~0.12 eV) and the lowest formation energy among all possible defects. Thus, the ionic conduction in c-Li 3N is expected to occur via an interstitial mechanism, in contrast to that in the well-known α-Li 3N phase which occurs via a vacancy mechanism.« less

Identifying randomized clinical trials in Spanish-language dermatology journals.

PubMed

Sanclemente, G; Pardo, H; Sánchez, S; Bonfill, X

2015-06-01

The necessary foundation for good clinical practice lies in knowledge derived from clinical research. Evidence from randomized clinical trials (RCTs) is the pillar on which decisions about therapy are based. To search exhaustively and rigorously to identify RCTs in dermatology journals published in Spanish. We located dermatology journals through the following search engines and indexes: PubMed, LILACS, SciELO, Periódica, Latindex, Índice Médico Español, C-17, IBECS, EMBASE, and IMBIOMED. We also sought information through dermatology associations and dermatologists in countries where Spanish was the usual language of publication, and we searched the Internet (Google). Afterwards we searched the journals electronically and manually to identify RCTs in all available volumes and issues, checking from the year publication started through 2012. Of 28 journals identified, we included 21 in the search. We found a total of 144 RCTs published since 1969; 78 (54%) were in Latin American journals and 66 (46%) were in Spanish journals. The most frequent disease contexts for RCTs in Spanish journals were psoriasis, mycoses, and acne vulgaris. In Latin American journals, the most frequent disease contexts were common warts, mycoses, acne vulgaris, and skin ulcers on the lower limbs. Manual searches identified more RCTs than electronic searches. Manual searches found a larger number of RCTs. Relatively fewer RCTs are published in Spanish and Latin American journals than in English-language journals. Internet facilitated access to full texts published by many journals; however, free open access to these texts is still unavailable and a large number of journal issues are still not posted online. Copyright © 2014 Elsevier España, S.L.U. and AEDV. All rights reserved.

Effectiveness of Treatment Approaches for Children and Adolescents with Reading Disabilities: A Meta-Analysis of Randomized Controlled Trials

PubMed Central

Galuschka, Katharina; Ise, Elena; Krick, Kathrin; Schulte-Körne, Gerd

2014-01-01

Children and adolescents with reading disabilities experience a significant impairment in the acquisition of reading and spelling skills. Given the emotional and academic consequences for children with persistent reading disorders, evidence-based interventions are critically needed. The present meta-analysis extracts the results of all available randomized controlled trials. The aims were to determine the effectiveness of different treatment approaches and the impact of various factors on the efficacy of interventions. The literature search for published randomized-controlled trials comprised an electronic search in the databases ERIC, PsycINFO, PubMed, and Cochrane, and an examination of bibliographical references. To check for unpublished trials, we searched the websites clinicaltrials.com and ProQuest, and contacted experts in the field. Twenty-two randomized controlled trials with a total of 49 comparisons of experimental and control groups could be included. The comparisons evaluated five reading fluency trainings, three phonemic awareness instructions, three reading comprehension trainings, 29 phonics instructions, three auditory trainings, two medical treatments, and four interventions with coloured overlays or lenses. One trial evaluated the effectiveness of sunflower therapy and another investigated the effectiveness of motor exercises. The results revealed that phonics instruction is not only the most frequently investigated treatment approach, but also the only approach whose efficacy on reading and spelling performance in children and adolescents with reading disabilities is statistically confirmed. The mean effect sizes of the remaining treatment approaches did not reach statistical significance. The present meta-analysis demonstrates that severe reading and spelling difficulties can be ameliorated with appropriate treatment. In order to be better able to provide evidence-based interventions to children and adolescent with reading disabilities, research should intensify the application of blinded randomized controlled trials. PMID:24587110

Architecture of marine food webs: To be or not be a 'small-world'.

PubMed

Marina, Tomás Ignacio; Saravia, Leonardo A; Cordone, Georgina; Salinas, Vanesa; Doyle, Santiago R; Momo, Fernando R

2018-01-01

The search for general properties in network structure has been a central issue for food web studies in recent years. One such property is the small-world topology that combines a high clustering and a small distance between nodes of the network. This property may increase food web resilience but make them more sensitive to the extinction of connected species. Food web theory has been developed principally from freshwater and terrestrial ecosystems, largely omitting marine habitats. If theory needs to be modified to accommodate observations from marine ecosystems, based on major differences in several topological characteristics is still on debate. Here we investigated if the small-world topology is a common structural pattern in marine food webs. We developed a novel, simple and statistically rigorous method to examine the largest set of complex marine food webs to date. More than half of the analyzed marine networks exhibited a similar or lower characteristic path length than the random expectation, whereas 39% of the webs presented a significantly higher clustering than its random counterpart. Our method proved that 5 out of 28 networks fulfilled both features of the small-world topology: short path length and high clustering. This work represents the first rigorous analysis of the small-world topology and its associated features in high-quality marine networks. We conclude that such topology is a structural pattern that is not maximized in marine food webs; thus it is probably not an effective model to study robustness, stability and feasibility of marine ecosystems.

Detection of IUPAC and IUPAC-like chemical names.

PubMed

Klinger, Roman; Kolárik, Corinna; Fluck, Juliane; Hofmann-Apitius, Martin; Friedrich, Christoph M

2008-07-01

Chemical compounds like small signal molecules or other biological active chemical substances are an important entity class in life science publications and patents. Several representations and nomenclatures for chemicals like SMILES, InChI, IUPAC or trivial names exist. Only SMILES and InChI names allow a direct structure search, but in biomedical texts trivial names and Iupac like names are used more frequent. While trivial names can be found with a dictionary-based approach and in such a way mapped to their corresponding structures, it is not possible to enumerate all IUPAC names. In this work, we present a new machine learning approach based on conditional random fields (CRF) to find mentions of IUPAC and IUPAC-like names in scientific text as well as its evaluation and the conversion rate with available name-to-structure tools. We present an IUPAC name recognizer with an F(1) measure of 85.6% on a MEDLINE corpus. The evaluation of different CRF orders and offset conjunction orders demonstrates the importance of these parameters. An evaluation of hand-selected patent sections containing large enumerations and terms with mixed nomenclature shows a good performance on these cases (F(1) measure 81.5%). Remaining recognition problems are to detect correct borders of the typically long terms, especially when occurring in parentheses or enumerations. We demonstrate the scalability of our implementation by providing results from a full MEDLINE run. We plan to publish the corpora, annotation guideline as well as the conditional random field model as a UIMA component.

Searching for Control: Priming Randomness Increases the Evaluation of Ritual Efficacy

ERIC Educational Resources Information Center

Legare, Cristine H.; Souza, André L.

2014-01-01

Reestablishing feelings of control after experiencing uncertainty has long been considered a fundamental motive for human behavior. We propose that rituals (i.e., socially stipulated, causally opaque practices) provide a means for coping with the aversive feelings associated with randomness due to the perception of a connection between ritual…

In Search of the Most Likely Value

ERIC Educational Resources Information Center

Letkowski, Jerzy

2014-01-01

Descripting Statistics provides methodology and tools for user-friendly presentation of random data. Among the summary measures that describe focal tendencies in random data, the mode is given the least amount of attention and it is frequently misinterpreted in many introductory textbooks on statistics. The purpose of the paper is to provide a…

Acupuncture for Children with Autism Spectrum Disorders: A Systematic Review of Randomized Clinical Trials

ERIC Educational Resources Information Center

Lee, Myeong Soo; Choi, Tae-Young; Shin, Byung-Cheul; Ernst, Edzard

2012-01-01

This study aimed to assess the effectiveness of acupuncture as a treatment for autism spectrum disorders (ASD). We searched the literature using 15 databases. Eleven randomized clinical trials (RCTs) met our inclusion criteria. Most had significant methodological weaknesses. The studies' statistical and clinical heterogeneity prevented us from…

A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

PubMed

Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

2010-08-01

The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

Searching for answers to clinical questions using google versus evidence-based summary resources: a randomized controlled crossover study.

PubMed

Kim, Sarang; Noveck, Helaine; Galt, James; Hogshire, Lauren; Willett, Laura; O'Rourke, Kerry

2014-06-01

To compare the speed and accuracy of answering clinical questions using Google versus summary resources. In 2011 and 2012, 48 internal medicine interns from two classes at Rutgers University Robert Wood Johnson Medical School, who had been trained to use three evidence-based summary resources, performed four-minute computer searches to answer 10 clinical questions. Half were randomized to initiate searches for answers to questions 1 to 5 using Google; the other half initiated searches using a summary resource. They then crossed over and used the other resource for questions 6 to 10. They documented the time spent searching and the resource where the answer was found. Time to correct response and percentage of correct responses were compared between groups using t test and general estimating equations. Of 480 questions administered, interns found answers for 393 (82%). Interns initiating searches in Google used a wider variety of resources than those starting with summary resources. No significant difference was found in mean time to correct response (138.5 seconds for Google versus 136.1 seconds for summary resource; P = .72). Mean correct response rate was 58.4% for Google versus 61.5% for summary resource (mean difference -3.1%; 95% CI -10.3% to 4.2%; P = .40). The authors found no significant differences in speed or accuracy between searches initiated using Google versus summary resources. Although summary resources are considered to provide the highest quality of evidence, improvements to allow for better speed and accuracy are needed.

Decision aids for patients.

PubMed

Lenz, Matthias; Buhse, Susanne; Kasper, Jürgen; Kupfer, Ramona; Richter, Tanja; Mühlhauser, Ingrid

2012-06-01

Patients want to be more involved in medical decision-making. To this end, some decision aids are now available. We present an overview of this subject, in which we explain the terms "shared decision-making", "decision aid", and "evidence-based patient information" and survey information on the available decision aids in German and other languages on the basis of a literature search in MEDLINE, EMBASE and PsycInfo and a current Cochrane Review. We also searched the Internet for providers of decision aids in Germany. Decision aids exist in the form of brochures, decision tables, videos, and computer programs; they address various topics in the prevention, diagnosis, and treatment of disease. They typically contain information on the advantages and disadvantages of the available options, as well as guidance for personal decision-making. They can be used alone or as a part of structured counseling or patient education. Minimal quality standards include an adequate evidence base, completeness, absence of bias, and intelligibility. Our search revealed 12 randomized controlled trials (RCTs) of decision aids in German and 106 RCTs of decision aids in other languages. These trials studied the outcome of the use of decision aids not just with respect to clinical developments, but also with respect to patient knowledge, adherence to treatment regimens, satisfaction, involvement in decision-making, autonomy preference, and decisional conflicts. Only a small fraction of the available decision aids were systematically developed and have been subjected to systematic evaluation. Patients are still not receiving the help in decision-making to which medical ethics entitles them. Structures need to be put in place for the sustainable development, evaluation and implementation of high-quality decision aids.

New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation.

PubMed

Antczak, Maciej; Popenda, Mariusz; Zok, Tomasz; Zurkowski, Michal; Adamiak, Ryszard W; Szachniuk, Marta

2018-04-15

Understanding the formation, architecture and roles of pseudoknots in RNA structures are one of the most difficult challenges in RNA computational biology and structural bioinformatics. Methods predicting pseudoknots typically perform this with poor accuracy, often despite experimental data incorporation. Existing bioinformatic approaches differ in terms of pseudoknots' recognition and revealing their nature. A few ways of pseudoknot classification exist, most common ones refer to a genus or order. Following the latter one, we propose new algorithms that identify pseudoknots in RNA structure provided in BPSEQ format, determine their order and encode in dot-bracket-letter notation. The proposed encoding aims to illustrate the hierarchy of RNA folding. New algorithms are based on dynamic programming and hybrid (combining exhaustive search and random walk) approaches. They evolved from elementary algorithm implemented within the workflow of RNA FRABASE 1.0, our database of RNA structure fragments. They use different scoring functions to rank dissimilar dot-bracket representations of RNA structure. Computational experiments show an advantage of new methods over the others, especially for large RNA structures. Presented algorithms have been implemented as new functionality of RNApdbee webserver and are ready to use at http://rnapdbee.cs.put.poznan.pl. mszachniuk@cs.put.poznan.pl. Supplementary data are available at Bioinformatics online.

Dual-state modulation of the contextual cueing effect: Evidence from eye movement recordings.

PubMed

Zhao, Guang; Liu, Qiang; Jiao, Jun; Zhou, Peiling; Li, Hong; Sun, Hong-jin

2012-06-08

The repeated configurations of random elements induce a better search performance than that of the displays of novel random configurations. The mechanism of such contextual cueing effect has been investigated through the use of the RT × Set Size function. There are divergent views on whether the contextual cueing effect is driven by attentional guidance or facilitation of initial perceptual processing or response selection. To explore this question, we used eye movement recording in this study, which offers information about the substages of the search task. The results suggest that the contextual cueing effect is contributed mainly by attentional guidance, and facilitation of response selection also plays a role.

A comparative study of controlled random search algorithms with application to inverse aerofoil design

NASA Astrophysics Data System (ADS)

Manzanares-Filho, N.; Albuquerque, R. B. F.; Sousa, B. S.; Santos, L. G. C.

2018-06-01

This article presents a comparative study of some versions of the controlled random search algorithm (CRSA) in global optimization problems. The basic CRSA, originally proposed by Price in 1977 and improved by Ali et al. in 1997, is taken as a starting point. Then, some new modifications are proposed to improve the efficiency and reliability of this global optimization technique. The performance of the algorithms is assessed using traditional benchmark test problems commonly invoked in the literature. This comparative study points out the key features of the modified algorithm. Finally, a comparison is also made in a practical engineering application, namely the inverse aerofoil shape design.

Molecule database framework: a framework for creating database applications with chemical structure search capability

PubMed Central

2013-01-01

Background Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Results Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes: • Support for multi-component compounds (mixtures) • Import and export of SD-files • Optional security (authorization) For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. Conclusions By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework. PMID:24325762

Molecule database framework: a framework for creating database applications with chemical structure search capability.

PubMed

Kiener, Joos

2013-12-11

Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

Image Re-Ranking Based on Topic Diversity.

PubMed

Qian, Xueming; Lu, Dan; Wang, Yaxiong; Zhu, Li; Tang, Yuan Yan; Wang, Meng

2017-08-01

Social media sharing Websites allow users to annotate images with free tags, which significantly contribute to the development of the web image retrieval. Tag-based image search is an important method to find images shared by users in social networks. However, how to make the top ranked result relevant and with diversity is challenging. In this paper, we propose a topic diverse ranking approach for tag-based image retrieval with the consideration of promoting the topic coverage performance. First, we construct a tag graph based on the similarity between each tag. Then, the community detection method is conducted to mine the topic community of each tag. After that, inter-community and intra-community ranking are introduced to obtain the final retrieved results. In the inter-community ranking process, an adaptive random walk model is employed to rank the community based on the multi-information of each topic community. Besides, we build an inverted index structure for images to accelerate the searching process. Experimental results on Flickr data set and NUS-Wide data sets show the effectiveness of the proposed approach.

Factors influencing the effectiveness of scalp cooling in the prevention of chemotherapy-induced alopecia.

PubMed

Komen, Manon M C; Smorenburg, Carolien H; van den Hurk, Corina J G; Nortier, Johan W R

2013-01-01

The success of scalp cooling in preventing or reducing chemotherapy-induced alopecia (CIA) is highly variable between patients and chemotherapy regimens. The outcome of hair preservation is often unpredictable and depends on various factors. Methods. We performed a structured search of literature published from 1970 to February 2012 for articles that reported on factors influencing the effectiveness of scalp cooling to prevent CIA in patients with cancer. Results. The literature search identified 192 reports, of which 32 studies were considered relevant. Randomized studies on scalp cooling are scarce and there is little information on the determinants of the result. The effectiveness of scalp cooling for hair preservation depends on dose and type of chemotherapy, with less favorable results at higher doses. Temperature seems to be an important determinant. Various studies suggest that a subcutaneous scalp temperature less than 22 °C is required for hair preservation. Conclusions. The effectiveness of scalp cooling for hair preservation varies by chemotherapy type and dose, and probably by the degree and duration of cooling.

Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

PubMed

Song, Yinglei; Liu, Chunmei; Malmberg, Russell; Pan, Fangfang; Cai, Liming

2005-01-01

Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

HDAPD: a web tool for searching the disease-associated protein structures

PubMed Central

2010-01-01

Background The protein structures of the disease-associated proteins are important for proceeding with the structure-based drug design to against a particular disease. Up until now, proteins structures are usually searched through a PDB id or some sequence information. However, in the HDAPD database presented here the protein structure of a disease-associated protein can be directly searched through the associated disease name keyed in. Description The search in HDAPD can be easily initiated by keying some key words of a disease, protein name, protein type, or PDB id. The protein sequence can be presented in FASTA format and directly copied for a BLAST search. HDAPD is also interfaced with Jmol so that users can observe and operate a protein structure with Jmol. The gene ontological data such as cellular components, molecular functions, and biological processes are provided once a hyperlink to Gene Ontology (GO) is clicked. Further, HDAPD provides a link to the KEGG map such that where the protein is placed and its relationship with other proteins in a metabolic pathway can be found from the map. The latest literatures namely titles, journals, authors, and abstracts searched from PubMed for the protein are also presented as a length controllable list. Conclusions Since the HDAPD data content can be routinely updated through a PHP-MySQL web page built, the new database presented is useful for searching the structures for some disease-associated proteins that may play important roles in the disease developing process for performing the structure-based drug design to against the diseases. PMID:20158919

Differences in Functional Outcomes for Adult Patients with Prosthodontically-Treated and -Untreated Shortened Dental Arches: A Systematic Review

PubMed Central

Khan, Saadika; Musekiwa, Alfred; Chikte, Usuf M. E.; Omar, Ridwaan

2014-01-01

This review examined differences in functional outcomes and patient satisfaction when shortened dental arches are left untreated compared to their restoration to complete arch lengths with different prosthodontic interventions. Methods A protocol was developed according to the criteria for a systematic review. All relevant databases were searched to identify appropriate clinical trials regardless of language or publication status. Predetermined eligibility criteria were applied, trial quality assessed and data extracted for each study. Relevant outcomes assessed were: functioning ability, patient satisfaction and harmful effects on oral structures. Results Searches yielded 101 articles: 81 from electronic databases and 20 from reference lists of retrieved articles (PEARLing searches). Sixty-nine citations were assessed for eligibility after removing 32 duplicate records. After reading titles and abstracts, a total of 41 records were excluded and the full-texts of the remaining 28 records were read. Only 21 records were included for the SR because 7 records were excluded after reading the full-text reports. These 21 records report the outcomes of four randomized controlled trials (RCTs) and one non-randomized clinical trial (CT) which were pre-specified and used for this review. No on-going studies were found and no eligible studies were excluded for failure to report the reviewer’s pre-specified outcomes. Outcomes were reported in the retrieved 21 articles. A narrative explanation of the pre-specified outcomes is reported for the 3 comparison groups (which were based on the different interventions used for the individual clinical trials). The shortened dental arch as a treatment option is encouraging in terms of functioning, patient satisfaction and cost-effectiveness. By using only high quality studies it was expected that the results would be more reliable when making conclusions and recommendations, but some of the included studies had to be downgraded due to methodological errors. PMID:24992473

Strategic search from long-term memory: an examination of semantic and autobiographical recall.

PubMed

Unsworth, Nash; Brewer, Gene A; Spillers, Gregory J

2014-01-01

Searching long-term memory is theoretically driven by both directed (search strategies) and random components. In the current study we conducted four experiments evaluating strategic search in semantic and autobiographical memory. Participants were required to generate either exemplars from the category of animals or the names of their friends for several minutes. Self-reported strategies suggested that participants typically relied on visualization strategies for both tasks and were less likely to rely on ordered strategies (e.g., alphabetic search). When participants were instructed to use particular strategies, the visualization strategy resulted in the highest levels of performance and the most efficient search, whereas ordered strategies resulted in the lowest levels of performance and fairly inefficient search. These results are consistent with the notion that retrieval from long-term memory is driven, in part, by search strategies employed by the individual, and that one particularly efficient strategy is to visualize various situational contexts that one has experienced in the past in order to constrain the search and generate the desired information.

Context matters: the structure of task goals affects accuracy in multiple-target visual search.

PubMed

Clark, Kait; Cain, Matthew S; Adcock, R Alison; Mitroff, Stephen R

2014-05-01

Career visual searchers such as radiologists and airport security screeners strive to conduct accurate visual searches, but despite extensive training, errors still occur. A key difference between searches in radiology and airport security is the structure of the search task: Radiologists typically scan a certain number of medical images (fixed objective), and airport security screeners typically search X-rays for a specified time period (fixed duration). Might these structural differences affect accuracy? We compared performance on a search task administered either under constraints that approximated radiology or airport security. Some displays contained more than one target because the presence of multiple targets is an established source of errors for career searchers, and accuracy for additional targets tends to be especially sensitive to contextual conditions. Results indicate that participants searching within the fixed objective framework produced more multiple-target search errors; thus, adopting a fixed duration framework could improve accuracy for career searchers. Copyright © 2013 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Costs and benefits to industry of online literature searches

NASA Technical Reports Server (NTRS)

Jensen, R. J.; Asbury, H. O.; King, R. G.

1980-01-01

A description is given of a client survey conducted by the NASA Industrial Application Center, U.S.C., examining user-identified dollar costs and benefits of an online computerized literature search. Telephone interviews were conducted on a random sample of clients using a Denver Research Institute questionnaire. Of the total 159 clients surveyed, over 53% identified dollar benefits. A direct relationship between client dollars invested and benefits derived from the search was shown. The ratio of dollar benefit to investment dollar averaged 2.9 to 1. Precise data on the end user's evaluation of the dollar value of an information search are presented.

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site.

PubMed

Kurcinski, Mateusz; Jamroz, Michal; Blaszczyk, Maciej; Kolinski, Andrzej; Kmiecik, Sebastian

2015-07-01

Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein-peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3

PubMed Central

Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

2011-01-01

One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA have backbone RMSD 0.8 – 1.5 Å from the reference structures determined by traditional NMR approaches. PMID:21706248

Flight plan optimization

NASA Astrophysics Data System (ADS)

Dharmaseelan, Anoop; Adistambha, Keyne D.

2015-05-01

Fuel cost accounts for 40 percent of the operating cost of an airline. Fuel cost can be minimized by planning a flight on optimized routes. The routes can be optimized by searching best connections based on the cost function defined by the airline. The most common algorithm that used to optimize route search is Dijkstra's. Dijkstra's algorithm produces a static result and the time taken for the search is relatively long. This paper experiments a new algorithm to optimize route search which combines the principle of simulated annealing and genetic algorithm. The experimental results of route search, presented are shown to be computationally fast and accurate compared with timings from generic algorithm. The new algorithm is optimal for random routing feature that is highly sought by many regional operators.

Tuning Monotonic Basin Hopping: Improving the Efficiency of Stochastic Search as Applied to Low-Thrust Trajectory Optimization

NASA Technical Reports Server (NTRS)

Englander, Jacob; Englander, Arnold

2014-01-01

Trajectory optimization methods using MBH have become well developed during the past decade. An essential component of MBH is a controlled random search through the multi-dimensional space of possible solutions. Historically, the randomness has been generated by drawing RVs from a uniform probability distribution. Here, we investigate the generating the randomness by drawing the RVs from Cauchy and Pareto distributions, chosen because of their characteristic long tails. We demonstrate that using Cauchy distributions (as first suggested by Englander significantly improves MBH performance, and that Pareto distributions provide even greater improvements. Improved performance is defined in terms of efficiency and robustness, where efficiency is finding better solutions in less time, and robustness is efficiency that is undiminished by (a) the boundary conditions and internal constraints of the optimization problem being solved, and (b) by variations in the parameters of the probability distribution. Robustness is important for achieving performance improvements that are not problem specific. In this work we show that the performance improvements are the result of how these long-tailed distributions enable MBH to search the solution space faster and more thoroughly. In developing this explanation, we use the concepts of sub-diffusive, normally-diffusive, and super-diffusive RWs originally developed in the field of statistical physics.

The efficacy of low-level laser treatment in reducing pain and swelling after endodontic surgery: a systematic review

NASA Astrophysics Data System (ADS)

Moshari, Amirabbas; Vatanpour, Mehdi; Zakershahrak, Mehrsa

2016-03-01

Introduction: LLLT in oral cavity believed to reduce pain after endodontic surgery and wisdom tooth removal, to accelerate wound healing and to have an anti-inflammatory and regenerative effect. The aim of this systematic review therefore was to assess the proof available for the efficacy of low-level laser treatment in reducing pain and swelling after endodontic surgery. Methods: The PubMed service of the U.S. National Library of Medicine was searched with applicable search strategies. No language restriction was applied. The last electronic search was accomplished on August 31, 2015. All randomized clinical trials on the efficiency of low-level laser treatment in reducing pain and swelling after endodontic surgery was considered for the Meta-analysis. Quality consideration of the included randomized clinical trials was appraised according to CONSORT guidelines. Results: Only two randomized clinical trials were attained. These studies clarified that laser treatment could reduce pain and swelling, but the results were not significant. Conclusions: Low-level laser therapy can be advantageous for the reduction of postoperative pain but there is no strong confirmation for its efficiency. Its clinical utility and applicability relating to endodontic surgery, Along with the optimal energy dosage and the number of laser treatments needed after surgery, still, demand further research and experiment.

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

PubMed Central

2010-01-01

Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl. Conclusions RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field. PMID:20459631

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures.

PubMed

Popenda, Mariusz; Szachniuk, Marta; Blazewicz, Marek; Wasik, Szymon; Burke, Edmund K; Blazewicz, Jacek; Adamiak, Ryszard W

2010-05-06

Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl. RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field.

Optimal fractional order PID design via Tabu Search based algorithm.

PubMed

Ateş, Abdullah; Yeroglu, Celaleddin

2016-01-01

This paper presents an optimization method based on the Tabu Search Algorithm (TSA) to design a Fractional-Order Proportional-Integral-Derivative (FOPID) controller. All parameter computations of the FOPID employ random initial conditions, using the proposed optimization method. Illustrative examples demonstrate the performance of the proposed FOPID controller design method. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Scaffold hopping in drug discovery using inductive logic programming.

PubMed

Tsunoyama, Kazuhisa; Amini, Ata; Sternberg, Michael J E; Muggleton, Stephen H

2008-05-01

In chemoinformatics, searching for compounds which are structurally diverse and share a biological activity is called scaffold hopping. Scaffold hopping is important since it can be used to obtain alternative structures when the compound under development has unexpected side-effects. Pharmaceutical companies use scaffold hopping when they wish to circumvent prior patents for targets of interest. We propose a new method for scaffold hopping using inductive logic programming (ILP). ILP uses the observed spatial relationships between pharmacophore types in pretested active and inactive compounds and learns human-readable rules describing the diverse structures of active compounds. The ILP-based scaffold hopping method is compared to two previous algorithms (chemically advanced template search, CATS, and CATS3D) on 10 data sets with diverse scaffolds. The comparison shows that the ILP-based method is significantly better than random selection while the other two algorithms are not. In addition, the ILP-based method retrieves new active scaffolds which were not found by CATS and CATS3D. The results show that the ILP-based method is at least as good as the other methods in this study. ILP produces human-readable rules, which makes it possible to identify the three-dimensional features that lead to scaffold hopping. A minor variant of a rule learnt by ILP for scaffold hopping was subsequently found to cover an inhibitor identified by an independent study. This provides a successful result in a blind trial of the effectiveness of ILP to generate rules for scaffold hopping. We conclude that ILP provides a valuable new approach for scaffold hopping.

Standard plane localization in ultrasound by radial component model and selective search.

PubMed

Ni, Dong; Yang, Xin; Chen, Xin; Chin, Chien-Ting; Chen, Siping; Heng, Pheng Ann; Li, Shengli; Qin, Jing; Wang, Tianfu

2014-11-01

Acquisition of the standard plane is crucial for medical ultrasound diagnosis. However, this process requires substantial experience and a thorough knowledge of human anatomy. Therefore it is very challenging for novices and even time consuming for experienced examiners. We proposed a hierarchical, supervised learning framework for automatically detecting the standard plane from consecutive 2-D ultrasound images. We tested this technique by developing a system that localizes the fetal abdominal standard plane from ultrasound video by detecting three key anatomical structures: the stomach bubble, umbilical vein and spine. We first proposed a novel radial component-based model to describe the geometric constraints of these key anatomical structures. We then introduced a novel selective search method which exploits the vessel probability algorithm to produce probable locations for the spine and umbilical vein. Next, using component classifiers trained by random forests, we detected the key anatomical structures at their probable locations within the regions constrained by the radial component-based model. Finally, a second-level classifier combined the results from the component detection to identify an ultrasound image as either a "fetal abdominal standard plane" or a "non- fetal abdominal standard plane." Experimental results on 223 fetal abdomen videos showed that the detection accuracy of our method was as high as 85.6% and significantly outperformed both the full abdomen and the separate anatomy detection methods without geometric constraints. The experimental results demonstrated that our system shows great promise for application to clinical practice. Copyright © 2014 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Interventions to reduce accidents in childhood: a systematic review.

PubMed

Barcelos, Raquel S; Del-Ponte, Bianca; Santos, Iná S

2017-12-30

To review the literature on interventions planned to prevent the incidence of injuries in childhood. The PubMed, Web of Science, and Bireme databases were searched by two independent reviewers, employing the single terms accidents, accident, injuries, injury, clinical trial, intervention, educational intervention, and multiple interventions, and their combinations, present in the article title or abstract, with no limits except period of publication (2006-2016) and studies in human subjects. Initially, 11,097 titles were located. Fifteen articles were selected for the review. Eleven were randomized trials (four carried out at the children's households, five in pediatric healthcare services, and two at schools), and four were non-randomized trials carried out at the children's households. Four of the randomized trials were analyzed by intention-to-treat and a protective effect of the intervention was observed: decrease in the number of risk factors, decrease in the number of medical consultations due to injuries, decrease in the prevalence of risk behaviors, and increase of the parents' knowledge regarding injury prevention in childhood. Traumatic injuries in childhood are amenable to primary prevention through strategies that consider the child's age and level of development, as well as structural aspects of the environment. Copyright © 2017 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

Utilizing bi-spectral index (BIS) for the monitoring of sedated adult ICU patients: a systematic review.

PubMed

Bilgili, Beliz; Montoya, Juan C; Layon, A J; Berger, Andrea L; Kirchner, H L; Gupta, Leena K; Gloss, David S

2017-03-01

The ideal level of sedation in the ICU is an ongoing source of scrutiny. At higher levels of sedation, the current scoring systems are not ideal. BIS may be able to improve both. We evaluated literature on effectiveness of BIS monitoring in sedated mechanically ventilated (MV) ICU patients compared to clinical sedation scores (CSS). For this systematic review, full text articles were searched in OVID, MEDLINE, EMBASE, and Cochrane databases from 1986 - 2014. Additional studies were identified searching bibliographies/abstracts from national/international Critical Care Medicine conferences and references from searched articles retrieved. Search terms were: 'Clinical sedation scale, Bi-spectral Index, Mechanical ventilation, Intensive care Unit'. Included were prospective, randomized and non-randomized studies comparing BIS monitoring with any CSS in MV adult (>18 yr old) ICU patients. Studies were graded for quality of evidence based on bias as established by the GRADE guidelines. Additional sources of bias were examined. There were five studies which met inclusion criteria. All five studies were either unclear or high risk for blinding of participants and blinding of outcome assessment. All papers had at least one source of additional high risk, or unclear/unstated. BIS monitoring in the mechanically ventilated ICU patient may decrease sedative drug dose, recall, and time to wake-up. The studies suggesting this are severely limited methodologically. BIS, when compared to subjective CSSs, is not, at this time, clearly indicated. An appropriately powered randomized, controlled study is needed to determine if this monitoring modality is of use on the ICU.

Automated parameterization of intermolecular pair potentials using global optimization techniques

NASA Astrophysics Data System (ADS)

Krämer, Andreas; Hülsmann, Marco; Köddermann, Thorsten; Reith, Dirk

2014-12-01

In this work, different global optimization techniques are assessed for the automated development of molecular force fields, as used in molecular dynamics and Monte Carlo simulations. The quest of finding suitable force field parameters is treated as a mathematical minimization problem. Intricate problem characteristics such as extremely costly and even abortive simulations, noisy simulation results, and especially multiple local minima naturally lead to the use of sophisticated global optimization algorithms. Five diverse algorithms (pure random search, recursive random search, CMA-ES, differential evolution, and taboo search) are compared to our own tailor-made solution named CoSMoS. CoSMoS is an automated workflow. It models the parameters' influence on the simulation observables to detect a globally optimal set of parameters. It is shown how and why this approach is superior to other algorithms. Applied to suitable test functions and simulations for phosgene, CoSMoS effectively reduces the number of required simulations and real time for the optimization task.

Cluster-Based Multipolling Sequencing Algorithm for Collecting RFID Data in Wireless LANs

NASA Astrophysics Data System (ADS)

Choi, Woo-Yong; Chatterjee, Mainak

2015-03-01

With the growing use of RFID (Radio Frequency Identification), it is becoming important to devise ways to read RFID tags in real time. Access points (APs) of IEEE 802.11-based wireless Local Area Networks (LANs) are being integrated with RFID networks that can efficiently collect real-time RFID data. Several schemes, such as multipolling methods based on the dynamic search algorithm and random sequencing, have been proposed. However, as the number of RFID readers associated with an AP increases, it becomes difficult for the dynamic search algorithm to derive the multipolling sequence in real time. Though multipolling methods can eliminate the polling overhead, we still need to enhance the performance of the multipolling methods based on random sequencing. To that extent, we propose a real-time cluster-based multipolling sequencing algorithm that drastically eliminates more than 90% of the polling overhead, particularly so when the dynamic search algorithm fails to derive the multipolling sequence in real time.

Dual representation of item positions in verbal short-term memory: Evidence for two access modes.

PubMed

Lange, Elke B; Verhaeghen, Paul; Cerella, John

Memory sets of N = 1~5 digits were exposed sequentially from left-to-right across the screen, followed by N recognition probes. Probes had to be compared to memory list items on identity only (Sternberg task) or conditional on list position. Positions were probed randomly or in left-to-right order. Search functions related probe response times to set size. Random probing led to ramped, "Sternbergian" functions whose intercepts were elevated by the location requirement. Sequential probing led to flat search functions-fast responses unaffected by set size. These results suggested that items in STM could be accessed either by a slow search-on-identity followed by recovery of an associated location tag, or in a single step by following item-to-item links in study order. It is argued that this dual coding of location information occurs spontaneously at study, and that either code can be utilised at retrieval depending on test demands.

A novel global Harmony Search method based on Ant Colony Optimisation algorithm

NASA Astrophysics Data System (ADS)

Fouad, Allouani; Boukhetala, Djamel; Boudjema, Fares; Zenger, Kai; Gao, Xiao-Zhi

2016-03-01

The Global-best Harmony Search (GHS) is a stochastic optimisation algorithm recently developed, which hybridises the Harmony Search (HS) method with the concept of swarm intelligence in the particle swarm optimisation (PSO) to enhance its performance. In this article, a new optimisation algorithm called GHSACO is developed by incorporating the GHS with the Ant Colony Optimisation algorithm (ACO). Our method introduces a novel improvisation process, which is different from that of the GHS in the following aspects. (i) A modified harmony memory (HM) representation and conception. (ii) The use of a global random switching mechanism to monitor the choice between the ACO and GHS. (iii) An additional memory consideration selection rule using the ACO random proportional transition rule with a pheromone trail update mechanism. The proposed GHSACO algorithm has been applied to various benchmark functions and constrained optimisation problems. Simulation results demonstrate that it can find significantly better solutions when compared with the original HS and some of its variants.

Protein structure determination by exhaustive search of Protein Data Bank derived databases.

PubMed

Stokes-Rees, Ian; Sliz, Piotr

2010-12-14

Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database.

SNP selection and classification of genome-wide SNP data using stratified sampling random forests.

PubMed

Wu, Qingyao; Ye, Yunming; Liu, Yang; Ng, Michael K

2012-09-01

For high dimensional genome-wide association (GWA) case-control data of complex disease, there are usually a large portion of single-nucleotide polymorphisms (SNPs) that are irrelevant with the disease. A simple random sampling method in random forest using default mtry parameter to choose feature subspace, will select too many subspaces without informative SNPs. Exhaustive searching an optimal mtry is often required in order to include useful and relevant SNPs and get rid of vast of non-informative SNPs. However, it is too time-consuming and not favorable in GWA for high-dimensional data. The main aim of this paper is to propose a stratified sampling method for feature subspace selection to generate decision trees in a random forest for GWA high-dimensional data. Our idea is to design an equal-width discretization scheme for informativeness to divide SNPs into multiple groups. In feature subspace selection, we randomly select the same number of SNPs from each group and combine them to form a subspace to generate a decision tree. The advantage of this stratified sampling procedure can make sure each subspace contains enough useful SNPs, but can avoid a very high computational cost of exhaustive search of an optimal mtry, and maintain the randomness of a random forest. We employ two genome-wide SNP data sets (Parkinson case-control data comprised of 408 803 SNPs and Alzheimer case-control data comprised of 380 157 SNPs) to demonstrate that the proposed stratified sampling method is effective, and it can generate better random forest with higher accuracy and lower error bound than those by Breiman's random forest generation method. For Parkinson data, we also show some interesting genes identified by the method, which may be associated with neurological disorders for further biological investigations.

Collinearity Impairs Local Element Visual Search

ERIC Educational Resources Information Center

Jingling, Li; Tseng, Chia-Huei

2013-01-01

In visual searches, stimuli following the law of good continuity attract attention to the global structure and receive attentional priority. Also, targets that have unique features are of high feature contrast and capture attention in visual search. We report on a salient global structure combined with a high orientation contrast to the…

Self-Adaptive Stepsize Search Applied to Optimal Structural Design

NASA Astrophysics Data System (ADS)

Nolle, L.; Bland, J. A.

Structural engineering often involves the design of space frames that are required to resist predefined external forces without exhibiting plastic deformation. The weight of the structure and hence the weight of its constituent members has to be as low as possible for economical reasons without violating any of the load constraints. Design spaces are usually vast and the computational costs for analyzing a single design are usually high. Therefore, not every possible design can be evaluated for real-world problems. In this work, a standard structural design problem, the 25-bar problem, has been solved using self-adaptive stepsize search (SASS), a relatively new search heuristic. This algorithm has only one control parameter and therefore overcomes the drawback of modern search heuristics, i.e. the need to first find a set of optimum control parameter settings for the problem at hand. In this work, SASS outperforms simulated-annealing, genetic algorithms, tabu search and ant colony optimization.

Meta-analysis of associations between childhood adversity and hippocampus and amygdala volume in non-clinical and general population samples.

PubMed

Calem, Maria; Bromis, Konstantinos; McGuire, Philip; Morgan, Craig; Kempton, Matthew J

2017-01-01

Studies of psychiatric populations have reported associations between childhood adversity and volumes of stress-related brain structures. This meta-analysis investigated these associations in non-clinical samples and therefore independent of the effects of severe mental health difficulties and their treatment. The MEDLINE database was searched for magnetic resonance imaging studies measuring brain structure in adults with and without childhood adversity. Fifteen eligible papers (1781 participants) reporting hippocampal volumes and/or amygdala volumes were pooled using a random effects meta-analysis. Those with childhood adversity had lower hippocampus volumes (hedges g = - 0.15, p  = 0.010). Controlling for gender, this difference became less evident (hedges g = - 0.12, p  = 0.124). This association differed depending on whether studies included participants with some psychopathology, though this may be due to differences in the type of adversity these studies examined. There was no strong evidence of any differences in amygdala volume. Childhood adversity may have only a modest impact on stress-related brain structures in those without significant mental health difficulties.

Structural and configurational properties of nanoconfined monolayer ice from first principles

PubMed Central

Corsetti, Fabiano; Matthews, Paul; Artacho, Emilio

2016-01-01

Understanding the structural tendencies of nanoconfined water is of great interest for nanoscience and biology, where nano/micro-sized objects may be separated by very few layers of water. Here we investigate the properties of ice confined to a quasi-2D monolayer by a featureless, chemically neutral potential, in order to characterize its intrinsic behaviour. We use density-functional theory simulations with a non-local van der Waals density functional. An ab initio random structure search reveals all the energetically competitive monolayer configurations to belong to only two of the previously-identified families, characterized by a square or honeycomb hydrogen-bonding network, respectively. We discuss the modified ice rules needed for each network, and propose a simple point dipole 2D lattice model that successfully explains the energetics of the square configurations. All identified stable phases for both networks are found to be non-polar (but with a topologically non-trivial texture for the square) and, hence, non-ferroelectric, in contrast to previous predictions from a five-site empirical force-field model. Our results are in good agreement with very recently reported experimental observations. PMID:26728125

Structural and configurational properties of nanoconfined monolayer ice from first principles

NASA Astrophysics Data System (ADS)

Corsetti, Fabiano; Matthews, Paul; Artacho, Emilio

2016-01-01

Understanding the structural tendencies of nanoconfined water is of great interest for nanoscience and biology, where nano/micro-sized objects may be separated by very few layers of water. Here we investigate the properties of ice confined to a quasi-2D monolayer by a featureless, chemically neutral potential, in order to characterize its intrinsic behaviour. We use density-functional theory simulations with a non-local van der Waals density functional. An ab initio random structure search reveals all the energetically competitive monolayer configurations to belong to only two of the previously-identified families, characterized by a square or honeycomb hydrogen-bonding network, respectively. We discuss the modified ice rules needed for each network, and propose a simple point dipole 2D lattice model that successfully explains the energetics of the square configurations. All identified stable phases for both networks are found to be non-polar (but with a topologically non-trivial texture for the square) and, hence, non-ferroelectric, in contrast to previous predictions from a five-site empirical force-field model. Our results are in good agreement with very recently reported experimental observations.

Protein structure database search and evolutionary classification.

PubMed

Yang, Jinn-Moon; Tung, Chi-Hua

2006-01-01

As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw].

Education in cardiopulmonary resuscitation in Russia: A systematic review of the available evidence

PubMed Central

Birkun, Alexei; Glotov, Maksim

2017-01-01

BACKGROUND: To summarise and appraise cumulative published scientific evidence relevant to cardiopulmonary resuscitation (CPR) education in Russia. DATA RESOURCES: We searched Medline, Scopus, Science Direct and Russian Science Citation Index databases from December 1991 to December 2016 to identify studies pertaining to the field of CPR education that were carried out by Russian researchers and/or investigated the topic of interest for Russia/Russian population. Reference lists of eligible publications, contents pages of relevant Russian journals and Google Scholar were also searched. There was no limitation based on publication language or study design. RESULTS: Of 7 964 unique citations identified, 22 studies were included. All studies were published from 2009 to 2016, mainly in Russian. Only three studies were reported to be randomized controlled. Non-medical individuals constituted 17% of studied populations. Most of the studies aimed to assess effects of CPR educational interventions, generally suggesting positive influence of the training conducted. The studies were highly heterogeneous as for methodological approaches, structure and duration of educational interventions, evaluation methods and criteria being used. Methodological quality was generally poor, with >40% publications not passing quality screening and only 2 studies meeting the criteria of moderate high quality. CONCLUSION: The results suggest paucity, low population coverage, high thematic and methodological heterogeneity and low quality of the studies addressing CPR education, which were carried out in the Russian Federation. There is a critical need in conducting methodologically consistent, large-scale, randomized, controlled studies evaluating and comparing efficiency of educational interventions for teaching CPR in different population categories of Russia. PMID:29123601

Vertices cannot be hidden from quantum spatial search for almost all random graphs

NASA Astrophysics Data System (ADS)

Glos, Adam; Krawiec, Aleksandra; Kukulski, Ryszard; Puchała, Zbigniew

2018-04-01

In this paper, we show that all nodes can be found optimally for almost all random Erdős-Rényi G(n,p) graphs using continuous-time quantum spatial search procedure. This works for both adjacency and Laplacian matrices, though under different conditions. The first one requires p=ω (log ^8(n)/n), while the second requires p≥ (1+ɛ )log (n)/n, where ɛ >0. The proof was made by analyzing the convergence of eigenvectors corresponding to outlying eigenvalues in the \\Vert \\cdot \\Vert _∞ norm. At the same time for p<(1-ɛ )log (n)/n, the property does not hold for any matrix, due to the connectivity issues. Hence, our derivation concerning Laplacian matrix is tight.

System Design under Uncertainty: Evolutionary Optimization of the Gravity Probe-B Spacecraft

NASA Technical Reports Server (NTRS)

Pullen, Samuel P.; Parkinson, Bradford W.

1994-01-01

This paper discusses the application of evolutionary random-search algorithms (Simulated Annealing and Genetic Algorithms) to the problem of spacecraft design under performance uncertainty. Traditionally, spacecraft performance uncertainty has been measured by reliability. Published algorithms for reliability optimization are seldom used in practice because they oversimplify reality. The algorithm developed here uses random-search optimization to allow us to model the problem more realistically. Monte Carlo simulations are used to evaluate the objective function for each trial design solution. These methods have been applied to the Gravity Probe-B (GP-B) spacecraft being developed at Stanford University for launch in 1999, Results of the algorithm developed here for GP-13 are shown, and their implications for design optimization by evolutionary algorithms are discussed.

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

Evaluating the Florida Urban Search and Rescue System: Its Future Structure and Direction

DTIC Science & Technology

2009-12-01

FLORIDA URBAN SEARCH AND RESCUE SYSTEM: ITS FUTURE STRUCTURE AND DIRECTION by John J. DeIorio, II December 2009 Thesis Advisor: Ellen...COVERED Master’s Thesis 4. TITLE AND SUBTITLE Evaluating the Florida Urban Search and Rescue System: Its Future Structure and Direction 6. AUTHOR(S...professional liability, the system is in jeopardy of ceasing to exist. If this were to occur, Florida could not adequately protect its citizens during

Methods for identifying SNP interactions: a review on variations of Logic Regression, Random Forest and Bayesian logistic regression.

PubMed

Chen, Carla Chia-Ming; Schwender, Holger; Keith, Jonathan; Nunkesser, Robin; Mengersen, Kerrie; Macrossan, Paula

2011-01-01

Due to advancements in computational ability, enhanced technology and a reduction in the price of genotyping, more data are being generated for understanding genetic associations with diseases and disorders. However, with the availability of large data sets comes the inherent challenges of new methods of statistical analysis and modeling. Considering a complex phenotype may be the effect of a combination of multiple loci, various statistical methods have been developed for identifying genetic epistasis effects. Among these methods, logic regression (LR) is an intriguing approach incorporating tree-like structures. Various methods have built on the original LR to improve different aspects of the model. In this study, we review four variations of LR, namely Logic Feature Selection, Monte Carlo Logic Regression, Genetic Programming for Association Studies, and Modified Logic Regression-Gene Expression Programming, and investigate the performance of each method using simulated and real genotype data. We contrast these with another tree-like approach, namely Random Forests, and a Bayesian logistic regression with stochastic search variable selection.

Finding the Optimal Nets for Self-Folding Kirigami

NASA Astrophysics Data System (ADS)

Araújo, N. A. M.; da Costa, R. A.; Dorogovtsev, S. N.; Mendes, J. F. F.

2018-05-01

Three-dimensional shells can be synthesized from the spontaneous self-folding of two-dimensional templates of interconnected panels, called nets. However, some nets are more likely to self-fold into the desired shell under random movements. The optimal nets are the ones that maximize the number of vertex connections, i.e., vertices that have only two of its faces cut away from each other in the net. Previous methods for finding such nets are based on random search, and thus, they do not guarantee the optimal solution. Here, we propose a deterministic procedure. We map the connectivity of the shell into a shell graph, where the nodes and links of the graph represent the vertices and edges of the shell, respectively. Identifying the nets that maximize the number of vertex connections corresponds to finding the set of maximum leaf spanning trees of the shell graph. This method allows us not only to design the self-assembly of much larger shell structures but also to apply additional design criteria, as a complete catalog of the maximum leaf spanning trees is obtained.

Diffusion Geometry Unravels the Emergence of Functional Clusters in Collective Phenomena.

PubMed

De Domenico, Manlio

2017-04-21

Collective phenomena emerge from the interaction of natural or artificial units with a complex organization. The interplay between structural patterns and dynamics might induce functional clusters that, in general, are different from topological ones. In biological systems, like the human brain, the overall functionality is often favored by the interplay between connectivity and synchronization dynamics, with functional clusters that do not coincide with anatomical modules in most cases. In social, sociotechnical, and engineering systems, the quest for consensus favors the emergence of clusters. Despite the unquestionable evidence for mesoscale organization of many complex systems and the heterogeneity of their interconnectivity, a way to predict and identify the emergence of functional modules in collective phenomena continues to elude us. Here, we propose an approach based on random walk dynamics to define the diffusion distance between any pair of units in a networked system. Such a metric allows us to exploit the underlying diffusion geometry to provide a unifying framework for the intimate relationship between metastable synchronization, consensus, and random search dynamics in complex networks, pinpointing the functional mesoscale organization of synthetic and biological systems.

Diffusion Geometry Unravels the Emergence of Functional Clusters in Collective Phenomena

NASA Astrophysics Data System (ADS)

De Domenico, Manlio

2017-04-01

Collective phenomena emerge from the interaction of natural or artificial units with a complex organization. The interplay between structural patterns and dynamics might induce functional clusters that, in general, are different from topological ones. In biological systems, like the human brain, the overall functionality is often favored by the interplay between connectivity and synchronization dynamics, with functional clusters that do not coincide with anatomical modules in most cases. In social, sociotechnical, and engineering systems, the quest for consensus favors the emergence of clusters. Despite the unquestionable evidence for mesoscale organization of many complex systems and the heterogeneity of their interconnectivity, a way to predict and identify the emergence of functional modules in collective phenomena continues to elude us. Here, we propose an approach based on random walk dynamics to define the diffusion distance between any pair of units in a networked system. Such a metric allows us to exploit the underlying diffusion geometry to provide a unifying framework for the intimate relationship between metastable synchronization, consensus, and random search dynamics in complex networks, pinpointing the functional mesoscale organization of synthetic and biological systems.

A Real-Time All-Atom Structural Search Engine for Proteins

PubMed Central

Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

2014-01-01

Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license). PMID:25079944

A real-time all-atom structural search engine for proteins.

PubMed

Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F

2014-07-01

Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).

Categorizing words through semantic memory navigation

NASA Astrophysics Data System (ADS)

Borge-Holthoefer, J.; Arenas, A.

2010-03-01

Semantic memory is the cognitive system devoted to storage and retrieval of conceptual knowledge. Empirical data indicate that semantic memory is organized in a network structure. Everyday experience shows that word search and retrieval processes provide fluent and coherent speech, i.e. are efficient. This implies either that semantic memory encodes, besides thousands of words, different kind of links for different relationships (introducing greater complexity and storage costs), or that the structure evolves facilitating the differentiation between long-lasting semantic relations from incidental, phenomenological ones. Assuming the latter possibility, we explore a mechanism to disentangle the underlying semantic backbone which comprises conceptual structure (extraction of categorical relations between pairs of words), from the rest of information present in the structure. To this end, we first present and characterize an empirical data set modeled as a network, then we simulate a stochastic cognitive navigation on this topology. We schematize this latter process as uncorrelated random walks from node to node, which converge to a feature vectors network. By doing so we both introduce a novel mechanism for information retrieval, and point at the problem of category formation in close connection to linguistic and non-linguistic experience.

Making working memory work: The effects of extended practice on focus capacity and the processes of updating, forward access, and random access

PubMed Central

Price, John M.; Colflesh, Gregory J. H.; Cerella, John; Verhaeghen, Paul

2014-01-01

We investigated the effects of 10 hours of practice on variations of the N-Back task to investigate the processes underlying possible expansion of the focus of attention within working memory. Using subtractive logic, we showed that random access (i.e., Sternberg-like search) yielded a modest effect (a 50% increase in speed) whereas the processes of forward access (i.e., retrieval in order, as in a standard N-Back task) and updating (i.e., changing the contents of working memory) were executed about 5 times faster after extended practice. We additionally found that extended practice increased working memory capacity as measured by the size of the focus of attention for the forward-access task, but not for variations where probing was in random order. This suggests that working memory capacity may depend on the type of search process engaged, and that certain working-memory-related cognitive processes are more amenable to practice than others. PMID:24486803

A systematic review of randomized controlled trials of interventions designed to decrease child abuse in high-risk families

PubMed Central

Levey, Elizabeth J.; Gelaye, Bizu; Bain, Paul; Rondon, Marta B.; Borba, Christina P.C.; Henderson, David C.; Williams, Michelle A.

2017-01-01

Child abuse is a global problem, and parents with histories of childhood abuse are at increased risk of abusing their offspring. The objective of this systematic review is to provide a clear overview of the existing literature of randomized controlled trials evaluating the effectiveness of interventions to prevent child abuse. PubMed, PsychINFO, Web of Science, Sociological Abstracts, and CINAHL were systematically searched and expanded by hand search. This review includes all randomized controlled trials (RCTs) of interventions designed to prevent abuse among mothers identified as high-risk. Of the eight studies identified, only three found statistically significant reductions in abuse by any measure, and only two found reductions in incidents reported to child protective services. While much has been written about child abuse in high-risk families, few RCTs have been performed. Only home visitation has a significant evidence base for reducing child abuse, and the findings vary considerably. Also, data from low- and middle-income countries are limited. PMID:28110205

TemperSAT: A new efficient fair-sampling random k-SAT solver

NASA Astrophysics Data System (ADS)

Fang, Chao; Zhu, Zheng; Katzgraber, Helmut G.

The set membership problem is of great importance to many applications and, in particular, database searches for target groups. Recently, an approach to speed up set membership searches based on the NP-hard constraint-satisfaction problem (random k-SAT) has been developed. However, the bottleneck of the approach lies in finding the solution to a large SAT formula efficiently and, in particular, a large number of independent solutions is needed to reduce the probability of false positives. Unfortunately, traditional random k-SAT solvers such as WalkSAT are biased when seeking solutions to the Boolean formulas. By porting parallel tempering Monte Carlo to the sampling of binary optimization problems, we introduce a new algorithm (TemperSAT) whose performance is comparable to current state-of-the-art SAT solvers for large k with the added benefit that theoretically it can find many independent solutions quickly. We illustrate our results by comparing to the currently fastest implementation of WalkSAT, WalkSATlm.

Quantum search algorithms on a regular lattice

NASA Astrophysics Data System (ADS)

Hein, Birgit; Tanner, Gregor

2010-07-01

Quantum algorithms for searching for one or more marked items on a d-dimensional lattice provide an extension of Grover’s search algorithm including a spatial component. We demonstrate that these lattice search algorithms can be viewed in terms of the level dynamics near an avoided crossing of a one-parameter family of quantum random walks. We give approximations for both the level splitting at the avoided crossing and the effectively two-dimensional subspace of the full Hilbert space spanning the level crossing. This makes it possible to give the leading order behavior for the search time and the localization probability in the limit of large lattice size including the leading order coefficients. For d=2 and d=3, these coefficients are calculated explicitly. Closed form expressions are given for higher dimensions.

Image Search Reranking With Hierarchical Topic Awareness.

PubMed

Tian, Xinmei; Yang, Linjun; Lu, Yijuan; Tian, Qi; Tao, Dacheng

2015-10-01

With much attention from both academia and industrial communities, visual search reranking has recently been proposed to refine image search results obtained from text-based image search engines. Most of the traditional reranking methods cannot capture both relevance and diversity of the search results at the same time. Or they ignore the hierarchical topic structure of search result. Each topic is treated equally and independently. However, in real applications, images returned for certain queries are naturally in hierarchical organization, rather than simple parallel relation. In this paper, a new reranking method "topic-aware reranking (TARerank)" is proposed. TARerank describes the hierarchical topic structure of search results in one model, and seamlessly captures both relevance and diversity of the image search results simultaneously. Through a structured learning framework, relevance and diversity are modeled in TARerank by a set of carefully designed features, and then the model is learned from human-labeled training samples. The learned model is expected to predict reranking results with high relevance and diversity for testing queries. To verify the effectiveness of the proposed method, we collect an image search dataset and conduct comparison experiments on it. The experimental results demonstrate that the proposed TARerank outperforms the existing relevance-based and diversified reranking methods.

SIMBAD : a sequence-independent molecular-replacement pipeline

DOE PAGES

Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.; ...

2018-06-08

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD , this approach has solved novel cases that have otherwise proved difficult to solve.« less

SIMBAD : a sequence-independent molecular-replacement pipeline

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

Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD , this approach has solved novel cases that have otherwise proved difficult to solve.« less

3D Protein structure prediction with genetic tabu search algorithm

PubMed Central

2010-01-01

Background Protein structure prediction (PSP) has important applications in different fields, such as drug design, disease prediction, and so on. In protein structure prediction, there are two important issues. The first one is the design of the structure model and the second one is the design of the optimization technology. Because of the complexity of the realistic protein structure, the structure model adopted in this paper is a simplified model, which is called off-lattice AB model. After the structure model is assumed, optimization technology is needed for searching the best conformation of a protein sequence based on the assumed structure model. However, PSP is an NP-hard problem even if the simplest model is assumed. Thus, many algorithms have been developed to solve the global optimization problem. In this paper, a hybrid algorithm, which combines genetic algorithm (GA) and tabu search (TS) algorithm, is developed to complete this task. Results In order to develop an efficient optimization algorithm, several improved strategies are developed for the proposed genetic tabu search algorithm. The combined use of these strategies can improve the efficiency of the algorithm. In these strategies, tabu search introduced into the crossover and mutation operators can improve the local search capability, the adoption of variable population size strategy can maintain the diversity of the population, and the ranking selection strategy can improve the possibility of an individual with low energy value entering into next generation. Experiments are performed with Fibonacci sequences and real protein sequences. Experimental results show that the lowest energy obtained by the proposed GATS algorithm is lower than that obtained by previous methods. Conclusions The hybrid algorithm has the advantages from both genetic algorithm and tabu search algorithm. It makes use of the advantage of multiple search points in genetic algorithm, and can overcome poor hill-climbing capability in the conventional genetic algorithm by using the flexible memory functions of TS. Compared with some previous algorithms, GATS algorithm has better performance in global optimization and can predict 3D protein structure more effectively. PMID:20522256

Persistence and Adaptation in Immunity: T Cells Balance the Extent and Thoroughness of Search

PubMed Central

Fricke, G. Matthew; Letendre, Kenneth A.; Moses, Melanie E.; Cannon, Judy L.

2016-01-01

Effective search strategies have evolved in many biological systems, including the immune system. T cells are key effectors of the immune response, required for clearance of pathogenic infection. T cell activation requires that T cells encounter antigen-bearing dendritic cells within lymph nodes, thus, T cell search patterns within lymph nodes may be a crucial determinant of how quickly a T cell immune response can be initiated. Previous work suggests that T cell motion in the lymph node is similar to a Brownian random walk, however, no detailed analysis has definitively shown whether T cell movement is consistent with Brownian motion. Here, we provide a precise description of T cell motility in lymph nodes and a computational model that demonstrates how motility impacts T cell search efficiency. We find that both Brownian and Lévy walks fail to capture the complexity of T cell motion. Instead, T cell movement is better described as a correlated random walk with a heavy-tailed distribution of step lengths. Using computer simulations, we identify three distinct factors that contribute to increasing T cell search efficiency: 1) a lognormal distribution of step lengths, 2) motion that is directionally persistent over short time scales, and 3) heterogeneity in movement patterns. Furthermore, we show that T cells move differently in specific frequently visited locations that we call “hotspots” within lymph nodes, suggesting that T cells change their movement in response to the lymph node environment. Our results show that like foraging animals, T cells adapt to environmental cues, suggesting that adaption is a fundamental feature of biological search. PMID:26990103

Competitive Employment for Youth with Autism Spectrum Disorders: Early Results from a Randomized Clinical Trial

ERIC Educational Resources Information Center

Wehman, Paul H.; Schall, Carol M.; McDonough, Jennifer; Kregel, John; Brooke, Valerie; Molinelli, Alissa; Ham, Whitney; Graham, Carolyn W.; Riehle, J. Erin; Collins, Holly T.; Thiss, Weston

2014-01-01

For most youth with autism spectrum disorders (ASD), employment upon graduation from high school or college is elusive. Employment rates are reported in many studies to be very low despite many years of intensive special education services. This paper presented the preliminary results of a randomized clinical trial of Project SEARCH plus ASD…

A Literature Review of Randomized Controlled Trials of the Organization of Care at the End of Life

ERIC Educational Resources Information Center

Thomas, Roger E.; Wilson, Donna; Sheps, Sam

2006-01-01

We searched nine electronic databases for randomized controlled trials (RCTs) about care at the end of life and found 23 RCTs. We assessed their quality using the criteria of the Cochrane Collaboration. The RCTs researched three themes: (a) the effect of providing palliative care through dedicated community teams on quality of life, on the…

Short-term Internet search using makes people rely on search engines when facing unknown issues.

PubMed

Wang, Yifan; Wu, Lingdan; Luo, Liang; Zhang, Yifen; Dong, Guangheng

2017-01-01

The Internet search engines, which have powerful search/sort functions and ease of use features, have become an indispensable tool for many individuals. The current study is to test whether the short-term Internet search training can make people more dependent on it. Thirty-one subjects out of forty subjects completed the search training study which included a pre-test, a six-day's training of Internet search, and a post-test. During the pre- and post- tests, subjects were asked to search online the answers to 40 unusual questions, remember the answers and recall them in the scanner. Un-learned questions were randomly presented at the recalling stage in order to elicited search impulse. Comparing to the pre-test, subjects in the post-test reported higher impulse to use search engines to answer un-learned questions. Consistently, subjects showed higher brain activations in dorsolateral prefrontal cortex and anterior cingulate cortex in the post-test than in the pre-test. In addition, there were significant positive correlations self-reported search impulse and brain responses in the frontal areas. The results suggest that a simple six-day's Internet search training can make people dependent on the search tools when facing unknown issues. People are easily dependent on the Internet search engines.

Short-term Internet search using makes people rely on search engines when facing unknown issues

PubMed Central

Wang, Yifan; Wu, Lingdan; Luo, Liang; Zhang, Yifen

2017-01-01

The Internet search engines, which have powerful search/sort functions and ease of use features, have become an indispensable tool for many individuals. The current study is to test whether the short-term Internet search training can make people more dependent on it. Thirty-one subjects out of forty subjects completed the search training study which included a pre-test, a six-day’s training of Internet search, and a post-test. During the pre- and post- tests, subjects were asked to search online the answers to 40 unusual questions, remember the answers and recall them in the scanner. Un-learned questions were randomly presented at the recalling stage in order to elicited search impulse. Comparing to the pre-test, subjects in the post-test reported higher impulse to use search engines to answer un-learned questions. Consistently, subjects showed higher brain activations in dorsolateral prefrontal cortex and anterior cingulate cortex in the post-test than in the pre-test. In addition, there were significant positive correlations self-reported search impulse and brain responses in the frontal areas. The results suggest that a simple six-day’s Internet search training can make people dependent on the search tools when facing unknown issues. People are easily dependent on the Internet search engines. PMID:28441408

Perspective: Role of structure prediction in materials discovery and design

NASA Astrophysics Data System (ADS)

Needs, Richard J.; Pickard, Chris J.

2016-05-01

Materials informatics owes much to bioinformatics and the Materials Genome Initiative has been inspired by the Human Genome Project. But there is more to bioinformatics than genomes, and the same is true for materials informatics. Here we describe the rapidly expanding role of searching for structures of materials using first-principles electronic-structure methods. Structure searching has played an important part in unraveling structures of dense hydrogen and in identifying the record-high-temperature superconducting component in hydrogen sulfide at high pressures. We suggest that first-principles structure searching has already demonstrated its ability to determine structures of a wide range of materials and that it will play a central and increasing part in materials discovery and design.

On the efficiency of a randomized mirror descent algorithm in online optimization problems

NASA Astrophysics Data System (ADS)

Gasnikov, A. V.; Nesterov, Yu. E.; Spokoiny, V. G.

2015-04-01

A randomized online version of the mirror descent method is proposed. It differs from the existing versions by the randomization method. Randomization is performed at the stage of the projection of a subgradient of the function being optimized onto the unit simplex rather than at the stage of the computation of a subgradient, which is common practice. As a result, a componentwise subgradient descent with a randomly chosen component is obtained, which admits an online interpretation. This observation, for example, has made it possible to uniformly interpret results on weighting expert decisions and propose the most efficient method for searching for an equilibrium in a zero-sum two-person matrix game with sparse matrix.

A Multi-Start Evolutionary Local Search for the Two-Echelon Location Routing Problem

NASA Astrophysics Data System (ADS)

Nguyen, Viet-Phuong; Prins, Christian; Prodhon, Caroline

This paper presents a new hybrid metaheuristic between a greedy randomized adaptive search procedure (GRASP) and an evolutionary/iterated local search (ELS/ILS), using Tabu list to solve the two-echelon location routing problem (LRP-2E). The GRASP uses in turn three constructive heuristics followed by local search to generate the initial solutions. From a solution of GRASP, an intensification strategy is carried out by a dynamic alternation between ELS and ILS. In this phase, each child is obtained by mutation and evaluated through a splitting procedure of giant tour followed by a local search. The tabu list, defined by two characteristics of solution (total cost and number of trips), is used to avoid searching a space already explored. The results show that our metaheuristic clearly outperforms all previously published methods on LRP-2E benchmark instances. Furthermore, it is competitive with the best meta-heuristic published for the single-echelon LRP.

Contextual cueing impairment in patients with age-related macular degeneration.

PubMed

Geringswald, Franziska; Herbik, Anne; Hoffmann, Michael B; Pollmann, Stefan

2013-09-12

Visual attention can be guided by past experience of regularities in our visual environment. In the contextual cueing paradigm, incidental learning of repeated distractor configurations speeds up search times compared to random search arrays. Concomitantly, fewer fixations and more direct scan paths indicate more efficient visual exploration in repeated search arrays. In previous work, we found that simulating a central scotoma in healthy observers eliminated this search facilitation. Here, we investigated contextual cueing in patients with age-related macular degeneration (AMD) who suffer from impaired foveal vision. AMD patients performed visual search using only their more severely impaired eye (n = 13) as well as under binocular viewing (n = 16). Normal-sighted controls developed a significant contextual cueing effect. In comparison, patients showed only a small nonsignificant advantage for repeated displays when searching with their worse eye. When searching binocularly, they profited from contextual cues, but still less than controls. Number of fixations and scan pattern ratios showed a comparable pattern as search times. Moreover, contextual cueing was significantly correlated with acuity in monocular search. Thus, foveal vision loss may lead to impaired guidance of attention by contextual memory cues.

GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution

PubMed Central

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational difficulty and the ever-increasing amount of structural data, however, it is in general not feasible to perform exhaustive all-against-all structure comparisons necessary for comprehensive classifications. To efficiently handle such situations, we have previously proposed a method, now called GIRAF. We herein describe further improvements in the GIRAF protein structure search and alignment method. The GIRAF method achieves extremely efficient search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. In addition, it produces refined atom-wise alignments by iterative applications of the Hungarian method to the bipartite graph defined for a pair of superimposed structures. By combining the refined alignments based on different local coordinate frames, it is made possible to align structures involving domain movements. We provide detailed accounts for the database design, the search and alignment algorithms as well as some benchmark results. PMID:27493524

Efficient RNA structure comparison algorithms.

PubMed

Arslan, Abdullah N; Anandan, Jithendar; Fry, Eric; Monschke, Keith; Ganneboina, Nitin; Bowerman, Jason

2017-12-01

Recently proposed relative addressing-based ([Formula: see text]) RNA secondary structure representation has important features by which an RNA structure database can be stored into a suffix array. A fast substructure search algorithm has been proposed based on binary search on this suffix array. Using this substructure search algorithm, we present a fast algorithm that finds the largest common substructure of given multiple RNA structures in [Formula: see text] format. The multiple RNA structure comparison problem is NP-hard in its general formulation. We introduced a new problem for comparing multiple RNA structures. This problem has more strict similarity definition and objective, and we propose an algorithm that solves this problem efficiently. We also develop another comparison algorithm that iteratively calls this algorithm to locate nonoverlapping large common substructures in compared RNAs. With the new resulting tools, we improved the RNASSAC website (linked from http://faculty.tamuc.edu/aarslan ). This website now also includes two drawing tools: one specialized for preparing RNA substructures that can be used as input by the search tool, and another one for automatically drawing the entire RNA structure from a given structure sequence.

Asymmetry in search.

PubMed

Kaindl, H; Kainz, G; Radda, K

2001-01-01

Most of the work on search in artificial intelligence (AI) deals with one search direction only-mostly forward search-although it is known that a structural asymmetry of the search graph causes differences in the efficiency of searching in the forward or the backward direction, respectively. In the case of symmetrical graph structure, however, current theory would not predict such differences in efficiency. In several classes of job sequencing problems, we observed a phenomenon of asymmetry in search that relates to the distribution of the are costs in the search graph. This phenomenon can be utilized for improving the search efficiency by a new algorithm that automatically selects the search direction. We demonstrate fur a class of job sequencing problems that, through the utilization of this phenomenon, much more difficult problems can be solved-according to our best knowledge-than by the best published approach, and on the same problems, the running time is much reduced. As a consequence, we propose to check given problems for asymmetrical distribution of are costs that may cause asymmetry in search.

Online Patent Searching: The Realities.

ERIC Educational Resources Information Center

Kaback, Stuart M.

1983-01-01

Considers patent subject searching capabilities of major online databases, noting patent claims, "deep-indexed" files, test searches, retrieval of related references, multi-database searching, improvements needed in indexing of chemical structures, full text searching, improvements needed in handling numerical data, and augmenting a…

Laboratory animal research published in plastic surgery journals in 2014 has extensive waste: A systematic review.

PubMed

Freshwater, M Felix

2015-11-01

Laboratory animal research must be designed in a manner that minimizes bias if it is to yield valid and reproducible results. In 2009, a survey that examined 271 animal studies found that 87% did not use randomization and 86% did not use blinding. This has been called "research waste" because it wasted time and resources. This systematic review measured the quantity of research waste in plastic surgery journals in 2014. The PRISMA-P protocol was used. SCOPUS and PubMed searches were done for all animal studies published in 2014 in Aesthetic Plast Surg, Aesthet Surg J, Ann Plast Surg, JPRAS, J Plast Surg Hand Surg and Plast Reconstr Surg. These were supplemented by manual searches of the 2014 issues not indexed. Articles were analyzed for descriptions of randomization, randomization methodology, allocation concealment, and blinding of the primary outcome assessment. Corresponding authors who mentioned randomization without elaborating were emailed for details. 112 of 154 articles met the inclusion criteria. Only 24/112 (21.4%) had blinding of the primary outcome measure, 28/110 (25.5%) of articles that required randomization mentioned it. While 12/28 articles clearly described randomizing the intervention, only 4/28 described the method of randomization, and 2/28 mentioned allocation concealment. Only two authors responded and described the randomization methodology. The quality of plastic surgery laboratory animal research published in 2014 was poor. Use of the National Centre for the Replacement Refinement & Reduction of Animals in Research's "Animal Research: Reporting In Vivo Experiments" (ARRIVE) Guidelines by authors, and enforcement of them by editors and reviewers could improve research quality and reduce waste. Copyright © 2015 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

A Systematic Review of Surgical Randomized Controlled Trials: Part 2. Funding Source, Conflict of Interest, and Sample Size in Plastic Surgery.

PubMed

Voineskos, Sophocles H; Coroneos, Christopher J; Ziolkowski, Natalia I; Kaur, Manraj N; Banfield, Laura; Meade, Maureen O; Chung, Kevin C; Thoma, Achilleas; Bhandari, Mohit

2016-02-01

The authors examined industry support, conflict of interest, and sample size in plastic surgery randomized controlled trials that compared surgical interventions. They hypothesized that industry-funded trials demonstrate statistically significant outcomes more often, and randomized controlled trials with small sample sizes report statistically significant results more frequently. An electronic search identified randomized controlled trials published between 2000 and 2013. Independent reviewers assessed manuscripts and performed data extraction. Funding source, conflict of interest, primary outcome direction, and sample size were examined. Chi-squared and independent-samples t tests were used in the analysis. The search identified 173 randomized controlled trials, of which 100 (58 percent) did not acknowledge funding status. A relationship between funding source and trial outcome direction was not observed. Both funding status and conflict of interest reporting improved over time. Only 24 percent (six of 25) of industry-funded randomized controlled trials reported authors to have independent control of data and manuscript contents. The mean number of patients randomized was 73 per trial (median, 43, minimum, 3, maximum, 936). Small trials were not found to be positive more often than large trials (p = 0.87). Randomized controlled trials with small sample size were common; however, this provides great opportunity for the field to engage in further collaboration and produce larger, more definitive trials. Reporting of trial funding and conflict of interest is historically poor, but it greatly improved over the study period. Underreporting at author and journal levels remains a limitation when assessing the relationship between funding source and trial outcomes. Improved reporting and manuscript control should be goals that both authors and journals can actively achieve.

The effects of Sahaja Yoga meditation on mental health: a systematic review.

PubMed

Hendriks, Tom

2018-05-30

Objectives To determine the efficacy of Sahaja Yoga (SY) meditation on mental health among clinical and healthy populations. Methods All publications on SY were eligible. Databases were searched up to November 2017, namely PubMed, MEDLINE (NLM), PsychINFO, and Scopus. An internet search (Google Scholar) was also conducted. The quality of the randomized controlled trails was assessed using the Cochrane Risk Assessment for Bias. The quality of cross-sectional studies, a non-randomized controlled trial and a cohort study was assessed with the Newcastle-Ottawa Quality Assessment Scale. Results We included a total of eleven studies; four randomized controlled trials, one non-randomized controlled trial, five cross-sectional studies, and one prospective cohort study. The studies included a total of 910 participants. Significant findings were reported in relation to the following outcomes: anxiety, depression, stress, subjective well-being, and psychological well-being. Two randomized studies were rated as high quality studies, two randomized studies as low quality studies. The quality of the non-randomized trial, the cross-sectional studies and the cohort study was high. Effect sizes could not be calculated in five studies due to unclear or incomplete reporting. Conclusions After reviewing the articles and taking the quality of the studies into account, it appears that SY may reduce depression and possibly anxiety. In addition, the practice of SY is also associated with increased subjective wellbeing and psychological well-beng. However, due to the limited number of publications, definite conclusions on the effects of SY cannot be made and more high quality randomized studies are needed to justify any firm conclusions on the beneficial effects of SY on mental health.

Inducing Behavioral Change in Seekers of Pro-Anorexia Content Using Internet Advertisements: Randomized Controlled Trial

PubMed Central

Brunstein-Klomek, Anat; Mandel, Or; Hadas, Arie; Fennig, Silvana

2018-01-01

Background The influence of pro-anorexia (pro-ana) websites is debated, with studies indicating both negative and positive effects, as well as significant variation in the effects of different websites for those suffering from eating disorders (EDs) and the general population. Online advertising, known to induce behavioral change both online and in the physical world, has not been used so far to modify the search behavior of people seeking pro-ana content. Objective The objective of this randomized controlled trial (RCT) was to examine if online advertisements (ads) can change online search behaviors of users who are looking for online pro-ana content. Methods Using the Bing Ads system, we conducted an RCT to randomly expose the searchers for pro-ana content to 10 different ads referring people to one of the three websites: the National Eating Disorders Association, the National Institutes of Mental Health, and MyProAna. MyProAna is a pro-ana website that was found in a previous study to be associated with less pathological online behaviors than other pro-ana websites. We followed participants exposed and unexposed to the ads to explore their past and future online searches. The ads were shown 25,554 times and clicked on 217 times. Results Exposure to the ads was associated with a decrease in searches for pro-ana and self-harm content. Reductions were greatest among those referred to MyProAna (reduction of 34.0% [73/215] and 37.2% [80/215] for pro-ana and self-harm, respectively) compared with users who were referred elsewhere (reduction of 15.47% [410/2650] and 3.21% [85/2650], respectively), and with users who were not shown the ads, who increased their behaviors (increase of 57.12% [6462/11,314] and 4.07% [461/11,314], respectively). In addition, those referred to MyProAna increased their search for treatment, as did control users, who did so to a lesser extent. However, users referred elsewhere decreased their searches for this content. Conclusions We found that referring users interested in ED-related content to specific pro-ana communities might lessen their maladaptive online search behavior. This suggests that those who are preoccupied with EDs can be redirected to less pathological online searches through appropriate pathways. Trial Registration ClinicalTrials.gov NCT03439553; https://clinicaltrials.gov/show/NCT03439553 (Archived by WebCite at http://www.webcitation.org/6xNYnxYlw) PMID:29472176

Inducing Behavioral Change in Seekers of Pro-Anorexia Content Using Internet Advertisements: Randomized Controlled Trial.

PubMed

Yom-Tov, Elad; Brunstein-Klomek, Anat; Mandel, Or; Hadas, Arie; Fennig, Silvana

2018-02-22

The influence of pro-anorexia (pro-ana) websites is debated, with studies indicating both negative and positive effects, as well as significant variation in the effects of different websites for those suffering from eating disorders (EDs) and the general population. Online advertising, known to induce behavioral change both online and in the physical world, has not been used so far to modify the search behavior of people seeking pro-ana content. The objective of this randomized controlled trial (RCT) was to examine if online advertisements (ads) can change online search behaviors of users who are looking for online pro-ana content. Using the Bing Ads system, we conducted an RCT to randomly expose the searchers for pro-ana content to 10 different ads referring people to one of the three websites: the National Eating Disorders Association, the National Institutes of Mental Health, and MyProAna. MyProAna is a pro-ana website that was found in a previous study to be associated with less pathological online behaviors than other pro-ana websites. We followed participants exposed and unexposed to the ads to explore their past and future online searches. The ads were shown 25,554 times and clicked on 217 times. Exposure to the ads was associated with a decrease in searches for pro-ana and self-harm content. Reductions were greatest among those referred to MyProAna (reduction of 34.0% [73/215] and 37.2% [80/215] for pro-ana and self-harm, respectively) compared with users who were referred elsewhere (reduction of 15.47% [410/2650] and 3.21% [85/2650], respectively), and with users who were not shown the ads, who increased their behaviors (increase of 57.12% [6462/11,314] and 4.07% [461/11,314], respectively). In addition, those referred to MyProAna increased their search for treatment, as did control users, who did so to a lesser extent. However, users referred elsewhere decreased their searches for this content. We found that referring users interested in ED-related content to specific pro-ana communities might lessen their maladaptive online search behavior. This suggests that those who are preoccupied with EDs can be redirected to less pathological online searches through appropriate pathways. ClinicalTrials.gov NCT03439553; https://clinicaltrials.gov/show/NCT03439553 (Archived by WebCite at http://www.webcitation.org/6xNYnxYlw). ©Elad Yom-Tov, Anat Brunstein-Klomek, Or Mandel, Arie Hadas, Silvana Fennig. Originally published in JMIR Mental Health (http://mental.jmir.org), 22.02.2018.

Multi-Objective Community Detection Based on Memetic Algorithm

PubMed Central

2015-01-01

Community detection has drawn a lot of attention as it can provide invaluable help in understanding the function and visualizing the structure of networks. Since single objective optimization methods have intrinsic drawbacks to identifying multiple significant community structures, some methods formulate the community detection as multi-objective problems and adopt population-based evolutionary algorithms to obtain multiple community structures. Evolutionary algorithms have strong global search ability, but have difficulty in locating local optima efficiently. In this study, in order to identify multiple significant community structures more effectively, a multi-objective memetic algorithm for community detection is proposed by combining multi-objective evolutionary algorithm with a local search procedure. The local search procedure is designed by addressing three issues. Firstly, nondominated solutions generated by evolutionary operations and solutions in dominant population are set as initial individuals for local search procedure. Then, a new direction vector named as pseudonormal vector is proposed to integrate two objective functions together to form a fitness function. Finally, a network specific local search strategy based on label propagation rule is expanded to search the local optimal solutions efficiently. The extensive experiments on both artificial and real-world networks evaluate the proposed method from three aspects. Firstly, experiments on influence of local search procedure demonstrate that the local search procedure can speed up the convergence to better partitions and make the algorithm more stable. Secondly, comparisons with a set of classic community detection methods illustrate the proposed method can find single partitions effectively. Finally, the method is applied to identify hierarchical structures of networks which are beneficial for analyzing networks in multi-resolution levels. PMID:25932646

Multi-objective community detection based on memetic algorithm.

PubMed

Wu, Peng; Pan, Li

2015-01-01

Community detection has drawn a lot of attention as it can provide invaluable help in understanding the function and visualizing the structure of networks. Since single objective optimization methods have intrinsic drawbacks to identifying multiple significant community structures, some methods formulate the community detection as multi-objective problems and adopt population-based evolutionary algorithms to obtain multiple community structures. Evolutionary algorithms have strong global search ability, but have difficulty in locating local optima efficiently. In this study, in order to identify multiple significant community structures more effectively, a multi-objective memetic algorithm for community detection is proposed by combining multi-objective evolutionary algorithm with a local search procedure. The local search procedure is designed by addressing three issues. Firstly, nondominated solutions generated by evolutionary operations and solutions in dominant population are set as initial individuals for local search procedure. Then, a new direction vector named as pseudonormal vector is proposed to integrate two objective functions together to form a fitness function. Finally, a network specific local search strategy based on label propagation rule is expanded to search the local optimal solutions efficiently. The extensive experiments on both artificial and real-world networks evaluate the proposed method from three aspects. Firstly, experiments on influence of local search procedure demonstrate that the local search procedure can speed up the convergence to better partitions and make the algorithm more stable. Secondly, comparisons with a set of classic community detection methods illustrate the proposed method can find single partitions effectively. Finally, the method is applied to identify hierarchical structures of networks which are beneficial for analyzing networks in multi-resolution levels.

A method of searching for related literature on protein structure analysis by considering a user's intention

PubMed Central

2015-01-01

Background In recent years, with advances in techniques for protein structure analysis, the knowledge about protein structure and function has been published in a vast number of articles. A method to search for specific publications from such a large pool of articles is needed. In this paper, we propose a method to search for related articles on protein structure analysis by using an article itself as a query. Results Each article is represented as a set of concepts in the proposed method. Then, by using similarities among concepts formulated from databases such as Gene Ontology, similarities between articles are evaluated. In this framework, the desired search results vary depending on the user's search intention because a variety of information is included in a single article. Therefore, the proposed method provides not only one input article (primary article) but also additional articles related to it as an input query to determine the search intention of the user, based on the relationship between two query articles. In other words, based on the concepts contained in the input article and additional articles, we actualize a relevant literature search that considers user intention by varying the degree of attention given to each concept and modifying the concept hierarchy graph. Conclusions We performed an experiment to retrieve relevant papers from articles on protein structure analysis registered in the Protein Data Bank by using three query datasets. The experimental results yielded search results with better accuracy than when user intention was not considered, confirming the effectiveness of the proposed method. PMID:25952498

The handsearching of 2 medical journals of Bahrain for reports of randomized controlled trials.

PubMed

Al-Hajeri, Amani A; Fedorowicz, Zbigniew; Amin, Fawzi A; Eisinga, Anne

2006-04-01

To identify reports of randomized trials by handsearching 2 Bahrain medical journals, which are indexed in the biomedical database EMBASE and to determine any added value of the handsearching by comparing the reports found by handsearching with what would have been found by searching EMBASE to examine (i) the precision and sensitivity of the EMBASE index term Randomized Controlled Trial (RCT) and (ii) The Cochrane Collaboration's systematic electronic search of EMBASE (which uses 4 index terms and 9 free-text terms). All issues of the Bahrain Medical Bulletin (BMB) (1979-2004) and the Journal of the Bahrain Medical Society (JBMS) (1989-2004) were handsearched in February 2005 for reports of RCTs or Controlled Clinical Trials (CCTs), according to Cochrane eligibility criteria. Out of 395 articles in BMB we found reports of 12 RCTs and 4 CCTs. Distribution by country of corresponding author: Jordan (4 RCTs, one CCT), Bahrain (one RCT, one CCT), India (3 RCTs, one CCT), Kuwait (one CCT), Saudi Arabia (2 RCTs), USA/Bahrain (one RCT), and Oman (one RCT); and by specialty: Anesthesia (8), Surgery (1) Pediatrics (1), Radiotherapy (1), Community Medicine (1), Sports Medicine (1), Obstetrics/Gynecology (3). The Journal of the Bahrain Medical Society included reports of 14 RCTs and 3 CCTs, out of 97 articles. Distribution by country of corresponding author: Jordan (9 RCTs, 2 CCTs), Bahrain (3 RCTs), Egypt (one RCT), Kuwait (one RCT), and Saudi Arabia (one RCT); and by specialty: Anesthesia (7), General Surgery (3), Obstetrics/Gynecology (1), Radiotherapy (1), Pediatrics (1), Orthopaedic Surgery (1), Education (1) Ear Nose and Throat (1) Ophthalmology (1). Overall, of the 33 reports of trials found by handsearching both journals, only 23 were included in EMBASE of which only 6 had been indexed with the term RCT. Of the 23 reports of trials included in EMBASE, 16 had been identified in the Collaboration s systematic search of EMBASE. Two reports of trials could have been retrieved by this search but there was insufficient information in the title and abstract to code these as trials. The EMBASE records for the remaining 5 reports of trials did not contain terms currently used by The Cochrane Collaboration to identify reports of randomized trials in this database. The handsearching of these journals will help minimize publication bias by locating randomized trials not previously identified and, through their inclusion in the Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library, will ensure reports of randomized trials will not remain buried through indexing bias.

Effect of fermented milk-based probiotic preparations on Helicobacter pylori eradication: a systematic review and meta-analysis of randomized-controlled trials.

PubMed

Sachdeva, Aarti; Nagpal, Jitender

2009-01-01

To evaluate the effect of fermented milk-based probiotic preparations on Helicobacter pylori eradication. Systematic review of randomized controlled trials. Electronic databases and hand search of reviews, bibliographies of books and abstracts and proceedings of international conferences. Included trials had to be randomized or quasi-randomized and controlled, using fermented milk-based probiotics in the intervention group, treating Helicobacter-infected patients and evaluating improvement or eradication of H. pylori as an outcome. The search identified 10 eligible randomized controlled trials. Data were available for 963 patients, of whom 498 were in the treatment group and 465 in the control group. The pooled odds ratio (studies n=9) for eradication by intention-to-treat analysis in the treatment versus control group was 1.91 (1.38-2.67; P<0.0001) using the fixed effects model; test for heterogeneity (Cochran's Q=5.44; P=0.488). The pooled risk difference was 0.10 (95% CI 0.05-0.15; P<0.0001) by the fixed effects model (Cochran's Q=13.41; P=0.144). The pooled odds ratio for the number of patients with any adverse effect was 0.51 (95% CI 0.10-2.57; P=0.41; random effects model; heterogeneity by Cochran's Q=68.5; P<0.0001). Fermented milk-based probiotic preparations improve H. pylori eradication rates by approximately 5-15%, whereas the effect on adverse effects is heterogeneous.

Detection of IUPAC and IUPAC-like chemical names

PubMed Central

Klinger, Roman; Kolářik, Corinna; Fluck, Juliane; Hofmann-Apitius, Martin; Friedrich, Christoph M.

2008-01-01

Motivation: Chemical compounds like small signal molecules or other biological active chemical substances are an important entity class in life science publications and patents. Several representations and nomenclatures for chemicals like SMILES, InChI, IUPAC or trivial names exist. Only SMILES and InChI names allow a direct structure search, but in biomedical texts trivial names and Iupac like names are used more frequent. While trivial names can be found with a dictionary-based approach and in such a way mapped to their corresponding structures, it is not possible to enumerate all IUPAC names. In this work, we present a new machine learning approach based on conditional random fields (CRF) to find mentions of IUPAC and IUPAC-like names in scientific text as well as its evaluation and the conversion rate with available name-to-structure tools. Results: We present an IUPAC name recognizer with an F1 measure of 85.6% on a MEDLINE corpus. The evaluation of different CRF orders and offset conjunction orders demonstrates the importance of these parameters. An evaluation of hand-selected patent sections containing large enumerations and terms with mixed nomenclature shows a good performance on these cases (F1 measure 81.5%). Remaining recognition problems are to detect correct borders of the typically long terms, especially when occurring in parentheses or enumerations. We demonstrate the scalability of our implementation by providing results from a full MEDLINE run. Availability: We plan to publish the corpora, annotation guideline as well as the conditional random field model as a UIMA component. Contact: roman.klinger@scai.fraunhofer.de PMID:18586724

Stochastic Control Synthesis of Systems with Structured Uncertainty

NASA Technical Reports Server (NTRS)

Padula, Sharon L. (Technical Monitor); Crespo, Luis G.

2003-01-01

This paper presents a study on the design of robust controllers by using random variables to model structured uncertainty for both SISO and MIMO feedback systems. Once the parameter uncertainty is prescribed with probability density functions, its effects are propagated through the analysis leading to stochastic metrics for the system's output. Control designs that aim for satisfactory performances while guaranteeing robust closed loop stability are attained by solving constrained non-linear optimization problems in the frequency domain. This approach permits not only to quantify the probability of having unstable and unfavorable responses for a particular control design but also to search for controls while favoring the values of the parameters with higher chance of occurrence. In this manner, robust optimality is achieved while the characteristic conservatism of conventional robust control methods is eliminated. Examples that admit closed form expressions for the probabilistic metrics of the output are used to elucidate the nature of the problem at hand and validate the proposed formulations.

Object Classification in Semi Structured Enviroment Using Forward-Looking Sonar

PubMed Central

dos Santos, Matheus; Ribeiro, Pedro Otávio; Núñez, Pedro; Botelho, Silvia

2017-01-01

The submarine exploration using robots has been increasing in recent years. The automation of tasks such as monitoring, inspection, and underwater maintenance requires the understanding of the robot’s environment. The object recognition in the scene is becoming a critical issue for these systems. On this work, an underwater object classification pipeline applied in acoustic images acquired by Forward-Looking Sonar (FLS) are studied. The object segmentation combines thresholding, connected pixels searching and peak of intensity analyzing techniques. The object descriptor extract intensity and geometric features of the detected objects. A comparison between the Support Vector Machine, K-Nearest Neighbors, and Random Trees classifiers are presented. An open-source tool was developed to annotate and classify the objects and evaluate their classification performance. The proposed method efficiently segments and classifies the structures in the scene using a real dataset acquired by an underwater vehicle in a harbor area. Experimental results demonstrate the robustness and accuracy of the method described in this paper. PMID:28961163

Extracting Near-Field Structures Related to Noise Production in High Speed Jet

NASA Astrophysics Data System (ADS)

Kan, Pinqing; Lewalle, Jacques; Syracuse University Team

2015-11-01

Jet noise research started with Lighthill's seminal work on aerodynamic sound in 1952. The current consensus is that jet noise has two main kinds of sources, the large turbulent structures and the fine-scale turbulence. Coherent structures and the noise they produce are the focus of this paper because they offer better odds for control and they are associated with the most energetic part of the acoustic spectrum. We develop an algorithm using cross-correlation, continuous wavelet and pattern recognition techniques to search for near-field (NF) structures associated with far-field (FF) acoustic noise at aft angles. An experimental data is analyzed which measured a cold circular jet of Mach 0.6 (Low et al. 2013). The events identified are short wave packets in the time-frequency domain, distorted by ambient perturbations. The statistics of the event properties, including intermittency, frequency and magnitude are consistent with observations from other researchers. We investigate the localization and time sequencing of the events and use ensemble average to bring out the distinct structures associated to noise production. The filtered signals including / excluding the events are compared and the results are further tested using synthetic and randomized signals. This work has been funded by Spectral Energies LLC through an Air Force Research Lab SBIR, an AFOSR Grant and Syracuse University.

Microscopy as a statistical, Rényi-Ulam, half-lie game: a new heuristic search strategy to accelerate imaging.

PubMed

Drumm, Daniel W; Greentree, Andrew D

2017-11-07

Finding a fluorescent target in a biological environment is a common and pressing microscopy problem. This task is formally analogous to the canonical search problem. In ideal (noise-free, truthful) search problems, the well-known binary search is optimal. The case of half-lies, where one of two responses to a search query may be deceptive, introduces a richer, Rényi-Ulam problem and is particularly relevant to practical microscopy. We analyse microscopy in the contexts of Rényi-Ulam games and half-lies, developing a new family of heuristics. We show the cost of insisting on verification by positive result in search algorithms; for the zero-half-lie case bisectioning with verification incurs a 50% penalty in the average number of queries required. The optimal partitioning of search spaces directly following verification in the presence of random half-lies is determined. Trisectioning with verification is shown to be the most efficient heuristic of the family in a majority of cases.

Fast protein tertiary structure retrieval based on global surface shape similarity.

PubMed

Sael, Lee; Li, Bin; La, David; Fang, Yi; Ramani, Karthik; Rustamov, Raif; Kihara, Daisuke

2008-09-01

Characterization and identification of similar tertiary structure of proteins provides rich information for investigating function and evolution. The importance of structure similarity searches is increasing as structure databases continue to expand, partly due to the structural genomics projects. A crucial drawback of conventional protein structure comparison methods, which compare structures by their main-chain orientation or the spatial arrangement of secondary structure, is that a database search is too slow to be done in real-time. Here we introduce a global surface shape representation by three-dimensional (3D) Zernike descriptors, which represent a protein structure compactly as a series expansion of 3D functions. With this simplified representation, the search speed against a few thousand structures takes less than a minute. To investigate the agreement between surface representation defined by 3D Zernike descriptor and conventional main-chain based representation, a benchmark was performed against a protein classification generated by the combinatorial extension algorithm. Despite the different representation, 3D Zernike descriptor retrieved proteins of the same conformation defined by combinatorial extension in 89.6% of the cases within the top five closest structures. The real-time protein structure search by 3D Zernike descriptor will open up new possibility of large-scale global and local protein surface shape comparison. 2008 Wiley-Liss, Inc.

Interpretation of the results of statistical measurements. [search for basic probability model

NASA Technical Reports Server (NTRS)

Olshevskiy, V. V.

1973-01-01

For random processes, the calculated probability characteristic, and the measured statistical estimate are used in a quality functional, which defines the difference between the two functions. Based on the assumption that the statistical measurement procedure is organized so that the parameters for a selected model are optimized, it is shown that the interpretation of experimental research is a search for a basic probability model.

Scaling laws of marine predator search behaviour.

PubMed

Sims, David W; Southall, Emily J; Humphries, Nicolas E; Hays, Graeme C; Bradshaw, Corey J A; Pitchford, Jonathan W; James, Alex; Ahmed, Mohammed Z; Brierley, Andrew S; Hindell, Mark A; Morritt, David; Musyl, Michael K; Righton, David; Shepard, Emily L C; Wearmouth, Victoria J; Wilson, Rory P; Witt, Matthew J; Metcalfe, Julian D

2008-02-28

Many free-ranging predators have to make foraging decisions with little, if any, knowledge of present resource distribution and availability. The optimal search strategy they should use to maximize encounter rates with prey in heterogeneous natural environments remains a largely unresolved issue in ecology. Lévy walks are specialized random walks giving rise to fractal movement trajectories that may represent an optimal solution for searching complex landscapes. However, the adaptive significance of this putative strategy in response to natural prey distributions remains untested. Here we analyse over a million movement displacements recorded from animal-attached electronic tags to show that diverse marine predators-sharks, bony fishes, sea turtles and penguins-exhibit Lévy-walk-like behaviour close to a theoretical optimum. Prey density distributions also display Lévy-like fractal patterns, suggesting response movements by predators to prey distributions. Simulations show that predators have higher encounter rates when adopting Lévy-type foraging in natural-like prey fields compared with purely random landscapes. This is consistent with the hypothesis that observed search patterns are adapted to observed statistical patterns of the landscape. This may explain why Lévy-like behaviour seems to be widespread among diverse organisms, from microbes to humans, as a 'rule' that evolved in response to patchy resource distributions.

Building a Better Fragment Library for De Novo Protein Structure Prediction

PubMed Central

de Oliveira, Saulo H. P.; Shi, Jiye; Deane, Charlotte M.

2015-01-01

Fragment-based approaches are the current standard for de novo protein structure prediction. These approaches rely on accurate and reliable fragment libraries to generate good structural models. In this work, we describe a novel method for structure fragment library generation and its application in fragment-based de novo protein structure prediction. The importance of correct testing procedures in assessing the quality of fragment libraries is demonstrated. In particular, the exclusion of homologs to the target from the libraries to correctly simulate a de novo protein structure prediction scenario, something which surprisingly is not always done. We demonstrate that fragments presenting different predominant predicted secondary structures should be treated differently during the fragment library generation step and that exhaustive and random search strategies should both be used. This information was used to develop a novel method, Flib. On a validation set of 41 structurally diverse proteins, Flib libraries presents both a higher precision and coverage than two of the state-of-the-art methods, NNMake and HHFrag. Flib also achieves better precision and coverage on the set of 275 protein domains used in the two previous experiments of the the Critical Assessment of Structure Prediction (CASP9 and CASP10). We compared Flib libraries against NNMake libraries in a structure prediction context. Of the 13 cases in which a correct answer was generated, Flib models were more accurate than NNMake models for 10. “Flib is available for download at: http://www.stats.ox.ac.uk/research/proteins/resources”. PMID:25901595

Faster quantum walk search on a weighted graph

NASA Astrophysics Data System (ADS)

Wong, Thomas G.

2015-09-01

A randomly walking quantum particle evolving by Schrödinger's equation searches for a unique marked vertex on the "simplex of complete graphs" in time Θ (N3 /4) . We give a weighted version of this graph that preserves vertex transitivity, and we show that the time to search on it can be reduced to nearly Θ (√{N }) . To prove this, we introduce two extensions to degenerate perturbation theory: an adjustment that distinguishes the weights of the edges and a method to determine how precisely the jumping rate of the quantum walk must be chosen.

A Survey in Indexing and Searching XML Documents.

ERIC Educational Resources Information Center

Luk, Robert W. P.; Leong, H. V.; Dillon, Tharam S.; Chan, Alvin T. S.; Croft, W. Bruce; Allan, James

2002-01-01

Discussion of XML focuses on indexing techniques for XML documents, grouping them into flat-file, semistructured, and structured indexing paradigms. Highlights include searching techniques, including full text search and multistage search; search result presentations; database and information retrieval system integration; XML query languages; and…

An approach in building a chemical compound search engine in oracle database.

PubMed

Wang, H; Volarath, P; Harrison, R

2005-01-01

A searching or identifying of chemical compounds is an important process in drug design and in chemistry research. An efficient search engine involves a close coupling of the search algorithm and database implementation. The database must process chemical structures, which demands the approaches to represent, store, and retrieve structures in a database system. In this paper, a general database framework for working as a chemical compound search engine in Oracle database is described. The framework is devoted to eliminate data type constrains for potential search algorithms, which is a crucial step toward building a domain specific query language on top of SQL. A search engine implementation based on the database framework is also demonstrated. The convenience of the implementation emphasizes the efficiency and simplicity of the framework.

In search of random noise

NASA Technical Reports Server (NTRS)

Kester, DO; Bontekoe, Tj. Romke

1994-01-01

In order to make the best high resolution images of IRAS data it is necessary to incorporate any knowledge about the instrument into a model: the IRAS model. This is necessary since every remaining systematic effect will be amplified by any high resolution technique into spurious artifacts in the images. The search for random noise is in fact the never-ending quest for better quality results, and can only be obtained by better models. The Dutch high-resolution effort has resulted in HIRAS which drives the MEMSYS5 algorithm. It is specifically designed for IRAS image construction. A detailed description of HIRAS with many results is in preparation. In this paper we emphasize many of the instrumental effects incorporated in the IRAS model, including our improved 100 micron IRAS response functions.

Overt attention in contextual cuing of visual search is driven by the attentional set, but not by the predictiveness of distractors.

PubMed

Beesley, Tom; Hanafi, Gunadi; Vadillo, Miguel A; Shanks, David R; Livesey, Evan J

2018-05-01

Two experiments examined biases in selective attention during contextual cuing of visual search. When participants were instructed to search for a target of a particular color, overt attention (as measured by the location of fixations) was biased strongly toward distractors presented in that same color. However, when participants searched for targets that could be presented in 1 of 2 possible colors, overt attention was not biased between the different distractors, regardless of whether these distractors predicted the location of the target (repeating) or did not (randomly arranged). These data suggest that selective attention in visual search is guided only by the demands of the target detection task (the attentional set) and not by the predictive validity of the distractor elements. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

An improved harmony search algorithm for emergency inspection scheduling

NASA Astrophysics Data System (ADS)

Kallioras, Nikos A.; Lagaros, Nikos D.; Karlaftis, Matthew G.

2014-11-01

The ability of nature-inspired search algorithms to efficiently handle combinatorial problems, and their successful implementation in many fields of engineering and applied sciences, have led to the development of new, improved algorithms. In this work, an improved harmony search (IHS) algorithm is presented, while a holistic approach for solving the problem of post-disaster infrastructure management is also proposed. The efficiency of IHS is compared with that of the algorithms of particle swarm optimization, differential evolution, basic harmony search and the pure random search procedure, when solving the districting problem that is the first part of post-disaster infrastructure management. The ant colony optimization algorithm is employed for solving the associated routing problem that constitutes the second part. The comparison is based on the quality of the results obtained, the computational demands and the sensitivity on the algorithmic parameters.

Modelling eye movements in a categorical search task

PubMed Central

Zelinsky, Gregory J.; Adeli, Hossein; Peng, Yifan; Samaras, Dimitris

2013-01-01

We introduce a model of eye movements during categorical search, the task of finding and recognizing categorically defined targets. It extends a previous model of eye movements during search (target acquisition model, TAM) by using distances from an support vector machine classification boundary to create probability maps indicating pixel-by-pixel evidence for the target category in search images. Other additions include functionality enabling target-absent searches, and a fixation-based blurring of the search images now based on a mapping between visual and collicular space. We tested this model on images from a previously conducted variable set-size (6/13/20) present/absent search experiment where participants searched for categorically defined teddy bear targets among random category distractors. The model not only captured target-present/absent set-size effects, but also accurately predicted for all conditions the numbers of fixations made prior to search judgements. It also predicted the percentages of first eye movements during search landing on targets, a conservative measure of search guidance. Effects of set size on false negative and false positive errors were also captured, but error rates in general were overestimated. We conclude that visual features discriminating a target category from non-targets can be learned and used to guide eye movements during categorical search. PMID:24018720

Expertise and processing distorted structure in chess

PubMed Central

Bartlett, James C.; Boggan, Amy L.; Krawczyk, Daniel C.

2013-01-01

A classic finding in research on human expertise and knowledge is that of enhanced memory for stimuli in a domain of expertise as compared to either stimuli outside that domain, or within-domain stimuli that have been degraded or distorted in some way. However, we do not understand how experts process degradation or distortion of stimuli within the expert domain (e.g., a face with the eyes, nose, and mouth in the wrong positions, or a chessboard with pieces placed randomly). Focusing on the domain of chess, we present new fMRI evidence that when experts view such distorted/within-domain stimuli, they engage an active search for structure—a kind of exploratory chunking—that involves a component of a prefrontal-parietal network linked to consciousness, attention and working memory. PMID:24348371

Genetic algorithms as global random search methods

NASA Technical Reports Server (NTRS)

Peck, Charles C.; Dhawan, Atam P.

1995-01-01

Genetic algorithm behavior is described in terms of the construction and evolution of the sampling distributions over the space of candidate solutions. This novel perspective is motivated by analysis indicating that the schema theory is inadequate for completely and properly explaining genetic algorithm behavior. Based on the proposed theory, it is argued that the similarities of candidate solutions should be exploited directly, rather than encoding candidate solutions and then exploiting their similarities. Proportional selection is characterized as a global search operator, and recombination is characterized as the search process that exploits similarities. Sequential algorithms and many deletion methods are also analyzed. It is shown that by properly constraining the search breadth of recombination operators, convergence of genetic algorithms to a global optimum can be ensured.

Genetic algorithms as global random search methods

NASA Technical Reports Server (NTRS)

Peck, Charles C.; Dhawan, Atam P.

1995-01-01

Genetic algorithm behavior is described in terms of the construction and evolution of the sampling distributions over the space of candidate solutions. This novel perspective is motivated by analysis indicating that that schema theory is inadequate for completely and properly explaining genetic algorithm behavior. Based on the proposed theory, it is argued that the similarities of candidate solutions should be exploited directly, rather than encoding candidate solution and then exploiting their similarities. Proportional selection is characterized as a global search operator, and recombination is characterized as the search process that exploits similarities. Sequential algorithms and many deletion methods are also analyzed. It is shown that by properly constraining the search breadth of recombination operators, convergence of genetic algorithms to a global optimum can be ensured.

A review of hospital characteristics associated with improved performance.

PubMed

Brand, Caroline A; Barker, Anna L; Morello, Renata T; Vitale, Michael R; Evans, Sue M; Scott, Ian A; Stoelwinder, Johannes U; Cameron, Peter A

2012-10-01

The objective of this review was to critically appraise the literature relating to associations between high-level structural and operational hospital characteristics and improved performance. The Cochrane Library, MEDLINE (Ovid), CINAHL, proQuest and PsychINFO were searched for articles published between January 1996 and May 2010. Reference lists of included articles were reviewed and key journals were hand searched for relevant articles. and data extraction Studies were included if they were systematic reviews or meta-analyses, randomized controlled trials, controlled before and after studies or observational studies (cohort and cross-sectional) that were multicentre, comparative performance studies. Two reviewers independently extracted data, assigned grades of evidence according to the Australian National Health and Medical Research Council guidelines and critically appraised the included articles. Data synthesis Fifty-seven studies were reported within 12 systematic reviews and 47 observational articles. There was heterogeneity in use and definition of performance outcomes. Hospital characteristics investigated were environment (incentives, market characteristics), structure (network membership, ownership, teaching status, geographical setting, service size) and operational design (innovativeness, leadership, organizational culture, public reporting and patient safety practices, information technology systems and decision support, service activity and planning, workforce design, staff training and education). The strongest evidence for an association with overall performance was identified for computerized physician order entry systems. Some evidence supported the associations with workforce design, use of financial incentives, nursing leadership and hospital volume. There is limited, mainly low-quality evidence, supporting the associations between hospital characteristics and healthcare performance. Further characteristic-specific systematic reviews are indicated.

Mixed-methods designs in mental health services research: a review.

PubMed

Palinkas, Lawrence A; Horwitz, Sarah M; Chamberlain, Patricia; Hurlburt, Michael S; Landsverk, John

2011-03-01

Despite increased calls for use of mixed-methods designs in mental health services research, how and why such methods are being used and whether there are any consistent patterns that might indicate a consensus about how such methods can and should be used are unclear. Use of mixed methods was examined in 50 peer-reviewed journal articles found by searching PubMed Central and 60 National Institutes of Health (NIH)-funded projects found by searching the CRISP database over five years (2005-2009). Studies were coded for aims and the rationale, structure, function, and process for using mixed methods. A notable increase was observed in articles published and grants funded over the study period. However, most did not provide an explicit rationale for using mixed methods, and 74% gave priority to use of quantitative methods. Mixed methods were used to accomplish five distinct types of study aims (assess needs for services, examine existing services, develop new or adapt existing services, evaluate services in randomized controlled trials, and examine service implementation), with three categories of rationale, seven structural arrangements based on timing and weighting of methods, five functions of mixed methods, and three ways of linking quantitative and qualitative data. Each study aim was associated with a specific pattern of use of mixed methods, and four common patterns were identified. These studies offer guidance for continued progress in integrating qualitative and quantitative methods in mental health services research consistent with efforts by NIH and other funding agencies to promote their use.

New Evidence for Strategic Differences between Static and Dynamic Search Tasks: An Individual Observer Analysis of Eye Movements

PubMed Central

Dickinson, Christopher A.; Zelinsky, Gregory J.

2013-01-01

Two experiments are reported that further explore the processes underlying dynamic search. In Experiment 1, observers’ oculomotor behavior was monitored while they searched for a randomly oriented T among oriented L distractors under static and dynamic viewing conditions. Despite similar search slopes, eye movements were less frequent and more spatially constrained under dynamic viewing relative to static, with misses also increasing more with target eccentricity in the dynamic condition. These patterns suggest that dynamic search involves a form of sit-and-wait strategy in which search is restricted to a small group of items surrounding fixation. To evaluate this interpretation, we developed a computational model of a sit-and-wait process hypothesized to underlie dynamic search. In Experiment 2 we tested this model by varying fixation position in the display and found that display positions optimized for a sit-and-wait strategy resulted in higher d′ values relative to a less optimal location. We conclude that different strategies, and therefore underlying processes, are used to search static and dynamic displays. PMID:23372555

Monte Carlo simulations within avalanche rescue

NASA Astrophysics Data System (ADS)

Reiweger, Ingrid; Genswein, Manuel; Schweizer, Jürg

2016-04-01

Refining concepts for avalanche rescue involves calculating suitable settings for rescue strategies such as an adequate probing depth for probe line searches or an optimal time for performing resuscitation for a recovered avalanche victim in case of additional burials. In the latter case, treatment decisions have to be made in the context of triage. However, given the low number of incidents it is rarely possible to derive quantitative criteria based on historical statistics in the context of evidence-based medicine. For these rare, but complex rescue scenarios, most of the associated concepts, theories, and processes involve a number of unknown "random" parameters which have to be estimated in order to calculate anything quantitatively. An obvious approach for incorporating a number of random variables and their distributions into a calculation is to perform a Monte Carlo (MC) simulation. We here present Monte Carlo simulations for calculating the most suitable probing depth for probe line searches depending on search area and an optimal resuscitation time in case of multiple avalanche burials. The MC approach reveals, e.g., new optimized values for the duration of resuscitation that differ from previous, mainly case-based assumptions.

GeneBee-net: Internet-based server for analyzing biopolymers

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

Brodsky, L.I.; Ivanov, V.V.; Nikolaev, V.K.

This work describes a network server for searching databanks of biopolymer structures and performing other biocomputing procedures; it is available via direct Internet connection. Basic server procedures are dedicated to homology (similarity) search of sequence and 3D structure of proteins. The homologies found could be used to build multiple alignments, predict protein and RNA secondary structure, and construct phylogenetic trees. In addition to traditional methods of sequence similarity search, the authors propose {open_quotes}non-matrix{close_quotes} (correlational) search. An analogous approach is used to identify regions of similar tertiary structure of proteins. Algorithm concepts and usage examples are presented for new methods. Servicemore » logic is based upon interaction of a client program and server procedures. The client program allows the compilation of queries and the processing of results of an analysis.« less

Structator: fast index-based search for RNA sequence-structure patterns

PubMed Central

2011-01-01

Background The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running time that is only linear in the size of sequence databases. Furthermore, established index data structures for fast sequence matching, like suffix trees or arrays, cannot benefit from the complementarity constraints introduced by the secondary structure of RNAs. Results We present a novel method and readily applicable software for time efficient matching of RNA sequence-structure patterns in sequence databases. Our approach is based on affix arrays, a recently introduced index data structure, preprocessed from the target database. Affix arrays support bidirectional pattern search, which is required for efficiently handling the structural constraints of the pattern. Structural patterns like stem-loops can be matched inside out, such that the loop region is matched first and then the pairing bases on the boundaries are matched consecutively. This allows to exploit base pairing information for search space reduction and leads to an expected running time that is sublinear in the size of the sequence database. The incorporation of a new chaining approach in the search of RNA sequence-structure patterns enables the description of molecules folding into complex secondary structures with multiple ordered patterns. The chaining approach removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our method runs up to two orders of magnitude faster than previous methods. Conclusions The presented method's sublinear expected running time makes it well suited for RNA sequence-structure pattern matching in large sequence databases. RNA molecules containing several stem-loop substructures can be described by multiple sequence-structure patterns and their matches are efficiently handled by a novel chaining method. Beyond our algorithmic contributions, we provide with Structator a complete and robust open-source software solution for index-based search of RNA sequence-structure patterns. The Structator software is available at http://www.zbh.uni-hamburg.de/Structator. PMID:21619640

When the lowest energy does not induce native structures: parallel minimization of multi-energy values by hybridizing searching intelligences.

PubMed

Lü, Qiang; Xia, Xiao-Yan; Chen, Rong; Miao, Da-Jun; Chen, Sha-Sha; Quan, Li-Jun; Li, Hai-Ou

2012-01-01

Protein structure prediction (PSP), which is usually modeled as a computational optimization problem, remains one of the biggest challenges in computational biology. PSP encounters two difficult obstacles: the inaccurate energy function problem and the searching problem. Even if the lowest energy has been luckily found by the searching procedure, the correct protein structures are not guaranteed to obtain. A general parallel metaheuristic approach is presented to tackle the above two problems. Multi-energy functions are employed to simultaneously guide the parallel searching threads. Searching trajectories are in fact controlled by the parameters of heuristic algorithms. The parallel approach allows the parameters to be perturbed during the searching threads are running in parallel, while each thread is searching the lowest energy value determined by an individual energy function. By hybridizing the intelligences of parallel ant colonies and Monte Carlo Metropolis search, this paper demonstrates an implementation of our parallel approach for PSP. 16 classical instances were tested to show that the parallel approach is competitive for solving PSP problem. This parallel approach combines various sources of both searching intelligences and energy functions, and thus predicts protein conformations with good quality jointly determined by all the parallel searching threads and energy functions. It provides a framework to combine different searching intelligence embedded in heuristic algorithms. It also constructs a container to hybridize different not-so-accurate objective functions which are usually derived from the domain expertise.

When the Lowest Energy Does Not Induce Native Structures: Parallel Minimization of Multi-Energy Values by Hybridizing Searching Intelligences

PubMed Central

Lü, Qiang; Xia, Xiao-Yan; Chen, Rong; Miao, Da-Jun; Chen, Sha-Sha; Quan, Li-Jun; Li, Hai-Ou

2012-01-01

Background Protein structure prediction (PSP), which is usually modeled as a computational optimization problem, remains one of the biggest challenges in computational biology. PSP encounters two difficult obstacles: the inaccurate energy function problem and the searching problem. Even if the lowest energy has been luckily found by the searching procedure, the correct protein structures are not guaranteed to obtain. Results A general parallel metaheuristic approach is presented to tackle the above two problems. Multi-energy functions are employed to simultaneously guide the parallel searching threads. Searching trajectories are in fact controlled by the parameters of heuristic algorithms. The parallel approach allows the parameters to be perturbed during the searching threads are running in parallel, while each thread is searching the lowest energy value determined by an individual energy function. By hybridizing the intelligences of parallel ant colonies and Monte Carlo Metropolis search, this paper demonstrates an implementation of our parallel approach for PSP. 16 classical instances were tested to show that the parallel approach is competitive for solving PSP problem. Conclusions This parallel approach combines various sources of both searching intelligences and energy functions, and thus predicts protein conformations with good quality jointly determined by all the parallel searching threads and energy functions. It provides a framework to combine different searching intelligence embedded in heuristic algorithms. It also constructs a container to hybridize different not-so-accurate objective functions which are usually derived from the domain expertise. PMID:23028708

Chaotic Traversal (CHAT): Very Large Graphs Traversal Using Chaotic Dynamics

NASA Astrophysics Data System (ADS)

Changaival, Boonyarit; Rosalie, Martin; Danoy, Grégoire; Lavangnananda, Kittichai; Bouvry, Pascal

2017-12-01

Graph Traversal algorithms can find their applications in various fields such as routing problems, natural language processing or even database querying. The exploration can be considered as a first stepping stone into knowledge extraction from the graph which is now a popular topic. Classical solutions such as Breadth First Search (BFS) and Depth First Search (DFS) require huge amounts of memory for exploring very large graphs. In this research, we present a novel memoryless graph traversal algorithm, Chaotic Traversal (CHAT) which integrates chaotic dynamics to traverse large unknown graphs via the Lozi map and the Rössler system. To compare various dynamics effects on our algorithm, we present an original way to perform the exploration of a parameter space using a bifurcation diagram with respect to the topological structure of attractors. The resulting algorithm is an efficient and nonresource demanding algorithm, and is therefore very suitable for partial traversal of very large and/or unknown environment graphs. CHAT performance using Lozi map is proven superior than the, commonly known, Random Walk, in terms of number of nodes visited (coverage percentage) and computation time where the environment is unknown and memory usage is restricted.

How effective are risk assessments/measures for predicting future aggressive behaviour in adults with intellectual disabilities (ID): A systematic review and meta-analysis.

PubMed

Lofthouse, Rachael; Golding, Laura; Totsika, Vasiliki; Hastings, Richard; Lindsay, William

2017-12-01

Risk assessments assist professionals in the identification and management of risk of aggression. The present study aimed to systematically review evidence on the efficacy of assessments for managing the risk of physical aggression in adults with intellectual disabilities (ID). A literature search was conducted using the databases PsycINFO, EMBASE, MEDLINE, Web of Science, and Google Scholar. Electronic and hand searches identified 14 studies that met the inclusion criteria. Standardised mean difference effect sizes Area Under Curve (AUC) were calculated for studies. Random effects subgroup analysis was used to compare different types of risk measures (Actuarial, Structured Professional Judgment and dynamic), and prospective vs. catch-up longitudinal study designs. Overall, evidence of predictive validity was found for risk measures with ID populations: (AUC)=0.724, 95% CI [0.681, 0.768]. There was no variation in the performance of different types of risk measures, or different study design. Risk assessment measures predict the likelihood of aggression in ID population and are comparable to those in mainstream populations. Further meta-analysis is necessary when risk measures are more established in this population. Copyright © 2017 Elsevier Ltd. All rights reserved.

Patients' evaluations of health care providers in the era of social networking: an analysis of physician-rating websites.

PubMed

Lagu, Tara; Hannon, Nicholas S; Rothberg, Michael B; Lindenauer, Peter K

2010-09-01

Internet-based social networking tools that allow users to share content have enabled a new form of public reporting of physician performance: the physician-rating website. To describe the structure and content of physician-rating websites and to assess the extent to which a patient might find them valuable. We searched Google for websites that allowed patients to review physicians in the US. We included websites that met predetermined criteria, identified common elements of these websites, and recorded website characteristics. We then searched the websites for reviews of a random sample of 300 Boston physicians. Finally, we separately analyzed quantitative and narrative reviews. We identified 33 physician-rating websites, which contained 190 reviews for 81 physicians. Most reviews were positive (88%). Six percent were negative, and six percent were neutral. Generalists and subspecialists did not significantly differ in number or nature of reviews. We identified several narrative reviews that appeared to be written by the physicians themselves. Physician-rating websites offer patients a novel way to provide feedback and obtain information about physician performance. Despite controversy surrounding these sites, their use by patients has been limited to date, and a majority of reviews appear to be positive.

A systematic search method for the identification of tightly packed transmembrane parallel alpha-helices.

PubMed

Akula, Nagaraju; Pattabiraman, Nagarajan

2005-06-01

Membrane proteins play a major role in number of biological processes such as signaling pathways. The determination of the three-dimensional structure of these proteins is increasingly important for our understanding of their structure-function relationships. Due to the difficulty in isolating membrane proteins for X-ray diffraction studies, computational techniques are being developed to generate the 3D structures of TM domains. Here, we present a systematic search method for the identification of energetically favorable and tightly packed transmembrane parallel alpha-helices. The first step in our systematic search method is the generation of 3D models for pairs of parallel helix bundles with all possible orientations followed by an energy-based filter to eliminate structures with severe non-bonded contacts. Then, a RMS-based filter was used to cluster these structures into families. Furthermore, these dimers were energy minimized using molecular mechanics force field. Finally, we identified the tightly packed parallel alpha-helices by using an interface surface area. To validate our search method, we compared our predicted GlycophorinA dimer structures with the reported NMR structures. With our search method, we are able to reproduce NMR structures of GPA with 0.9A RMSD. In addition, by considering the reported mutational data on GxxxG motif interactions, twenty percent of our predicted dimers are within in the 2.0A RMSD. The dimers obtained from our method were used to generate parallel trimeric and tetramer TM structures of GPA and found that the structure of GPA might exist only in a dimer form as reported earlier.

A new method to improve network topological similarity search: applied to fold recognition

PubMed Central

Lhota, John; Hauptman, Ruth; Hart, Thomas; Ng, Clara; Xie, Lei

2015-01-01

Motivation: Similarity search is the foundation of bioinformatics. It plays a key role in establishing structural, functional and evolutionary relationships between biological sequences. Although the power of the similarity search has increased steadily in recent years, a high percentage of sequences remain uncharacterized in the protein universe. Thus, new similarity search strategies are needed to efficiently and reliably infer the structure and function of new sequences. The existing paradigm for studying protein sequence, structure, function and evolution has been established based on the assumption that the protein universe is discrete and hierarchical. Cumulative evidence suggests that the protein universe is continuous. As a result, conventional sequence homology search methods may be not able to detect novel structural, functional and evolutionary relationships between proteins from weak and noisy sequence signals. To overcome the limitations in existing similarity search methods, we propose a new algorithmic framework—Enrichment of Network Topological Similarity (ENTS)—to improve the performance of large scale similarity searches in bioinformatics. Results: We apply ENTS to a challenging unsolved problem: protein fold recognition. Our rigorous benchmark studies demonstrate that ENTS considerably outperforms state-of-the-art methods. As the concept of ENTS can be applied to any similarity metric, it may provide a general framework for similarity search on any set of biological entities, given their representation as a network. Availability and implementation: Source code freely available upon request Contact: lxie@iscb.org PMID:25717198

Towards computational improvement of DNA database indexing and short DNA query searching.

PubMed

Stojanov, Done; Koceski, Sašo; Mileva, Aleksandra; Koceska, Nataša; Bande, Cveta Martinovska

2014-09-03

In order to facilitate and speed up the search of massive DNA databases, the database is indexed at the beginning, employing a mapping function. By searching through the indexed data structure, exact query hits can be identified. If the database is searched against an annotated DNA query, such as a known promoter consensus sequence, then the starting locations and the number of potential genes can be determined. This is particularly relevant if unannotated DNA sequences have to be functionally annotated. However, indexing a massive DNA database and searching an indexed data structure with millions of entries is a time-demanding process. In this paper, we propose a fast DNA database indexing and searching approach, identifying all query hits in the database, without having to examine all entries in the indexed data structure, limiting the maximum length of a query that can be searched against the database. By applying the proposed indexing equation, the whole human genome could be indexed in 10 hours on a personal computer, under the assumption that there is enough RAM to store the indexed data structure. Analysing the methodology proposed by Reneker, we observed that hits at starting positions [Formula: see text] are not reported, if the database is searched against a query shorter than [Formula: see text] nucleotides, such that [Formula: see text] is the length of the DNA database words being mapped and [Formula: see text] is the length of the query. A solution of this drawback is also presented.

Evidence-based practice: extending the search to find material for the systematic review

PubMed Central

Helmer, Diane; Savoie, Isabelle; Green, Carolyn; Kazanjian, Arminée

2001-01-01

Background: Cochrane-style systematic reviews increasingly require the participation of librarians. Guidelines on the appropriate search strategy to use for systematic reviews have been proposed. However, research evidence supporting these recommendations is limited. Objective: This study investigates the effectiveness of various systematic search methods used to uncover randomized controlled trials (RCTs) for systematic reviews. Effectiveness is defined as the proportion of relevant material uncovered for the systematic review using extended systematic review search methods. The following extended systematic search methods are evaluated: searching subject-specific or specialized databases (including trial registries), hand searching, scanning reference lists, and communicating personally. Methods: Two systematic review projects were prospectively monitored regarding the method used to identify items as well as the type of items retrieved. The proportion of RCTs identified by each systematic search method was calculated. Results: The extended systematic search methods uncovered 29.2% of all items retrieved for the systematic reviews. The search of specialized databases was the most effective method, followed by scanning of reference lists, communicating personally, and hand searching. Although the number of items identified through hand searching was small, these unique items would otherwise have been missed. Conclusions: Extended systematic search methods are effective tools for uncovering material for the systematic review. The quality of the items uncovered has yet to be assessed and will be key in evaluating the value of the systematic search methods. PMID:11837256

Practicing evidence based medicine at the bedside: a randomized controlled pilot study in undergraduate medical students assessing the practicality of tablets, smartphones, and computers in clinical life.

PubMed

Friederichs, Hendrik; Marschall, Bernhard; Weissenstein, Anne

2014-12-05

Practicing evidence-based medicine is an important aspect of providing good medical care. Accessing external information through literature searches on computer-based systems can effectively achieve integration in clinical care. We conducted a pilot study using smartphones, tablets, and stationary computers as search devices at the bedside. The objective was to determine possible differences between the various devices and assess students' internet use habits. In a randomized controlled pilot study, 120 students were divided in three groups. One control group solved clinical problems on a computer and two intervention groups used mobile devices at the bedside. In a questionnaire, students were asked to report their internet use habits as well as their satisfaction with their respective search tool using a 5-point Likert scale. Of 120 surveys, 94 (78.3%) complete data sets were analyzed. The mobility of the tablet (3.90) and the smartphone (4.39) was seen as a significant advantage over the computer (2.38, p < .001). However, for performing an effective literature search at the bedside, the computer (3.22) was rated superior to both tablet computers (2.13) and smartphones (1.68). No significant differences were detected between tablets and smartphones except satisfaction with screen size (tablet 4.10, smartphone 2.00, p < .001). Using a mobile device at the bedside to perform an extensive search is not suitable for students who prefer using computers. However, mobility is regarded as a substantial advantage, and therefore future applications might facilitate quick and simple searches at the bedside.

The Use of Web Search Engines in Information Science Research.

ERIC Educational Resources Information Center

Bar-Ilan, Judit

2004-01-01

Reviews the literature on the use of Web search engines in information science research, including: ways users interact with Web search engines; social aspects of searching; structure and dynamic nature of the Web; link analysis; other bibliometric applications; characterizing information on the Web; search engine evaluation and improvement; and…

Analysis of correlations and search for evidence of deterministic chaos in rhythmic motor control by the human brain

NASA Astrophysics Data System (ADS)

Roberts, Sean; Eykholt, R.; Thaut, Michael H.

2000-08-01

We investigate rhythmic finger tapping in both the presence and the absence of a metronome. We examine both the time intervals between taps and the time lags between the stimulus tones from the metronome and the response taps by the subject. We analyze the correlations in these data sets, and we search for evidence of deterministic chaos, as opposed to randomness, in the fluctuations.

LigandBox: A database for 3D structures of chemical compounds

PubMed Central

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

LigandBox: A database for 3D structures of chemical compounds.

PubMed

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

Rational evolutionary design: the theory of in vitro protein evolution.

PubMed

Voigt, C A; Kauffman, S; Wang, Z G

2000-01-01

Directed evolution uses a combination of powerful search techniques to generate proteins with improved properties. Part of the success is due to the stochastic element of random mutagenesis; improvements can be made without a detailed description of the complex interactions that constitute function or stability. However, optimization is not a conglomeration of random processes. Rather, it requires both knowledge of the system that is being optimized and a logical series of techniques that best explores the pathways of evolution (Eigen et al., 1988). The weighing of parameters associated with mutation, recombination, and screening to achieve the maximum fitness improvement is the beginning of rational evolutionary design. The optimal mutation rate is strongly influenced by the finite number of mutants that can be screened. A smooth fitness landscape implies that many mutations can be accumulated without disrupting the fitness. This has the effect of lowering the required library size to sample a higher mutation rate. As the sequence ascends the fitness landscape, the optimal mutation rate decreases as the probability of discovering improved mutations also decreases. Highly coupled regions require that many mutations be simultaneously made to generate a positive mutant. Therefore, positive mutations are discovered at uncoupled positions as the fitness of the parent increases. The benefit of recombination is twofold: it combines good mutations and searches more sequence space in a meaningful way. Recombination is most beneficial when the number of mutants that can be screened is limited and the landscape is of an intermediate ruggedness. The structure of schema in proteins leads to the conclusion that many cut points are required. The number of parents and their sequence identity are determined by the balance between exploration and exploitation. Many disparate parents can explore more space, but at the risk of losing information. The required screening effort is related to the number of uphill paths, which decreases more rapidly for rugged landscapes. Noise in the fitness measurements causes a dramatic increase in the required mutant library size, thus implying a smaller optimal mutation rate. Because of strict limitations on the number of mutants that can be screened, there is motivation to optimize the content of the mutant library. By restricting mutations to regions of the gene that are expected to show improvement, a greater return can be made with the same number of mutants. Initial studies with subtilisin E have shown that structurally tolerant positions tend to be where positive activity mutants are made during directed evolution. Mutant fitness information is produced by the screening step that has the potential to provide insight into the structure of the fitness landscape, thus aiding the setting of experimental parameters. By analyzing the mutant fitness distribution and targeting specific regions of the sequence, in vitro evolution can be accelerated. However, when expediting the search, there is a trade-off between rapid improvement and the quality of the long-term solution. The benefit of neutrality has yet to be captured with in vitro protein evolution. Neutral theory predicts the punctuated emergence of novel structure and function, however, with current methods, the required time scale is not feasible. Utilizing neutral evolution to accelerate the discovery of new functional and structural solutions requires a theory that predicts the behavior of mutational pathways between networks. Because the transition from neutral to adaptive evolution requires a multi-mutational switch, increasing the mutation rate decreases the time required for a punctuated change to occur. By limiting the search to the less coupled region of the sequence (smooth portion of the fitness landscape), the required larger mutation rate can be tolerated. Advances in directed evolution will be achieved when the driving forces behind such proce

Toward a human-centered hyperlipidemia management system: the interaction between internal and external information on relational data search.

PubMed

Gong, Yang; Zhang, Jiajie

2011-04-01

In a distributed information search task, data representation and cognitive distribution jointly affect user search performance in terms of response time and accuracy. Guided by UFuRT (User, Function, Representation, Task), a human-centered framework, we proposed a search model and task taxonomy. The model defines its application in the context of healthcare setting. The taxonomy clarifies the legitimate operations for each type of search task of relational data. We then developed experimental prototypes of hyperlipidemia data displays. Based on the displays, we tested the search tasks performance through two experiments. The experiments are of a within-subject design with a random sample of 24 participants. The results support our hypotheses and validate the prediction of the model and task taxonomy. In this study, representation dimensions, data scales, and search task types are the main factors in determining search efficiency and effectiveness. Specifically, the more external representations provided on the interface the better search task performance of users. The results also suggest the ideal search performance occurs when the question type and its corresponding data scale representation match. The implications of the study lie in contributing to the effective design of search interface for relational data, especially laboratory results, which could be more effectively designed in electronic medical records.

Effects of flicker rate, complexity, and color combinations of Chinese characters and backgrounds on visual search performance with varying flicker types.

PubMed

Huang, Kuo-Chen; Lin, Rung-Tai; Wu, Chih-Fu

2011-08-01

This study investigated the effects of number of strokes in Chinese characters, flicker rate, flicker type, and character/background color combination on search performance. 37 participants ages 14 to 18 years were randomly assigned to each flicker-type condition. The search field contained 36 characters arranged in a 6 x 6 matrix. Participants were asked to search for the target characters among the surrounding distractors and count how many target characters were displayed in the search array. Analysis indicated that the character/background color combination significantly affected search times. The color combinations of white/purple and white/green yielded search times greater than those for black/white and black/yellow combinations. A significant effect for flicker type on search time was also identified. Rotating characters facilitated search time, compared with twinkling ones. The number of strokes and the flicker rates also had positive effects on search performances. For flicker rate, the search accuracy for 0.5 Hz was greater than that for 1.0 Hz, and the latter was also greater than that for 2.0 Hz. Results are applicable to web advertisement designs containing dynamic characters, in terms of how to best capture readers' attention by various means of dynamic character presentation.

An AI-based approach to structural damage identification by modal analysis

NASA Technical Reports Server (NTRS)

Glass, B. J.; Hanagud, S.

1990-01-01

Flexible-structure damage is presently addressed by a combined model- and parameter-identification approach which employs the AI methodologies of classification, heuristic search, and object-oriented model knowledge representation. The conditions for model-space search convergence to the best model are discussed in terms of search-tree organization and initial model parameter error. In the illustrative example of a truss structure presented, the use of both model and parameter identification is shown to lead to smaller parameter corrections than would be required by parameter identification alone.

Spatial Query for Planetary Data

NASA Technical Reports Server (NTRS)

Shams, Khawaja S.; Crockett, Thomas M.; Powell, Mark W.; Joswig, Joseph C.; Fox, Jason M.

2011-01-01

Science investigators need to quickly and effectively assess past observations of specific locations on a planetary surface. This innovation involves a location-based search technology that was adapted and applied to planetary science data to support a spatial query capability for mission operations software. High-performance location-based searching requires the use of spatial data structures for database organization. Spatial data structures are designed to organize datasets based on their coordinates in a way that is optimized for location-based retrieval. The particular spatial data structure that was adapted for planetary data search is the R+ tree.

Index Compression and Efficient Query Processing in Large Web Search Engines

ERIC Educational Resources Information Center

Ding, Shuai

2013-01-01

The inverted index is the main data structure used by all the major search engines. Search engines build an inverted index on their collection to speed up query processing. As the size of the web grows, the length of the inverted list structures, which can easily grow to hundreds of MBs or even GBs for common terms (roughly linear in the size of…

Visual search for object categories is predicted by the representational architecture of high-level visual cortex

PubMed Central

Alvarez, George A.; Nakayama, Ken; Konkle, Talia

2016-01-01

Visual search is a ubiquitous visual behavior, and efficient search is essential for survival. Different cognitive models have explained the speed and accuracy of search based either on the dynamics of attention or on similarity of item representations. Here, we examined the extent to which performance on a visual search task can be predicted from the stable representational architecture of the visual system, independent of attentional dynamics. Participants performed a visual search task with 28 conditions reflecting different pairs of categories (e.g., searching for a face among cars, body among hammers, etc.). The time it took participants to find the target item varied as a function of category combination. In a separate group of participants, we measured the neural responses to these object categories when items were presented in isolation. Using representational similarity analysis, we then examined whether the similarity of neural responses across different subdivisions of the visual system had the requisite structure needed to predict visual search performance. Overall, we found strong brain/behavior correlations across most of the higher-level visual system, including both the ventral and dorsal pathways when considering both macroscale sectors as well as smaller mesoscale regions. These results suggest that visual search for real-world object categories is well predicted by the stable, task-independent architecture of the visual system. NEW & NOTEWORTHY Here, we ask which neural regions have neural response patterns that correlate with behavioral performance in a visual processing task. We found that the representational structure across all of high-level visual cortex has the requisite structure to predict behavior. Furthermore, when directly comparing different neural regions, we found that they all had highly similar category-level representational structures. These results point to a ubiquitous and uniform representational structure in high-level visual cortex underlying visual object processing. PMID:27832600

Confirming preferences or collecting data? Information search strategies and romantic partner selection.

PubMed

Hennessy, Michael H; Fishbein, Marty; Curtis, Brenda; Barrett, Daniel

2008-03-01

This article investigates two kinds of information search strategies in the context of selecting romantic partners. Confirmatory searching occurs when people ask for more information about a romantic partner in order to validate or confirm their assessment. Balanced searches are characterized by a search for risk information for partners rated as attractive and for attractiveness information about partners rated as risky in order to attain a more complete evaluation. A factorial survey computer program randomly constructed five types of partner descriptions and college-age respondents evaluated nine descriptions in terms of both health risk and romantic attractiveness outcomes. The results show little evidence of balanced search strategies: for all vignette types the respondents searched for attractiveness information. Regression analysis of the search outcomes showed no difference between males and females in the desire for attractiveness or risk information, the amount of additional information desired, or the proportion of descriptions for which more information was desired. However, an attractive physical appearance did increase the amount of additional information desired and the proportion of vignettes for which more information was desired. The results were generally inconsistent with a balanced search hypothesis; a better characterization of the respondents' strategy might be "confirmatory bias."

Effects of life review on mental health and well-being among cancer patients: A systematic review.

PubMed

Zhang, Xiaoling; Xiao, Huimin; Chen, Ying

2017-09-01

Cancer patients often experience psychological distress. Life review has increasingly been used to enhance their mental health and well-being. However, no systematic review has synthesized the evidence, and its effects remain unclear. To examine and synthesize the best available evidence on the effects of life review on mental health and well-being among cancer patients. Systematic review of randomized controlled trials and clinical controlled trials. Twelve electronic databases were searched for published studies reported in English or Chinese, from inception to September 2016. Other supplementary sources, such as related websites, professional books, reference lists, and author contacts were also used for published or unpublished studies. A comprehensive literature search was conducted to identify eligible randomized controlled trials or clinical controlled trials about the effects of life review on cancer patients. Study selection, quality assessment, and data extraction were independently performed by two reviewers. The results were synthesized without meta-analysis in this review. Fifteen studies (899 participants) were identified; of that total, nine studies were rated as strong in quality, while six studies were of moderate quality. In addition to structured life review interviews, other elements such as memory prompts and a legacy product were integrated into life review programs. A majority of studies indicated that life review programs benefited cancer patients by reducing depression and anxiety, as well as improving their sense of hope, self-esteem and quality of life. Life review can improve mental health and well-being among cancer patients. This suggests that life review can be integrated into typical cancer treatment to enhance patients' mental health and well-being. More research with rigorous design is necessary to further explore the effects of life review. Copyright © 2017 Elsevier Ltd. All rights reserved.

Changes & Challenges: Hot Topics in a New Era of Schools. Proceedings of the Education Law Association Winter Seminar (Park City, UT, March 15-18, 2001). Seminar Outlines.

ERIC Educational Resources Information Center

Education Law Association, Dayton, OH.

The following are outlines presented by individuals at the Education Law Association 2001 winter seminar: "Academic Freedom and the Religiously Affiliated University" (the freedom to teach, research, and publish has never been--and still is not--without limits); "How Random and Suspicionless May School Searches Be" (random and suspicionless drug…

Sparse Forward-Backward for Fast Training of Conditional Random Fields

DTIC Science & Technology

2006-01-01

knowledge- based systems. Proceedings of the 6th Conference on Uncertainty in Artifcial Intelligence , 1990. Appears to be unavailable. [4] Michael I...response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and...task, the NetTalk text-to-speech data set [5], we can now train a conditional random field (CRF) in about 6 hours for which training previously

Understanding and comparisons of different sampling approaches for the Fourier Amplitudes Sensitivity Test (FAST)

PubMed Central

Xu, Chonggang; Gertner, George

2013-01-01

Fourier Amplitude Sensitivity Test (FAST) is one of the most popular uncertainty and sensitivity analysis techniques. It uses a periodic sampling approach and a Fourier transformation to decompose the variance of a model output into partial variances contributed by different model parameters. Until now, the FAST analysis is mainly confined to the estimation of partial variances contributed by the main effects of model parameters, but does not allow for those contributed by specific interactions among parameters. In this paper, we theoretically show that FAST analysis can be used to estimate partial variances contributed by both main effects and interaction effects of model parameters using different sampling approaches (i.e., traditional search-curve based sampling, simple random sampling and random balance design sampling). We also analytically calculate the potential errors and biases in the estimation of partial variances. Hypothesis tests are constructed to reduce the effect of sampling errors on the estimation of partial variances. Our results show that compared to simple random sampling and random balance design sampling, sensitivity indices (ratios of partial variances to variance of a specific model output) estimated by search-curve based sampling generally have higher precision but larger underestimations. Compared to simple random sampling, random balance design sampling generally provides higher estimation precision for partial variances contributed by the main effects of parameters. The theoretical derivation of partial variances contributed by higher-order interactions and the calculation of their corresponding estimation errors in different sampling schemes can help us better understand the FAST method and provide a fundamental basis for FAST applications and further improvements. PMID:24143037

Understanding and comparisons of different sampling approaches for the Fourier Amplitudes Sensitivity Test (FAST).

PubMed

Xu, Chonggang; Gertner, George

2011-01-01

Fourier Amplitude Sensitivity Test (FAST) is one of the most popular uncertainty and sensitivity analysis techniques. It uses a periodic sampling approach and a Fourier transformation to decompose the variance of a model output into partial variances contributed by different model parameters. Until now, the FAST analysis is mainly confined to the estimation of partial variances contributed by the main effects of model parameters, but does not allow for those contributed by specific interactions among parameters. In this paper, we theoretically show that FAST analysis can be used to estimate partial variances contributed by both main effects and interaction effects of model parameters using different sampling approaches (i.e., traditional search-curve based sampling, simple random sampling and random balance design sampling). We also analytically calculate the potential errors and biases in the estimation of partial variances. Hypothesis tests are constructed to reduce the effect of sampling errors on the estimation of partial variances. Our results show that compared to simple random sampling and random balance design sampling, sensitivity indices (ratios of partial variances to variance of a specific model output) estimated by search-curve based sampling generally have higher precision but larger underestimations. Compared to simple random sampling, random balance design sampling generally provides higher estimation precision for partial variances contributed by the main effects of parameters. The theoretical derivation of partial variances contributed by higher-order interactions and the calculation of their corresponding estimation errors in different sampling schemes can help us better understand the FAST method and provide a fundamental basis for FAST applications and further improvements.

Child language interventions in public health: a systematic literature review.

PubMed

De Cesaro, Bruna Campos; Gurgel, Léia Gonçalves; Nunes, Gabriela Pisoni Canedo; Reppold, Caroline Tozzi

2013-01-01

Systematically review the literature on interventions in children's language in primary health care. One searched the electronic databases (January 1980 to March 2013) MEDLINE (accessed by PubMed), Scopus, Lilacs and Scielo. The search terms used were "child language", "primary health care", "randomized controlled trial" and "intervention studies" (in English, Portuguese and Spanish). There were included any randomized controlled trials that addressed the issues child language and primary health care. The analysis was based on the type of language intervention conducted in primary health care. Seven studies were included and used intervention strategies such as interactive video, guidance for parents and group therapy. Individuals of both genders were included in the seven studies. The age of the children participant in the samples of the articles included in this review ranged from zero to 11 years. These seven studies used approaches that included only parents, parents and children or just children. The mainly intervention in language on primary health care, used in randomized controlled trials, involved the use of interactional video. Several professionals, beyond speech and language therapist, been inserted in the language interventions on primary health care, demonstrating the importance of interdisciplinary work. None of the articles mentioned aspects related to hearing. There was scarcity of randomized controlled trials that address on language and public health, either in Brazil or internationally.

Prey should hide more randomly when a predator attacks more persistently.

PubMed

Gal, Shmuel; Alpern, Steve; Casas, Jérôme

2015-12-06

When being searched for and then (if found) pursued by a predator, a prey animal has a choice between choosing very randomly among hiding locations so as to be hard to find or alternatively choosing a location from which it is more likely to successfully flee if found. That is, the prey can choose to be hard to find or hard to catch, if found. In our model, capture of prey requires both finding it and successfully pursuing it. We model this dilemma as a zero-sum repeated game between predator and prey, with the eventual capture probability as the pay-off to the predator. We find that the more random hiding strategy is better when the chances of repeated pursuit, which are known to be related to area topography, are high. Our results extend earlier results of Gal and Casas, where there was at most only a single pursuit. In that model, hiding randomly was preferred by the prey when the predator has only a few looks. Thus, our new multistage model shows that the effect of more potential looks is opposite. Our results can be viewed as a generalization of search games to the repeated game context and are in accordance with observed escape behaviour of different animals. © 2015 The Author(s).

Prey should hide more randomly when a predator attacks more persistently

PubMed Central

Gal, Shmuel; Alpern, Steve; Casas, Jérôme

2015-01-01

When being searched for and then (if found) pursued by a predator, a prey animal has a choice between choosing very randomly among hiding locations so as to be hard to find or alternatively choosing a location from which it is more likely to successfully flee if found. That is, the prey can choose to be hard to find or hard to catch, if found. In our model, capture of prey requires both finding it and successfully pursuing it. We model this dilemma as a zero-sum repeated game between predator and prey, with the eventual capture probability as the pay-off to the predator. We find that the more random hiding strategy is better when the chances of repeated pursuit, which are known to be related to area topography, are high. Our results extend earlier results of Gal and Casas, where there was at most only a single pursuit. In that model, hiding randomly was preferred by the prey when the predator has only a few looks. Thus, our new multistage model shows that the effect of more potential looks is opposite. Our results can be viewed as a generalization of search games to the repeated game context and are in accordance with observed escape behaviour of different animals. PMID:26631332

Making working memory work: the effects of extended practice on focus capacity and the processes of updating, forward access, and random access.

PubMed

Price, John M; Colflesh, Gregory J H; Cerella, John; Verhaeghen, Paul

2014-05-01

We investigated the effects of 10h of practice on variations of the N-Back task to investigate the processes underlying possible expansion of the focus of attention within working memory. Using subtractive logic, we showed that random access (i.e., Sternberg-like search) yielded a modest effect (a 50% increase in speed) whereas the processes of forward access (i.e., retrieval in order, as in a standard N-Back task) and updating (i.e., changing the contents of working memory) were executed about 5 times faster after extended practice. We additionally found that extended practice increased working memory capacity as measured by the size of the focus of attention for the forward-access task, but not for variations where probing was in random order. This suggests that working memory capacity may depend on the type of search process engaged, and that certain working-memory-related cognitive processes are more amenable to practice than others. Copyright © 2014 Elsevier B.V. All rights reserved.

A systematic review of randomized controlled trials of interventions designed to decrease child abuse in high-risk families.

PubMed

Levey, Elizabeth J; Gelaye, Bizu; Bain, Paul; Rondon, Marta B; Borba, Christina P C; Henderson, David C; Williams, Michelle A

2017-03-01

Child abuse is a global problem, and parents with histories of childhood abuse are at increased risk of abusing their offspring. The objective of this systematic review is to provide a clear overview of the existing literature of randomized controlled trials evaluating the effectiveness of interventions to prevent child abuse. PubMed, PsychINFO, Web of Science, Sociological Abstracts, and CINAHL were systematically searched and expanded by hand search. This review includes all randomized controlled trials (RCTs) of interventions designed to prevent abuse among mothers identified as high-risk. Of the eight studies identified, only three found statistically significant reductions in abuse by any measure, and only two found reductions in incidents reported to child protective services. While much has been written about child abuse in high-risk families, few RCTs have been performed. Only home visitation has a significant evidence base for reducing child abuse, and the findings vary considerably. Also, data from low- and middle-income countries are limited. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

The Clinical Effects of Aromatherapy Massage on Reducing Pain for the Cancer Patients: Meta-Analysis of Randomized Controlled Trials.

PubMed

Chen, Ting-Hao; Tung, Tao-Hsin; Chen, Pei-Shih; Wang, Shu-Hui; Chao, Chuang-Min; Hsiung, Nan-Hsing; Chi, Ching-Chi

2016-01-01

Purpose. Aromatherapy massage is an alternative treatment in reducing the pain of the cancer patients. This study was to investigate whether aromatherapy massage could improve the pain of the cancer patients. Methods. We searched PubMed and Cochrane Library for relevant randomized controlled trials without language limitations between 1 January 1990 and 31 July 2015 with a priori defined inclusion and exclusion criteria. The search terms included aromatherapy, essential oil, pain, ache, cancer, tumor, and carcinoma. There were 7 studies which met the selection criteria and 3 studies were eventually included among 63 eligible publications. Results. This meta-analysis included three randomized controlled trials with a total of 278 participants (135 participants in the massage with essential oil group and 143 participants in the control (usual care) group). Compared with the control group, the massage with essential oil group had nonsignificant effect on reducing the pain (standardized mean difference = 0.01; 95% CI [-0.23,0.24]). Conclusion. Aromatherapy massage does not appear to reduce pain of the cancer patients. Further rigorous studies should be conducted with more objective measures.

Completeness of reporting in abstracts from clinical trials of pre-harvest interventions against foodborne pathogens.

PubMed

Snedeker, Kate G; Canning, Paisley; Totton, Sarah C; Sargeant, Jan M

2012-04-01

Abstracts are the most commonly read part of a journal article, and play an important role as summaries of the articles, and search and screening tools. However, research on abstracts in human biomedicine has shown that abstracts often do not report key methodological features and results. Little research has been done to examine reporting of such features in abstracts from papers detailing pre-harvest food safety trials. Thus, the objective of this study was to assess the quality of reporting of key factors in abstracts detailing trials of pre-harvest food safety interventions. A systematic search algorithm was used to identify all in vivo trials of pre-harvest interventions against foodborne pathogens in PubMed and CAB Direct published from 1999 to October 2009. References were screened for relevance, and 150 were randomly chosen for inclusion in the study. A checklist based on the CONSORT abstract extension and the REFLECT Statement was used to assess the reporting of methodological features and results. All screening and assessment was performed by two independent reviewers with disagreements resolved by consensus. The systematic search returned 3554 unique citations; 356 were found to be relevant and 150 were randomly selected for inclusion. The abstracts were from 51 different journals, and 13 out of 150 were structured. Of the 124 abstracts that reported whether the trial design was deliberate disease challenge or natural exposure, 113 were deliberate challenge and 11 natural exposure. 103 abstracts detailed studies involving poultry, 20 cattle and 15 swine. Most abstracts reported the production stage of the animals (135/150), a hypothesis or objective (123/150), and results for all treatment groups (136/150). However, few abstracts reported on how animals were grouped in housing (25/150), the location of the study (5/150), the primary outcome (2/126), level of treatment allocation (15/150), sample size (63/150) or whether study units were lost to follow up (4/150). Forty-eight (48/150) abstracts reported the name, mode of administration, dose and duration of the intervention(s), while 102 (102/150) reported at least one of these elements. Nine (9/150) abstracts specified that allocation of study units to treatments was randomized, and none of the abstracts reported whether blinding was used (0/150). These results reveal gaps in reporting of methodological features and results. Thus, improving reporting quality in abstracts should be a crucial goal to be pursued by authors, reviewers and journal editors. Copyright © 2011 Elsevier B.V. All rights reserved.

An improved stochastic fractal search algorithm for 3D protein structure prediction.

PubMed

Zhou, Changjun; Sun, Chuan; Wang, Bin; Wang, Xiaojun

2018-05-03

Protein structure prediction (PSP) is a significant area for biological information research, disease treatment, and drug development and so on. In this paper, three-dimensional structures of proteins are predicted based on the known amino acid sequences, and the structure prediction problem is transformed into a typical NP problem by an AB off-lattice model. This work applies a novel improved Stochastic Fractal Search algorithm (ISFS) to solve the problem. The Stochastic Fractal Search algorithm (SFS) is an effective evolutionary algorithm that performs well in exploring the search space but falls into local minimums sometimes. In order to avoid the weakness, Lvy flight and internal feedback information are introduced in ISFS. In the experimental process, simulations are conducted by ISFS algorithm on Fibonacci sequences and real peptide sequences. Experimental results prove that the ISFS performs more efficiently and robust in terms of finding the global minimum and avoiding getting stuck in local minimums.

A Particle Swarm Optimization-Based Approach with Local Search for Predicting Protein Folding.

PubMed

Yang, Cheng-Hong; Lin, Yu-Shiun; Chuang, Li-Yeh; Chang, Hsueh-Wei

2017-10-01

The hydrophobic-polar (HP) model is commonly used for predicting protein folding structures and hydrophobic interactions. This study developed a particle swarm optimization (PSO)-based algorithm combined with local search algorithms; specifically, the high exploration PSO (HEPSO) algorithm (which can execute global search processes) was combined with three local search algorithms (hill-climbing algorithm, greedy algorithm, and Tabu table), yielding the proposed HE-L-PSO algorithm. By using 20 known protein structures, we evaluated the performance of the HE-L-PSO algorithm in predicting protein folding in the HP model. The proposed HE-L-PSO algorithm exhibited favorable performance in predicting both short and long amino acid sequences with high reproducibility and stability, compared with seven reported algorithms. The HE-L-PSO algorithm yielded optimal solutions for all predicted protein folding structures. All HE-L-PSO-predicted protein folding structures possessed a hydrophobic core that is similar to normal protein folding.

Rapid search for tertiary fragments reveals protein sequence–structure relationships

PubMed Central

Zhou, Jianfu; Grigoryan, Gevorg

2015-01-01

Finding backbone substructures from the Protein Data Bank that match an arbitrary query structural motif, composed of multiple disjoint segments, is a problem of growing relevance in structure prediction and protein design. Although numerous protein structure search approaches have been proposed, methods that address this specific task without additional restrictions and on practical time scales are generally lacking. Here, we propose a solution, dubbed MASTER, that is both rapid, enabling searches over the Protein Data Bank in a matter of seconds, and provably correct, finding all matches below a user-specified root-mean-square deviation cutoff. We show that despite the potentially exponential time complexity of the problem, running times in practice are modest even for queries with many segments. The ability to explore naturally plausible structural and sequence variations around a given motif has the potential to synthesize its design principles in an automated manner; so we go on to illustrate the utility of MASTER to protein structural biology. We demonstrate its capacity to rapidly establish structure–sequence relationships, uncover the native designability landscapes of tertiary structural motifs, identify structural signatures of binding, and automatically rewire protein topologies. Given the broad utility of protein tertiary fragment searches, we hope that providing MASTER in an open-source format will enable novel advances in understanding, predicting, and designing protein structure. PMID:25420575

Structures of Aln (n= 27, 28, 29, and 30) clusters with double-tetrahedron structures

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

Zhang, W.; Lu, W. C.; Sun, J.

2008-01-31

Global search for lowest-energy structures of neutral aluminum clusters Al{sub n} (n = 27, 28, 29 and 30) was performed using a genetic algorithm (GA) coupled with a tight-binding (TB) method. Structural candidates obtained from our GA search were further optimized with first-principles calculations. It is found that the medium-sized aluminum clusters Al{sub 27} to Al{sub 30} favor double-tetrahedron structures.

Directed intermittent search for a hidden target on a dendritic tree

NASA Astrophysics Data System (ADS)

Newby, Jay M.; Bressloff, Paul C.

2009-08-01

Motivated by experimental observations of active (motor-driven) intracellular transport in neuronal dendrites, we analyze a stochastic model of directed intermittent search on a tree network. A particle injected from the cell body or soma into the primary branch of the dendritic tree randomly switches between a stationary search phase and a mobile nonsearch phase that is biased in the forward direction. A (synaptic) target is presented somewhere within the tree, which the particle can locate if it is within a certain range and in the searching phase. We approximate the moment generating function using Green’s function methods. The moment generating function is then used to compute the hitting probability and conditional mean first passage time to the target. We show that in contrast to a previously explored finite interval case, there is a range of parameters for which a bidirectional search strategy is more efficient than a unidirectional one in finding the target.

A k-Vector Approach to Sampling, Interpolation, and Approximation

NASA Astrophysics Data System (ADS)

Mortari, Daniele; Rogers, Jonathan

2013-12-01

The k-vector search technique is a method designed to perform extremely fast range searching of large databases at computational cost independent of the size of the database. k-vector search algorithms have historically found application in satellite star-tracker navigation systems which index very large star catalogues repeatedly in the process of attitude estimation. Recently, the k-vector search algorithm has been applied to numerous other problem areas including non-uniform random variate sampling, interpolation of 1-D or 2-D tables, nonlinear function inversion, and solution of systems of nonlinear equations. This paper presents algorithms in which the k-vector search technique is used to solve each of these problems in a computationally-efficient manner. In instances where these tasks must be performed repeatedly on a static (or nearly-static) data set, the proposed k-vector-based algorithms offer an extremely fast solution technique that outperforms standard methods.

Statistical patterns of visual search for hidden objects

PubMed Central

Credidio, Heitor F.; Teixeira, Elisângela N.; Reis, Saulo D. S.; Moreira, André A.; Andrade Jr, José S.

2012-01-01

The movement of the eyes has been the subject of intensive research as a way to elucidate inner mechanisms of cognitive processes. A cognitive task that is rather frequent in our daily life is the visual search for hidden objects. Here we investigate through eye-tracking experiments the statistical properties associated with the search of target images embedded in a landscape of distractors. Specifically, our results show that the twofold process of eye movement, composed of sequences of fixations (small steps) intercalated by saccades (longer jumps), displays characteristic statistical signatures. While the saccadic jumps follow a log-normal distribution of distances, which is typical of multiplicative processes, the lengths of the smaller steps in the fixation trajectories are consistent with a power-law distribution. Moreover, the present analysis reveals a clear transition between a directional serial search to an isotropic random movement as the difficulty level of the searching task is increased. PMID:23226829

Searching for patterns in remote sensing image databases using neural networks

NASA Technical Reports Server (NTRS)

Paola, Justin D.; Schowengerdt, Robert A.

1995-01-01

We have investigated a method, based on a successful neural network multispectral image classification system, of searching for single patterns in remote sensing databases. While defining the pattern to search for and the feature to be used for that search (spectral, spatial, temporal, etc.) is challenging, a more difficult task is selecting competing patterns to train against the desired pattern. Schemes for competing pattern selection, including random selection and human interpreted selection, are discussed in the context of an example detection of dense urban areas in Landsat Thematic Mapper imagery. When applying the search to multiple images, a simple normalization method can alleviate the problem of inconsistent image calibration. Another potential problem, that of highly compressed data, was found to have a minimal effect on the ability to detect the desired pattern. The neural network algorithm has been implemented using the PVM (Parallel Virtual Machine) library and nearly-optimal speedups have been obtained that help alleviate the long process of searching through imagery.

Outcomes validity and reliability of the modified Rankin scale: implications for stroke clinical trials: a literature review and synthesis.

PubMed

Banks, Jamie L; Marotta, Charles A

2007-03-01

The modified Rankin scale (mRS), a clinician-reported measure of global disability, is widely applied for evaluating stroke patient outcomes and as an end point in randomized clinical trials. Extensive evidence on the validity of the mRS exists across a large but fragmented literature. As new treatments for acute ischemic stroke are submitted for agency approval, an appreciation of the mRS's attributes, specifically its relationship to other stroke evaluation scales, would be valuable for decision-makers to properly assess the impact of a new drug on treatment paradigms. The purpose of this report is to assemble and systematically assess the properties of the mRS to provide decision-makers with pertinent evaluative information. A Medline search was conducted to identify reports in the peer-reviewed medical literature (1957-2006) that provide information on the structure, validation, scoring, and psychometric properties of the mRS and its use in clinical trials. The selection of articles was based on defined criteria that included relevance, study design and use of appropriate statistical methods. Of 224 articles identified by the literature search, 50 were selected for detailed assessment. Inter-rater reliability with the mRS is moderate and improves with structured interviews (kappa 0.56 versus 0.78); strong test-re-test reliability (kappa=0.81 to 0.95) has been reported. Numerous studies demonstrate the construct validity of the mRS by its relationships to physiological indicators such as stroke type, lesion size, perfusion and neurological impairment. Convergent validity between the mRS and other disability scales is well documented. Patient comorbidities and socioeconomic factors should be considered in properly applying and interpreting the mRS. Recent analyses suggest that randomized clinical trials of acute stroke treatments may require a smaller sample size if the mRS is used as a primary end point rather than the Barthel Index. Multiple types of evidence attest to the validity and reliability of the mRS. The reported data support the view that the mRS is a valuable instrument for assessing the impact of new stroke treatments.

Analysis of ehealth search perspectives among female college students in the health professions using Q methodology.

PubMed

Stellefson, Michael; Hanik, Bruce; Chaney, J Don; Tennant, Bethany

2012-04-27

The current "Millennial Generation" of college students majoring in the health professions has unprecedented access to the Internet. Although some research has been initiated among medical professionals to investigate the cognitive basis for health information searches on the Internet, little is known about Internet search practices among health and medical professional students. To systematically identify health professional college student perspectives of personal eHealth search practices. Q methodology was used to examine subjective perspectives regarding personal eHealth search practices among allied health students majoring in a health education degree program. Thirteen (n = 13) undergraduate students were interviewed about their attitudes and experiences conducting eHealth searches. From the interviews, 36 statements were used in a structured ranking task to identify clusters and determine which specific perceptions of eHealth search practices discriminated students into different groups. Scores on an objective measure of eHealth literacy were used to help categorize participant perspectives. Q-technique factor analysis of the rankings identified 3 clusters of respondents with differing views on eHealth searches that generally coincided with participants' objective eHealth literacy scores. The proficient resourceful students (pattern/structure coefficient range 0.56-0.80) described themselves as using multiple resources to obtain eHealth information, as opposed to simply relying on Internet search engines. The intermediate reluctant students (pattern/structure coefficient range 0.75-0.90) reported engaging only Internet search engines to locate eHealth information, citing undeveloped evaluation skills when considering sources of information located on the Internet. Both groups of advanced students reported not knowing how to use Boolean operators to conduct Internet health searches. The basic hubristic students (pattern/structure coefficient range 0.54-0.76) described themselves as independent procrastinators when searching for eHealth information. Interestingly, basic hubristic students represented the only cluster of participants to describe themselves as (1) having received instruction on using the Internet to conduct eHealth searches, and (2) possessing relative confidence when completing a search task. Subjective perspectives of eHealth search practices differed among students possessing different levels of eHealth literacy. These multiple perspectives present both challenges and opportunities for empowering college students in the health professions to use the Internet to obtain and appraise evidence-based health information using the Internet.

Analysis of eHealth Search Perspectives Among Female College Students in the Health Professions Using Q Methodology

PubMed Central

Hanik, Bruce; Chaney, J. Don; Tennant, Bethany

2012-01-01

Background The current “Millennial Generation” of college students majoring in the health professions has unprecedented access to the Internet. Although some research has been initiated among medical professionals to investigate the cognitive basis for health information searches on the Internet, little is known about Internet search practices among health and medical professional students. Objective To systematically identify health professional college student perspectives of personal eHealth search practices. Methods Q methodology was used to examine subjective perspectives regarding personal eHealth search practices among allied health students majoring in a health education degree program. Thirteen (n = 13) undergraduate students were interviewed about their attitudes and experiences conducting eHealth searches. From the interviews, 36 statements were used in a structured ranking task to identify clusters and determine which specific perceptions of eHealth search practices discriminated students into different groups. Scores on an objective measure of eHealth literacy were used to help categorize participant perspectives. Results Q-technique factor analysis of the rankings identified 3 clusters of respondents with differing views on eHealth searches that generally coincided with participants’ objective eHealth literacy scores. The proficient resourceful students (pattern/structure coefficient range 0.56-0.80) described themselves as using multiple resources to obtain eHealth information, as opposed to simply relying on Internet search engines. The intermediate reluctant students (pattern/structure coefficient range 0.75-0.90) reported engaging only Internet search engines to locate eHealth information, citing undeveloped evaluation skills when considering sources of information located on the Internet. Both groups of advanced students reported not knowing how to use Boolean operators to conduct Internet health searches. The basic hubristic students (pattern/structure coefficient range 0.54-0.76) described themselves as independent procrastinators when searching for eHealth information. Interestingly, basic hubristic students represented the only cluster of participants to describe themselves as (1) having received instruction on using the Internet to conduct eHealth searches, and (2) possessing relative confidence when completing a search task. Conclusions Subjective perspectives of eHealth search practices differed among students possessing different levels of eHealth literacy. These multiple perspectives present both challenges and opportunities for empowering college students in the health professions to use the Internet to obtain and appraise evidence-based health information using the Internet. PMID:22543437

A pilot randomized controlled trial comparing effectiveness of prism glasses, visual search training and standard care in hemianopia.

PubMed

Rowe, F J; Conroy, E J; Bedson, E; Cwiklinski, E; Drummond, A; García-Fiñana, M; Howard, C; Pollock, A; Shipman, T; Dodridge, C; MacIntosh, C; Johnson, S; Noonan, C; Barton, G; Sackley, C

2017-10-01

Pilot trial to compare prism therapy and visual search training, for homonymous hemianopia, to standard care (information only). Prospective, multicentre, parallel, single-blind, three-arm RCT across fifteen UK acute stroke units. Stroke survivors with homonymous hemianopia. Arm a (Fresnel prisms) for minimum 2 hours, 5 days per week over 6 weeks. Arm b (visual search training) for minimum 30 minutes, 5 days per week over 6 weeks. Arm c (standard care-information only). Adult stroke survivors (>18 years), stable hemianopia, visual acuity better than 0.5 logMAR, refractive error within ±5 dioptres, ability to read/understand English and provide consent. Primary outcomes were change in visual field area from baseline to 26 weeks and calculation of sample size for a definitive trial. Secondary measures included Rivermead Mobility Index, Visual Function Questionnaire 25/10, Nottingham Extended Activities of Daily Living, Euro Qual, Short Form-12 questionnaires and Radner reading ability. Measures were post-randomization at baseline and 6, 12 and 26 weeks. Randomization block lists stratified by site and partial/complete hemianopia. Allocations disclosed to patients. Primary outcome assessor blind to treatment allocation. Eighty-seven patients were recruited: 27-Fresnel prisms, 30-visual search training and 30-standard care; 69% male; mean age 69 years (SD 12). At 26 weeks, full results for 24, 24 and 22 patients, respectively, were compared to baseline. Sample size calculation for a definitive trial determined as 269 participants per arm for a 200 degree 2 visual field area change at 90% power. Non-significant relative change in area of visual field was 5%, 8% and 3.5%, respectively, for the three groups. Visual Function Questionnaire responses improved significantly from baseline to 26 weeks with visual search training (60 [SD 19] to 68.4 [SD 20]) compared to Fresnel prisms (68.5 [SD 16.4] to 68.2 [18.4]: 7% difference) and standard care (63.7 [SD 19.4] to 59.8 [SD 22.7]: 10% difference), P=.05. Related adverse events were common with Fresnel prisms (69.2%; typically headaches). No significant change occurred for area of visual field area across arms over follow-up. Visual search training had significant improvement in vision-related quality of life. Prism therapy produced adverse events in 69%. Visual search training results warrant further investigation. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Physical examination in undergraduate medical education in the field of general practice - a scoping review.

PubMed

Moßhammer, Dirk; Graf, Joachim; Joos, Stefanie; Hertkorn, Rebekka

2017-11-25

Physical examination (PE) is an essential clinical skill and a central part of a physician's daily activity. Teaching of PE has been integrated into medical school by many clinical disciplines with respective specific examination procedures. For instance, PE teaching in general practice may include a full-body examination approach. Studies show that PE-skills of medical students often need enhancement. The aim of this article was to scope the literature regarding the teaching and research of PE within general practice during undergraduate medical education. We evaluated a wide breadth of literature relating to the content, study design, country of research institution and year of publication. Literature search in Medline along the PRISMA-P protocol was performed by search syntax ("physical examination" AND "medical education" AND "undergraduate" AND general practice) considering Medline MeSH (Medical Subject Heading)-Terms and Medline search term tree structure. Independent title, abstract and full-text screening with defined inclusion and exclusion criteria was performed. Full texts were analyzed by publication year, country of origin, study design and content (by categorizing articles along their main topic according to qualitative content analysis of Mayring). One-hundred seven articles were included. The annual number of publications ranged from 4 to 14 and had a slightly rising trend since 2000. Nearly half of the publications originated from the United States (n = 54), 33 from Canada and the United Kingdom. Overall, intervention studies represented the largest group (n = 60, including uncontrolled and controlled studies, randomized and non-randomized), followed by cross-sectional studies (n = 29). The 117 studies could be assigned to five categories "teaching methods (n = 53)", "teaching quality (n = 33)", "performance evaluation and examination formats (n=19)", "students' views (n = 8)" and "patients' and standardized patients' views (n=4)". The present work shows a wide spectrum of teaching and research activities and a certain level of evidence for the effectiveness of individual teaching methods. It can be used as orientation and impulse generator for the further development of medical education in the field of PE.

Glycan fragment database: a database of PDB-based glycan 3D structures.

PubMed

Jo, Sunhwan; Im, Wonpil

2013-01-01

The glycan fragment database (GFDB), freely available at http://www.glycanstructure.org, is a database of the glycosidic torsion angles derived from the glycan structures in the Protein Data Bank (PDB). Analogous to protein structure, the structure of an oligosaccharide chain in a glycoprotein, referred to as a glycan, can be characterized by the torsion angles of glycosidic linkages between relatively rigid carbohydrate monomeric units. Knowledge of accessible conformations of biologically relevant glycans is essential in understanding their biological roles. The GFDB provides an intuitive glycan sequence search tool that allows the user to search complex glycan structures. After a glycan search is complete, each glycosidic torsion angle distribution is displayed in terms of the exact match and the fragment match. The exact match results are from the PDB entries that contain the glycan sequence identical to the query sequence. The fragment match results are from the entries with the glycan sequence whose substructure (fragment) or entire sequence is matched to the query sequence, such that the fragment results implicitly include the influences from the nearby carbohydrate residues. In addition, clustering analysis based on the torsion angle distribution can be performed to obtain the representative structures among the searched glycan structures.

Multiple-variable neighbourhood search for the single-machine total weighted tardiness problem

NASA Astrophysics Data System (ADS)

Chung, Tsui-Ping; Fu, Qunjie; Liao, Ching-Jong; Liu, Yi-Ting

2017-07-01

The single-machine total weighted tardiness (SMTWT) problem is a typical discrete combinatorial optimization problem in the scheduling literature. This problem has been proved to be NP hard and thus provides a challenging area for metaheuristics, especially the variable neighbourhood search algorithm. In this article, a multiple variable neighbourhood search (m-VNS) algorithm with multiple neighbourhood structures is proposed to solve the problem. Special mechanisms named matching and strengthening operations are employed in the algorithm, which has an auto-revising local search procedure to explore the solution space beyond local optimality. Two aspects, searching direction and searching depth, are considered, and neighbourhood structures are systematically exchanged. Experimental results show that the proposed m-VNS algorithm outperforms all the compared algorithms in solving the SMTWT problem.

Randomized Controlled Trials Evaluating Effect of Television Advertising on Food Intake in Children: Why Such a Sensitive Topic is Lacking Top-Level Evidence?

PubMed

Gregori, Dario; Ballali, Simonetta; Vecchio, Maria Gabriella; Sciré, Antonella Silvia; Foltran, Francesca; Berchialla, Paola

2014-01-01

The aim of this study was to perform a systematic review of evidence coming from randomized controlled trials (RCT) aimed at assessing the effect of television advertising on food intake in children from 4 to 12 years old. Randomized controlled trials were searched in PubMed database and included if they assessed the effect of direct exposure to television food advertising over the actual energy intake of children. Seven studies out of 2166 fulfilled the inclusion criteria. The association between television advertising and energy intake is based on a very limited set of randomized researches lacking a solid ground of first-level evidence.

Does structured patient education improve the recovery and clinical outcomes of patients with neck pain? A systematic review from the Ontario Protocol for Traffic Injury Management (OPTIMa) Collaboration.

PubMed

Yu, Hainan; Côté, Pierre; Southerst, Danielle; Wong, Jessica J; Varatharajan, Sharanya; Shearer, Heather M; Gross, Douglas P; van der Velde, Gabrielle M; Carroll, Linda J; Mior, Silvano A; Ameis, Arthur; Jacobs, Craig L; Taylor-Vaisey, Anne L

2016-12-01

In 2008, the Bone and Joint Decade 2000 to 2010 Task Force on Neck Pain and Its Associated Disorders recommended patient education for the management of neck pain. However, the effectiveness of education interventions has recently been challenged. To update the findings of the Bone and Joint Decade 2000 to 2010 Task Force on Neck Pain and Its Associated Disorders and evaluate the effectiveness of structured patient education for the management of patients with whiplash-associated disorders (WAD) or neck pain and associated disorders (NAD). Systematic review of the literature and best-evidence synthesis. Randomized controlled trials that compared structured patient education with other conservative interventions. Self-rated recovery, functional recovery (eg, disability, return to activities, work, or school), pain intensity, health-related quality of life, psychological outcomes such as depression or fear, or adverse effects. We systematically searched eight electronic databases (MEDLINE, EMBASE, CINAHL, PsycINFO, the Cochrane Central Register of Controlled Trials, DARE, PubMed, and ICL) from 2000 to 2012. Randomized controlled trials, cohort studies, and case-control studies meeting our selection criteria were eligible for critical appraisal. Random pairs of independent reviewers critically appraised eligible studies using the Scottish Intercollegiate Guidelines Network criteria. Scientifically admissible studies were summarized in evidence tables and synthesized following best-evidence synthesis principles. We retrieved 4,477 articles. Of those, nine were eligible for critical appraisal and six were scientifically admissible. Four admissible articles investigated patients with WAD and two targeted patients with NAD. All structured patient education interventions included advice on activation or exercises delivered orally combined with written information or as written information alone. Overall, as a therapeutic intervention, structured patient education was equal or less effective than other conservative treatments including massage, supervised exercise, and physiotherapy. However, structured patient education may provide small benefits when combined with physiotherapy. Either mode of delivery (ie, oral or written education) provides similar results in patients with recent WAD. This review adds to the Bone and Joint Decade 2000 to 2010 Task Force on Neck Pain and Its Associated Disorders by defining more specifically the role of structured patient education in the management of WAD and NAD. Results suggest that structured patient education alone cannot be expected to yield large benefits in clinical effectiveness compared with other conservative interventions for patients with WAD or NAD. Moreover, structured patient education may be of benefit during the recovery of patients with WAD when used as an adjunct therapy to physiotherapy or emergency room care. These benefits are small and short lived. Copyright © 2014 Elsevier Inc. All rights reserved.

Model of community emergence in weighted social networks

NASA Astrophysics Data System (ADS)

Kumpula, J. M.; Onnela, J.-P.; Saramäki, J.; Kertész, J.; Kaski, K.

2009-04-01

Over the years network theory has proven to be rapidly expanding methodology to investigate various complex systems and it has turned out to give quite unparalleled insight to their structure, function, and response through data analysis, modeling, and simulation. For social systems in particular the network approach has empirically revealed a modular structure due to interplay between the network topology and link weights between network nodes or individuals. This inspired us to develop a simple network model that could catch some salient features of mesoscopic community and macroscopic topology formation during network evolution. Our model is based on two fundamental mechanisms of network sociology for individuals to find new friends, namely cyclic closure and focal closure, which are mimicked by local search-link-reinforcement and random global attachment mechanisms, respectively. In addition we included to the model a node deletion mechanism by removing all its links simultaneously, which corresponds for an individual to depart from the network. Here we describe in detail the implementation of our model algorithm, which was found to be computationally efficient and produce many empirically observed features of large-scale social networks. Thus this model opens a new perspective for studying such collective social phenomena as spreading, structure formation, and evolutionary processes.

Improved Genetic Algorithm Based on the Cooperation of Elite and Inverse-elite

NASA Astrophysics Data System (ADS)

Kanakubo, Masaaki; Hagiwara, Masafumi

In this paper, we propose an improved genetic algorithm based on the combination of Bee system and Inverse-elitism, both are effective strategies for the improvement of GA. In the Bee system, in the beginning, each chromosome tries to find good solution individually as global search. When some chromosome is regarded as superior one, the other chromosomes try to find solution around there. However, since chromosomes for global search are generated randomly, Bee system lacks global search ability. On the other hand, in the Inverse-elitism, an inverse-elite whose gene values are reversed from the corresponding elite is produced. This strategy greatly contributes to diversification of chromosomes, but it lacks local search ability. In the proposed method, the Inverse-elitism with Pseudo-simplex method is employed for global search of Bee system in order to strengthen global search ability. In addition, it also has strong local search ability. The proposed method has synergistic effects of the three strategies. We confirmed validity and superior performance of the proposed method by computer simulations.

A feature-weighting account of priming in conjunction search.

PubMed

Becker, Stefanie I; Horstmann, Gernot

2009-02-01

Previous research on the priming effect in conjunction search has shown that repeating the target and distractor features across displays speeds mean response times but does not improve search efficiency: Repetitions do not reduce the set size effect-that is, the effect of the number of distractor items-but only modulate the intercept of the search function. In the present study, we investigated whether priming modulates search efficiency when a conjunctively defined target randomly changes between red and green. The results from an eyetracking experiment show that repeating the target across trials reduced the set size effect and, thus, did enhance search efficiency. Moreover, the probability of selecting the target as the first item in the display was higher when the target-distractor displays were repeated across trials than when they changed. Finally, red distractors were selected more frequently than green distractors when the previous target had been red (and vice versa). Taken together, these results indicate that priming in conjunction search modulates processes concerned with guiding attention to the target, by assigning more attentional weight to features sharing the previous target's color.

'Googling' Gout: Exploring perceptions about gout through a linguistic analysis of online search activities.

PubMed

Jordan, Kayla N; Pennebaker, James W; Petrie, Keith J; Dalbeth, Nicola

2018-05-21

To understand what terms people seeking information about gout use most frequently in online searches and explore the psychological and emotional tone of these searches. A large de-identified dataset of search histories from major search engines was analyzed. Participants who searched for gout (n=1,117), arthritis (arthritis search control group, n=2,036, age and sex-matched), and a random set of age and sex-matched participants (general control group, n=2,150) were included. Searches were analyzed using Meaning Extraction Helper and Linguistic Inquiry and Word Count. The most frequent unique searches in the gout search group included gout-related and food-related terms. Those who searched for gout were most likely to search for words related to eating or avoidance. In contrast, those who searched for arthritis were more likely to search for disease or health-related words. Compared with the general control group, higher information seeking was observed for the gout and arthritis search groups. Compared with the general control group, both the gout and arthritis search groups searched for more food-related words, and fewer leisure and sexual words. The searches of both the gout and arthritis search groups were lower in positivity and higher in sadness words. The perception of gout as a condition managed by dietary strategies aligns with online information-seeking about the disease and its management. In contrast, people searching about arthritis focus more on medical strategies. Linguistic analyses reflect greater disability in social and leisure activities and lower positive emotion for those searching for gout or arthritis. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

A Search Model for Imperfectly Detected Targets

NASA Technical Reports Server (NTRS)

Ahumada, Albert

2012-01-01

Under the assumptions that 1) the search region can be divided up into N non-overlapping sub-regions that are searched sequentially, 2) the probability of detection is unity if a sub-region is selected, and 3) no information is available to guide the search, there are two extreme case models. The search can be done perfectly, leading to a uniform distribution over the number of searches required, or the search can be done with no memory, leading to a geometric distribution for the number of searches required with a success probability of 1/N. If the probability of detection P is less than unity, but the search is done otherwise perfectly, the searcher will have to search the N regions repeatedly until detection occurs. The number of searches is thus the sum two random variables. One is N times the number of full searches (a geometric distribution with success probability P) and the other is the uniform distribution over the integers 1 to N. The first three moments of this distribution were computed, giving the mean, standard deviation, and the kurtosis of the distribution as a function of the two parameters. The model was fit to the data presented last year (Ahumada, Billington, & Kaiwi, 2 required to find a single pixel target on a simulated horizon. The model gave a good fit to the three moments for all three observers.

Load Balancing in Structured P2P Networks

NASA Astrophysics Data System (ADS)

Zhu, Yingwu

In this chapter we start by addressing the importance and necessity of load balancing in structured P2P networks, due to three main reasons. First, structured P2P networks assume uniform peer capacities while peer capacities are heterogeneous in deployed P2P networks. Second, resorting to pseudo-uniformity of the hash function used to generate node IDs and data item keys leads to imbalanced overlay address space and item distribution. Lastly, placement of data items cannot be randomized in some applications (e.g., range searching). We then present an overview of load aggregation and dissemination techniques that are required by many load balancing algorithms. Two techniques are discussed including tree structure-based approach and gossip-based approach. They make different tradeoffs between estimate/aggregate accuracy and failure resilience. To address the issue of load imbalance, three main solutions are described: virtual server-based approach, power of two choices, and address-space and item balancing. While different in their designs, they all aim to improve balance on the address space and data item distribution. As a case study, the chapter discusses a virtual server-based load balancing algorithm that strives to ensure fair load distribution among nodes and minimize load balancing cost in bandwidth. Finally, the chapter concludes with future research and a summary.

Enhanced oxygen vacancy diffusion in Ta2O5 resistive memory devices due to infinitely adaptive crystal structure

NASA Astrophysics Data System (ADS)

Jiang, Hao; Stewart, Derek A.

2016-04-01

Metal oxide resistive memory devices based on Ta2O5 have demonstrated high switching speed, long endurance, and low set voltage. However, the physical origin of this improved performance is still unclear. Ta2O5 is an important archetype of a class of materials that possess an adaptive crystal structure that can respond easily to the presence of defects. Using first principles nudged elastic band calculations, we show that this adaptive crystal structure leads to low energy barriers for in-plane diffusion of oxygen vacancies in λ phase Ta2O5. Identified diffusion paths are associated with collective motion of neighboring atoms. The overall vacancy diffusion is anisotropic with higher diffusion barriers found for oxygen vacancy movement between Ta-O planes. Coupled with the fact that oxygen vacancy formation energy in Ta2O5 is relatively small, our calculated low diffusion barriers can help explain the low set voltage in Ta2O5 based resistive memory devices. Our work shows that other oxides with adaptive crystal structures could serve as potential candidates for resistive random access memory devices. We also discuss some general characteristics for ideal resistive RAM oxides that could be used in future computational material searches.

Identification of problems in search strategies in Cochrane Reviews.

PubMed

Franco, Juan Víctor Ariel; Garrote, Virginia Laura; Escobar Liquitay, Camila Micaela; Vietto, Valeria

2018-05-15

Search strategies are essential for the adequate retrieval of studies in a systematic review (SR). Our objective was to identify problems in the design and reporting of search strategies in a sample of new Cochrane SRs first published in The Cochrane Library in 2015. We took a random sample of 70 new Cochrane SRs of interventions published in 2015. We evaluated their design and reporting of search strategies using the recommendations from the Cochrane Handbook for Systematic Reviews of Interventions, the Methodological Expectations of Cochrane Intervention Reviews, and the Peer Review of Electronic Search Strategies evidence-based guideline. Most reviews complied with the reporting standards in the Cochrane Handbook and the Methodological Expectations of Cochrane Intervention Reviews; however, 8 SRs did not search trials registers, 3 SRs included language restrictions, and there was inconsistent reporting of contact with individuals and searches of the gray literature. We found problems in the design of the search strategies in 73% of reviews (95% CI, 60-84%) and 53% of these contained problems (95% CI, 38-69%) that could limit both the sensitivity and precision of the search strategies. We found limitations in the design and reporting of search strategies. We consider that a greater adherence to the guidelines could improve their quality. Copyright © 2018 John Wiley & Sons, Ltd.

Network meta-analyses could be improved by searching more sources and by involving a librarian.

PubMed

Li, Lun; Tian, Jinhui; Tian, Hongliang; Moher, David; Liang, Fuxiang; Jiang, Tongxiao; Yao, Liang; Yang, Kehu

2014-09-01

Network meta-analyses (NMAs) aim to rank the benefits (or harms) of interventions, based on all available randomized controlled trials. Thus, the identification of relevant data is critical. We assessed the conduct of the literature searches in NMAs. Published NMAs were retrieved by searching electronic bibliographic databases and other sources. Two independent reviewers selected studies and five trained reviewers abstracted data regarding literature searches, in duplicate. Search method details were examined using descriptive statistics. Two hundred forty-nine NMAs were included. Eight used previous systematic reviews to identify primary studies without further searching, and five did not report any literature searches. In the 236 studies that used electronic databases to identify primary studies, the median number of databases was 3 (interquartile range: 3-5). MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials were the most commonly used databases. The most common supplemental search methods included reference lists of included studies (48%), reference lists of previous systematic reviews (40%), and clinical trial registries (32%). None of these supplemental methods was conducted in more than 50% of the NMAs. Literature searches in NMAs could be improved by searching more sources, and by involving a librarian or information specialist. Copyright © 2014 Elsevier Inc. All rights reserved.

Hard x ray imaging graphics development and literature search

NASA Technical Reports Server (NTRS)

Emslie, A. Gordon

1991-01-01

This report presents work performed between June 1990 and June 1991 and has the following objectives: (1) a comprehensive literature search of imaging technology and coded aperture imaging as well as relevant topics relating to solar flares; (2) an analysis of random number generators; and (3) programming simulation models of hard x ray telescopes. All programs are compatible with NASA/MSFC Space Science LAboratory VAX Cluster and are written in VAX FORTRAN and VAX IDL (Interactive Data Language).

Hybrid geometric-random template-placement algorithm for gravitational wave searches from compact binary coalescences

NASA Astrophysics Data System (ADS)

Roy, Soumen; Sengupta, Anand S.; Thakor, Nilay

2017-05-01

Astrophysical compact binary systems consisting of neutron stars and black holes are an important class of gravitational wave (GW) sources for advanced LIGO detectors. Accurate theoretical waveform models from the inspiral, merger, and ringdown phases of such systems are used to filter detector data under the template-based matched-filtering paradigm. An efficient grid over the parameter space at a fixed minimal match has a direct impact on the overall time taken by these searches. We present a new hybrid geometric-random template placement algorithm for signals described by parameters of two masses and one spin magnitude. Such template banks could potentially be used in GW searches from binary neutron stars and neutron star-black hole systems. The template placement is robust and is able to automatically accommodate curvature and boundary effects with no fine-tuning. We also compare these banks against vanilla stochastic template banks and show that while both are equally efficient in the fitting-factor sense, the bank sizes are ˜25 % larger in the stochastic method. Further, we show that the generation of the proposed hybrid banks can be sped up by nearly an order of magnitude over the stochastic bank. Generic issues related to optimal implementation are discussed in detail. These improvements are expected to directly reduce the computational cost of gravitational wave searches.

Evidence of Levy walk foraging patterns in human hunter-gatherers.

PubMed

Raichlen, David A; Wood, Brian M; Gordon, Adam D; Mabulla, Audax Z P; Marlowe, Frank W; Pontzer, Herman

2014-01-14

When searching for food, many organisms adopt a superdiffusive, scale-free movement pattern called a Lévy walk, which is considered optimal when foraging for heterogeneously located resources with little prior knowledge of distribution patterns [Viswanathan GM, da Luz MGE, Raposo EP, Stanley HE (2011) The Physics of Foraging: An Introduction to Random Searches and Biological Encounters]. Although memory of food locations and higher cognition may limit the benefits of random walk strategies, no studies to date have fully explored search patterns in human foraging. Here, we show that human hunter-gatherers, the Hadza of northern Tanzania, perform Lévy walks in nearly one-half of all foraging bouts. Lévy walks occur when searching for a wide variety of foods from animal prey to underground tubers, suggesting that, even in the most cognitively complex forager on Earth, such patterns are essential to understanding elementary foraging mechanisms. This movement pattern may be fundamental to how humans experience and interact with the world across a wide range of ecological contexts, and it may be adaptive to food distribution patterns on the landscape, which previous studies suggested for organisms with more limited cognition. Additionally, Lévy walks may have become common early in our genus when hunting and gathering arose as a major foraging strategy, playing an important role in the evolution of human mobility.

A randomized controlled trial comparing 2 interventions for visual field loss with standard occupational therapy during inpatient stroke rehabilitation.

PubMed

Mödden, Claudia; Behrens, Marion; Damke, Iris; Eilers, Norbert; Kastrup, Andreas; Hildebrandt, Helmut

2012-06-01

Compensatory and restorative treatments have been developed to improve visual field defects after stroke. However, no controlled trials have compared these interventions with standard occupational therapy (OT). A total of 45 stroke participants with visual field defect admitted for inpatient rehabilitation were randomized to restorative computerized training (RT) using computer-based stimulation of border areas of their visual field defects or to a computer-based compensatory therapy (CT) teaching a visual search strategy. OT, in which different compensation strategies were used to train for activities of daily living, served as standard treatment for the active control group. Each treatment group received 15 single sessions of 30 minutes distributed over 3 weeks. The primary outcome measures were visual field expansion for RT, visual search performance for CT, and reading performance for both treatments. Visual conjunction search, alertness, and the Barthel Index were secondary outcomes. Compared with OT, CT resulted in a better visual search performance, and RT did not result in a larger expansion of the visual field. Intragroup pre-post comparisons demonstrated that CT improved all defined outcome parameters and RT several, whereas OT only improved one. CT improved functional deficits after visual field loss compared with standard OT and may be the intervention of choice during inpatient rehabilitation. A larger trial that includes lesion location in the analysis is recommended.

Searching for bumps and ellipses on the ground and in the sky: no advantage for the ground plane.

PubMed

Jóhannesson, Omar I; Sigurdardottir, Kristín Ósk; Kristjánsson, Arni

2013-11-01

A staple of modern theories of vision is that the visual system has evolved to perceive cues containing the most predictive information about the layout of the environment. This entails the prediction that - other things being equal - visual performance in a familiar setting should be superior to performance in an unfamiliar one. Visual performance should therefore be better on the familiar ground plane compared to an implied sky or wall plane. We tested this comparing visual search for stimuli presented in an implied ground plane with search on a 180° rotated search display so that the stimuli appeared in an implied "sky" plane, and with search in a random layout implying no depth. This was tested for stimuli with, or without, curvature discontinuities, that have previously been shown to be strong cues for shape analysis. Surprisingly, no advantage of the ground plane over the sky plane was observed, while a strong effect of layout regularity was seen. Similarly, in experiment 2 there was little effect of placing the stimuli on an implied wall plane compared to the ground or the sky. The results are not explained by assuming that curvature discontinuities are such strong cues that they overshadow any effect of depth-plane, since there was a strong effect of regular versus random layout, which should also have disappeared under this account. The results argue instead for a very strong effect of layout regularity, unrelated to environmental regularities in evolutionary history, since there was no ground-plane benefit. Copyright © 2013 Elsevier B.V. All rights reserved.

Temporal stability of visual search-driven biometrics

NASA Astrophysics Data System (ADS)

Yoon, Hong-Jun; Carmichael, Tandy R.; Tourassi, Georgia

2015-03-01

Previously, we have shown the potential of using an individual's visual search pattern as a possible biometric. That study focused on viewing images displaying dot-patterns with different spatial relationships to determine which pattern can be more effective in establishing the identity of an individual. In this follow-up study we investigated the temporal stability of this biometric. We performed an experiment with 16 individuals asked to search for a predetermined feature of a random-dot pattern as we tracked their eye movements. Each participant completed four testing sessions consisting of two dot patterns repeated twice. One dot pattern displayed concentric circles shifted to the left or right side of the screen overlaid with visual noise, and participants were asked which side the circles were centered on. The second dot-pattern displayed a number of circles (between 0 and 4) scattered on the screen overlaid with visual noise, and participants were asked how many circles they could identify. Each session contained 5 untracked tutorial questions and 50 tracked test questions (200 total tracked questions per participant). To create each participant's "fingerprint", we constructed a Hidden Markov Model (HMM) from the gaze data representing the underlying visual search and cognitive process. The accuracy of the derived HMM models was evaluated using cross-validation for various time-dependent train-test conditions. Subject identification accuracy ranged from 17.6% to 41.8% for all conditions, which is significantly higher than random guessing (1/16 = 6.25%). The results suggest that visual search pattern is a promising, temporally stable personalized fingerprint of perceptual organization.

Effects of Link Annotations on Search Performance in Layered and Unlayered Hierarchically Organized Information Spaces.

ERIC Educational Resources Information Center

Fraser, Landon; Locatis, Craig

2001-01-01

Investigated the effects of link annotations on high school user search performance in Web hypertext environments having deep (layered) and shallow link structures. Results confirmed previous research that shallow link structures are better than deep (layered) link structures, and also showed that annotations had virtually no effect on search…

Bootstrapping on Undirected Binary Networks Via Statistical Mechanics

NASA Astrophysics Data System (ADS)

Fushing, Hsieh; Chen, Chen; Liu, Shan-Yu; Koehl, Patrice

2014-09-01

We propose a new method inspired from statistical mechanics for extracting geometric information from undirected binary networks and generating random networks that conform to this geometry. In this method an undirected binary network is perceived as a thermodynamic system with a collection of permuted adjacency matrices as its states. The task of extracting information from the network is then reformulated as a discrete combinatorial optimization problem of searching for its ground state. To solve this problem, we apply multiple ensembles of temperature regulated Markov chains to establish an ultrametric geometry on the network. This geometry is equipped with a tree hierarchy that captures the multiscale community structure of the network. We translate this geometry into a Parisi adjacency matrix, which has a relative low energy level and is in the vicinity of the ground state. The Parisi adjacency matrix is then further optimized by making block permutations subject to the ultrametric geometry. The optimal matrix corresponds to the macrostate of the original network. An ensemble of random networks is then generated such that each of these networks conforms to this macrostate; the corresponding algorithm also provides an estimate of the size of this ensemble. By repeating this procedure at different scales of the ultrametric geometry of the network, it is possible to compute its evolution entropy, i.e. to estimate the evolution of its complexity as we move from a coarse to a fine description of its geometric structure. We demonstrate the performance of this method on simulated as well as real data networks.

The rate of decline of joint space width in patients with osteoarthritis of the knee: a systematic review and meta-analysis of randomized placebo-controlled trials of chondroitin sulfate .

PubMed

Hochberg, Marc C; Zhan, Min; Langenberg, Patricia

2008-11-01

Chondroitin sulfate has been shown to relieve pain and improve functional limitation in patients with osteoarthritis (OA) of the knee in numerous clinical trials and meta-analyses. Its role as a potential structure-modifying drug for knee OA, however, remains controversial. To perform a meta-analysis of randomized double-blind placebo-controlled clinical trials to assess the efficacy of chondroitin sulfate as a structure-modifying drug for knee OA. A Medline search was conducted from 1996 through 2007 and five articles that reported results from three trials were identified; one additional trial was identified through review of presentations at annual rheumatology meetings. There was no evidence of heterogeneity across the trials and results were pooled using a fixed effects meta-analysis. Pooled results demonstrated a small significant effect of chondroitin sulfate on the reduction in rate of decline in minimum joint space width of 0.07 mm/year (95% CI 0.03, 0.10) that corresponded to an effect size of 0.26 (95% CI 0.14, 0.38) (p < 0.0001). This result was robust in sensitivity analyses. The individual studies included in the meta-analysis varied in the number of patients enrolled and the techniques used to acquire knee radiographs and to measure joint space width. These results demonstrate that chondroitin sulfate is effective for reducing the rate of decline in minimum joint space width in patients with OA of the knee. Chondroitin sulfate may have a role as a structure-modifying agent in the management of patients with knee OA.

A probabilistic framework for identifying biosignatures using Pathway Complexity

NASA Astrophysics Data System (ADS)

Marshall, Stuart M.; Murray, Alastair R. G.; Cronin, Leroy

2017-11-01

One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random structures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can easily be distinguished from non-living material assemblies. Many complex artefacts, from ordinary bioproducts to human tools, though they are not living things, are ultimately produced by biological processes-whether those processes occur at the scale of cells or societies, they are the consequences of living systems. While these objects are not living, they cannot randomly form, as they are the product of a biological organism and hence are either technological or cultural biosignatures. A generalized approach that aims to evaluate complex objects as possible biosignatures could be useful to explore the cosmos for new life forms. However, it is not obvious how it might be possible to create such a self-contained approach. This would require us to prove rigorously that a given artefact is too complex to have formed by chance. In this paper, we present a new type of complexity measure, which we call `Pathway Complexity', that allows us not only to threshold the abiotic-biotic divide, but also to demonstrate a probabilistic approach based on object abundance and complexity which can be used to unambiguously assign complex objects as biosignatures. We hope that this approach will not only open up the search for biosignatures beyond the Earth, but also allow us to explore the Earth for new types of biology, and to determine when a complex chemical system discovered in the laboratory could be considered alive. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Structure prediction and molecular simulation of gases diffusion pathways in hydrogenase.

PubMed

Sundaram, Shanthy; Tripathi, Ashutosh; Gupta, Vipul

2010-10-06

Although hydrogen is considered to be one of the most promising future energy sources and the technical aspects involved in using it have advanced considerably, the future supply of hydrogen from renewable sources is still unsolved. The [Fe]- hydrogenase enzymes are highly efficient H(2) catalysts found in ecologically and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlamydomonas reinhardtii. While these enzymes can occur in several forms, H(2) catalysis takes place at a unique [FeS] prosthetic group or H-cluster, located at the active site. 3D structure of the protein hydA1 hydrogenase from Chlamydomonas reinhardtti was predicted using the MODELER 8v2 software. Conserved region was depicted from the NCBI CDD Search. Template selection was done on the basis NCBI BLAST results. For single template 1FEH was used and for multiple templates 1FEH and 1HFE were used. The result of the Homology modeling was verified by uploading the file to SAVS server. On the basis of the SAVS result 3D structure predicted using single template was chosen for performing molecular simulation. For performing molecular simulation three strategies were used. First the molecular simulation of the protein was performed in solvated box containing bulk water. Then 100 H(2) molecules were randomly inserted in the solvated box and two simulations of 50 and 100 ps were performed. Similarly 100 O(2) molecules were randomly placed in the solvated box and again 50 and 100 ps simulation were performed. Energy minimization was performed before each simulation was performed. Conformations were saved after each simulation. Analysis of the gas diffusion was done on the basis of RMSD, Radius of Gyration and no. of gas molecule/ps plot.

Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search

PubMed Central

Alocci, Davide; Mariethoz, Julien; Horlacher, Oliver; Bolleman, Jerven T.; Campbell, Matthew P.; Lisacek, Frederique

2015-01-01

Resource description framework (RDF) and Property Graph databases are emerging technologies that are used for storing graph-structured data. We compare these technologies through a molecular biology use case: glycan substructure search. Glycans are branched tree-like molecules composed of building blocks linked together by chemical bonds. The molecular structure of a glycan can be encoded into a direct acyclic graph where each node represents a building block and each edge serves as a chemical linkage between two building blocks. In this context, Graph databases are possible software solutions for storing glycan structures and Graph query languages, such as SPARQL and Cypher, can be used to perform a substructure search. Glycan substructure searching is an important feature for querying structure and experimental glycan databases and retrieving biologically meaningful data. This applies for example to identifying a region of the glycan recognised by a glycan binding protein (GBP). In this study, 19,404 glycan structures were selected from GlycomeDB (www.glycome-db.org) and modelled for being stored into a RDF triple store and a Property Graph. We then performed two different sets of searches and compared the query response times and the results from both technologies to assess performance and accuracy. The two implementations produced the same results, but interestingly we noted a difference in the query response times. Qualitative measures such as portability were also used to define further criteria for choosing the technology adapted to solving glycan substructure search and other comparable issues. PMID:26656740

Proactive Personality and the Successful Job Search : A Field Investigation with College Graduates

ERIC Educational Resources Information Center

Brown, Douglas J.; Cober, Richard T.; Kane, Kevin; Levy, Paul E.; Shalhoop, Jarrett

2006-01-01

The current article tests a model of proactive personality and job search success with a sample of 180 graduating college students. Using structural equation modeling, the authors tested a theoretical model that specified the relations among proactive personality, job search self-efficacy, job search behaviors, job search effort, and job search…

The Concept of the "Imploded Boolean Search": A Case Study with Undergraduate Chemistry Students

ERIC Educational Resources Information Center

Tomaszewski, Robert

2016-01-01

Critical thinking and analytical problem-solving skills in research involves using different search strategies. A proposed concept for an "Imploded Boolean Search" combines three unique identifiable field types to perform a search: keyword(s), numerical value(s), and a chemical structure or reaction. The object of this type of search is…

Effects of exercise on functional aerobic capacity in adults with fibromyalgia syndrome: A systematic review of randomized controlled trials.

PubMed

García-Hermoso, Antonio; Saavedra, Jose M; Escalante, Yolanda

2015-01-01

Patients with fibromyalgia present a reduced capacity of upper and lower limb physical performance and affect their independence in performing everyday activities. The purpose of the present systematic review was to summarize evidence for the effectiveness and structure of exercise programs on functional aerobic capacity in patients with fibromyalgia syndrome. Keyword searches were made of seven databases. The systematic review was limited to English language studies of people with FM that evaluated the effects of exercise programs on functional aerobic capacity (6-minute walk test). The criteria for inclusion were satisfied by 12 randomized controlled trial (RCT) studies. The main cumulative evidence indicates that the programs based on aerobic exercise alone and on aquatic exercises have large (effect size = 0.85) and moderate (effect size = 0.44) effects. Aerobic and aquatic exercises at the proper intensity favour the increased functional aerobic capacity of fibromyalgia patients; however, most works do not adequately detail the intensity of the exercises. Moderate intensity exercise (aerobic and aquatic exercise) performed at least two times per week and 30-60 minutes a day is effective for increasing functional aerobic capacity, favouring the daily activities of daily living in this population.