Social influence bias: a randomized experiment.

Science.gov (United States)

Muchnik, Lev; Aral, Sinan; Taylor, Sean J

2013-08-09

Our society is increasingly relying on the digitized, aggregated opinions of others to make decisions. We therefore designed and analyzed a large-scale randomized experiment on a social news aggregation Web site to investigate whether knowledge of such aggregates distorts decision-making. Prior ratings created significant bias in individual rating behavior, and positive and negative social influences created asymmetric herding effects. Whereas negative social influence inspired users to correct manipulated ratings, positive social influence increased the likelihood of positive ratings by 32% and created accumulating positive herding that increased final ratings by 25% on average. This positive herding was topic-dependent and affected by whether individuals were viewing the opinions of friends or enemies. A mixture of changing opinion and greater turnout under both manipulations together with a natural tendency to up-vote on the site combined to create the herding effects. Such findings will help interpret collective judgment accurately and avoid social influence bias in collective intelligence in the future.

Stationary Probability and First-Passage Time of Biased Random Walk

International Nuclear Information System (INIS)

Li Jing-Wen; Tang Shen-Li; Xu Xin-Ping

2016-01-01

In this paper, we consider the stationary probability and first-passage time of biased random walk on 1D chain, where at each step the walker moves to the left and right with probabilities p and q respectively (0 ⩽ p, q ⩽ 1, p + q = 1). We derive exact analytical results for the stationary probability and first-passage time as a function of p and q for the first time. Our results suggest that the first-passage time shows a double power-law F ∼ (N − 1) γ , where the exponent γ = 2 for N < |p − q| −1 and γ = 1 for N > |p − q| −1 . Our study sheds useful insights into the biased random-walk process. (paper)

Randomized clinical trials in dentistry: Risks of bias, risks of random errors, reporting quality, and methodologic quality over the years 1955-2013.

Directory of Open Access Journals (Sweden)

Humam Saltaji

Full Text Available To examine the risks of bias, risks of random errors, reporting quality, and methodological quality of randomized clinical trials of oral health interventions and the development of these aspects over time.We included 540 randomized clinical trials from 64 selected systematic reviews. We extracted, in duplicate, details from each of the selected randomized clinical trials with respect to publication and trial characteristics, reporting and methodologic characteristics, and Cochrane risk of bias domains. We analyzed data using logistic regression and Chi-square statistics.Sequence generation was assessed to be inadequate (at unclear or high risk of bias in 68% (n = 367 of the trials, while allocation concealment was inadequate in the majority of trials (n = 464; 85.9%. Blinding of participants and blinding of the outcome assessment were judged to be inadequate in 28.5% (n = 154 and 40.5% (n = 219 of the trials, respectively. A sample size calculation before the initiation of the study was not performed/reported in 79.1% (n = 427 of the trials, while the sample size was assessed as adequate in only 17.6% (n = 95 of the trials. Two thirds of the trials were not described as double blinded (n = 358; 66.3%, while the method of blinding was appropriate in 53% (n = 286 of the trials. We identified a significant decrease over time (1955-2013 in the proportion of trials assessed as having inadequately addressed methodological quality items (P < 0.05 in 30 out of the 40 quality criteria, or as being inadequate (at high or unclear risk of bias in five domains of the Cochrane risk of bias tool: sequence generation, allocation concealment, incomplete outcome data, other sources of bias, and overall risk of bias.The risks of bias, risks of random errors, reporting quality, and methodological quality of randomized clinical trials of oral health interventions have improved over time; however, further efforts that contribute to the development of more stringent

Local literature bias in genetic epidemiology: an empirical evaluation of the Chinese literature.

Directory of Open Access Journals (Sweden)

Zhenglun Pan

2005-12-01

Full Text Available BACKGROUND: Postulated epidemiological associations are subject to several biases. We evaluated whether the Chinese literature on human genome epidemiology may offer insights on the operation of selective reporting and language biases. METHODS AND FINDINGS: We targeted 13 gene-disease associations, each already assessed by meta-analyses, including at least 15 non-Chinese studies. We searched the Chinese Journal Full-Text Database for additional Chinese studies on the same topics. We identified 161 Chinese studies on 12 of these gene-disease associations; only 20 were PubMed-indexed (seven English full-text. Many studies (14-35 per topic were available for six topics, covering diseases common in China. With one exception, the first Chinese study appeared with a time lag (2-21 y after the first non-Chinese study on the topic. Chinese studies showed significantly more prominent genetic effects than non-Chinese studies, and 48% were statistically significant per se, despite their smaller sample size (median sample size 146 versus 268, p < 0.001. The largest genetic effects were often seen in PubMed-indexed Chinese studies (65% statistically significant per se. Non-Chinese studies of Asian-descent populations (27% significant per se also tended to show somewhat more prominent genetic effects than studies of non-Asian descent (17% significant per se. CONCLUSION: Our data provide evidence for the interplay of selective reporting and language biases in human genome epidemiology. These biases may not be limited to the Chinese literature and point to the need for a global, transparent, comprehensive outlook in molecular population genetics and epidemiologic studies in general.

Genetic diversity and sex-bias dispersal of plateau pika in Tibetan plateau.

Science.gov (United States)

Zhang, Liangzhi; Qu, Jiapeng; Li, Kexin; Li, Wenjing; Yang, Min; Zhang, Yanming

2017-10-01

Dispersal is an important aspect in organism's life history which could influence the rate and outcome of evolution of organism. Plateau pika is the keystone species in community of grasslands in Tibetan Plateau. In this study, we combine genetic and field data to character the population genetic pattern and dispersal dynamics in plateau pika ( Ochotona curzoniae ). Totally, 1,352 individual samples were collected, and 10 microsatellite loci were analyzed. Results revealed that plateau pika possessed high genetic diversity and inbreeding coefficient in a fine-scale population. Dispersal distance is short and restricted in about 20 m. An effective sex-biased dispersal strategy is employed by plateau pika: males disperse in breeding period for mating while females do it after reproduction for offspring and resource. Inbreeding avoiding was shown as the common driving force of dispersal, together with the other two factors, environment and resource. In addition, natal dispersal is female biased. More detailed genetic analyzes are needed to confirm the role of inbreeding avoidance and resource competition as ultimate cause of dispersal patterns in plateau pika.

Sex-biased dispersal creates spatial genetic structure in a parthenogenetic ant with a dependent-lineage reproductive system.

Science.gov (United States)

Kuhn, A; Bauman, D; Darras, H; Aron, S

2017-10-01

Reproduction and dispersal are key aspects of species life history that influence spatial genetic structure in populations. Several ant species in the genus Cataglyphis have evolved a unique breeding system in which new reproductives (that is, queens and males) are produced asexually by parthenogenesis; in contrast, non-reproductives (that is, workers) are produced via sexual reproduction by mates from distinct genetic lineages. We investigated how these two coexisting reproductive methods affect population-level spatial genetic structure using the ant Cataglyphis mauritanica as a model. We obtained genotypes for queens and their male mates from 338 colonies, and we found that the two lineages present in the study population occurred with equal frequency. Furthermore, analysis of spatial genetic structure revealed strong sex-biased dispersal. Because queens were produced by parthenogenesis and because they dispersed over short distances, there was an extreme level of spatial structuring: a mosaic of patches composed of clonal queens was formed. Males, on the other hand, dispersed over several hundred metres and, thus, across patches, ensuring successful interlineage mating.

[Elucidation of key genes in sex determination in genetics teaching].

Science.gov (United States)

Li, Meng; He, Zhumei

2014-06-01

Sex is an important and complex feature of organisms, which is controlled by the genetic and environmental factors. The genetic factors, i.e., genes, are vital in sex determination. However, not all the related genes play the same roles, and some key genes play a vital role in the sex determination and differentiation. With the development of the modern genetics, a great progress on the key genes has been made in sex determination. In this review, we summarize the mechanism of sex determination and the strategy of how to study the key genes in sex determination. It will help us to understand the mechanism of sex determination better in the teaching of genetics.

Internet-based cognitive bias modification for obsessive compulsive disorder : study protocol for a randomized controlled trial

NARCIS (Netherlands)

Williams, Alishia D; Pajak, Rosanna; O'Moore, Kathleen; Andrews, Gavin; Grisham, Jessica R

2014-01-01

BACKGROUND: Cognitive bias modification (CBM) interventions have demonstrated efficacy in augmenting core biases implicated in psychopathology. The current randomized controlled trial (RCT) will evaluate the efficacy of an internet-delivered positive imagery cognitive bias modification intervention

Are most samples of animals systematically biased? Consistent individual trait differences bias samples despite random sampling.

Science.gov (United States)

Biro, Peter A

2013-02-01

Sampling animals from the wild for study is something nearly every biologist has done, but despite our best efforts to obtain random samples of animals, 'hidden' trait biases may still exist. For example, consistent behavioral traits can affect trappability/catchability, independent of obvious factors such as size and gender, and these traits are often correlated with other repeatable physiological and/or life history traits. If so, systematic sampling bias may exist for any of these traits. The extent to which this is a problem, of course, depends on the magnitude of bias, which is presently unknown because the underlying trait distributions in populations are usually unknown, or unknowable. Indeed, our present knowledge about sampling bias comes from samples (not complete population censuses), which can possess bias to begin with. I had the unique opportunity to create naturalized populations of fish by seeding each of four small fishless lakes with equal densities of slow-, intermediate-, and fast-growing fish. Using sampling methods that are not size-selective, I observed that fast-growing fish were up to two-times more likely to be sampled than slower-growing fish. This indicates substantial and systematic bias with respect to an important life history trait (growth rate). If correlations between behavioral, physiological and life-history traits are as widespread as the literature suggests, then many animal samples may be systematically biased with respect to these traits (e.g., when collecting animals for laboratory use), and affect our inferences about population structure and abundance. I conclude with a discussion on ways to minimize sampling bias for particular physiological/behavioral/life-history types within animal populations.

MARRT: Medial Axis biased rapidly-exploring random trees

KAUST Repository

Denny, Jory

2014-05-01

© 2014 IEEE. Motion planning is a difficult and widely studied problem in robotics. Current research aims not only to find feasible paths, but to ensure paths have certain properties, e.g., shortest or safest paths. This is difficult for current state-of-the-art sampling-based techniques as they typically focus on simply finding any path. Despite this difficulty, sampling-based techniques have shown great success in planning for a wide range of applications. Among such planners, Rapidly-Exploring Random Trees (RRTs) search the planning space by biasing exploration toward unexplored regions. This paper introduces a novel RRT variant, Medial Axis RRT (MARRT), which biases tree exploration to the medial axis of free space by pushing all configurations from expansion steps towards the medial axis. We prove that this biasing increases the tree\\'s clearance from obstacles. Improving obstacle clearance is useful where path safety is important, e.g., path planning for robots performing tasks in close proximity to the elderly. Finally, we experimentally analyze MARRT, emphasizing its ability to effectively map difficult passages while increasing obstacle clearance, and compare it to contemporary RRT techniques.

Geometrically biased random walks in bacteria-driven micro-shuttles

International Nuclear Information System (INIS)

Angelani, Luca; Di Leonardo, Roberto

2010-01-01

Micron-sized objects having asymmetric boundaries can rectify the chaotic motions of an active bacterial suspension and perform geometrically biased random walks. Using numerical simulations in a planar geometry, we show that arrow-shaped micro-shuttles, constrained to move in one dimension (1D) in a bath of self-propelled micro-organisms, spontaneously perform unidirectional translational motions with a strongly shape-dependent speed. Relaxing the 1D constraint, a random motion in the whole plane sets in at long times, due to random changes in shuttle orientation caused by bacterial collisions. The complex dynamics arising from the mechanical interactions between bacteria and the object boundaries can be described by a Gaussian stochastic force with a shape-dependent mean and a self-correlation decaying exponentially on the timescale of seconds.

Testing for biases in selection on avian reproductive traits and partitioning direct and indirect selection using quantitative genetic models.

Science.gov (United States)

Reed, Thomas E; Gienapp, Phillip; Visser, Marcel E

2016-10-01

Key life history traits such as breeding time and clutch size are frequently both heritable and under directional selection, yet many studies fail to document microevolutionary responses. One general explanation is that selection estimates are biased by the omission of correlated traits that have causal effects on fitness, but few valid tests of this exist. Here, we show, using a quantitative genetic framework and six decades of life-history data on two free-living populations of great tits Parus major, that selection estimates for egg-laying date and clutch size are relatively unbiased. Predicted responses to selection based on the Robertson-Price Identity were similar to those based on the multivariate breeder's equation (MVBE), indicating that unmeasured covarying traits were not missing from the analysis. Changing patterns of phenotypic selection on these traits (for laying date, linked to climate change) therefore reflect changing selection on breeding values, and genetic constraints appear not to limit their independent evolution. Quantitative genetic analysis of correlational data from pedigreed populations can be a valuable complement to experimental approaches to help identify whether apparent associations between traits and fitness are biased by missing traits, and to parse the roles of direct versus indirect selection across a range of environments. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Empirical evidence of study design biases in randomized trials

DEFF Research Database (Denmark)

Page, Matthew J.; Higgins, Julian P. T.; Clayton, Gemma

2016-01-01

search September 2012), and searched Ovid MEDLINE and Ovid EMBASE for studies indexed from Jan 2012-May 2015. Data were extracted by one author and verified by another. We combined estimates of average bias (e.g. ratio of odds ratios (ROR) or difference in standardised mean differences (dSMD)) in meta......-analyses using the random-effects model. Analyses were stratified by type of outcome ("mortality" versus "other objective" versus "subjective"). Direction of effect was standardised so that ROR SMD ... studies). For these characteristics, the average bias appeared to be larger in trials of subjective outcomes compared with other objective outcomes. Also, intervention effects for subjective outcomes appear to be exaggerated in trials with lack of/unclear blinding of participants (versus blinding) (dSMD...

Bias detection and certified reference materials for random measurands

Science.gov (United States)

Rukhin, Andrew L.

2015-12-01

A problem that frequently occurs in metrology is the bias checking of data obtained by a laboratory against the specified value and uncertainty estimate given in the certificate of analysis. The measurand—a property of a certified reference material (CRM)—is supposed to be random with a normal distribution whose parameters are given by the certificate specifications. The laboratory’s data from subsequent measurements of the CRM (a CRM experiment) are summarized by the sample mean value and its uncertainty which is commonly based on a repeatability standard deviation. New confidence intervals for the lab’s bias are derived. Although they may lack intuitive appeal, those obtained by using higher order asymptotic methods, compared and contrasted in this paper, are recommended.

Bias in random forest variable importance measures: Illustrations, sources and a solution

Directory of Open Access Journals (Sweden)

Hothorn Torsten

2007-01-01

Full Text Available Abstract Background Variable importance measures for random forests have been receiving increased attention as a means of variable selection in many classification tasks in bioinformatics and related scientific fields, for instance to select a subset of genetic markers relevant for the prediction of a certain disease. We show that random forest variable importance measures are a sensible means for variable selection in many applications, but are not reliable in situations where potential predictor variables vary in their scale of measurement or their number of categories. This is particularly important in genomics and computational biology, where predictors often include variables of different types, for example when predictors include both sequence data and continuous variables such as folding energy, or when amino acid sequence data show different numbers of categories. Results Simulation studies are presented illustrating that, when random forest variable importance measures are used with data of varying types, the results are misleading because suboptimal predictor variables may be artificially preferred in variable selection. The two mechanisms underlying this deficiency are biased variable selection in the individual classification trees used to build the random forest on one hand, and effects induced by bootstrap sampling with replacement on the other hand. Conclusion We propose to employ an alternative implementation of random forests, that provides unbiased variable selection in the individual classification trees. When this method is applied using subsampling without replacement, the resulting variable importance measures can be used reliably for variable selection even in situations where the potential predictor variables vary in their scale of measurement or their number of categories. The usage of both random forest algorithms and their variable importance measures in the R system for statistical computing is illustrated and

Genetic anticipation in BRCA1/2 families after controlling for ascertainment bias and cohort effect

Science.gov (United States)

Guindalini, Rodrigo Santa Cruz; Song, Andrew; Fackenthal, James D.; Olopade, Olufunmilayo I.; Huo, Dezheng

2016-01-01

Background Genetic anticipation, the earlier onset of disease in successive generations, has been reported in hereditary breast and ovarian cancer syndrome (HBOC), but little is known about its underlying mechanisms. Ascertainment bias is a reason that has been suggested in previous studies. Likewise, cohort effect, which may be due to environmental factors, can be misinterpreted as genetic anticipation. Methods We conducted a review of pedigrees in 176 kindreds segregating deleterious mutations in BRCA1/2 genes who had at least two consecutive generations of the same cancer (breast or ovarian). Using mutation probabilities as analytical weights in weighted random-effect models, we calculated generational differences in age of onset of breast/ovarian cancer. Then we further controlled for ascertainment bias by excluding probands and adjusted for birth cohort effect in the anticipation models. Results The mean age of breast cancer for the probands’ generation was 41.9 years, which was 6.8 years and 9.8 years earlier than the parents’ and grandparents’ generations, respectively. The anticipation effect for breast cancer remained significant after excluding probands. There was a birth cohort effect: patients born in 1930s and 1940s had breast cancer 5.0 and 7.6 years earlier than patients born before 1920. The difference in breast cancer age of onset across generations was no longer significant after adjusting for birth cohort effect. Conclusions The observed anticipation effect was mainly driven by a decrease in age of onset across birth cohorts, underscoring the need for risk reducing interventions that target changing environmental/lifestyle factors in BRCA1/2 carriers. PMID:26992017

Time-delayed fronts from biased random walks

International Nuclear Information System (INIS)

Fort, Joaquim; Pujol, Toni

2007-01-01

We generalize a previous model of time-delayed reaction-diffusion fronts (Fort and Mendez 1999 Phys. Rev. Lett. 82 867) to allow for a bias in the microscopic random walk of particles or individuals. We also present a second model which takes the time order of events (diffusion and reproduction) into account. As an example, we apply them to the human invasion front across the USA in the 19th century. The corrections relative to the previous model are substantial. Our results are relevant to physical and biological systems with anisotropic fronts, including particle diffusion in disordered lattices, population invasions, the spread of epidemics, etc

Random-Resistor-Random-Temperature Kirchhoff-Law-Johnson-Noise (RRRT-KLJN Key Exchange

Directory of Open Access Journals (Sweden)

Kish Laszlo B.

2016-03-01

Full Text Available We introduce two new Kirchhoff-law-Johnson-noise (KLJN secure key distribution schemes which are generalizations of the original KLJN scheme. The first of these, the Random-Resistor (RR- KLJN scheme, uses random resistors with values chosen from a quasi-continuum set. It is well-known since the creation of the KLJN concept that such a system could work in cryptography, because Alice and Bob can calculate the unknown resistance value from measurements, but the RR-KLJN system has not been addressed in prior publications since it was considered impractical. The reason for discussing it now is the second scheme, the Random Resistor Random Temperature (RRRT- KLJN key exchange, inspired by a recent paper of Vadai, Mingesz and Gingl, wherein security was shown to be maintained at non-zero power flow. In the RRRT-KLJN secure key exchange scheme, both the resistances and their temperatures are continuum random variables. We prove that the security of the RRRT-KLJN scheme can prevail at a non-zero power flow, and thus the physical law guaranteeing security is not the Second Law of Thermodynamics but the Fluctuation-Dissipation Theorem. Alice and Bob know their own resistances and temperatures and can calculate the resistance and temperature values at the other end of the communication channel from measured voltage, current and power-flow data in the wire. However, Eve cannot determine these values because, for her, there are four unknown quantities while she can set up only three equations. The RRRT-KLJN scheme has several advantages and makes all former attacks on the KLJN scheme invalid or incomplete.

Bias analysis applied to Agricultural Health Study publications to estimate non-random sources of uncertainty.

Science.gov (United States)

Lash, Timothy L

2007-11-26

The associations of pesticide exposure with disease outcomes are estimated without the benefit of a randomized design. For this reason and others, these studies are susceptible to systematic errors. I analyzed studies of the associations between alachlor and glyphosate exposure and cancer incidence, both derived from the Agricultural Health Study cohort, to quantify the bias and uncertainty potentially attributable to systematic error. For each study, I identified the prominent result and important sources of systematic error that might affect it. I assigned probability distributions to the bias parameters that allow quantification of the bias, drew a value at random from each assigned distribution, and calculated the estimate of effect adjusted for the biases. By repeating the draw and adjustment process over multiple iterations, I generated a frequency distribution of adjusted results, from which I obtained a point estimate and simulation interval. These methods were applied without access to the primary record-level dataset. The conventional estimates of effect associating alachlor and glyphosate exposure with cancer incidence were likely biased away from the null and understated the uncertainty by quantifying only random error. For example, the conventional p-value for a test of trend in the alachlor study equaled 0.02, whereas fewer than 20% of the bias analysis iterations yielded a p-value of 0.02 or lower. Similarly, the conventional fully-adjusted result associating glyphosate exposure with multiple myleoma equaled 2.6 with 95% confidence interval of 0.7 to 9.4. The frequency distribution generated by the bias analysis yielded a median hazard ratio equal to 1.5 with 95% simulation interval of 0.4 to 8.9, which was 66% wider than the conventional interval. Bias analysis provides a more complete picture of true uncertainty than conventional frequentist statistical analysis accompanied by a qualitative description of study limitations. The latter approach is

Bias analysis applied to Agricultural Health Study publications to estimate non-random sources of uncertainty

Directory of Open Access Journals (Sweden)

Lash Timothy L

2007-11-01

Full Text Available Abstract Background The associations of pesticide exposure with disease outcomes are estimated without the benefit of a randomized design. For this reason and others, these studies are susceptible to systematic errors. I analyzed studies of the associations between alachlor and glyphosate exposure and cancer incidence, both derived from the Agricultural Health Study cohort, to quantify the bias and uncertainty potentially attributable to systematic error. Methods For each study, I identified the prominent result and important sources of systematic error that might affect it. I assigned probability distributions to the bias parameters that allow quantification of the bias, drew a value at random from each assigned distribution, and calculated the estimate of effect adjusted for the biases. By repeating the draw and adjustment process over multiple iterations, I generated a frequency distribution of adjusted results, from which I obtained a point estimate and simulation interval. These methods were applied without access to the primary record-level dataset. Results The conventional estimates of effect associating alachlor and glyphosate exposure with cancer incidence were likely biased away from the null and understated the uncertainty by quantifying only random error. For example, the conventional p-value for a test of trend in the alachlor study equaled 0.02, whereas fewer than 20% of the bias analysis iterations yielded a p-value of 0.02 or lower. Similarly, the conventional fully-adjusted result associating glyphosate exposure with multiple myleoma equaled 2.6 with 95% confidence interval of 0.7 to 9.4. The frequency distribution generated by the bias analysis yielded a median hazard ratio equal to 1.5 with 95% simulation interval of 0.4 to 8.9, which was 66% wider than the conventional interval. Conclusion Bias analysis provides a more complete picture of true uncertainty than conventional frequentist statistical analysis accompanied by a

DNA based random key generation and management for OTP encryption.

Science.gov (United States)

Zhang, Yunpeng; Liu, Xin; Sun, Manhui

2017-09-01

One-time pad (OTP) is a principle of key generation applied to the stream ciphering method which offers total privacy. The OTP encryption scheme has proved to be unbreakable in theory, but difficult to realize in practical applications. Because OTP encryption specially requires the absolute randomness of the key, its development has suffered from dense constraints. DNA cryptography is a new and promising technology in the field of information security. DNA chromosomes storing capabilities can be used as one-time pad structures with pseudo-random number generation and indexing in order to encrypt the plaintext messages. In this paper, we present a feasible solution to the OTP symmetric key generation and transmission problem with DNA at the molecular level. Through recombinant DNA technology, by using only sender-receiver known restriction enzymes to combine the secure key represented by DNA sequence and the T vector, we generate the DNA bio-hiding secure key and then place the recombinant plasmid in implanted bacteria for secure key transmission. The designed bio experiments and simulation results show that the security of the transmission of the key is further improved and the environmental requirements of key transmission are reduced. Analysis has demonstrated that the proposed DNA-based random key generation and management solutions are marked by high security and usability. Published by Elsevier B.V.

Randomness determines practical security of BB84 quantum key distribution

Science.gov (United States)

Li, Hong-Wei; Yin, Zhen-Qiang; Wang, Shuang; Qian, Yong-Jun; Chen, Wei; Guo, Guang-Can; Han, Zheng-Fu

2015-11-01

Unconditional security of the BB84 quantum key distribution protocol has been proved by exploiting the fundamental laws of quantum mechanics, but the practical quantum key distribution system maybe hacked by considering the imperfect state preparation and measurement respectively. Until now, different attacking schemes have been proposed by utilizing imperfect devices, but the general security analysis model against all of the practical attacking schemes has not been proposed. Here, we demonstrate that the general practical attacking schemes can be divided into the Trojan horse attack, strong randomness attack and weak randomness attack respectively. We prove security of BB84 protocol under randomness attacking models, and these results can be applied to guarantee the security of the practical quantum key distribution system.

Ascertainment bias causes false signal of anticipation in genetic prion disease.

Science.gov (United States)

Minikel, Eric Vallabh; Zerr, Inga; Collins, Steven J; Ponto, Claudia; Boyd, Alison; Klug, Genevieve; Karch, André; Kenny, Joanna; Collinge, John; Takada, Leonel T; Forner, Sven; Fong, Jamie C; Mead, Simon; Geschwind, Michael D

2014-10-02

Anticipation is the phenomenon whereby age of onset in genetic disease decreases in successive generations. Three independent reports have claimed anticipation in Creutzfeldt-Jakob disease (CJD) caused by the c.598G > A mutation in PRNP encoding a p.Glu200Lys (E200K) substitution in the prion protein. If confirmed, this finding would carry clear implications for genetic counseling. We analyzed pedigrees with this mutation from four prion centers worldwide (n = 217 individuals with the mutation) to analyze age of onset and death in affected and censored individuals. We show through simulation that selective ascertainment of individuals whose onset falls within the historical window since the mutation's 1989 discovery is sufficient to create robust false signals both of anticipation and of heritability of age of onset. In our data set, the number of years of anticipation observed depends upon how strictly the data are limited by the ascertainment window. Among individuals whose disease was directly observed at a study center, a 28-year difference between parent and child age of onset is observed (p = 0.002), but including individuals ascertained retrospectively through family history reduces this figure to 7 years (p = 0.005). Applying survival analysis to the most thoroughly ascertained subset of data eliminates the signal of anticipation. Moreover, even non-CJD deaths exhibit 16 years anticipation (p = 0.002), indicating that ascertainment bias can entirely explain observed anticipation. We suggest that reports of anticipation in genetic prion disease are driven entirely by ascertainment bias. Guidelines for future studies claiming statistical evidence for anticipation are suggested. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Navigational efficiency in a biased and correlated random walk model of individual animal movement.

Science.gov (United States)

Bailey, Joseph D; Wallis, Jamie; Codling, Edward A

2018-01-01

Understanding how an individual animal is able to navigate through its environment is a key question in movement ecology that can give insight into observed movement patterns and the mechanisms behind them. Efficiency of navigation is important for behavioral processes at a range of different spatio-temporal scales, including foraging and migration. Random walk models provide a standard framework for modeling individual animal movement and navigation. Here we consider a vector-weighted biased and correlated random walk (BCRW) model for directed movement (taxis), where external navigation cues are balanced with forward persistence. We derive a mathematical approximation of the expected navigational efficiency for any BCRW of this form and confirm the model predictions using simulations. We demonstrate how the navigational efficiency is related to the weighting given to forward persistence and external navigation cues, and highlight the counter-intuitive result that for low (but realistic) levels of error on forward persistence, a higher navigational efficiency is achieved by giving more weighting to this indirect navigation cue rather than direct navigational cues. We discuss and interpret the relevance of these results for understanding animal movement and navigation strategies. © 2017 by the Ecological Society of America.

Modeling Random Telegraph Noise Under Switched Bias Conditions Using Cyclostationary RTS Noise

NARCIS (Netherlands)

van der Wel, A.P.; Klumperink, Eric A.M.; Vandamme, L.K.J.; Nauta, Bram

In this paper, we present measurements and simulation of random telegraph signal (RTS) noise in n-channel MOSFETs under periodic large signal gate-source excitation (switched bias conditions). This is particularly relevant to analog CMOS circuit design where large signal swings occur and where LF

Biasing the random walk of a molecular motor

Energy Technology Data Exchange (ETDEWEB)

Astumian, R Dean [Department of Physics, University of Maine, Orono, ME 04469-5709 (United States)

2005-11-30

Biomolecular motors are often described in mechanical terms, with analogy to cars, turbines, judo throws, levers, etc. It is important to remember however that because of their small size, and because of the aqueous environment in which molecular motors move, viscous drag and thermal noise dominate the inertial forces that drive macroscopic machines. The sequence of motions-conformational changes-by which a motor protein moves can best be described as a random walk, with transitions from one state to another occurring by thermal activation over energy barriers. In this paper I will address the question of how this random walk is biased by a non-equilibrium chemical reaction (ATP hydrolysis) so that the motor molecule moves preferentially (with almost unit certainty) in one direction, even when an external force is applied to drive it in the opposite direction. I will also discuss how these 'soft matter' motors can achieve thermodynamic efficiencies of nearly 100%.

Biasing the random walk of a molecular motor

International Nuclear Information System (INIS)

Astumian, R Dean

2005-01-01

Biomolecular motors are often described in mechanical terms, with analogy to cars, turbines, judo throws, levers, etc. It is important to remember however that because of their small size, and because of the aqueous environment in which molecular motors move, viscous drag and thermal noise dominate the inertial forces that drive macroscopic machines. The sequence of motions-conformational changes-by which a motor protein moves can best be described as a random walk, with transitions from one state to another occurring by thermal activation over energy barriers. In this paper I will address the question of how this random walk is biased by a non-equilibrium chemical reaction (ATP hydrolysis) so that the motor molecule moves preferentially (with almost unit certainty) in one direction, even when an external force is applied to drive it in the opposite direction. I will also discuss how these 'soft matter' motors can achieve thermodynamic efficiencies of nearly 100%

Bias correction for the estimation of sensitivity indices based on random balance designs

International Nuclear Information System (INIS)

Tissot, Jean-Yves; Prieur, Clémentine

2012-01-01

This paper deals with the random balance design method (RBD) and its hybrid approach, RBD-FAST. Both these global sensitivity analysis methods originate from Fourier amplitude sensitivity test (FAST) and consequently face the main problems inherent to discrete harmonic analysis. We present here a general way to correct a bias which occurs when estimating sensitivity indices (SIs) of any order – except total SI of single factor or group of factors – by the random balance design method (RBD) and its hybrid version, RBD-FAST. In the RBD case, this positive bias has been recently identified in a paper by Xu and Gertner [1]. Following their work, we propose a bias correction method for first-order SIs estimates in RBD. We then extend the correction method to the SIs of any order in RBD-FAST. At last, we suggest an efficient strategy to estimate all the first- and second-order SIs using RBD-FAST. - Highlights: ► We provide a bias correction method for the global sensitivity analysis methods: RBD and RBD-FAST. ► In RBD, first-order sensitivity estimates are corrected. ► In RBD-FAST, sensitivity indices of any order and closed sensitivity indices are corrected. ► We propose an efficient strategy to estimate all the first- and second-order indices of a model.

Design of a randomized trial of diabetes genetic risk testing to motivate behavior change: the Genetic Counseling/lifestyle Change (GC/LC) Study for Diabetes Prevention.

Science.gov (United States)

Grant, Richard W; Meigs, James B; Florez, Jose C; Park, Elyse R; Green, Robert C; Waxler, Jessica L; Delahanty, Linda M; O'Brien, Kelsey E

2011-10-01

The efficacy of diabetes genetic risk testing to motivate behavior change for diabetes prevention is currently unknown. This paper presents key issues in the design and implementation of one of the first randomized trials (The Genetic Counseling/Lifestyle Change (GC/LC) Study for Diabetes Prevention) to test whether knowledge of diabetes genetic risk can motivate patients to adopt healthier behaviors. Because individuals may react differently to receiving 'higher' vs 'lower' genetic risk results, we designed a 3-arm parallel group study to separately test the hypotheses that: (1) patients receiving 'higher' diabetes genetic risk results will increase healthy behaviors compared to untested controls, and (2) patients receiving 'lower' diabetes genetic risk results will decrease healthy behaviors compared to untested controls. In this paper we describe several challenges to implementing this study, including: (1) the application of a novel diabetes risk score derived from genetic epidemiology studies to a clinical population, (2) the use of the principle of Mendelian randomization to efficiently exclude 'average' diabetes genetic risk patients from the intervention, and (3) the development of a diabetes genetic risk counseling intervention that maintained the ethical need to motivate behavior change in both 'higher' and 'lower' diabetes genetic risk result recipients. Diabetes genetic risk scores were developed by aggregating the results of 36 diabetes-associated single nucleotide polymorphisms. Relative risk for type 2 diabetes was calculated using Framingham Offspring Study outcomes, grouped by quartiles into 'higher', 'average' (middle two quartiles) and 'lower' genetic risk. From these relative risks, revised absolute risks were estimated using the overall absolute risk for the study group. For study efficiency, we excluded all patients receiving 'average' diabetes risk results from the subsequent intervention. This post-randomization allocation strategy was

Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution.

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Bera, Bidhan Ch; Virmani, Nitin; Kumar, Naveen; Anand, Taruna; Pavulraj, S; Rash, Adam; Elton, Debra; Rash, Nicola; Bhatia, Sandeep; Sood, Richa; Singh, Raj Kumar; Tripathi, Bhupendra Nath

2017-08-23

Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) were analyzed to elucidate the genetic and evolutionary relationships in a novel perspective. The group - specific consensus amino acid substitutions were identified in all polymerase genes of EIVs that led to divergence of EIVs into various clades. The consistent amino acid changes were also detected in the Florida clade 2 EIVs circulating in Europe and Asia since 2007. To study the codon usage patterns, a total of 281,324 codons of polymerase genes of EIV H3N8 isolates from 1963 to 2015 were systemically analyzed. The polymerase genes of EIVs exhibit a weak codon usage bias. The ENc-GC3s and Neutrality plots indicated that natural selection is the major influencing factor of codon usage bias, and that the impact of mutation pressure is comparatively minor. The methods for estimating host imposed translation pressure suggested that the polymerase acidic (PA) gene seems to be under less translational pressure compared to polymerase basic 1 (PB1) and polymerase basic 2 (PB2) genes. The multivariate statistical analysis of polymerase genes divided EIVs into four evolutionary diverged clusters - Pre-divergent, Eurasian, Florida sub-lineage 1 and 2. Various lineage specific amino acid substitutions observed in all polymerase genes of EIVs and especially, clade 2 EIVs underwent major variations which led to the emergence of a phylogenetically distinct group of EIVs originating from Richmond/1/07. The codon usage bias was low in all the polymerase genes of EIVs that was influenced by the multiple factors such as the nucleotide compositions, mutation pressure, aromaticity and hydropathicity. However, natural selection was the major influencing factor in defining the

Personalized Genetic Risk Counseling to Motivate Diabetes Prevention: A randomized trial

OpenAIRE

Grant, Richard W.; O’Brien, Kelsey E.; Waxler, Jessica L.; Vassy, Jason L.; Delahanty, Linda M.; Bissett, Laurie G.; Green, Robert C.; Stember, Katherine G.; Guiducci, Candace; Park, Elyse R.; Florez, Jose C.; Meigs, James B.

2013-01-01

OBJECTIVE To examine whether diabetes genetic risk testing and counseling can improve diabetes prevention behaviors. RESEARCH DESIGN AND METHODS We conducted a randomized trial of diabetes genetic risk counseling among overweight patients at increased phenotypic risk for type 2 diabetes. Participants were randomly allocated to genetic testing versus no testing. Genetic risk was calculated by summing 36 single nucleotide polymorphisms associated with type 2 diabetes. Participants in the top an...

Genetic association of telomere length with hepatocellular carcinoma risk: A Mendelian randomization analysis.

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Cheng, Yue; Yu, Chengxiao; Huang, Mingtao; Du, Fangzhi; Song, Ci; Ma, Zijian; Zhai, Xiangjun; Yang, Yuan; Liu, Jibin; Bei, Jin-Xin; Jia, Weihua; Jin, Guangfu; Li, Shengping; Zhou, Weiping; Liu, Jianjun; Dai, Juncheng; Hu, Zhibin

2017-10-01

Observational studies show an association between telomere length and Hepatocellular carcinoma (HCC) risk, but the relationship is controversial. Particularly, it remains unclear whether the association is due to confounding or biases inherent in conventional epidemiological studies. Here, we applied Mendelian randomization approach to evaluate whether telomere length is causally associated with HCC risk. Individual-level data were from HBV-related HCC Genome-wide association studies (1,538 HBV positive HCC patients and 1,465 HBV positive controls). Genetic risk score, as proxy for actual measured telomere length, derived from nine telomere length-associated genetic variants was used to evaluate the effect of telomere length on HCC risk. We observed a significant risk signal between genetically increased telomere length and HBV-related HCC risk (OR=2.09, 95% CI 1.32-3.31, P=0.002). Furthermore, a U-shaped curve was fitted by the restricted cubic spline curve, which indicated that either short or long telomere length would increase HCC risk (P=0.0022 for non-linearity test). Subgroup analysis did not reveal significant heterogeneity between different age, gender, smoking status and drinking status groups. Our results indicated that a genetic background that favors longer or shorter telomere length may increase HBV-related HCC risk-a U-shaped association. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bias, accuracy and impact of indirect genetic effects in infectious diseases

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Debby eLipschutz-Powell

2012-10-01

Full Text Available Selection for improved host response to infectious disease offers a desirable alternative to chemical treatment but has proven difficult in practice, due to low heritability estimates of disease traits. Disease data from field studies is often binary, indicating whether an individual has become infected or not following exposure to an infectious disease. Numerous studies have shown that from this data one can infer genetic variation in individuals’ underlying susceptibility. In a previous study, we showed that with an Indirect Genetic Effect (IGE model it is possible to capture some genetic variation in infectivity, if present, as well as in susceptibility. Infectivity is the propensity of transmitting infection upon contact with a susceptible individual. It is an important factor determining the severity of an epidemic. However, there are severe shortcomings with the Standard IGE models as they do not accommodate the dynamic nature of disease data. Here we adjust the Standard IGE model to (1 make expression of infectivity dependent on the individuals’ disease status (Case Model and (2 to include timing of infection (Case-ordered Model. The models are evaluated by comparing impact of selection, bias and accuracy of each model using simulated binary disease data. These were generated for populations with known variation in susceptibility and infectivity thus allowing comparisons between estimated and true breeding values. Overall the Case Model provided better estimates for host genetic susceptibility and infectivity compared to the Standard Model in terms of bias, impact and accuracy. Furthermore, these estimates were strongly influenced by epidemiological characteristics. However, surprisingly, the Case Ordered model performed considerably worse than the Standard and the Case Models, pointing towards limitations in incorporating disease dynamics into conventional variance component estimation methodology and software used in animal breeding.

Randomized controlled trial of attention bias modification in a racially diverse, socially anxious, alcohol dependent sample.

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Clerkin, Elise M; Magee, Joshua C; Wells, Tony T; Beard, Courtney; Barnett, Nancy P

2016-12-01

Attention biases may be an important treatment target for both alcohol dependence and social anxiety. This is the first ABM trial to investigate two (vs. one) targets of attention bias within a sample with co-occurring symptoms of social anxiety and alcohol dependence. Additionally, we used trial-level bias scores (TL-BS) to capture the phenomena of attention bias in a more ecologically valid, dynamic way compared to traditional attention bias scores. Adult participants (N = 86; 41% Female; 52% African American; 40% White) with elevated social anxiety symptoms and alcohol dependence were randomly assigned to an 8-session training condition in this 2 (Social Anxiety ABM vs. Social Anxiety Control) by 2 (Alcohol ABM vs. Alcohol Control) design. Symptoms of social anxiety, alcohol dependence, and attention bias were assessed across time. Multilevel models estimated the trajectories for each measure within individuals, and tested whether these trajectories differed according to the randomized training conditions. Across time, there were significant or trending decreases in all attention TL-BS parameters (but not traditional attention bias scores) and most symptom measures. However, there were not significant differences in the trajectories of change between any ABM and control conditions for any symptom measures. These findings add to previous evidence questioning the robustness of ABM and point to the need to extend the effects of ABM to samples that are racially diverse and/or have co-occurring psychopathology. The results also illustrate the potential importance of calculating trial-level attention bias scores rather than only including traditional bias scores. Copyright © 2016 Elsevier Ltd. All rights reserved.

Randomized Controlled Trial of Attention Bias Modification in a Racially Diverse, Socially Anxious, Alcohol Dependent Sample

Science.gov (United States)

Clerkin, Elise M.; Magee, Joshua C.; Wells, Tony T.; Beard, Courtney; Barnett, Nancy P.

2016-01-01

Objective Attention biases may be an important treatment target for both alcohol dependence and social anxiety. This is the first ABM trial to investigate two (vs. one) targets of attention bias within a sample with co-occurring symptoms of social anxiety and alcohol dependence. Additionally, we used trial-level bias scores (TL-BS) to capture the phenomena of attention bias in a more ecologically valid, dynamic way compared to traditional attention bias scores. Method Adult participants (N=86; 41% Female; 52% African American; 40% White) with elevated social anxiety symptoms and alcohol dependence were randomly assigned to an 8-session training condition in this 2 (Social Anxiety ABM vs. Social Anxiety Control) by 2 (Alcohol ABM vs. Alcohol Control) design. Symptoms of social anxiety, alcohol dependence, and attention bias were assessed across time. Results Multilevel models estimated the trajectories for each measure within individuals, and tested whether these trajectories differed according to the randomized training conditions. Across time, there were significant or trending decreases in all attention TL-BS parameters (but not traditional attention bias scores) and most symptom measures. However, there were not significant differences in the trajectories of change between any ABM and control conditions for any symptom measures. Conclusions These findings add to previous evidence questioning the robustness of ABM and point to the need to extend the effects of ABM to samples that are racially diverse and/or have co-occurring psychopathology. The results also illustrate the potential importance of calculating trial-level attention bias scores rather than only including traditional bias scores. PMID:27591918

Resistance and resistance fluctuations in random resistor networks under biased percolation.

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Pennetta, Cecilia; Reggiani, L; Trefán, Gy; Alfinito, E

2002-06-01

We consider a two-dimensional random resistor network (RRN) in the presence of two competing biased processes consisting of the breaking and recovering of elementary resistors. These two processes are driven by the joint effects of an electrical bias and of the heat exchange with a thermal bath. The electrical bias is set up by applying a constant voltage or, alternatively, a constant current. Monte Carlo simulations are performed to analyze the network evolution in the full range of bias values. Depending on the bias strength, electrical failure or steady state are achieved. Here we investigate the steady state of the RRN focusing on the properties of the non-Ohmic regime. In constant-voltage conditions, a scaling relation is found between /(0) and V/V(0), where is the average network resistance, (0) the linear regime resistance, and V0 the threshold value for the onset of nonlinearity. A similar relation is found in constant-current conditions. The relative variance of resistance fluctuations also exhibits a strong nonlinearity whose properties are investigated. The power spectral density of resistance fluctuations presents a Lorentzian spectrum and the amplitude of fluctuations shows a significant non-Gaussian behavior in the prebreakdown region. These results compare well with electrical breakdown measurements in thin films of composites and of other conducting materials.

Genetic clusters and sex-biased gene flow in a unicolonial Formica ant

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Chapuisat Michel

2009-03-01

Full Text Available Abstract Background Animal societies are diverse, ranging from small family-based groups to extraordinarily large social networks in which many unrelated individuals interact. At the extreme of this continuum, some ant species form unicolonial populations in which workers and queens can move among multiple interconnected nests without eliciting aggression. Although unicoloniality has been mostly studied in invasive ants, it also occurs in some native non-invasive species. Unicoloniality is commonly associated with very high queen number, which may result in levels of relatedness among nestmates being so low as to raise the question of the maintenance of altruism by kin selection in such systems. However, the actual relatedness among cooperating individuals critically depends on effective dispersal and the ensuing pattern of genetic structuring. In order to better understand the evolution of unicoloniality in native non-invasive ants, we investigated the fine-scale population genetic structure and gene flow in three unicolonial populations of the wood ant F. paralugubris. Results The analysis of geo-referenced microsatellite genotypes and mitochondrial haplotypes revealed the presence of cryptic clusters of genetically-differentiated nests in the three populations of F. paralugubris. Because of this spatial genetic heterogeneity, members of the same clusters were moderately but significantly related. The comparison of nuclear (microsatellite and mitochondrial differentiation indicated that effective gene flow was male-biased in all populations. Conclusion The three unicolonial populations exhibited male-biased and mostly local gene flow. The high number of queens per nest, exchanges among neighbouring nests and restricted long-distance gene flow resulted in large clusters of genetically similar nests. The positive relatedness among clustermates suggests that kin selection may still contribute to the maintenance of altruism in unicolonial

Analysis of Secret Key Randomness Exploiting the Radio Channel Variability

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Taghrid Mazloum

2015-01-01

Full Text Available A few years ago, physical layer based techniques have started to be considered as a way to improve security in wireless communications. A well known problem is the management of ciphering keys, both regarding the generation and distribution of these keys. A way to alleviate such difficulties is to use a common source of randomness for the legitimate terminals, not accessible to an eavesdropper. This is the case of the fading propagation channel, when exact or approximate reciprocity applies. Although this principle has been known for long, not so many works have evaluated the effect of radio channel properties in practical environments on the degree of randomness of the generated keys. To this end, we here investigate indoor radio channel measurements in different environments and settings at either 2.4625 GHz or 5.4 GHz band, of particular interest for WIFI related standards. Key bits are extracted by quantizing the complex channel coefficients and their randomness is evaluated using the NIST test suite. We then look at the impact of the carrier frequency, the channel variability in the space, time, and frequency degrees of freedom used to construct a long secret key, in relation to the nature of the radio environment such as the LOS/NLOS character.

Genetic anticipation in BRCA1/BRCA2 families after controlling for ascertainment bias and cohort effect.

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Guindalini, Rodrigo Santa Cruz; Song, Andrew; Fackenthal, James D; Olopade, Olufunmilayo I; Huo, Dezheng

2016-06-15

Genetic anticipation, the earlier onset of disease in successive generations, has been reported in hereditary breast and ovarian cancer syndrome (HBOC), but little is known about its underlying mechanisms. Ascertainment bias has been suggested as a reason in previous studies. Likewise, cohort effect, which may be caused by environmental factors, can be misinterpreted as genetic anticipation. The authors reviewed the pedigrees of 176 kindreds, segregating those with deleterious mutations in breast cancer genes 1 and 2 (BRCA1/BRCA2) who had at least 2 consecutive generations of the same cancer (breast or ovarian). By using mutation probabilities as analytical weights in weighted random-effect models, generational differences in the age at onset of breast/ovarian cancer were calculated. The analyses were further controlled for ascertainment bias by excluding probands and adjusting for birth-cohort effect in the anticipation models. The mean age at the onset of breast cancer for the probands' generation was 41.9 years, which was 6.8 years and 9.8 years earlier than the parents' and grandparents' generations, respectively. The anticipation effect for breast cancer remained significant after excluding the probands. There was a birth-cohort effect: patients who were born in 1930s and 1940s had breast cancer 5.0 years and 7.6 years earlier than patients who were born before 1920. The difference in breast cancer age of onset across generations was no longer significant after adjusting for birth-cohort effect. The observed anticipation effect was driven mainly by a decrease in age of onset across birth cohorts, underscoring the need for risk-reducing interventions that target changing environmental/lifestyle factors in BRCA1/BRCA2 carriers. Cancer 2016;122:1913-20. © 2016 American Cancer Society. © 2016 American Cancer Society.

Genetic biasing through cultural transmission: do simple Bayesian models of language evolution generalize?

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Dediu, Dan

2009-08-07

The recent Bayesian approaches to language evolution and change seem to suggest that genetic biases can impact on the characteristics of language, but, at the same time, that its cultural transmission can partially free it from these same genetic constraints. One of the current debates centres on the striking differences between sampling and a posteriori maximising Bayesian learners, with the first converging on the prior bias while the latter allows a certain freedom to language evolution. The present paper shows that this difference disappears if populations more complex than a single teacher and a single learner are considered, with the resulting behaviours more similar to the sampler. This suggests that generalisations based on the language produced by Bayesian agents in such homogeneous single agent chains are not warranted. It is not clear which of the assumptions in such models are responsible, but these findings seem to support the rising concerns on the validity of the "acquisitionist" assumption, whereby the locus of language change and evolution is taken to be the first language acquirers (children) as opposed to the competent language users (the adults).

A genetically mediated bias in decision making driven by failure of amygdala control.

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Roiser, Jonathan P; de Martino, Benedetto; Tan, Geoffrey C Y; Kumaran, Dharshan; Seymour, Ben; Wood, Nicholas W; Dolan, Raymond J

2009-05-06

Genetic variation at the serotonin transporter-linked polymorphic region (5-HTTLPR) is associated with altered amygdala reactivity and lack of prefrontal regulatory control. Similar regions mediate decision-making biases driven by contextual cues and ambiguity, for example the "framing effect." We hypothesized that individuals hemozygous for the short (s) allele at the 5-HTTLPR would be more susceptible to framing. Participants, selected as homozygous for either the long (la) or s allele, performed a decision-making task where they made choices between receiving an amount of money for certain and taking a gamble. A strong bias was evident toward choosing the certain option when the option was phrased in terms of gains and toward gambling when the decision was phrased in terms of losses (the frame effect). Critically, this bias was significantly greater in the ss group compared with the lala group. In simultaneously acquired functional magnetic resonance imaging data, the ss group showed greater amygdala during choices made in accord, compared with those made counter to the frame, an effect not seen in the lala group. These differences were also mirrored by differences in anterior cingulate-amygdala coupling between the genotype groups during decision making. Specifically, lala participants showed increased coupling during choices made counter to, relative to those made in accord with, the frame, with no such effect evident in ss participants. These data suggest that genetically mediated differences in prefrontal-amygdala interactions underpin interindividual differences in economic decision making.

Bias, precision and statistical power of analysis of covariance in the analysis of randomized trials with baseline imbalance: a simulation study

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2014-01-01

Background Analysis of variance (ANOVA), change-score analysis (CSA) and analysis of covariance (ANCOVA) respond differently to baseline imbalance in randomized controlled trials. However, no empirical studies appear to have quantified the differential bias and precision of estimates derived from these methods of analysis, and their relative statistical power, in relation to combinations of levels of key trial characteristics. This simulation study therefore examined the relative bias, precision and statistical power of these three analyses using simulated trial data. Methods 126 hypothetical trial scenarios were evaluated (126 000 datasets), each with continuous data simulated by using a combination of levels of: treatment effect; pretest-posttest correlation; direction and magnitude of baseline imbalance. The bias, precision and power of each method of analysis were calculated for each scenario. Results Compared to the unbiased estimates produced by ANCOVA, both ANOVA and CSA are subject to bias, in relation to pretest-posttest correlation and the direction of baseline imbalance. Additionally, ANOVA and CSA are less precise than ANCOVA, especially when pretest-posttest correlation ≥ 0.3. When groups are balanced at baseline, ANCOVA is at least as powerful as the other analyses. Apparently greater power of ANOVA and CSA at certain imbalances is achieved in respect of a biased treatment effect. Conclusions Across a range of correlations between pre- and post-treatment scores and at varying levels and direction of baseline imbalance, ANCOVA remains the optimum statistical method for the analysis of continuous outcomes in RCTs, in terms of bias, precision and statistical power. PMID:24712304

Effects of social approval bias on self-reported fruit and vegetable consumption: a randomized controlled trial

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Marcus Al C

2008-06-01

Full Text Available Abstract Background Self-reports of dietary intake in the context of nutrition intervention research can be biased by the tendency of respondents to answer consistent with expected norms (social approval bias. The objective of this study was to assess the potential influence of social approval bias on self-reports of fruit and vegetable intake obtained using both food frequency questionnaire (FFQ and 24-hour recall methods. Methods A randomized blinded trial compared reported fruit and vegetable intake among subjects exposed to a potentially biasing prompt to that from control subjects. Subjects included 163 women residing in Colorado between 35 and 65 years of age who were randomly selected and recruited by telephone to complete what they were told would be a future telephone survey about health. Randomly half of the subjects then received a letter prior to the interview describing this as a study of fruit and vegetable intake. The letter included a brief statement of the benefits of fruits and vegetables, a 5-A-Day sticker, and a 5-a-Day refrigerator magnet. The remainder received the same letter, but describing the study purpose only as a more general nutrition survey, with neither the fruit and vegetable message nor the 5-A-Day materials. Subjects were then interviewed on the telephone within 10 days following the letters using an eight-item FFQ and a limited 24-hour recall to estimate fruit and vegetable intake. All interviewers were blinded to the treatment condition. Results By the FFQ method, subjects who viewed the potentially biasing prompts reported consuming more fruits and vegetables than did control subjects (5.2 vs. 3.7 servings per day, p Conclusion Self-reports of fruit and vegetable intake using either a food frequency questionnaire or a limited 24-hour recall are both susceptible to substantial social approval bias. Valid assessments of intervention effects in nutritional intervention trials may require objective measures of

Simultaneous transmission for an encrypted image and a double random-phase encryption key

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Yuan, Sheng; Zhou, Xin; Li, Da-Hai; Zhou, Ding-Fu

2007-06-01

We propose a method to simultaneously transmit double random-phase encryption key and an encrypted image by making use of the fact that an acceptable decryption result can be obtained when only partial data of the encrypted image have been taken in the decryption process. First, the original image data are encoded as an encrypted image by a double random-phase encryption technique. Second, a double random-phase encryption key is encoded as an encoded key by the Rivest-Shamir-Adelman (RSA) public-key encryption algorithm. Then the amplitude of the encrypted image is modulated by the encoded key to form what we call an encoded image. Finally, the encoded image that carries both the encrypted image and the encoded key is delivered to the receiver. Based on such a method, the receiver can have an acceptable result and secure transmission can be guaranteed by the RSA cipher system.

Regularity of the Speed of Biased Random Walk in a One-Dimensional Percolation Model

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Gantert, Nina; Meiners, Matthias; Müller, Sebastian

2018-03-01

We consider biased random walks on the infinite cluster of a conditional bond percolation model on the infinite ladder graph. Axelson-Fisk and Häggström established for this model a phase transition for the asymptotic linear speed \\overline{v} of the walk. Namely, there exists some critical value λ c>0 such that \\overline{v}>0 if λ \\in (0,λ c) and \\overline{v}=0 if λ ≥ λ c. We show that the speed \\overline{v} is continuous in λ on (0,∞) and differentiable on (0,λ c/2). Moreover, we characterize the derivative as a covariance. For the proof of the differentiability of \\overline{v} on (0,λ c/2), we require and prove a central limit theorem for the biased random walk. Additionally, we prove that the central limit theorem fails to hold for λ ≥ λ c/2.

Dynamic approach to space and habitat use based on biased random bridges.

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Simon Benhamou

Full Text Available BACKGROUND: Although habitat use reflects a dynamic process, most studies assess habitat use statically as if an animal's successively recorded locations reflected a point rather than a movement process. By relying on the activity time between successive locations instead of the local density of individual locations, movement-based methods can substantially improve the biological relevance of utilization distribution (UD estimates (i.e. the relative frequencies with which an animal uses the various areas of its home range, HR. One such method rests on Brownian bridges (BBs. Its theoretical foundation (purely and constantly diffusive movements is paradoxically inconsistent with both HR settlement and habitat selection. An alternative involves movement-based kernel density estimation (MKDE through location interpolation, which may be applied to various movement behaviours but lacks a sound theoretical basis. METHODOLOGY/PRINCIPAL FINDINGS: I introduce the concept of a biased random (advective-diffusive bridge (BRB and show that the MKDE method is a practical means to estimate UDs based on simplified (isotropically diffusive BRBs. The equation governing BRBs is constrained by the maximum delay between successive relocations warranting constant within-bridge advection (allowed to vary between bridges but remains otherwise similar to the BB equation. Despite its theoretical inconsistencies, the BB method can therefore be applied to animals that regularly reorientate within their HRs and adapt their movements to the habitats crossed, provided that they were relocated with a high enough frequency. CONCLUSIONS/SIGNIFICANCE: Biased random walks can approximate various movement types at short times from a given relocation. Their simplified form constitutes an effective trade-off between too simple, unrealistic movement models, such as Brownian motion, and more sophisticated and realistic ones, such as biased correlated random walks (BCRWs, which are too

An Assessment of the Risk of Bias in Randomized Controlled Trial Reports Published in Prosthodontic and Implant Dentistry Journals.

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Papageorgiou, Spyridon N; Kloukos, Dimitrios; Petridis, Haralampos; Pandis, Nikolaos

2015-01-01

The objective of this study was to assess the risk of bias of randomized controlled trials (RCTs) published in prosthodontic and implant dentistry journals. The last 30 issues of 9 journals in the field of prosthodontic and implant dentistry (Clinical Implant Dentistry and Related Research, Clinical Oral Implants Research, Implant Dentistry, International Journal of Oral & Maxillofacial Implants, International Journal of Periodontics and Restorative Dentistry, International Journal of Prosthodontics, Journal of Dentistry, Journal of Oral Rehabilitation, and Journal of Prosthetic Dentistry) were hand-searched for RCTs. Risk of bias was assessed using the Cochrane Collaboration's risk of bias tool and analyzed descriptively. From the 3,667 articles screened, a total of 147 RCTs were identified and included. The number of published RCTs increased with time. The overall distribution of a high risk of bias assessment varied across the domains of the Cochrane risk of bias tool: 8% for random sequence generation, 18% for allocation concealment, 41% for masking, 47% for blinding of outcome assessment, 7% for incomplete outcome data, 12% for selective reporting, and 41% for other biases. The distribution of high risk of bias for RCTs published in the selected prosthodontic and implant dentistry journals varied among journals and ranged from 8% to 47%, which can be considered as substantial.

Randomly biased investments and the evolution of public goods on interdependent networks

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Chen, Wei; Wu, Te; Li, Zhiwu; Wang, Long

2017-08-01

Deciding how to allocate resources between interdependent systems is significant to optimize efficiency. We study the effects of heterogeneous contribution, induced by such interdependency, on the evolution of cooperation, through implementing the public goods games on two-layer networks. The corresponding players on different layers try to share a fixed amount of resources as the initial investment properly. The symmetry breaking of investments between players located on different layers is able to either prevent investments from, or extract them out of the deadlock. Results show that a moderate investment heterogeneity is best favorable for the evolution of cooperation, and random allocation of investment bias suppresses the cooperators at a wide range of the investment bias and the enhancement effect. Further studies on time evolution with different initial strategy configurations show that the non-interdependent cooperators along the interface of interdependent cooperators also are an indispensable factor in facilitating cooperative behavior. Our main results are qualitatively unchanged even diversifying investment bias that is subject to uniform distribution. Our study may shed light on the understanding of the origin of cooperative behavior on interdependent networks.

Genetic parameters for quail body weights using a random ...

African Journals Online (AJOL)

A model including fixed and random linear regressions is described for analyzing body weights at different ages. In this study, (co)variance components, heritabilities for quail weekly weights and genetic correlations among these weights were estimated using a random regression model by DFREML under DXMRR option.

Key-space analysis of double random phase encryption technique

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Monaghan, David S.; Gopinathan, Unnikrishnan; Naughton, Thomas J.; Sheridan, John T.

2007-09-01

We perform a numerical analysis on the double random phase encryption/decryption technique. The key-space of an encryption technique is the set of possible keys that can be used to encode data using that technique. In the case of a strong encryption scheme, many keys must be tried in any brute-force attack on that technique. Traditionally, designers of optical image encryption systems demonstrate only how a small number of arbitrary keys cannot decrypt a chosen encrypted image in their system. However, this type of demonstration does not discuss the properties of the key-space nor refute the feasibility of an efficient brute-force attack. To clarify these issues we present a key-space analysis of the technique. For a range of problem instances we plot the distribution of decryption errors in the key-space indicating the lack of feasibility of a simple brute-force attack.

Deep Random based Key Exchange protocol resisting unlimited MITM

OpenAIRE

de Valroger, Thibault

2018-01-01

We present a protocol enabling two legitimate partners sharing an initial secret to mutually authenticate and to exchange an encryption session key. The opponent is an active Man In The Middle (MITM) with unlimited computation and storage capacities. The resistance to unlimited MITM is obtained through the combined use of Deep Random secrecy, formerly introduced and proved as unconditionally secure against passive opponent for key exchange, and universal hashing techniques. We prove the resis...

Random amplified polymorphic DNA based genetic characterization ...

African Journals Online (AJOL)

Random amplified polymorphic DNA based genetic characterization of four important species of Bamboo, found in Raigad district, Maharashtra State, India. ... Bambusoideae are differentiated from other members of the family by the presence of petiolate blades with parallel venation and stamens are three, four, six or more, ...

Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality.

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Jones, Beryl M; Kingwell, Callum J; Wcislo, William T; Robinson, Gene E

2017-01-11

Developmental plasticity may accelerate the evolution of phenotypic novelty through genetic accommodation, but studies of genetic accommodation often lack knowledge of the ancestral state to place selected traits in an evolutionary context. A promising approach for assessing genetic accommodation involves using a comparative framework to ask whether ancestral plasticity is related to the evolution of a particular trait. Bees are an excellent group for such comparisons because caste-based societies (eusociality) have evolved multiple times independently and extant species exhibit different modes of eusociality. We measured brain and abdominal gene expression in a facultatively eusocial bee, Megalopta genalis, and assessed whether plasticity in this species is functionally linked to eusocial traits in other bee lineages. Caste-biased abdominal genes in M. genalis overlapped significantly with caste-biased genes in obligately eusocial bees. Moreover, caste-biased genes in M. genalis overlapped significantly with genes shown to be rapidly evolving in multiple studies of 10 bee species, particularly for genes in the glycolysis pathway and other genes involved in metabolism. These results provide support for the idea that eusociality can evolve via genetic accommodation, with plasticity in facultatively eusocial species like M. genalis providing a substrate for selection during the evolution of caste in obligately eusocial lineages. © 2017 The Author(s).

Random multiple key streams for encryption with added CBC mode of operation

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P. Penchalaiah

2016-09-01

For the first time, in this paper, we present a construction method to generate multiple random keys from a core-key with highest possible immunity to crack. We are with a particular emphasis on novel technique to secure user data, we have designed a secure and cost effective new cryptosystem called Rbits (Random bits cypher. In different directions we identify that Rbits having highest immunity to crack and presenting various analysis tests in support from this viewpoint and the analyzed results are reported.

Benefits of being biased!

Indian Academy of Sciences (India)

Administrator

Journal of Genetics, Vol. 83, No. 2, August 2004. Keywords. codon bias; alcohol dehydrogenase; Darwinian ... RESEARCH COMMENTARY. Benefits of being biased! SUTIRTH DEY*. Evolutionary Biology Laboratory, Evolutionary & Organismal Biology Unit,. Jawaharlal Nehru Centre for Advanced Scientific Research,.

Correction of confounding bias in non-randomized studies by appropriate weighting.

Science.gov (United States)

Schmoor, Claudia; Gall, Christine; Stampf, Susanne; Graf, Erika

2011-03-01

In non-randomized studies, the assessment of a causal effect of treatment or exposure on outcome is hampered by possible confounding. Applying multiple regression models including the effects of treatment and covariates on outcome is the well-known classical approach to adjust for confounding. In recent years other approaches have been promoted. One of them is based on the propensity score and considers the effect of possible confounders on treatment as a relevant criterion for adjustment. Another proposal is based on using an instrumental variable. Here inference relies on a factor, the instrument, which affects treatment but is thought to be otherwise unrelated to outcome, so that it mimics randomization. Each of these approaches can basically be interpreted as a simple reweighting scheme, designed to address confounding. The procedures will be compared with respect to their fundamental properties, namely, which bias they aim to eliminate, which effect they aim to estimate, and which parameter is modelled. We will expand our overview of methods for analysis of non-randomized studies to methods for analysis of randomized controlled trials and show that analyses of both study types may target different effects and different parameters. The considerations will be illustrated using a breast cancer study with a so-called Comprehensive Cohort Study design, including a randomized controlled trial and a non-randomized study in the same patient population as sub-cohorts. This design offers ideal opportunities to discuss and illustrate the properties of the different approaches. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hacking on decoy-state quantum key distribution system with partial phase randomization

Science.gov (United States)

Sun, Shi-Hai; Jiang, Mu-Sheng; Ma, Xiang-Chun; Li, Chun-Yan; Liang, Lin-Mei

2014-04-01

Quantum key distribution (QKD) provides means for unconditional secure key transmission between two distant parties. However, in practical implementations, it suffers from quantum hacking due to device imperfections. Here we propose a hybrid measurement attack, with only linear optics, homodyne detection, and single photon detection, to the widely used vacuum + weak decoy state QKD system when the phase of source is partially randomized. Our analysis shows that, in some parameter regimes, the proposed attack would result in an entanglement breaking channel but still be able to trick the legitimate users to believe they have transmitted secure keys. That is, the eavesdropper is able to steal all the key information without discovered by the users. Thus, our proposal reveals that partial phase randomization is not sufficient to guarantee the security of phase-encoding QKD systems with weak coherent states.

Hacking on decoy-state quantum key distribution system with partial phase randomization.

Science.gov (United States)

Sun, Shi-Hai; Jiang, Mu-Sheng; Ma, Xiang-Chun; Li, Chun-Yan; Liang, Lin-Mei

2014-04-23

Quantum key distribution (QKD) provides means for unconditional secure key transmission between two distant parties. However, in practical implementations, it suffers from quantum hacking due to device imperfections. Here we propose a hybrid measurement attack, with only linear optics, homodyne detection, and single photon detection, to the widely used vacuum + weak decoy state QKD system when the phase of source is partially randomized. Our analysis shows that, in some parameter regimes, the proposed attack would result in an entanglement breaking channel but still be able to trick the legitimate users to believe they have transmitted secure keys. That is, the eavesdropper is able to steal all the key information without discovered by the users. Thus, our proposal reveals that partial phase randomization is not sufficient to guarantee the security of phase-encoding QKD systems with weak coherent states.

Random amplified polymorphic DNA (RAPD) markers reveal genetic ...

African Journals Online (AJOL)

The present study evaluated genetic variability of superior bael genotypes collected from different parts of Andaman Islands, India using fruit characters and random amplified polymorphic DNA (RAPD) markers. Genomic DNA extracted from leaf material using cetyl trimethyl ammonium bromide (CTAB) method was ...

Information filtering via biased random walk on coupled social network.

Science.gov (United States)

Nie, Da-Cheng; Zhang, Zi-Ke; Dong, Qiang; Sun, Chongjing; Fu, Yan

2014-01-01

The recommender systems have advanced a great deal in the past two decades. However, most researchers focus their attentions on mining the similarities among users or objects in recommender systems and overlook the social influence which plays an important role in users' purchase process. In this paper, we design a biased random walk algorithm on coupled social networks which gives recommendation results based on both social interests and users' preference. Numerical analyses on two real data sets, Epinions and Friendfeed, demonstrate the improvement of recommendation performance by taking social interests into account, and experimental results show that our algorithm can alleviate the user cold-start problem more effectively compared with the mass diffusion and user-based collaborative filtering methods.

Social Desirability Bias in the Reporting of Alcohol Consumption: A Randomized Trial.

Science.gov (United States)

Kypri, Kypros; Wilson, Amanda; Attia, John; Sheeran, Paschal; Miller, Peter; McCambridge, Jim

2016-05-01

To investigate reporting of alcohol consumption, we manipulated the contexts of questions in ways designed to induce social desirability bias. We undertook a two-arm, parallel-group, individually randomized trial at an Australian public university. Students were recruited by email to a web-based "Research Project on Student Health Behavior." Respondents answered nine questions about their physical activity, diet, and smoking. They were unknowingly randomized to a group presented with either (A) three questions about their alcohol consumption or (B) seven questions about their alcohol dependence and problems (under a prominent header labeled "Alcohol Use Disorders Identification Test"), followed by the same three alcohol consumption questions from (A). A total of 3,594 students (mean age = 27, SD = 10) responded and were randomized: 1,778 to Group A and 1,816 to Group B. Outcome measures were the number of days they drank alcohol, the typical number of drinks they consumed per drinking day, and the number of days they consumed six or more drinks. The primary analysis included participants with any alcohol consumption in the preceding 4 weeks (1,304 in Group A; 1,340 in Group B) using between-group, two-tailed t tests. In Groups A and B, respectively, means (and SDs) of the number of days drinking were 5.89 (5.92) versus 6.06 (6.12), p = .49; typical number of drinks per drinking day: 4.02 (3.87) versus 3.82 (3.76), p = .17; and number of days consuming six or more drinks: 1.69 (2.94) versus 1.67 (3.25), p = .56. We could not reject the null hypothesis because earlier questions about alcohol dependence and problems showed no sign of biasing the respondents' subsequent reports of alcohol consumption. These data support the validity of university students' reporting of alcohol consumption in web-based studies.

Genetic relationships among Rosa species based on random ...

African Journals Online (AJOL)

To investigate the genetic diversity of Rosa accessions, random amplified polymorphism DNA (RAPD) approach was employed. Nine of ten primers amplified 138 scorable RAPD loci with 111 polymorphic bands (80%). Percentages of polymorphic bands ranged from 75 to 100%. Sizes of amplified DNA fragments ranged ...

Explicit Bias Toward High-Income-Country Research: A Randomized, Blinded, Crossover Experiment Of English Clinicians.

Science.gov (United States)

Harris, Matthew; Marti, Joachim; Watt, Hillary; Bhatti, Yasser; Macinko, James; Darzi, Ara W

2017-11-01

Unconscious bias may interfere with the interpretation of research from some settings, particularly from lower-income countries. Most studies of this phenomenon have relied on indirect outcomes such as article citation counts and publication rates; few have addressed or proven the effect of unconscious bias in evidence interpretation. In this randomized, blinded crossover experiment in a sample of 347 English clinicians, we demonstrate that changing the source of a research abstract from a low- to a high-income country significantly improves how it is viewed, all else being equal. Using fixed-effects models, we measured differences in ratings for strength of evidence, relevance, and likelihood of referral to a peer. Having a high-income-country source had a significant overall impact on respondents' ratings of relevance and recommendation to a peer. Unconscious bias can have far-reaching implications for the diffusion of knowledge and innovations from low-income countries.

Encoding plaintext by Fourier transform hologram in double random phase encoding using fingerprint keys

Science.gov (United States)

Takeda, Masafumi; Nakano, Kazuya; Suzuki, Hiroyuki; Yamaguchi, Masahiro

2012-09-01

It has been shown that biometric information can be used as a cipher key for binary data encryption by applying double random phase encoding. In such methods, binary data are encoded in a bit pattern image, and the decrypted image becomes a plain image when the key is genuine; otherwise, decrypted images become random images. In some cases, images decrypted by imposters may not be fully random, such that the blurred bit pattern can be partially observed. In this paper, we propose a novel bit coding method based on a Fourier transform hologram, which makes images decrypted by imposters more random. Computer experiments confirm that the method increases the randomness of images decrypted by imposters while keeping the false rejection rate as low as in the conventional method.

Encoding plaintext by Fourier transform hologram in double random phase encoding using fingerprint keys

International Nuclear Information System (INIS)

Takeda, Masafumi; Nakano, Kazuya; Suzuki, Hiroyuki; Yamaguchi, Masahiro

2012-01-01

It has been shown that biometric information can be used as a cipher key for binary data encryption by applying double random phase encoding. In such methods, binary data are encoded in a bit pattern image, and the decrypted image becomes a plain image when the key is genuine; otherwise, decrypted images become random images. In some cases, images decrypted by imposters may not be fully random, such that the blurred bit pattern can be partially observed. In this paper, we propose a novel bit coding method based on a Fourier transform hologram, which makes images decrypted by imposters more random. Computer experiments confirm that the method increases the randomness of images decrypted by imposters while keeping the false rejection rate as low as in the conventional method. (paper)

Genetic diversity of Santalum album using random amplified ...

African Journals Online (AJOL)

In the present study Random Amplified Polymorphic DNA (RAPD) technique was used to accesses the genetic diversity among 30 accessions of S. album collected from different parts of South India. A total of 248 polymorphic amplicons were obtained from 30 primers. The value of Jaccard coefficient ranged from 0.66 to ...

Genes: Interactions with Language on Three Levels—Inter-Individual Variation, Historical Correlations and Genetic Biasing

Science.gov (United States)

Dediu, Dan

The complex inter-relationships between genetics and linguistics encompass all four scales highlighted by the contributions to this book and, together with cultural transmission, the genetics of language holds the promise to offer a unitary understanding of this fascinating phenomenon. There are inter-individual differences in genetic makeup which contribute to the obvious fact that we are not identical in the way we understand and use language and, by studying them, we will be able to both better treat and enhance ourselves. There are correlations between the genetic configuration of human groups and their languages, reflecting the historical processes shaping them, and there also seem to exist genes which can influence some characteristics of language, biasing it towards or against certain states by altering the way language is transmitted across generations. Besides the joys of pure knowledge, the understanding of these three aspects of genetics relevant to language will potentially trigger advances in medicine, linguistics, psychology or the understanding of our own past and, last but not least, a profound change in the way we regard one of the emblems of being human: our capacity for language.

Analysis of double random phase encryption from a key-space perspective

Science.gov (United States)

Monaghan, David S.; Situ, Guohai; Ryle, James; Gopinathan, Unnikrishnan; Naughton, Thomas J.; Sheridan, John T.

2007-09-01

The main advantage of the double random phase encryption technique is its physical implementation however to allow us to analyse its behaviour we perform the encryption/decryption numerically. A typically strong encryption scheme will have an extremely large key-space, which will make the probable success of any brute force attack on that algorithm miniscule. Traditionally, designers of optical image encryption systems only demonstrate how a small number of arbitrary keys cannot decrypt a chosen encrypted image in their system. We analyse this algorithm from a key-space perspective. The key-space of an encryption algorithm can be defined as the set of possible keys that can be used to encode data using that algorithm. For a range of problem instances we plot the distribution of decryption errors in the key-space indicating the lack of feasibility of a simple brute force attack.

A strong deletion bias in nonallelic gene conversion.

Directory of Open Access Journals (Sweden)

Raquel Assis

Full Text Available Gene conversion is the unidirectional transfer of genetic information between orthologous (allelic or paralogous (nonallelic genomic segments. Though a number of studies have examined nucleotide replacements, little is known about length difference mutations produced by gene conversion. Here, we investigate insertions and deletions produced by nonallelic gene conversion in 338 Drosophila and 10,149 primate paralogs. Using a direct phylogenetic approach, we identify 179 insertions and 614 deletions in Drosophila paralogs, and 132 insertions and 455 deletions in primate paralogs. Thus, nonallelic gene conversion is strongly deletion-biased in both lineages, with almost 3.5 times as many conversion-induced deletions as insertions. In primates, the deletion bias is considerably stronger for long indels and, in both lineages, the per-site rate of gene conversion is orders of magnitudes higher than that of ordinary mutation. Due to this high rate, deletion-biased nonallelic gene conversion plays a key role in genome size evolution, leading to the cooperative shrinkage and eventual disappearance of selectively neutral paralogs.

Information verification cryptosystem using one-time keys based on double random phase encoding and public-key cryptography

Science.gov (United States)

Zhao, Tieyu; Ran, Qiwen; Yuan, Lin; Chi, Yingying; Ma, Jing

2016-08-01

A novel image encryption system based on double random phase encoding (DRPE) and RSA public-key algorithm is proposed. The main characteristic of the system is that each encryption process produces a new decryption key (even for the same plaintext), thus the encryption system conforms to the feature of the one-time pad (OTP) cryptography. The other characteristic of the system is the use of fingerprint key. Only with the rightful authorization will the true decryption be obtained, otherwise the decryption will result in noisy images. So the proposed system can be used to determine whether the ciphertext is falsified by attackers. In addition, the system conforms to the basic agreement of asymmetric cryptosystem (ACS) due to the combination with the RSA public-key algorithm. The simulation results show that the encryption scheme has high robustness against the existing attacks.

A permutation test to analyse systematic bias and random measurement errors of medical devices via boosting location and scale models.

Science.gov (United States)

Mayr, Andreas; Schmid, Matthias; Pfahlberg, Annette; Uter, Wolfgang; Gefeller, Olaf

2017-06-01

Measurement errors of medico-technical devices can be separated into systematic bias and random error. We propose a new method to address both simultaneously via generalized additive models for location, scale and shape (GAMLSS) in combination with permutation tests. More precisely, we extend a recently proposed boosting algorithm for GAMLSS to provide a test procedure to analyse potential device effects on the measurements. We carried out a large-scale simulation study to provide empirical evidence that our method is able to identify possible sources of systematic bias as well as random error under different conditions. Finally, we apply our approach to compare measurements of skin pigmentation from two different devices in an epidemiological study.

Bias Correction and Random Error Characterization for the Assimilation of HRDI Line-of-Sight Wind Measurements

Science.gov (United States)

Tangborn, Andrew; Menard, Richard; Ortland, David; Einaudi, Franco (Technical Monitor)

2001-01-01

A new approach to the analysis of systematic and random observation errors is presented in which the error statistics are obtained using forecast data rather than observations from a different instrument type. The analysis is carried out at an intermediate retrieval level, instead of the more typical state variable space. This method is carried out on measurements made by the High Resolution Doppler Imager (HRDI) on board the Upper Atmosphere Research Satellite (UARS). HRDI, a limb sounder, is the only satellite instrument measuring winds in the stratosphere, and the only instrument of any kind making global wind measurements in the upper atmosphere. HRDI measures doppler shifts in the two different O2 absorption bands (alpha and B) and the retrieved products are tangent point Line-of-Sight wind component (level 2 retrieval) and UV winds (level 3 retrieval). This analysis is carried out on a level 1.9 retrieval, in which the contributions from different points along the line-of-sight have not been removed. Biases are calculated from O-F (observed minus forecast) LOS wind components and are separated into a measurement parameter space consisting of 16 different values. The bias dependence on these parameters (plus an altitude dependence) is used to create a bias correction scheme carried out on the level 1.9 retrieval. The random error component is analyzed by separating the gamma and B band observations and locating observation pairs where both bands are very nearly looking at the same location at the same time. It is shown that the two observation streams are uncorrelated and that this allows the forecast error variance to be estimated. The bias correction is found to cut the effective observation error variance in half.

Exchange bias mechanism in FM/FM/AF spin valve systems in the presence of random unidirectional anisotropy field at the AF interface: The role played by the interface roughness due to randomness

Science.gov (United States)

Yüksel, Yusuf

2018-05-01

We propose an atomistic model and present Monte Carlo simulation results regarding the influence of FM/AF interface structure on the hysteresis mechanism and exchange bias behavior for a spin valve type FM/FM/AF magnetic junction. We simulate perfectly flat and roughened interface structures both with uncompensated interfacial AF moments. In order to simulate rough interface effect, we introduce the concept of random exchange anisotropy field induced at the interface, and acting on the interface AF spins. Our results yield that different types of the random field distributions of anisotropy field may lead to different behavior of exchange bias.

Selection bias in genetic-epidemiological studies of cleft lip and palate

Energy Technology Data Exchange (ETDEWEB)

Christensen, K.; Holm, N.V.; Kock, K. (Odense Univ. (Denmark)); Olsen, J. (Aarhus Univ. (Denmark)); Fogh-Anderson, P.

1992-09-01

The possible impact of selection bias in genetic and epidemiological studies of cleft lip and palate was studied, using three nationwide ascertainment sources and an autopsy study in a 10% sample of the Danish population. A total of 670 cases were identified. Two national record systems, when used together, were found suitable for ascertaining facial cleft in live births. More than 95% ascertainment was obtained by means of surgical files for cleft lip (with or without cleft palate) without associated malformations/syndromes. However, surgical files could be a poor source for studying isolated cleft palate (CP) (only a 60% and biased ascertainment), and they cannot be used to study the prevalence of associated malformations or syndromes in facial cleft cases. The male:female ratio was 0.88 in surgically treated cases of CP and was 1.5 in nonoperated CP cases, making the overall sex ratio for CP 1.1 (95% confidence limits 0.86-1.4) The sex ratio for CP without associated malformation was 1.1 (95% confidence limits 0.84-1.6). One of the major test criteria in CP multifactorial threshold models (higher CP liability among male CP relatives) must be reconsidered, if other investigations confirm that a CP sex-ratio reversal to male predominance occurs when high ascertainment is achieved. 24 refs., 1 fig., 4 tabs.

A random-key encoded harmony search approach for energy-efficient production scheduling with shared resources

Science.gov (United States)

Garcia-Santiago, C. A.; Del Ser, J.; Upton, C.; Quilligan, F.; Gil-Lopez, S.; Salcedo-Sanz, S.

2015-11-01

When seeking near-optimal solutions for complex scheduling problems, meta-heuristics demonstrate good performance with affordable computational effort. This has resulted in a gravitation towards these approaches when researching industrial use-cases such as energy-efficient production planning. However, much of the previous research makes assumptions about softer constraints that affect planning strategies and about how human planners interact with the algorithm in a live production environment. This article describes a job-shop problem that focuses on minimizing energy consumption across a production facility of shared resources. The application scenario is based on real facilities made available by the Irish Center for Manufacturing Research. The formulated problem is tackled via harmony search heuristics with random keys encoding. Simulation results are compared to a genetic algorithm, a simulated annealing approach and a first-come-first-served scheduling. The superior performance obtained by the proposed scheduler paves the way towards its practical implementation over industrial production chains.

Genetic diversity of two Tunisian sheep breeds using random ...

African Journals Online (AJOL)

Random amplified polymorphic DNA (RAPD) markers were used to study genetic diversity and population structure in six sheep populations belonging to two native Tunisian breeds (the Barbarine and the Western thin tail). A total of 96 samples were typed using eight RAPD primers. 62 bands were scored, of which 44 ...

Genetic variability of cultivated cowpea in Benin assessed by random amplified polymorphic DNA

NARCIS (Netherlands)

Zannou, A.; Kossou, D.K.; Ahanchédé, A.; Zoundjihékpon, J.; Agbicodo, E.; Struik, P.C.; Sanni, A.

2008-01-01

Characterization of genetic diversity among cultivated cowpea [Vigna unguiculata (L.) Walp.] varieties is important to optimize the use of available genetic resources by farmers, local communities, researchers and breeders. Random amplified polymorphic DNA (RAPD) markers were used to evaluate the

Estimation of genetic parameters related to eggshell strength using random regression models.

Science.gov (United States)

Guo, J; Ma, M; Qu, L; Shen, M; Dou, T; Wang, K

2015-01-01

This study examined the changes in eggshell strength and the genetic parameters related to this trait throughout a hen's laying life using random regression. The data were collected from a crossbred population between 2011 and 2014, where the eggshell strength was determined repeatedly for 2260 hens. Using random regression models (RRMs), several Legendre polynomials were employed to estimate the fixed, direct genetic and permanent environment effects. The residual effects were treated as independently distributed with heterogeneous variance for each test week. The direct genetic variance was included with second-order Legendre polynomials and the permanent environment with third-order Legendre polynomials. The heritability of eggshell strength ranged from 0.26 to 0.43, the repeatability ranged between 0.47 and 0.69, and the estimated genetic correlations between test weeks was high at > 0.67. The first eigenvalue of the genetic covariance matrix accounted for about 97% of the sum of all the eigenvalues. The flexibility and statistical power of RRM suggest that this model could be an effective method to improve eggshell quality and to reduce losses due to cracked eggs in a breeding plan.

Bias modification training can alter approach bias and chocolate consumption.

Science.gov (United States)

Schumacher, Sophie E; Kemps, Eva; Tiggemann, Marika

2016-01-01

Recent evidence has demonstrated that bias modification training has potential to reduce cognitive biases for attractive targets and affect health behaviours. The present study investigated whether cognitive bias modification training could be applied to reduce approach bias for chocolate and affect subsequent chocolate consumption. A sample of 120 women (18-27 years) were randomly assigned to an approach-chocolate condition or avoid-chocolate condition, in which they were trained to approach or avoid pictorial chocolate stimuli, respectively. Training had the predicted effect on approach bias, such that participants trained to approach chocolate demonstrated an increased approach bias to chocolate stimuli whereas participants trained to avoid such stimuli showed a reduced bias. Further, participants trained to avoid chocolate ate significantly less of a chocolate muffin in a subsequent taste test than participants trained to approach chocolate. Theoretically, results provide support for the dual process model's conceptualisation of consumption as being driven by implicit processes such as approach bias. In practice, approach bias modification may be a useful component of interventions designed to curb the consumption of unhealthy foods. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multivariate Meta-Analysis of Genetic Association Studies: A Simulation Study.

Directory of Open Access Journals (Sweden)

Binod Neupane

Full Text Available In a meta-analysis with multiple end points of interests that are correlated between or within studies, multivariate approach to meta-analysis has a potential to produce more precise estimates of effects by exploiting the correlation structure between end points. However, under random-effects assumption the multivariate estimation is more complex (as it involves estimation of more parameters simultaneously than univariate estimation, and sometimes can produce unrealistic parameter estimates. Usefulness of multivariate approach to meta-analysis of the effects of a genetic variant on two or more correlated traits is not well understood in the area of genetic association studies. In such studies, genetic variants are expected to roughly maintain Hardy-Weinberg equilibrium within studies, and also their effects on complex traits are generally very small to modest and could be heterogeneous across studies for genuine reasons. We carried out extensive simulation to explore the comparative performance of multivariate approach with most commonly used univariate inverse-variance weighted approach under random-effects assumption in various realistic meta-analytic scenarios of genetic association studies of correlated end points. We evaluated the performance with respect to relative mean bias percentage, and root mean square error (RMSE of the estimate and coverage probability of corresponding 95% confidence interval of the effect for each end point. Our simulation results suggest that multivariate approach performs similarly or better than univariate method when correlations between end points within or between studies are at least moderate and between-study variation is similar or larger than average within-study variation for meta-analyses of 10 or more genetic studies. Multivariate approach produces estimates with smaller bias and RMSE especially for the end point that has randomly or informatively missing summary data in some individual studies, when

Particle swarm optimization with random keys applied to the nuclear reactor reload problem

Energy Technology Data Exchange (ETDEWEB)

Meneses, Anderson Alvarenga de Moura [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia (COPPE). Programa de Engenharia Nuclear; Fundacao Educacional de Macae (FUNEMAC), RJ (Brazil). Faculdade Professor Miguel Angelo da Silva Santos; Machado, Marcelo Dornellas; Medeiros, Jose Antonio Carlos Canedo; Schirru, Roberto [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia (COPPE). Programa de Engenharia Nuclear]. E-mails: ameneses@con.ufrj.br; marcelo@lmp.ufrj.br; canedo@lmp.ufrj.br; schirru@lmp.ufrj.br

2007-07-01

In 1995, Kennedy and Eberhart presented the Particle Swarm Optimization (PSO), an Artificial Intelligence metaheuristic technique to optimize non-linear continuous functions. The concept of Swarm Intelligence is based on the socials aspects of intelligence, it means, the ability of individuals to learn with their own experience in a group as well as to take advantage of the performance of other individuals. Some PSO models for discrete search spaces have been developed for combinatorial optimization, although none of them presented satisfactory results to optimize a combinatorial problem as the nuclear reactor fuel reloading problem (NRFRP). In this sense, we developed the Particle Swarm Optimization with Random Keys (PSORK) in previous research to solve Combinatorial Problems. Experiences demonstrated that PSORK performed comparable to or better than other techniques. Thus, PSORK metaheuristic is being applied in optimization studies of the NRFRP for Angra 1 Nuclear Power Plant. Results will be compared with Genetic Algorithms and the manual method provided by a specialist. In this experience, the problem is being modeled for an eight-core symmetry and three-dimensional geometry, aiming at the minimization of the Nuclear Enthalpy Power Peaking Factor as well as the maximization of the cycle length. (author)

Particle swarm optimization with random keys applied to the nuclear reactor reload problem

International Nuclear Information System (INIS)

Meneses, Anderson Alvarenga de Moura; Fundacao Educacional de Macae; Machado, Marcelo Dornellas; Medeiros, Jose Antonio Carlos Canedo; Schirru, Roberto

2007-01-01

In 1995, Kennedy and Eberhart presented the Particle Swarm Optimization (PSO), an Artificial Intelligence metaheuristic technique to optimize non-linear continuous functions. The concept of Swarm Intelligence is based on the socials aspects of intelligence, it means, the ability of individuals to learn with their own experience in a group as well as to take advantage of the performance of other individuals. Some PSO models for discrete search spaces have been developed for combinatorial optimization, although none of them presented satisfactory results to optimize a combinatorial problem as the nuclear reactor fuel reloading problem (NRFRP). In this sense, we developed the Particle Swarm Optimization with Random Keys (PSORK) in previous research to solve Combinatorial Problems. Experiences demonstrated that PSORK performed comparable to or better than other techniques. Thus, PSORK metaheuristic is being applied in optimization studies of the NRFRP for Angra 1 Nuclear Power Plant. Results will be compared with Genetic Algorithms and the manual method provided by a specialist. In this experience, the problem is being modeled for an eight-core symmetry and three-dimensional geometry, aiming at the minimization of the Nuclear Enthalpy Power Peaking Factor as well as the maximization of the cycle length. (author)

Cryptographic analysis on the key space of optical phase encryption algorithm based on the design of discrete random phase mask

Science.gov (United States)

Lin, Chao; Shen, Xueju; Li, Zengyan

2013-07-01

The key space of phase encryption algorithm using discrete random phase mask is investigated by numerical simulation in this paper. Random phase mask with finite and discrete phase levels is considered as the core component in most practical optical encryption architectures. The key space analysis is based on the design criteria of discrete random phase mask. The role of random amplitude mask and random phase mask in optical encryption system is identified from the perspective of confusion and diffusion. The properties of discrete random phase mask in a practical double random phase encoding scheme working in both amplitude encoding (AE) and phase encoding (PE) modes are comparably analyzed. The key space of random phase encryption algorithm is evaluated considering both the encryption quality and the brute-force attack resistibility. A method for enlarging the key space of phase encryption algorithm is also proposed to enhance the security of optical phase encryption techniques.

Childhood adiposity and risk of type 1 diabetes: A Mendelian randomization study.

Directory of Open Access Journals (Sweden)

J C Censin

2017-08-01

Full Text Available The incidence of type 1 diabetes (T1D is increasing globally. One hypothesis is that increasing childhood obesity rates may explain part of this increase, but, as T1D is rare, intervention studies are challenging to perform. The aim of this study was to assess this hypothesis with a Mendelian randomization approach that uses genetic variants as instrumental variables to test for causal associations.We created a genetic instrument of 23 single nucleotide polymorphisms (SNPs associated with childhood adiposity in children aged 2-10 years. Summary-level association results for these 23 SNPs with childhood-onset (<17 years T1D were extracted from a meta-analysis of genome-wide association study with 5,913 T1D cases and 8,828 reference samples. Using inverse-variance weighted Mendelian randomization analysis, we found support for an effect of childhood adiposity on T1D risk (odds ratio 1.32, 95% CI 1.06-1.64 per standard deviation score in body mass index [SDS-BMI]. A sensitivity analysis provided evidence of horizontal pleiotropy bias (p = 0.04 diluting the estimates towards the null. We therefore applied Egger regression and multivariable Mendelian randomization methods to control for this type of bias and found evidence in support of a role of childhood adiposity in T1D (odds ratio in Egger regression, 2.76, 95% CI 1.40-5.44. Limitations of our study include that underlying genes and their mechanisms for most of the genetic variants included in the score are not known. Mendelian randomization requires large sample sizes, and power was limited to provide precise estimates. This research has been conducted using data from the Early Growth Genetics (EGG Consortium, the Genetic Investigation of Anthropometric Traits (GIANT Consortium, the Tobacco and Genetics (TAG Consortium, and the Social Science Genetic Association Consortium (SSGAC, as well as meta-analysis results from a T1D genome-wide association study.This study provides genetic support for a

Importance biasing quality criterion based on contribution response theory

International Nuclear Information System (INIS)

Borisov, N.M.; Panin, M.P.

2001-01-01

The report proposes a visual criterion of importance biasing both of forward and adjoint simulation. The similarity of contribution Monte Carlo and importance biasing random collision event distribution is proved. The conservation of total number of random trajectory crossings of surfaces, which separate the source and the detector is proposed as importance biasing quality criterion. The use of this criterion is demonstrated on the example of forward vs. adjoint importance biasing in gamma ray deep penetration problem. The larger amount of published data on forward field characteristics than on adjoint leads to the more accurate approximation of adjoint importance function in comparison to forward, for it adjoint importance simulation is more effective than forward. The proposed criterion indicates it visually, showing the most uniform distribution of random trajectory crossing events for the most effective importance biasing parameters and pointing to the direction of tuning importance biasing parameters. (orig.)

Internet-based cognitive bias modification for obsessive compulsive disorder: study protocol for a randomized controlled trial.

Science.gov (United States)

Williams, Alishia D; Pajak, Rosanna; O'Moore, Kathleen; Andrews, Gavin; Grisham, Jessica R

2014-05-29

Cognitive bias modification (CBM) interventions have demonstrated efficacy in augmenting core biases implicated in psychopathology. The current randomized controlled trial (RCT) will evaluate the efficacy of an internet-delivered positive imagery cognitive bias modification intervention for obsessive compulsive disorder (OCD) when compared to a control condition. Patients meeting diagnostic criteria for a current or lifetime diagnosis of OCD will be recruited via the research arm of a not-for-profit clinical and research unit in Australia. The minimum sample size for each group (alpha set at 0.05, power at .80) was identified as 29, but increased to 35 to allow for 20% attrition. We will measure the impact of CBM on interpretations bias using the OC Bias Measure (The Ambiguous Scenarios Test for OCD ;AST-OCD) and OC-beliefs (The Obsessive Beliefs Questionnaire-TRIP; OBQ-TRIP). Secondary outcome measures include the Dimensional Obsessive-Compulsive Scale (DOCS), the Patient Health Questionnaire (PHQ-9), The Kessler Psychological Distress Scale (K10), and the Word Sentence Association Test for OCD (WSAO). Change in diagnostic status will be indexed using the OCD Mini International Neuropsychiatric Interview (M.I.N.I) Module at baseline and follow-up. Intent-to-treat (ITT) marginal and mixed-effect models using restricted maximum likelihood (REML) estimation will be used to evaluate the primary hypotheses. Stability of bias change will be assessed at 1-month follow-up. A limitation of the online nature of the study is the inability to include a behavioral outcome measure. The trial was registered on 10 October 2013 with the Australian New Zealand Clinical Trials Registry (ACTRN12613001130752).

An Attribute Involved Public Key Cryptosystem Based on P-Sylow Subgroups and Randomization

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Sumalatha GUNNALA

2018-04-01

Full Text Available The Asymmetric Key Cryptosystem (AKC or Public Key Encryption (PKE is a mechanism used to encrypt the messages by using public key and decrypt the enciphered messages by using private key. Of late, the Attribute-Based Encryption (ABE is an expansion of asymmetric key encryption scheme that allows users to encrypt and decrypt the plaintext messages using the key based on the user’s credentials, called attributes, like social security number, PAN (Permanent Account Number, email ids or Aadhar number etc. Most of the existing ABE schemes rely on the multiple attributes from which the access control policies are derived. These policies define the users’ private keys, required for the decryption process and access to the confidential information. In this paper, we proposed a new attribute based asymmetric cryptosystem that uses the features of both the schemes: PKE and ABE. Here, we used a value of an attribute, personal to the user, for the encryption and the decryption process. This scheme assures that the receiver will only be able to access the secret data if recipient is shared with the valid attribute value. The asymmetric nature is this scheme is based on the concept of p-sylow sub-group assumption. In addition, the randomization factor is used in the encipherment process to strengthen the cipher further. The development of this cryptosystem is an embodiment where the merits of randomized asymmetric encryption technique and the attribute based encryption are integrated to achieve the authentication on top of confidentiality to secure the information transmission over the public networks.

Implementing a generic method for bias correction in statistical models using random effects, with spatial and population dynamics examples

DEFF Research Database (Denmark)

Thorson, James T.; Kristensen, Kasper

2016-01-01

Statistical models play an important role in fisheries science when reconciling ecological theory with available data for wild populations or experimental studies. Ecological models increasingly include both fixed and random effects, and are often estimated using maximum likelihood techniques...... configurations of an age-structured population dynamics model. This simulation experiment shows that the epsilon-method and the existing bias-correction method perform equally well in data-rich contexts, but the epsilon-method is slightly less biased in data-poor contexts. We then apply the epsilon......-method to a spatial regression model when estimating an index of population abundance, and compare results with an alternative bias-correction algorithm that involves Markov-chain Monte Carlo sampling. This example shows that the epsilon-method leads to a biologically significant difference in estimates of average...

Bias in clinical intervention research

DEFF Research Database (Denmark)

Gluud, Lise Lotte

2006-01-01

Research on bias in clinical trials may help identify some of the reasons why investigators sometimes reach the wrong conclusions about intervention effects. Several quality components for the assessment of bias control have been suggested, but although they seem intrinsically valid, empirical...... evidence is needed to evaluate their effects on the extent and direction of bias. This narrative review summarizes the findings of methodological studies on the influence of bias in clinical trials. A number of methodological studies suggest that lack of adequate randomization in published trial reports...

Validity of Qualis database as a predictor of evidence hierarchy and risk of bias in randomized controlled trials: a case study in dentistry

Directory of Open Access Journals (Sweden)

Christiane Alves Ferreira

2011-01-01

Full Text Available OBJECTIVE: To evaluate the validity of the Qualis database in identifying the levels of scientific evidence and the quality of randomized controlled trials indexed in the Lilacs database. METHODS: We selected 40 open-access journals and performed a page-by-page hand search, to identify published articles according to the type of study during a period of six years. Classification of studies was performed by independent reviewers assessed for their reliability. Randomized controlled trials were identified for separate evaluation of risk of bias using four dimensions: generation of allocation sequence, allocation concealment, blinding, and incomplete outcome data. The Qualis classification was considered to be the outcome variable. The statistical tests used included Kappa, Spearman's correlation, Kendall-tau and ordinal regressions. RESULTS: Studies with low levels of scientific evidence received similar Qualis classifications when compared to studies with high levels of evidence. In addition, randomized controlled trials with a high risk of bias for the generation of allocation sequences and allocation concealment were more likely to be published in journals with higher Qualis levels. DISCUSSION: The hierarchy level of the scientific evidence as classified by type of research design, as well as by the validity of studies according to the bias control level, was not correlated or associated with Qualis stratification. CONCLUSION: Qualis classifications for journals are not an approximate or indirect predictor of the validity of randomized controlled trials published in these journals and are therefore not a legitimate or appropriate indicator of the validity of randomized controlled trials.

Large-scale galaxy bias

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Jeong, Donghui; Desjacques, Vincent; Schmidt, Fabian

2018-01-01

Here, we briefly introduce the key results of the recent review (arXiv:1611.09787), whose abstract is as following. This review presents a comprehensive overview of galaxy bias, that is, the statistical relation between the distribution of galaxies and matter. We focus on large scales where cosmic density fields are quasi-linear. On these scales, the clustering of galaxies can be described by a perturbative bias expansion, and the complicated physics of galaxy formation is absorbed by a finite set of coefficients of the expansion, called bias parameters. The review begins with a detailed derivation of this very important result, which forms the basis of the rigorous perturbative description of galaxy clustering, under the assumptions of General Relativity and Gaussian, adiabatic initial conditions. Key components of the bias expansion are all leading local gravitational observables, which include the matter density but also tidal fields and their time derivatives. We hence expand the definition of local bias to encompass all these contributions. This derivation is followed by a presentation of the peak-background split in its general form, which elucidates the physical meaning of the bias parameters, and a detailed description of the connection between bias parameters and galaxy (or halo) statistics. We then review the excursion set formalism and peak theory which provide predictions for the values of the bias parameters. In the remainder of the review, we consider the generalizations of galaxy bias required in the presence of various types of cosmological physics that go beyond pressureless matter with adiabatic, Gaussian initial conditions: primordial non-Gaussianity, massive neutrinos, baryon-CDM isocurvature perturbations, dark energy, and modified gravity. Finally, we discuss how the description of galaxy bias in the galaxies' rest frame is related to clustering statistics measured from the observed angular positions and redshifts in actual galaxy catalogs.

Internet-delivered attention bias modification training in individuals with social anxiety disorder - a double blind randomized controlled trial

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Carlbring Per

2012-06-01

Full Text Available Abstract Background Computerized cognitive bias modification for social anxiety disorder has in several well conducted trials shown great promise with as many as 72% no longer fulfilling diagnostic criteria after a 4 week training program. To test if the same program can be transferred from a clinical setting to an internet delivered home based treatment the authors conducted a randomized, double-blind placebo-controlled trial. Methods After a diagnostic interview 79 participants were randomized to one of two attention training programs using a probe detection task. In the active condition the participant was trained to direct attention away from threat, whereas in the placebo condition the probe appeared with equal frequency in the position of the threatening and neutral faces. Results Results were analyzed on an intention-to-treat basis, including all randomized participants. Immediate and 4-month follow-up results revealed a significant time effect on all measured dimensions (social anxiety scales, general anxiety and depression levels, quality of life. However, there were no time x group interactions. The lack of differences in the two groups was also mirrored by the infinitesimal between group effect size both at post test and at 4-month follow-up. Conclusion We conclude that computerized attention bias modification may need to be altered before dissemination for the Internet. Trial registration ISRCTN01715124

On Generating Optimal Signal Probabilities for Random Tests: A Genetic Approach

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M. Srinivas

1996-01-01

Full Text Available Genetic Algorithms are robust search and optimization techniques. A Genetic Algorithm based approach for determining the optimal input distributions for generating random test vectors is proposed in the paper. A cost function based on the COP testability measure for determining the efficacy of the input distributions is discussed. A brief overview of Genetic Algorithms (GAs and the specific details of our implementation are described. Experimental results based on ISCAS-85 benchmark circuits are presented. The performance of our GAbased approach is compared with previous results. While the GA generates more efficient input distributions than the previous methods which are based on gradient descent search, the overheads of the GA in computing the input distributions are larger.

Are languages really independent from genes? If not, what would a genetic bias affecting language diversity look like?

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Dediu, Dan

2011-04-01

It is generally accepted that the relationship between human genes and language is very complex and multifaceted. This has its roots in the “regular” complexity governing the interplay among genes and between genes and environment for most phenotypes, but with the added layer of supraontogenetic and supra-individual processes defining culture. At the coarsest level, focusing on the species, it is clear that human-specific--but not necessarily faculty-specific--genetic factors subtend our capacity for language and a currently very productive research program is aiming at uncovering them. At the other end of the spectrum, it is uncontroversial that individual-level variations in different aspects related to speech and language have an important genetic component and their discovery and detailed characterization have already started to revolutionize the way we think about human nature. However, at the intermediate, glossogenetic/population level, the relationship becomes controversial, partly due to deeply ingrained beliefs about language acquisition and universality and partly because of confusions with a different type of gene-languages correlation due to shared history. Nevertheless, conceptual, mathematical and computational models--and, recently, experimental evidence from artificial languages and songbirds--have repeatedly shown that genetic biases affecting the acquisition or processing of aspects of language and speech can be amplified by population-level intergenerational cultural processes and made manifest either as fixed “universal” properties of language or as structured linguistic diversity. Here, I review several such models as well as the recently proposed case of a causal relationship between the distribution of tone languages and two genes related to brain growth and development, ASPM and Microcephalin, and I discuss the relevance of such genetic biasing for language evolution, change, and diversity.

Directional Bias and Pheromone for Discovery and Coverage on Networks

Energy Technology Data Exchange (ETDEWEB)

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 and 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.

Applications of random forest feature selection for fine-scale genetic population assignment.

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Sylvester, Emma V A; Bentzen, Paul; Bradbury, Ian R; Clément, Marie; Pearce, Jon; Horne, John; Beiko, Robert G

2018-02-01

Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine-learning algorithms (random forest, regularized random forest and guided regularized random forest) compared with F ST ranking for selection of single nucleotide polymorphisms (SNP) for fine-scale population assignment. We applied these methods to an unpublished SNP data set for Atlantic salmon ( Salmo salar ) and a published SNP data set for Alaskan Chinook salmon ( Oncorhynchus tshawytscha ). In each species, we identified the minimum panel size required to obtain a self-assignment accuracy of at least 90% using each method to create panels of 50-700 markers Panels of SNPs identified using random forest-based methods performed up to 7.8 and 11.2 percentage points better than F ST -selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self-assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each data set, respectively, a level of accuracy never reached for these species using F ST -selected panels. Our results demonstrate a role for machine-learning approaches in marker selection across large genomic data sets to improve assignment for management and conservation of exploited populations.

Identification of Protein Complexes from Tandem Affinity Purification/Mass Spectrometry Data via Biased Random Walk.

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Cai, Bingjing; Wang, Haiying; Zheng, Huiru; Wang, Hui

2015-01-01

Systematic identification of protein complexes from protein-protein interaction networks (PPIs) is an important application of data mining in life science. Over the past decades, various new clustering techniques have been developed based on modelling PPIs as binary relations. Non-binary information of co-complex relations (prey/bait) in PPIs data derived from tandem affinity purification/mass spectrometry (TAP-MS) experiments has been unfairly disregarded. In this paper, we propose a Biased Random Walk based algorithm for detecting protein complexes from TAP-MS data, resulting in the random walk with restarting baits (RWRB). RWRB is developed based on Random walk with restart. The main contribution of RWRB is the incorporation of co-complex relations in TAP-MS PPI networks into the clustering process, by implementing a new restarting strategy during the process of random walk. Through experimentation on un-weighted and weighted TAP-MS data sets, we validated biological significance of our results by mapping them to manually curated complexes. Results showed that, by incorporating non-binary, co-membership information, significant improvement has been achieved in terms of both statistical measurements and biological relevance. Better accuracy demonstrates that the proposed method outperformed several state-of-the-art clustering algorithms for the detection of protein complexes in TAP-MS data.

Exercise for depression in older adults: a meta-analysis of randomized controlled trials adjusting for publication bias

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Felipe B. Schuch

Full Text Available Objective: To evaluate the antidepressant effects of exercise in older adults, using randomized controlled trial (RCT data. Methods: We conducted a meta-analysis of exercise in older adults, addressing limitations of previous works. RCTs of exercise interventions in older people with depression (≥ 60 years comparing exercise vs. control were eligible. A random-effects meta-analysis calculating the standardized mean difference (SMD (95% confidence interval [95%CI], meta-regressions, and trim, fill, and fail-safe number analyses were conducted. Results: Eight RCTs were included, representing 138 participants in exercise arms and 129 controls. Exercise had a large and significant effect on depression (SMD = -0.90 [95%CI -0.29 to -1.51], with a fail-safe number of 71 studies. Significant effects were found for 1 mixed aerobic and anaerobic interventions, 2 at moderate intensity, 3 that were group-based, 4 that utilized mixed supervised and unsupervised formats, and 5 in people without other clinical comorbidities. Conclusion: Adjusting for publication bias increased the beneficial effects of exercise in three subgroup analysis, suggesting that previous meta-analyses have underestimated the benefits of exercise due to publication bias. We advocate that exercise be considered as a routine component of the management of depression in older adults.

Application of bias factor method using random sampling technique for prediction accuracy improvement of critical eigenvalue of BWR

International Nuclear Information System (INIS)

Ito, Motohiro; Endo, Tomohiro; Yamamoto, Akio; Kuroda, Yusuke; Yoshii, Takashi

2017-01-01

The bias factor method based on the random sampling technique is applied to the benchmark problem of Peach Bottom Unit 2. Validity and availability of the present method, i.e. correction of calculation results and reduction of uncertainty, are confirmed in addition to features and performance of the present method. In the present study, core characteristics in cycle 3 are corrected with the proposed method using predicted and 'measured' critical eigenvalues in cycles 1 and 2. As the source of uncertainty, variance-covariance of cross sections is considered. The calculation results indicate that bias between predicted and measured results, and uncertainty owing to cross section can be reduced. Extension to other uncertainties such as thermal hydraulics properties will be a future task. (author)

Blocked Randomization with Randomly Selected Block Sizes

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Jimmy Efird

2010-12-01

Full Text Available When planning a randomized clinical trial, careful consideration must be given to how participants are selected for various arms of a study. Selection and accidental bias may occur when participants are not assigned to study groups with equal probability. A simple random allocation scheme is a process by which each participant has equal likelihood of being assigned to treatment versus referent groups. However, by chance an unequal number of individuals may be assigned to each arm of the study and thus decrease the power to detect statistically significant differences between groups. Block randomization is a commonly used technique in clinical trial design to reduce bias and achieve balance in the allocation of participants to treatment arms, especially when the sample size is small. This method increases the probability that each arm will contain an equal number of individuals by sequencing participant assignments by block. Yet still, the allocation process may be predictable, for example, when the investigator is not blind and the block size is fixed. This paper provides an overview of blocked randomization and illustrates how to avoid selection bias by using random block sizes.

Genetic conservation and paddlefish propagation

Science.gov (United States)

Sloss, Brian L.; Klumb, Robert A.; Heist, Edward J.

2009-01-01

The conservation of genetic diversity of our natural resources is overwhelmingly one of the central foci of 21st century management practices. Three recommendations related to the conservation of paddlefish Polyodon spathula genetic diversity are to (1) identify genetic diversity at both nuclear and mitochondrial DNA loci using a suggested list of 20 sampling locations, (2) use genetic diversity estimates to develop genetic management units, and (3) identify broodstock sources to minimize effects of supplemental stocking on the genetic integrity of native paddlefish populations. We review previous genetic work on paddlefish and described key principles and concepts associated with maintaining genetic diversity within and among paddlefish populations and also present a genetic case study of current paddlefish propagation at the U.S. Fish and Wildlife Service Gavins Point National Fish Hatchery. This study confirmed that three potential sources of broodfish were genetically indistinguishable at the loci examined, allowing the management agencies cooperating on this program flexibility in sampling gametes. This study also showed significant bias in the hatchery occurred in terms of male reproductive contribution, which resulted in a shift in the genetic diversity of progeny compared to the broodfish. This shift was shown to result from differential male contributions, partially attributed to the mode of egg fertilization. Genetic insights enable implementation of a paddlefish propagation program within an adaptive management strategy that conserves inherent genetic diversity while achieving demographic goals.

Genetic diversity analysis of various red spider mite- resistant ...

African Journals Online (AJOL)

User

2011-05-02

May 2, 2011 ... 3Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Ya'an, 625014, P. R. ... Random amplified polymorphic DNA (RAPD) is a DNA ..... spider mite-resistant, bumper, high-quality and disease-.

Study books on ADHD genetics: balanced or biased?

Science.gov (United States)

Te Meerman, Sanne; Batstra, Laura; Hoekstra, Rink; Grietens, Hans

2017-06-01

Academic study books are essential assets for disseminating knowledge about ADHD to future healthcare professionals. This study examined if they are balanced with regard to genetics. We selected and analyzed study books (N=43) used in (pre) master's programmes at 10 universities in the Netherlands. Because the mere behaviourally informed quantitative genetics give a much higher effect size of the genetic involvement in ADHD, it is important that study books contrast these findings with molecular genetics' outcomes. The latter studies use real genetic data, and their low effect sizes expose the potential weaknesses of quantitative genetics, like underestimating the involvement of the environment. Only a quarter of books mention both effect sizes and contrast these findings, while another quarter does not discuss any effect size. Most importantly, however, roughly half of the books in our sample mention only the effect sizes from quantitative genetic studies without addressing the low explained variance of molecular genetic studies. This may confuse readers by suggesting that the weakly associated genes support the quite spectacular, but potentially flawed estimates of twin, family and adoption studies, while they actually contradict them.

Information hiding based on double random-phase encoding and public-key cryptography.

Science.gov (United States)

Sheng, Yuan; Xin, Zhou; Alam, Mohammed S; Xi, Lu; Xiao-Feng, Li

2009-03-02

A novel information hiding method based on double random-phase encoding (DRPE) and Rivest-Shamir-Adleman (RSA) public-key cryptosystem is proposed. In the proposed technique, the inherent diffusion property of DRPE is cleverly utilized to make up the diffusion insufficiency of RSA public-key cryptography, while the RSA cryptosystem is utilized for simultaneous transmission of the cipher text and the two phase-masks, which is not possible under the DRPE technique. This technique combines the complementary advantages of the DPRE and RSA encryption techniques and brings security and convenience for efficient information transmission. Extensive numerical simulation results are presented to verify the performance of the proposed technique.

The key role of patrilineal inheritance in shaping the genetic variation of Dagestan highlanders.

Science.gov (United States)

Caciagli, Laura; Bulayeva, Kazima; Bulayev, Oleg; Bertoncini, Stefania; Taglioli, Luca; Pagani, Luca; Paoli, Giorgio; Tofanelli, Sergio

2009-12-01

The Caucasus region is a complex cultural and ethnic mosaic, comprising populations that speak Caucasian, Indo-European and Altaic languages. Isolated mountain villages (auls) in Dagestan still preserve high level of genetic and cultural diversity and have patriarchal societies with a long history of isolation. The aim of this study was to understand the genetic history of five Dagestan highland auls with distinct ethnic affiliation (Avars, Chechens-Akkins, Kubachians, Laks, Tabasarans) using markers on the male-specific region of the Y chromosome. The groups analyzed here are all Muslims but speak different languages all belonging to the Nakh-Dagestanian linguistic family. The results show that the Dagestan ethnic groups share a common Y-genetic background, with deep-rooted genealogies and rare alleles, dating back to an early phase in the post-glacial recolonization of Europe. Geography and stochastic factors, such as founder effect and long-term genetic drift, driven by the rigid structuring of societies in groups of patrilineal descent, most likely acted as mutually reinforcing key factors in determining the high degree of Y-genetic divergence among these ethnic groups.

Genetic algorithms with memory- and elitism-based immigrants in dynamic environments.

Science.gov (United States)

Yang, Shengxiang

2008-01-01

In recent years the genetic algorithm community has shown a growing interest in studying dynamic optimization problems. Several approaches have been devised. The random immigrants and memory schemes are two major ones. The random immigrants scheme addresses dynamic environments by maintaining the population diversity while the memory scheme aims to adapt genetic algorithms quickly to new environments by reusing historical information. This paper investigates a hybrid memory and random immigrants scheme, called memory-based immigrants, and a hybrid elitism and random immigrants scheme, called elitism-based immigrants, for genetic algorithms in dynamic environments. In these schemes, the best individual from memory or the elite from the previous generation is retrieved as the base to create immigrants into the population by mutation. This way, not only can diversity be maintained but it is done more efficiently to adapt genetic algorithms to the current environment. Based on a series of systematically constructed dynamic problems, experiments are carried out to compare genetic algorithms with the memory-based and elitism-based immigrants schemes against genetic algorithms with traditional memory and random immigrants schemes and a hybrid memory and multi-population scheme. The sensitivity analysis regarding some key parameters is also carried out. Experimental results show that the memory-based and elitism-based immigrants schemes efficiently improve the performance of genetic algorithms in dynamic environments.

An Authenticated Key Agreement Scheme Based on Cyclic Automorphism Subgroups of Random Orders

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Yang Jun

2017-01-01

Full Text Available Group-based cryptography is viewed as a modern cryptographic candidate solution to blocking quantum computer attacks, and key exchange protocols on the Internet are one of the primitives to ensure the security of communication. In 2016 Habeeb et al proposed a “textbook” key exchange protocol based on the semidirect product of two groups, which is insecure for use in real-world applications. In this paper, after discarding the unnecessary disguising notion of semidirect product in the protocol, we establish a simplified yet enhanced authenticated key agreement scheme based on cyclic automorphism subgroups of random orders by making hybrid use of certificates and symmetric-key encryption as challenge-and-responses in the public-key setting. Its passive security is formally analyzed, which is relative to the cryptographic hardness assumption of a computational number-theoretic problem. Cryptanalysis of this scheme shows that it is secure against the intruder-in-the-middle attack even in the worst case of compromising the signatures, and provides explicit key confirmation to both parties.

Random regression models to estimate genetic parameters for milk production of Guzerat cows using orthogonal Legendre polynomials

Directory of Open Access Journals (Sweden)

Maria Gabriela Campolina Diniz Peixoto

2014-05-01

Full Text Available The objective of this work was to compare random regression models for the estimation of genetic parameters for Guzerat milk production, using orthogonal Legendre polynomials. Records (20,524 of test-day milk yield (TDMY from 2,816 first-lactation Guzerat cows were used. TDMY grouped into 10-monthly classes were analyzed for additive genetic effect and for environmental and residual permanent effects (random effects, whereas the contemporary group, calving age (linear and quadratic effects and mean lactation curve were analized as fixed effects. Trajectories for the additive genetic and permanent environmental effects were modeled by means of a covariance function employing orthogonal Legendre polynomials ranging from the second to the fifth order. Residual variances were considered in one, four, six, or ten variance classes. The best model had six residual variance classes. The heritability estimates for the TDMY records varied from 0.19 to 0.32. The random regression model that used a second-order Legendre polynomial for the additive genetic effect, and a fifth-order polynomial for the permanent environmental effect is adequate for comparison by the main employed criteria. The model with a second-order Legendre polynomial for the additive genetic effect, and that with a fourth-order for the permanent environmental effect could also be employed in these analyses.

Sex-biased dispersal at different geographical scales in a cooperative breeder from fragmented rainforest.

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Carl Vangestel

Full Text Available Dispersal affects both social behavior and population structure and is therefore a key determinant of long-term population persistence. However, dispersal strategies and responses to spatial habitat alteration may differ between sexes. Here we analyzed spatial and temporal variation in ten polymorphic microsatellite DNA loci of male and female Cabanis's greenbuls (Phyllastrephuscabanisi, a cooperative breeder of Afrotropical rainforest, to quantify rates of gene flow and fine-grained genetic structuring within and among fragmented populations. We found genetic evidence for female-biased dispersal at small spatial scales, but not at the landscape level. Local autocorrelation analysis provided evidence of positive genetic structure within 300 m distance ranges, which is consistent with behavioral observations of short-distance natal dispersal. At a landscape scale, individual-based autocorrelation values decreased over time while levels of admixture increased, possibly indicating increased gene flow over the past decade.

Population stochasticity, random determination of handedness, and the genetic basis of antisymmetry.

Science.gov (United States)

Kamimura, Yoshitaka

2011-12-07

Conspicuous lateral asymmetries of organisms are classified into two major categories: antisymmetry (AS), characterized by almost equal frequencies of dextral and sinistral morphs, and directional asymmetry (DA), in which one morph dominates. I compared and characterized two types of genes, both with existing examples, in their roles in the evolutionary transitions between AS and DA for the first time. Handedness genes (HGs) determine the chirality in a strict sense, while randomization genes (RGs) randomize the chirality. A theory predicts that, in an AS population maintained by HGs under negative frequency-dependent selection, RGs harness fluctuation of the morph frequencies as their driving force and thus increase their frequency until half of the population flips the phenotype. These predictions were confirmed by simulations. Consequently, RGs mask the genetic effects of HGs, which provides a possible explanation for the apparent lack of a genetic basis for AS in empirical AS studies. Copyright © 2011 Elsevier Ltd. All rights reserved.

A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals.

Science.gov (United States)

Silva, Marina; Oliveira, Marisa; Vieira, Daniel; Brandão, Andreia; Rito, Teresa; Pereira, Joana B; Fraser, Ross M; Hudson, Bob; Gandini, Francesca; Edwards, Ceiridwen; Pala, Maria; Koch, John; Wilson, James F; Pereira, Luísa; Richards, Martin B; Soares, Pedro

2017-03-23

India is a patchwork of tribal and non-tribal populations that speak many different languages from various language families. Indo-European, spoken across northern and central India, and also in Pakistan and Bangladesh, has been frequently connected to the so-called "Indo-Aryan invasions" from Central Asia ~3.5 ka and the establishment of the caste system, but the extent of immigration at this time remains extremely controversial. South India, on the other hand, is dominated by Dravidian languages. India displays a high level of endogamy due to its strict social boundaries, and high genetic drift as a result of long-term isolation which, together with a very complex history, makes the genetic study of Indian populations challenging. We have combined a detailed, high-resolution mitogenome analysis with summaries of autosomal data and Y-chromosome lineages to establish a settlement chronology for the Indian Subcontinent. Maternal lineages document the earliest settlement ~55-65 ka (thousand years ago), and major population shifts in the later Pleistocene that explain previous dating discrepancies and neutrality violation. Whilst current genome-wide analyses conflate all dispersals from Southwest and Central Asia, we were able to tease out from the mitogenome data distinct dispersal episodes dating from between the Last Glacial Maximum to the Bronze Age. Moreover, we found an extremely marked sex bias by comparing the different genetic systems. Maternal lineages primarily reflect earlier, pre-Holocene processes, and paternal lineages predominantly episodes within the last 10 ka. In particular, genetic influx from Central Asia in the Bronze Age was strongly male-driven, consistent with the patriarchal, patrilocal and patrilineal social structure attributed to the inferred pastoralist early Indo-European society. This was part of a much wider process of Indo-European expansion, with an ultimate source in the Pontic-Caspian region, which carried closely related Y

Biometrics based key management of double random phase encoding scheme using error control codes

Science.gov (United States)

Saini, Nirmala; Sinha, Aloka

2013-08-01

In this paper, an optical security system has been proposed in which key of the double random phase encoding technique is linked to the biometrics of the user to make it user specific. The error in recognition due to the biometric variation is corrected by encoding the key using the BCH code. A user specific shuffling key is used to increase the separation between genuine and impostor Hamming distance distribution. This shuffling key is then further secured using the RSA public key encryption to enhance the security of the system. XOR operation is performed between the encoded key and the feature vector obtained from the biometrics. The RSA encoded shuffling key and the data obtained from the XOR operation are stored into a token. The main advantage of the present technique is that the key retrieval is possible only in the simultaneous presence of the token and the biometrics of the user which not only authenticates the presence of the original input but also secures the key of the system. Computational experiments showed the effectiveness of the proposed technique for key retrieval in the decryption process by using the live biometrics of the user.

Genetic analysis of body weights of individually fed beef bulls in South Africa using random regression models.

Science.gov (United States)

Selapa, N W; Nephawe, K A; Maiwashe, A; Norris, D

2012-02-08

The aim of this study was to estimate genetic parameters for body weights of individually fed beef bulls measured at centralized testing stations in South Africa using random regression models. Weekly body weights of Bonsmara bulls (N = 2919) tested between 1999 and 2003 were available for the analyses. The model included a fixed regression of the body weights on fourth-order orthogonal Legendre polynomials of the actual days on test (7, 14, 21, 28, 35, 42, 49, 56, 63, 70, 77, and 84) for starting age and contemporary group effects. Random regressions on fourth-order orthogonal Legendre polynomials of the actual days on test were included for additive genetic effects and additional uncorrelated random effects of the weaning-herd-year and the permanent environment of the animal. Residual effects were assumed to be independently distributed with heterogeneous variance for each test day. Variance ratios for additive genetic, permanent environment and weaning-herd-year for weekly body weights at different test days ranged from 0.26 to 0.29, 0.37 to 0.44 and 0.26 to 0.34, respectively. The weaning-herd-year was found to have a significant effect on the variation of body weights of bulls despite a 28-day adjustment period. Genetic correlations amongst body weights at different test days were high, ranging from 0.89 to 1.00. Heritability estimates were comparable to literature using multivariate models. Therefore, random regression model could be applied in the genetic evaluation of body weight of individually fed beef bulls in South Africa.

Cognitive Bias in Systems Verification

Science.gov (United States)

Larson, Steve

2012-01-01

Working definition of cognitive bias: Patterns by which information is sought and interpreted that can lead to systematic errors in decisions. Cognitive bias is used in diverse fields: Economics, Politics, Intelligence, Marketing, to name a few. Attempts to ground cognitive science in physical characteristics of the cognitive apparatus exceed our knowledge. Studies based on correlations; strict cause and effect is difficult to pinpoint. Effects cited in the paper and discussed here have been replicated many times over, and appear sound. Many biases have been described, but it is still unclear whether they are all distinct. There may only be a handful of fundamental biases, which manifest in various ways. Bias can effect system verification in many ways . Overconfidence -> Questionable decisions to deploy. Availability -> Inability to conceive critical tests. Representativeness -> Overinterpretation of results. Positive Test Strategies -> Confirmation bias. Debiasing at individual level very difficult. The potential effect of bias on the verification process can be managed, but not eliminated. Worth considering at key points in the process.

A Bayesian phylogenetic approach to estimating the stability of linguistic features and the genetic biasing of tone.

Science.gov (United States)

Dediu, Dan

2011-02-07

Language is a hallmark of our species and understanding linguistic diversity is an area of major interest. Genetic factors influencing the cultural transmission of language provide a powerful and elegant explanation for aspects of the present day linguistic diversity and a window into the emergence and evolution of language. In particular, it has recently been proposed that linguistic tone-the usage of voice pitch to convey lexical and grammatical meaning-is biased by two genes involved in brain growth and development, ASPM and Microcephalin. This hypothesis predicts that tone is a stable characteristic of language because of its 'genetic anchoring'. The present paper tests this prediction using a Bayesian phylogenetic framework applied to a large set of linguistic features and language families, using multiple software implementations, data codings, stability estimations, linguistic classifications and outgroup choices. The results of these different methods and datasets show a large agreement, suggesting that this approach produces reliable estimates of the stability of linguistic data. Moreover, linguistic tone is found to be stable across methods and datasets, providing suggestive support for the hypothesis of genetic influences on its distribution.

A Genetic Investigation of Sex Bias in the Prevalence of Attention-Deficit/Hyperactivity Disorder

DEFF Research Database (Denmark)

Martin, Joanna; Walters, Raymond K; Demontis, Ditte

2017-01-01

BACKGROUND: Attention-deficit/hyperactivity disorder (ADHD) shows substantial heritability and is two to seven times more common in male individuals than in female individuals. We examined two putative genetic mechanisms underlying this sex bias: sex-specific heterogeneity and higher burden of risk...... disorder and congenital malformations), potentially indicating some clinical and etiological heterogeneity. Polygenic risk score analysis did not support a higher burden of ADHD common risk variants in female cases (odds ratio [confidence interval] = 1.02 [0.98-1.06], p = .28). In contrast, epidemiological...... using two methods suggested near complete sharing of common variant effects across sexes, with rg estimates close to 1. Analyses of population data, however, indicated that female individuals with ADHD may be at especially high risk for certain comorbid developmental conditions (i.e., autism spectrum...

Genetic evaluation of European quails by random regression models

Directory of Open Access Journals (Sweden)

Flaviana Miranda Gonçalves

2012-09-01

Full Text Available The objective of this study was to compare different random regression models, defined from different classes of heterogeneity of variance combined with different Legendre polynomial orders for the estimate of (covariance of quails. The data came from 28,076 observations of 4,507 female meat quails of the LF1 lineage. Quail body weights were determined at birth and 1, 14, 21, 28, 35 and 42 days of age. Six different classes of residual variance were fitted to Legendre polynomial functions (orders ranging from 2 to 6 to determine which model had the best fit to describe the (covariance structures as a function of time. According to the evaluated criteria (AIC, BIC and LRT, the model with six classes of residual variances and of sixth-order Legendre polynomial was the best fit. The estimated additive genetic variance increased from birth to 28 days of age, and dropped slightly from 35 to 42 days. The heritability estimates decreased along the growth curve and changed from 0.51 (1 day to 0.16 (42 days. Animal genetic and permanent environmental correlation estimates between weights and age classes were always high and positive, except for birth weight. The sixth order Legendre polynomial, along with the residual variance divided into six classes was the best fit for the growth rate curve of meat quails; therefore, they should be considered for breeding evaluation processes by random regression models.

Assessing Risk of Bias in Randomized Controlled Trials for Autism Spectrum Disorder

Directory of Open Access Journals (Sweden)

Paola Matiko Martins Okuda

2017-11-01

Full Text Available AimTo determine construct validity and reliability indicators of the Cochrane risk of bias (RoB tool in the context of randomized clinical trials (RCTs for autism spectrum disorder (ASD.MethodsConfirmatory factor analysis was used to evaluate a unidimensional model consisting of 9 RoB categorical indicators evaluated across 94 RCTs addressing interventions for ASD.ResultsOnly five of the nine original RoB items returned good fit indices and so were retained in the analysis. Only one of this five had very high factor loadings. The remaining four indicators had more measurement error than common variance with the RoB latent factor. Together, the five indicators showed poor reliability (ω = 0.687; 95% CI: 0.613–0.761.ConclusionAlthough the Cochrane model of RoB for ASD exhibited good fit indices, the majorities of the items have more residual variance than common variance and, therefore, did not adequately capture the RoB in ASD intervention trials.

Biases in casino betting

Directory of Open Access Journals (Sweden)

James Sundali

2006-07-01

Full Text Available We examine two departures of individual perceptions of randomness from probability theory: the hot hand and the gambler's fallacy, and their respective opposites. This paper's first contribution is to use data from the field (individuals playing roulette in a casino to demonstrate the existence and impact of these biases that have been previously documented in the lab. Decisions in the field are consistent with biased beliefs, although we observe significant individual heterogeneity in the population. A second contribution is to separately identify these biases within a given individual, then to examine their within-person correlation. We find a positive and significant correlation across individuals between hot hand and gambler's fallacy biases, suggesting a common (root cause of the two related errors. We speculate as to the source of this correlation (locus of control, and suggest future research which could test this speculation.

Measuring Agricultural Bias

DEFF Research Database (Denmark)

Jensen, Henning Tarp; Robinson, Sherman; Tarp, Finn

The measurement issue is the key issue in the literature on trade policy-induced agri-cultural price incentive bias. This paper introduces a general equilibrium effective rate of protection (GE-ERP) measure, which extends and generalizes earlier partial equilibrium nominal protection measures...... shares and intersectoral linkages - are crucial for determining the sign and magnitude of trade policy bias. The GE-ERP measure is therefore uniquely suited to capture the full impact of trade policies on agricultural price incentives. A Monte Carlo procedure confirms that the results are robust....... For the 15 sample countries, the results indicate that the agricultural price incentive bias, which was generally perceived to exist during the 1980s, was largely eliminated during the 1990s. The results also demonstrate that general equilibrium effects and country-specific characteristics - including trade...

Mendelian Randomization Study of Body Mass Index and Colorectal Cancer Risk

DEFF Research Database (Denmark)

Thrift, Aaron P.; Gong, Jian; Peters, Ulrike

2015-01-01

Background: High body mass index (BMI) is consistently linked to increased risk of colorectal cancer for men, whereas the association is less clear for women. As risk estimates from observational studies may be biased and/or confounded, we conducted a Mendelian randomization study to estimate...... the causal association between BMI and colorectal cancer. Methods: We used data from 10,226 colorectal cancer cases and 10,286 controls of European ancestry. The Mendelian randomization analysis used a weighted genetic risk score, derived from 77 genome-wide association study–identified variants associated......, rather than overall obesity, is a more important risk factor for men requires further investigation. Impact: Overall, conventional epidemiologic and Mendelian randomization studies suggest a strong association between obesity and the risk of colorectal cancer....

Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas?

Science.gov (United States)

Brooks, T M; Cuttelod, A; Faith, D P; Garcia-Moreno, J; Langhammer, P; Pérez-Espona, S

2015-02-19

'Key biodiversity areas' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl. 4, 326-337. (doi:10.1111/j.1752-4571.2010.00157.x)) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site's share of a threatened species' population; expand these to include the proportion of the species' genetic diversity unique to a site; (ii) expand criterion for 'threatened species' to consider 'threatened taxa' and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites.

Genetic parameters for body condition score, body weight, milk yield, and fertility estimated using random regression models.

Science.gov (United States)

Berry, D P; Buckley, F; Dillon, P; Evans, R D; Rath, M; Veerkamp, R F

2003-11-01

Genetic (co)variances between body condition score (BCS), body weight (BW), milk yield, and fertility were estimated using a random regression animal model extended to multivariate analysis. The data analyzed included 81,313 BCS observations, 91,937 BW observations, and 100,458 milk test-day yields from 8725 multiparous Holstein-Friesian cows. A cubic random regression was sufficient to model the changing genetic variances for BCS, BW, and milk across different days in milk. The genetic correlations between BCS and fertility changed little over the lactation; genetic correlations between BCS and interval to first service and between BCS and pregnancy rate to first service varied from -0.47 to -0.31, and from 0.15 to 0.38, respectively. This suggests that maximum genetic gain in fertility from indirect selection on BCS should be based on measurements taken in midlactation when the genetic variance for BCS is largest. Selection for increased BW resulted in shorter intervals to first service, but more services and poorer pregnancy rates; genetic correlations between BW and pregnancy rate to first service varied from -0.52 to -0.45. Genetic selection for higher lactation milk yield alone through selection on increased milk yield in early lactation is likely to have a more deleterious effect on genetic merit for fertility than selection on higher milk yield in late lactation.

Randomized dynamical decoupling strategies and improved one-way key rates for quantum cryptography

Energy Technology Data Exchange (ETDEWEB)

Kern, Oliver

2009-05-25

The present thesis deals with various methods of quantum error correction. It is divided into two parts. In the first part, dynamical decoupling methods are considered which have the task of suppressing the influence of residual imperfections in a quantum memory. Such imperfections might be given by couplings between the finite dimensional quantum systems (qudits) constituting the quantum memory, for instance. The suppression is achieved by altering the dynamics of an imperfect quantum memory with the help of a sequence of local unitary operations applied to the qudits. Whereas up to now the operations of such decoupling sequences have been constructed in a deterministic fashion, strategies are developed in this thesis which construct the operations by random selection from a suitable set. Formulas are derived which estimate the average performance of such strategies. As it turns out, randomized decoupling strategies offer advantages and disadvantages over deterministic ones. It is possible to benefit from the advantages of both kind of strategies by designing combined strategies. Furthermore, it is investigated if and how the discussed decoupling strategies can be employed to protect a quantum computation running on the quantum memory. It is shown that a purely randomized decoupling strategy may be used by applying the decoupling operations and adjusted gates of the quantum algorithm in an alternating fashion. Again this method can be enhanced by the means of deterministic methods in order to obtain a combined decoupling method for quantum computations analogously to the combining strategies for quantum memories. The second part of the thesis deals with quantum error-correcting codes and protocols for quantum key distribution. The focus is on the BB84 and the 6-state protocol making use of only one-way communication during the error correction and privacy amplification steps. It is shown that by adding additional errors to the preliminary key (a process called

Randomized dynamical decoupling strategies and improved one-way key rates for quantum cryptography

International Nuclear Information System (INIS)

Kern, Oliver

2009-01-01

The present thesis deals with various methods of quantum error correction. It is divided into two parts. In the first part, dynamical decoupling methods are considered which have the task of suppressing the influence of residual imperfections in a quantum memory. Such imperfections might be given by couplings between the finite dimensional quantum systems (qudits) constituting the quantum memory, for instance. The suppression is achieved by altering the dynamics of an imperfect quantum memory with the help of a sequence of local unitary operations applied to the qudits. Whereas up to now the operations of such decoupling sequences have been constructed in a deterministic fashion, strategies are developed in this thesis which construct the operations by random selection from a suitable set. Formulas are derived which estimate the average performance of such strategies. As it turns out, randomized decoupling strategies offer advantages and disadvantages over deterministic ones. It is possible to benefit from the advantages of both kind of strategies by designing combined strategies. Furthermore, it is investigated if and how the discussed decoupling strategies can be employed to protect a quantum computation running on the quantum memory. It is shown that a purely randomized decoupling strategy may be used by applying the decoupling operations and adjusted gates of the quantum algorithm in an alternating fashion. Again this method can be enhanced by the means of deterministic methods in order to obtain a combined decoupling method for quantum computations analogously to the combining strategies for quantum memories. The second part of the thesis deals with quantum error-correcting codes and protocols for quantum key distribution. The focus is on the BB84 and the 6-state protocol making use of only one-way communication during the error correction and privacy amplification steps. It is shown that by adding additional errors to the preliminary key (a process called

Domain-size-dependent exchange bias in Co/LaFeO3

Energy Technology Data Exchange (ETDEWEB)

Scholl, A.; Nolting, F.; Seo, J.W.; Ohldag, H.; Stohr, J.; Raoux,S.; Locquet, J.-P.; Fompeyrine, J.

2004-09-22

X-ray microscopy using magnetic linear dichroism of a zero-field-grown, multi-domain Co/LaFeO{sub 3} ferromagnet/antiferromagnet sample shows a local exchange bias of random direction and magnitude. A statistical analysis of the local bias of individual, micron-size magnetic domains demonstrates an increasing bias field with decreasing domain size as expected for a random distribution of pinned, uncompensated spins, which are believed to mediate the interface coupling. A linear dependence with the inverse domain diameter is found.

Genetic correlations between body condition scores and fertility in dairy cattle using bivariate random regression models.

Science.gov (United States)

De Haas, Y; Janss, L L G; Kadarmideen, H N

2007-10-01

Genetic correlations between body condition score (BCS) and fertility traits in dairy cattle were estimated using bivariate random regression models. BCS was recorded by the Swiss Holstein Association on 22,075 lactating heifers (primiparous cows) from 856 sires. Fertility data during first lactation were extracted for 40,736 cows. The fertility traits were days to first service (DFS), days between first and last insemination (DFLI), calving interval (CI), number of services per conception (NSPC) and conception rate to first insemination (CRFI). A bivariate model was used to estimate genetic correlations between BCS as a longitudinal trait by random regression components, and daughter's fertility at the sire level as a single lactation measurement. Heritability of BCS was 0.17, and heritabilities for fertility traits were low (0.01-0.08). Genetic correlations between BCS and fertility over the lactation varied from: -0.45 to -0.14 for DFS; -0.75 to 0.03 for DFLI; from -0.59 to -0.02 for CI; from -0.47 to 0.33 for NSPC and from 0.08 to 0.82 for CRFI. These results show (genetic) interactions between fat reserves and reproduction along the lactation trajectory of modern dairy cows, which can be useful in genetic selection as well as in management. Maximum genetic gain in fertility from indirect selection on BCS should be based on measurements taken in mid lactation when the genetic variance for BCS is largest, and the genetic correlations between BCS and fertility is strongest.

Genetic diversity among four Eucalyptus species (myrtaceae) based ...

African Journals Online (AJOL)

The results indicate that 16 positive and 13 negative markers were detected. The marker fragments size ranged between 175 to 630 bp for the negative markers and 235 to 945 bp for the positive markers. Key words: Eucalyptus, random amplified polymorphic DNA (RAPD), genetic diversity, DNA fingerprinting PCR, ...

The bias of weighted dark matter halos from peak theory

CERN Document Server

Verde, Licia; Simpson, Fergus; Alvarez-Gaume, Luis; Heavens, Alan; Matarrese, Sabino

2014-01-01

We give an analytical form for the weighted correlation function of peaks in a Gaussian random field. In a cosmological context, this approach strictly describes the formation bias and is the main result here. Nevertheless, we show its validity and applicability to the evolved cosmological density field and halo field, using Gaussian random field realisations and dark matter N-body numerical simulations. Using this result from peak theory we compute the bias of peaks (and dark matter halos) and show that it reproduces results from the simulations at the ${\\mathcal O}(10\\%)$ level. Our analytical formula for the bias predicts a scale-dependent bias with two characteristics: a broad band shape which, however, is most affected by the choice of weighting scheme and evolution bias, and a more robust, narrow feature localised at the BAO scale, an effect that is confirmed in simulations. This scale-dependent bias smooths the BAO feature but, conveniently, does not move it. We provide a simple analytic formula to des...

Bias due to two-stage residual-outcome regression analysis in genetic association studies.

Science.gov (United States)

Demissie, Serkalem; Cupples, L Adrienne

2011-11-01

Association studies of risk factors and complex diseases require careful assessment of potential confounding factors. Two-stage regression analysis, sometimes referred to as residual- or adjusted-outcome analysis, has been increasingly used in association studies of single nucleotide polymorphisms (SNPs) and quantitative traits. In this analysis, first, a residual-outcome is calculated from a regression of the outcome variable on covariates and then the relationship between the adjusted-outcome and the SNP is evaluated by a simple linear regression of the adjusted-outcome on the SNP. In this article, we examine the performance of this two-stage analysis as compared with multiple linear regression (MLR) analysis. Our findings show that when a SNP and a covariate are correlated, the two-stage approach results in biased genotypic effect and loss of power. Bias is always toward the null and increases with the squared-correlation between the SNP and the covariate (). For example, for , 0.1, and 0.5, two-stage analysis results in, respectively, 0, 10, and 50% attenuation in the SNP effect. As expected, MLR was always unbiased. Since individual SNPs often show little or no correlation with covariates, a two-stage analysis is expected to perform as well as MLR in many genetic studies; however, it produces considerably different results from MLR and may lead to incorrect conclusions when independent variables are highly correlated. While a useful alternative to MLR under , the two -stage approach has serious limitations. Its use as a simple substitute for MLR should be avoided. © 2011 Wiley Periodicals, Inc.

Impact of Selection Bias on Estimation of Subsequent Event Risk

NARCIS (Netherlands)

Hu, Yi Juan; Schmidt, Amand F.; Dudbridge, Frank; Holmes, Michael V; Brophy, James M.; Tragante, Vinicius; Li, Ziyi; Liao, Peizhou; Quyyumi, Arshed A.; McCubrey, Raymond O.; Horne, Benjamin D.; Hingorani, Aroon D; Asselbergs, Folkert W; Patel, Riyaz S.; Long, Qi; Åkerblom, Axel; Algra, Ale; Allayee, Hooman; Almgren, Peter; Anderson, Jeffrey L.; Andreassi, Maria G.; Anselmi, Chiara V.; Ardissino, Diego; Arsenault, Benoit J.; Ballantyne, Christie M.; Baranova, Ekaterina V.; Behloui, Hassan; Bergmeijer, Thomas O; Bezzina, Connie R; Bjornsson, Eythor; Body, Simon C.; Boeckx, Bram; Boersma, Eric H.; Boerwinkle, Eric; Bogaty, Peter; Braund, Peter S; Breitling, Lutz P.; Brenner, Hermann; Briguori, Carlo; Brugts, Jasper J.; Burkhardt, Ralph; Cameron, Vicky A.; Carlquist, John F.; Carpeggiani, Clara; Carruthers, Kathryn F.; Casu, Gavino; Condorelli, Gianluigi; Cresci, Sharon; Danchin, Nicolas; de Faire, Ulf; Deanfield, John; Delgado, Graciela; Deloukas, Panos; Direk, Kenan; Doughty, Robert N.; Drexel, Heinz; Duarte, Nubia E.; Dubé, Marie Pierre; Dufresne, Line; Engert, James C; Eriksson, Niclas; Fitzpatrick, Natalie; Foco, Luisa; Ford, Ian; Fox, Keith A; Gigante, Bruna; Gijsberts, Crystel M.; Girelli, Domenico; Gong, Yan; Gudbjartsson, Daniel F.; Hagström, Emil; Hartiala, Jaana; Hazen, Stanley L.; Held, Claes; Helgadottir, Anna; Hemingway, Harry; Heydarpour, Mahyar; Hoefer, Imo E.; Hovingh, G. Kees; Hubacek, Jaroslav A; James, Stefan; Johnson, Julie A; Jukema, J Wouter; Kaczor, Marcin P.; Kaminski, Karol A.; Kettner, Jiri; Kiliszek, Marek; Kleber, Marcus; Klungel, Olaf H.; Kofink, Daniel; Kohonen, Mika; Kotti, Salma; Kuukasjärvi, Pekka; Lagerqvist, Bo; Lambrechts, Diether; Lang, Chim C; Laurikka, Jari O.; Leander, Karin; Lee, Vei Vei; Lehtimäki, Terho; Leiherer, Andreas; Lenzini, Petra A.; Levin, Daniel; Lindholm, Daniel; Lokki, Marja-Liisa; Lotufo, Paulo A; Lyytikäinen, Leo-Pekka; Mahmoodi, B. Khan; Maitland-Van Der Zee, Anke H.; Martinelli, Nicola; März, Winfried; Marziliano, Nicola; McPherson, Ruth; Melander, Olle; Mons, Ute; Muehlschlegel, Jochen D.; Muhlestein, Joseph B.; Nelson, Cristopher P.; Cheh, Chris Newton; Olivieri, Oliviero; Opolski, Grzegorz; Palmer, Colin Na; Pare, Guillaume; Pasterkamp, Gerard; Pepine, Carl J; Pepinski, Witold; Pereira, Alexandre C.; Pilbrow, Anna P.; Pilote, Louise; Pitha, Jan; Ploski, Rafal; Richards, A. Mark; Saely, Christoph H.; Samani, Nilesh J; Samman-Tahhan, Ayman; Sanak, Marek; Sandesara, Pratik B.; Sattar, Naveed; Scholz, Markus; Siegbahn, Agneta; Simon, Tabassome; Sinisalo, Juha; Smith, J. Gustav; Spertus, John A.; Stefansson, Kari; Stewart, Alexandre F R; Stott, David J.; Szczeklik, Wojciech; Szpakowicz, Anna; Tanck, Michael W.T.; Tang, Wilson H.; Tardif, Jean-Claude; Ten Berg, Jur M.; Teren, Andrej; Thanassoulis, George; Thiery, Joachim; Thorgeirsson, Gudmundur; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Timmis, Adam; Trompet, Stella; Van de Werf, Frans; van der Graaf, Yolanda; Van Der Haarst, Pim; van der Laan, Sander W; Vilmundarson, Ragnar O.; Virani, Salim S.; Visseren, Frank L J; Vlachopoulou, Efthymia; Wallentin, Lars; Waltenberger, Johannes; Wauters, Els; Wilde, Arthur A M

2017-01-01

Background - Studies of recurrent or subsequent disease events may be susceptible to bias caused by selection of subjects who both experience and survive the primary indexing event. Currently, the magnitude of any selection bias, particularly for subsequent time-to-event analysis in genetic

Possible End to an Endless Quest? Cognitive Bias Modification for Excessive Multiplayer Online Gamers.

Science.gov (United States)

Rabinovitz, Sharon; Nagar, Maayan

2015-10-01

Cognitive biases have previously been recognized as key mechanisms that contribute to the development, maintenance, and relapse of addictive behaviors. The same mechanisms have been recently found in problematic computer gaming. The present study aims to investigate whether excessive massively multiplayer online role-playing gamers (EG) demonstrate an approach bias toward game-related cues compared to neutral stimuli; to test whether these automatic action tendencies can be implicitly modified in a single session training; and to test whether this training affects game urges and game-seeking behavior. EG (n=38) were randomly assigned to a condition in which they were implicitly trained to avoid or to approach gaming cues by pushing or pulling a joystick, using a computerized intervention (cognitive bias modification via the Approach Avoidance Task). EG demonstrated an approach bias for gaming cues compared with neutral, movie cues. Single session training significantly decreased automatic action tendencies to approach gaming cues. These effects occurred outside subjective awareness. Furthermore, approach bias retraining reduced subjective urges and intentions to play, as well as decreased game-seeking behavior. Retraining automatic processes may be beneficial in changing addictive impulses in EG. Yet, large-scale trials and long-term follow-up are warranted. The results extend the application of cognitive bias modification from substance use disorders to behavioral addictions, and specifically to Internet gaming disorder. Theoretical implications are discussed.

Clinical effectiveness of attentional bias modification training in abstinent alcoholic patients

NARCIS (Netherlands)

Schoenmakers, T.M.; Bruin, de M.; Lux, I.F.M.; Goertz, A.G.; Kerkhof, van D.H.A.T.; Wiers, R.W.

2010-01-01

A new training to decrease attentional bias (attentional bias modification training, ABM) was tested in a randomized controlled experimental study with alcohol-dependent patients as an addition to cognitive behavioral therapy. In alcohol dependence, attentional bias has been associated with severity

Genetic analyses of partial egg production in Japanese quail using multi-trait random regression models.

Science.gov (United States)

Karami, K; Zerehdaran, S; Barzanooni, B; Lotfi, E

2017-12-01

1. The aim of the present study was to estimate genetic parameters for average egg weight (EW) and egg number (EN) at different ages in Japanese quail using multi-trait random regression (MTRR) models. 2. A total of 8534 records from 900 quail, hatched between 2014 and 2015, were used in the study. Average weekly egg weights and egg numbers were measured from second until sixth week of egg production. 3. Nine random regression models were compared to identify the best order of the Legendre polynomials (LP). The most optimal model was identified by the Bayesian Information Criterion. A model with second order of LP for fixed effects, second order of LP for additive genetic effects and third order of LP for permanent environmental effects (MTRR23) was found to be the best. 4. According to the MTRR23 model, direct heritability for EW increased from 0.26 in the second week to 0.53 in the sixth week of egg production, whereas the ratio of permanent environment to phenotypic variance decreased from 0.48 to 0.1. Direct heritability for EN was low, whereas the ratio of permanent environment to phenotypic variance decreased from 0.57 to 0.15 during the production period. 5. For each trait, estimated genetic correlations among weeks of egg production were high (from 0.85 to 0.98). Genetic correlations between EW and EN were low and negative for the first two weeks, but they were low and positive for the rest of the egg production period. 6. In conclusion, random regression models can be used effectively for analysing egg production traits in Japanese quail. Response to selection for increased egg weight would be higher at older ages because of its higher heritability and such a breeding program would have no negative genetic impact on egg production.

Genetic correlations among body condition score, yield and fertility in multiparous cows using random regression models

OpenAIRE

Bastin, Catherine; Gillon, Alain; Massart, Xavier; Bertozzi, Carlo; Vanderick, Sylvie; Gengler, Nicolas

2010-01-01

Genetic correlations between body condition score (BCS) in lactation 1 to 3 and four economically important traits (days open, 305-days milk, fat, and protein yields recorded in the first 3 lactations) were estimated on about 12,500 Walloon Holstein cows using 4-trait random regression models. Results indicated moderate favorable genetic correlations between BCS and days open (from -0.46 to -0.62) and suggested the use of BCS for indirect selection on fertility. However, unfavorable genetic c...

Estimating low-bias frequency response using random decrement

DEFF Research Database (Denmark)

Brincker, Rune; Brandt, Anders

2011-01-01

It is well known that in order to minimize the influence of leakage bias in frequency response function (FRF) estimates, smooth windows should be applied in the FFT processing. It is also normal practice to use self windowing excitation signals whenever possible. However, in many cases FRFs have...

Efficient bias correction for magnetic resonance image denoising.

Science.gov (United States)

Mukherjee, Partha Sarathi; Qiu, Peihua

2013-05-30

Magnetic resonance imaging (MRI) is a popular radiology technique that is used for visualizing detailed internal structure of the body. Observed MRI images are generated by the inverse Fourier transformation from received frequency signals of a magnetic resonance scanner system. Previous research has demonstrated that random noise involved in the observed MRI images can be described adequately by the so-called Rician noise model. Under that model, the observed image intensity at a given pixel is a nonlinear function of the true image intensity and of two independent zero-mean random variables with the same normal distribution. Because of such a complicated noise structure in the observed MRI images, denoised images by conventional denoising methods are usually biased, and the bias could reduce image contrast and negatively affect subsequent image analysis. Therefore, it is important to address the bias issue properly. To this end, several bias-correction procedures have been proposed in the literature. In this paper, we study the Rician noise model and the corresponding bias-correction problem systematically and propose a new and more effective bias-correction formula based on the regression analysis and Monte Carlo simulation. Numerical studies show that our proposed method works well in various applications. Copyright © 2012 John Wiley & Sons, Ltd.

Variable-bias coin tossing

International Nuclear Information System (INIS)

Colbeck, Roger; Kent, Adrian

2006-01-01

Alice is a charismatic quantum cryptographer who believes her parties are unmissable; Bob is a (relatively) glamorous string theorist who believes he is an indispensable guest. To prevent possibly traumatic collisions of self-perception and reality, their social code requires that decisions about invitation or acceptance be made via a cryptographically secure variable-bias coin toss (VBCT). This generates a shared random bit by the toss of a coin whose bias is secretly chosen, within a stipulated range, by one of the parties; the other party learns only the random bit. Thus one party can secretly influence the outcome, while both can save face by blaming any negative decisions on bad luck. We describe here some cryptographic VBCT protocols whose security is guaranteed by quantum theory and the impossibility of superluminal signaling, setting our results in the context of a general discussion of secure two-party computation. We also briefly discuss other cryptographic applications of VBCT

Variable-bias coin tossing

Science.gov (United States)

Colbeck, Roger; Kent, Adrian

2006-03-01

Alice is a charismatic quantum cryptographer who believes her parties are unmissable; Bob is a (relatively) glamorous string theorist who believes he is an indispensable guest. To prevent possibly traumatic collisions of self-perception and reality, their social code requires that decisions about invitation or acceptance be made via a cryptographically secure variable-bias coin toss (VBCT). This generates a shared random bit by the toss of a coin whose bias is secretly chosen, within a stipulated range, by one of the parties; the other party learns only the random bit. Thus one party can secretly influence the outcome, while both can save face by blaming any negative decisions on bad luck. We describe here some cryptographic VBCT protocols whose security is guaranteed by quantum theory and the impossibility of superluminal signaling, setting our results in the context of a general discussion of secure two-party computation. We also briefly discuss other cryptographic applications of VBCT.

Characteristics, causes and evolutionary consequences of male-biased mutation.

Science.gov (United States)

Ellegren, Hans

2007-01-07

Mutation has traditionally been considered a random process, but this paradigm is challenged by recent evidence of divergence rate heterogeneity in different genomic regions. One facet of mutation rate variation is the propensity for genetic change to correlate with the number of germ cell divisions, reflecting the replication-dependent origin of many mutations. Haldane was the first to connect this association of replication and mutation to the difference in the number of cell divisions in oogenesis (low) and spermatogenesis (usually high), and the resulting sex difference in the rate of mutation. The concept of male-biased mutation has been thoroughly analysed in recent years using an evolutionary approach, in which sequence divergence of autosomes and/or sex chromosomes are compared to allow inference about the relative contribution of mothers and fathers in the accumulation of mutations. For instance, assuming that a neutral sequence is analysed, that rate heterogeneity owing to other factors is cancelled out by the investigation of many loci and that the effect of ancestral polymorphism is properly taken into account, the male-to-female mutation rate ratio, alpham, can be solved from the observed difference in rate of X and Y chromosome divergence. The male mutation bias is positively correlated with the relative excess of cell divisions in the male compared to the female germ line, as evidenced by a generation time effect: in mammals, alpham is estimated at approximately 4-6 in primates, approximately 3 in carnivores and approximately 2 in small rodents. Another life-history correlate is sexual selection: when there is intense sperm competition among males, increased sperm production will be associated with a larger number of mitotic cell divisions in spermatogenesis and hence an increase in alpham. Male-biased mutation has implications for important aspects of evolutionary biology such as mate choice in relation to mutation load, sexual selection and the

ROBINS-I: a tool for assessing risk of bias in non-randomised studies of interventions

OpenAIRE

Sterne, Jonathan AC; Hern?n, Miguel A; Reeves, Barnaby C; Savovi?, Jelena; Berkman, Nancy D; Viswanathan, Meera; Henry, David; Altman, Douglas G; Ansari, Mohammed T; Boutron, Isabelle; Carpenter, James R; Chan, An-Wen; Churchill, Rachel; Deeks, Jonathan J; Hr?bjartsson, Asbj?rn

2016-01-01

Non-randomized studies of the effects of interventions are critical to many areas of health care evaluation, but their results may be biased. It is therefore important to understand and appraise their strengths and weaknesses. We developed ROBINS-I (“Risk Of Bias In Non-randomized Studies - of Interventions”), a new tool for evaluating risk of bias in estimates of the comparative effectiveness (harm or benefit) of interventions from studies that did not use randomization to allocate units (in...

Editorial Bias in Crowd-Sourced Political Information.

Directory of Open Access Journals (Sweden)

Joshua L Kalla

Full Text Available The Internet has dramatically expanded citizens' access to and ability to engage with political information. On many websites, any user can contribute and edit "crowd-sourced" information about important political figures. One of the most prominent examples of crowd-sourced information on the Internet is Wikipedia, a free and open encyclopedia created and edited entirely by users, and one of the world's most accessed websites. While previous studies of crowd-sourced information platforms have found them to be accurate, few have considered biases in what kinds of information are included. We report the results of four randomized field experiments that sought to explore what biases exist in the political articles of this collaborative website. By randomly assigning factually true but either positive or negative and cited or uncited information to the Wikipedia pages of U.S. senators, we uncover substantial evidence of an editorial bias toward positivity on Wikipedia: Negative facts are 36% more likely to be removed by Wikipedia editors than positive facts within 12 hours and 29% more likely within 3 days. Although citations substantially increase an edit's survival time, the editorial bias toward positivity is not eliminated by inclusion of a citation. We replicate this study on the Wikipedia pages of deceased as well as recently retired but living senators and find no evidence of an editorial bias in either. Our results demonstrate that crowd-sourced information is subject to an editorial bias that favors the politically active.

Editorial Bias in Crowd-Sourced Political Information.

Science.gov (United States)

Kalla, Joshua L; Aronow, Peter M

2015-01-01

The Internet has dramatically expanded citizens' access to and ability to engage with political information. On many websites, any user can contribute and edit "crowd-sourced" information about important political figures. One of the most prominent examples of crowd-sourced information on the Internet is Wikipedia, a free and open encyclopedia created and edited entirely by users, and one of the world's most accessed websites. While previous studies of crowd-sourced information platforms have found them to be accurate, few have considered biases in what kinds of information are included. We report the results of four randomized field experiments that sought to explore what biases exist in the political articles of this collaborative website. By randomly assigning factually true but either positive or negative and cited or uncited information to the Wikipedia pages of U.S. senators, we uncover substantial evidence of an editorial bias toward positivity on Wikipedia: Negative facts are 36% more likely to be removed by Wikipedia editors than positive facts within 12 hours and 29% more likely within 3 days. Although citations substantially increase an edit's survival time, the editorial bias toward positivity is not eliminated by inclusion of a citation. We replicate this study on the Wikipedia pages of deceased as well as recently retired but living senators and find no evidence of an editorial bias in either. Our results demonstrate that crowd-sourced information is subject to an editorial bias that favors the politically active.

Genetic parameters for residual feed intake in a random population of Pekin duck

Directory of Open Access Journals (Sweden)

Yunsheng Zhang

2017-02-01

Full Text Available Objective The feed intake (FI and feed efficiency are economically important traits in ducks. To obtain insight into this economically important trait, we designed an experiment based on the residual feed intake (RFI and feed conversion ratio (FCR of a random population Pekin duck. Methods Two thousand and twenty pedigreed random population Pekin ducks were established from 90 males mated to 450 females in two hatches. Traits analyzed in the study were body weight at the 42th day (BW42, 15 to 42 days average daily gain (ADG, 15 to 42 days FI, 15 to 42 days FCR, and 15 to 42 days RFI to assess their genetic inter-relationships. The genetic parameters for feed efficiency traits were estimated using restricted maximum likelihood (REML methodology applied to a sire-dam model for all traits using the ASREML software. Results Estimates heritability of BW42, ADG, FI, FCR, and RFI were 0.39, 0.38, 0.33, 0.38, and 0.41, respectively. The genetic correlation was high between RFI and FI (0.77 and moderate between RFI and FCR (0.54. The genetic correlation was high and moderate between FCR and ADG (−0.80, and between FCR and BW42 (−0.64, and between FCR and FI (0.49, respectively. Conclusion Thus, selection on RFI was expected to improve feed efficiency, and reduce FI. Selection on RFI thus improves the feed efficiency of animals without impairing their FI and increase growth rate.

Examining the impact of genetic testing for type 2 diabetes on health behaviors: study protocol for a randomized controlled trial

Directory of Open Access Journals (Sweden)

Voils Corrine I

2012-08-01

Full Text Available Abstract Background We describe the study design, procedures, and development of the risk counseling protocol used in a randomized controlled trial to evaluate the impact of genetic testing for diabetes mellitus (DM on psychological, health behavior, and clinical outcomes. Methods/Design Eligible patients are aged 21 to 65 years with body mass index (BMI ≥27 kg/m2 and no prior diagnosis of DM. At baseline, conventional DM risk factors are assessed, and blood is drawn for possible genetic testing. Participants are randomized to receive conventional risk counseling for DM with eye disease counseling or with genetic test results. The counseling protocol was pilot tested to identify an acceptable graphical format for conveying risk estimates and match the length of the eye disease to genetic counseling. Risk estimates are presented with a vertical bar graph denoting risk level with colors and descriptors. After receiving either genetic counseling regarding risk for DM or control counseling on eye disease, brief lifestyle counseling for prevention of DM is provided to all participants. Discussion A standardized risk counseling protocol is being used in a randomized trial of 600 participants. Results of this trial will inform policy about whether risk counseling should include genetic counseling. Trial registration ClinicalTrials.gov Identifier NCT01060540

Efficient algorithms for extracting biological key pathways with global constraints

DEFF Research Database (Denmark)

Baumbach, Jan; Friedrich, T.; Kötzing, T.

2012-01-01

The integrated analysis of data of different types and with various interdependencies is one of the major challenges in computational biology. Recently, we developed KeyPathwayMiner, a method that combines biological networks modeled as graphs with disease-specific genetic expression data gained....... Here we present an alternative approach that avoids a certain bias towards hub nodes: We now aim for extracting all maximal connected sub-networks where all but at most K nodes are expressed in all cases but in total (!) at most L, i.e. accumulated over all cases and all nodes in a solution. We call...... this strategy GLONE (global node exceptions); the previous problem we call INES (individual node exceptions). Since finding GLONE-components is computationally hard, we developed an Ant Colony Optimization algorithm and implemented it with the KeyPathwayMiner Cytoscape framework as an alternative to the INES...

The cosmic microwave background radiation power spectrum as a random bit generator for symmetric- and asymmetric-key cryptography.

Science.gov (United States)

Lee, Jeffrey S; Cleaver, Gerald B

2017-10-01

In this note, the Cosmic Microwave Background (CMB) Radiation is shown to be capable of functioning as a Random Bit Generator, and constitutes an effectively infinite supply of truly random one-time pad values of arbitrary length. It is further argued that the CMB power spectrum potentially conforms to the FIPS 140-2 standard. Additionally, its applicability to the generation of a (n × n) random key matrix for a Vernam cipher is established.

Ascertainment biases in SNP chips affect measures of population divergence

DEFF Research Database (Denmark)

Albrechtsen, Anders; Nielsen, Finn Cilius; Nielsen, Rasmus

2010-01-01

Chip-based high-throughput genotyping has facilitated genome-wide studies of genetic diversity. Many studies have utilized these large data sets to make inferences about the demographic history of human populations using measures of genetic differentiation such as F(ST) or principal component...... on direct sequencing. In addition, we also analyze publicly available genome-wide data. We demonstrate that the ascertainment biases will distort measures of human diversity and possibly change conclusions drawn from these measures in some times unexpected ways. We also show that details of the genotyping...... analyses. However, the single nucleotide polymorphism (SNP) chip data suffer from ascertainment biases caused by the SNP discovery process in which a small number of individuals from selected populations are used as discovery panels. In this study, we investigate the effect of the ascertainment bias...

Large-scale galaxy bias

Science.gov (United States)

Desjacques, Vincent; Jeong, Donghui; Schmidt, Fabian

2018-02-01

This review presents a comprehensive overview of galaxy bias, that is, the statistical relation between the distribution of galaxies and matter. We focus on large scales where cosmic density fields are quasi-linear. On these scales, the clustering of galaxies can be described by a perturbative bias expansion, and the complicated physics of galaxy formation is absorbed by a finite set of coefficients of the expansion, called bias parameters. The review begins with a detailed derivation of this very important result, which forms the basis of the rigorous perturbative description of galaxy clustering, under the assumptions of General Relativity and Gaussian, adiabatic initial conditions. Key components of the bias expansion are all leading local gravitational observables, which include the matter density but also tidal fields and their time derivatives. We hence expand the definition of local bias to encompass all these contributions. This derivation is followed by a presentation of the peak-background split in its general form, which elucidates the physical meaning of the bias parameters, and a detailed description of the connection between bias parameters and galaxy statistics. We then review the excursion-set formalism and peak theory which provide predictions for the values of the bias parameters. In the remainder of the review, we consider the generalizations of galaxy bias required in the presence of various types of cosmological physics that go beyond pressureless matter with adiabatic, Gaussian initial conditions: primordial non-Gaussianity, massive neutrinos, baryon-CDM isocurvature perturbations, dark energy, and modified gravity. Finally, we discuss how the description of galaxy bias in the galaxies' rest frame is related to clustering statistics measured from the observed angular positions and redshifts in actual galaxy catalogs.

Bias, Confounding, and Interaction: Lions and Tigers, and Bears, Oh My!

Science.gov (United States)

Vetter, Thomas R; Mascha, Edward J

2017-09-01

Epidemiologists seek to make a valid inference about the causal effect between an exposure and a disease in a specific population, using representative sample data from a specific population. Clinical researchers likewise seek to make a valid inference about the association between an intervention and outcome(s) in a specific population, based upon their randomly collected, representative sample data. Both do so by using the available data about the sample variable to make a valid estimate about its corresponding or underlying, but unknown population parameter. Random error in an experiment can be due to the natural, periodic fluctuation or variation in the accuracy or precision of virtually any data sampling technique or health measurement tool or scale. In a clinical research study, random error can be due to not only innate human variability but also purely chance. Systematic error in an experiment arises from an innate flaw in the data sampling technique or measurement instrument. In the clinical research setting, systematic error is more commonly referred to as systematic bias. The most commonly encountered types of bias in anesthesia, perioperative, critical care, and pain medicine research include recall bias, observational bias (Hawthorne effect), attrition bias, misclassification or informational bias, and selection bias. A confounding variable is a factor associated with both the exposure of interest and the outcome of interest. A confounding variable (confounding factor or confounder) is a variable that correlates (positively or negatively) with both the exposure and outcome. Confounding is typically not an issue in a randomized trial because the randomized groups are sufficiently balanced on all potential confounding variables, both observed and nonobserved. However, confounding can be a major problem with any observational (nonrandomized) study. Ignoring confounding in an observational study will often result in a "distorted" or incorrect estimate of

Fault diagnosis in spur gears based on genetic algorithm and random forest

Science.gov (United States)

Cerrada, Mariela; Zurita, Grover; Cabrera, Diego; Sánchez, René-Vinicio; Artés, Mariano; Li, Chuan

2016-03-01

There are growing demands for condition-based monitoring of gearboxes, and therefore new methods to improve the reliability, effectiveness, accuracy of the gear fault detection ought to be evaluated. Feature selection is still an important aspect in machine learning-based diagnosis in order to reach good performance of the diagnostic models. On the other hand, random forest classifiers are suitable models in industrial environments where large data-samples are not usually available for training such diagnostic models. The main aim of this research is to build up a robust system for the multi-class fault diagnosis in spur gears, by selecting the best set of condition parameters on time, frequency and time-frequency domains, which are extracted from vibration signals. The diagnostic system is performed by using genetic algorithms and a classifier based on random forest, in a supervised environment. The original set of condition parameters is reduced around 66% regarding the initial size by using genetic algorithms, and still get an acceptable classification precision over 97%. The approach is tested on real vibration signals by considering several fault classes, one of them being an incipient fault, under different running conditions of load and velocity.

Cluster-randomized Studies in Educational Research: Principles and Methodological Aspects.

Science.gov (United States)

Dreyhaupt, Jens; Mayer, Benjamin; Keis, Oliver; Öchsner, Wolfgang; Muche, Rainer

2017-01-01

An increasing number of studies are being performed in educational research to evaluate new teaching methods and approaches. These studies could be performed more efficiently and deliver more convincing results if they more strictly applied and complied with recognized standards of scientific studies. Such an approach could substantially increase the quality in particular of prospective, two-arm (intervention) studies that aim to compare two different teaching methods. A key standard in such studies is randomization, which can minimize systematic bias in study findings; such bias may result if the two study arms are not structurally equivalent. If possible, educational research studies should also achieve this standard, although this is not yet generally the case. Some difficulties and concerns exist, particularly regarding organizational and methodological aspects. An important point to consider in educational research studies is that usually individuals cannot be randomized, because of the teaching situation, and instead whole groups have to be randomized (so-called "cluster randomization"). Compared with studies with individual randomization, studies with cluster randomization normally require (significantly) larger sample sizes and more complex methods for calculating sample size. Furthermore, cluster-randomized studies require more complex methods for statistical analysis. The consequence of the above is that a competent expert with respective special knowledge needs to be involved in all phases of cluster-randomized studies. Studies to evaluate new teaching methods need to make greater use of randomization in order to achieve scientifically convincing results. Therefore, in this article we describe the general principles of cluster randomization and how to implement these principles, and we also outline practical aspects of using cluster randomization in prospective, two-arm comparative educational research studies.

The persistence of the attentional bias to regularities in a changing environment.

Science.gov (United States)

Yu, Ru Qi; Zhao, Jiaying

2015-10-01

The environment often is stable, but some aspects may change over time. The challenge for the visual system is to discover and flexibly adapt to the changes. We examined how attention is shifted in the presence of changes in the underlying structure of the environment. In six experiments, observers viewed four simultaneous streams of objects while performing a visual search task. In the first half of each experiment, the stream in the structured location contained regularities, the shapes in the random location were randomized, and gray squares appeared in two neutral locations. In the second half, the stream in the structured or the random location may change. In the first half of all experiments, visual search was facilitated in the structured location, suggesting that attention was consistently biased toward regularities. In the second half, this bias persisted in the structured location when no change occurred (Experiment 1), when the regularities were removed (Experiment 2), or when new regularities embedded in the original or novel stimuli emerged in the previously random location (Experiments 3 and 6). However, visual search was numerically but no longer reliably faster in the structured location when the initial regularities were removed and new regularities were introduced in the previously random location (Experiment 4), or when novel random stimuli appeared in the random location (Experiment 5). This suggests that the attentional bias was weakened. Overall, the results demonstrate that the attentional bias to regularities was persistent but also sensitive to changes in the environment.

Does attention bias modification improve attentional control? A double-blind randomized experiment with individuals with social anxiety disorder.

Science.gov (United States)

Heeren, Alexandre; Mogoaşe, Cristina; McNally, Richard J; Schmitz, Anne; Philippot, Pierre

2015-01-01

People with anxiety disorders often exhibit an attentional bias for threat. Attention bias modification (ABM) procedure may reduce this bias, thereby diminishing anxiety symptoms. In ABM, participants respond to probes that reliably follow non-threatening stimuli (e.g., neutral faces) such that their attention is directed away from concurrently presented threatening stimuli (e.g., disgust faces). Early studies showed that ABM reduced anxiety more than control procedures lacking any contingency between valenced stimuli and probes. However, recent work suggests that no-contingency training and training toward threat cues can be as effective as ABM in reducing anxiety, implying that any training may increase executive control over attention, thereby helping people inhibit their anxious thoughts. Extending this work, we randomly assigned participants with DSM-IV diagnosed social anxiety disorder to either training toward non-threat (ABM), training toward threat, or no-contingency condition, and we used the attention network task (ANT) to assess all three components of attention. After two training sessions, subjects in all three conditions exhibited indistinguishably significant declines from baseline to post-training in self-report and behavioral measures of anxiety on an impromptu speech task. Moreover, all groups exhibited similarly significant improvements on the alerting and executive (but not orienting) components of attention. Implications for ABM research are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Sex-biased natal dispersal and inbreeding avoidance in American black bears as revealed by spatial genetic analyses.

Science.gov (United States)

Costello, Cecily M; Creel, Scott R; Kalinowski, Steven T; Vu, Ninh V; Quigley, Howard B

2008-11-01

We tested the hypothesis that sex-biased natal dispersal reduces close inbreeding in American black bears, a solitary species that exhibits nearly complete male dispersal and female philopatry. Using microsatellite DNA and spatial data from reproductively mature bears (>or= 4 years old), we examined the spatial genetic structure of two distinct populations in New Mexico from 1993 to 2000. As predicted, relatedness (r) and the frequency of close relationships (parent-offspring or full siblings) decreased with distance among female dyads, but little change was observed among male or opposite-sex dyads. Neighbouring females were more closely related than neighbouring males. The potential for inbreeding was low. Most opposite-sex pairs that lived sufficiently close to facilitate mating were unrelated, and few were close relatives. We found no evidence that bears actively avoided inbreeding in their selection of mates from this nearby pool, as mean r and relationship frequencies did not differ between potential and actual mating pairs (determined by parentage analysis). These basic patterns were apparent in both study areas despite a nearly two-fold difference in density. However, the sex bias in dispersal was less pronounced in the lower-density area, based on proportions of bears with male and female relatives residing nearby. This result suggests that male bears may respond to reduced competition by decreasing their rate or distance of dispersal. Evidence supports the hypothesis that inbreeding avoidance is achieved by means of male-biased dispersal but also indicates that competition (for mates or resources) modifies dispersal patterns.

Measuring agricultural policy bias

DEFF Research Database (Denmark)

Jensen, Henning Tarp; Robinson, Sherman; Tarp, Finn

2010-01-01

Measurement is a key issue in the literature on price incentive bias induced by trade policy. We introduce a general equilibrium measure of the relative effective rate of protection, which generalizes earlier protection measures. For our fifteen sample countries, results indicate that the agricul...

Risk of bias and confounding of observational studies of Zika virus infection: A scoping review of research protocols.

Science.gov (United States)

Reveiz, Ludovic; Haby, Michelle M; Martínez-Vega, Ruth; Pinzón-Flores, Carlos E; Elias, Vanessa; Smith, Emma; Pinart, Mariona; Broutet, Nathalie; Becerra-Posada, Francisco; Aldighieri, Sylvain; Van Kerkhove, Maria D

2017-01-01

Given the severity and impact of the current Zika virus (ZIKV) outbreak in the Americas, numerous countries have rushed to develop research studies to assess ZIKV and its potential health consequences. In an effort to ensure that studies are comprehensive, both internally and externally valid, and with reliable results, the World Health Organization, the Pan American Health Organization, Institut Pasteur, the networks of Fiocruz, the Consortia for the Standardization of Influenza Seroepidemiology (CONSISE) and the International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC) have generated six standardized clinical and epidemiological research protocols and questionnaires to address key public health questions on ZIKV. We conducted a systematic search of ongoing study protocols related to ZIKV research. We analyzed the content of protocols of 32 cohort studies and 13 case control studies for systematic bias that could produce erroneous results. Additionally we aimed to characterize the risks of bias and confounding in observational studies related to ZIKV and to propose ways to minimize them, including the use of six newly standardized research protocols. Observational studies of ZIKV face an array of challenges, including measurement of exposure and outcomes (microcephaly and Guillain-Barré Syndrome). Potential confounders need to be measured where known and controlled for in the analysis. Selection bias due to non-random selection is a significant issue, particularly in the case-control design, and losses to follow-up is equally important for the cohort design. Observational research seeking to answer key questions on the ZIKV should consider these restrictions and take precautions to minimize bias in an effort to provide reliable and valid results. Utilization of the standardized research protocols developed by the WHO, PAHO, Institut Pasteur, and CONSISE will harmonize the key methodological aspects of each study design to minimize bias at

Risk of bias and confounding of observational studies of Zika virus infection: A scoping review of research protocols.

Directory of Open Access Journals (Sweden)

Ludovic Reveiz

Full Text Available Given the severity and impact of the current Zika virus (ZIKV outbreak in the Americas, numerous countries have rushed to develop research studies to assess ZIKV and its potential health consequences. In an effort to ensure that studies are comprehensive, both internally and externally valid, and with reliable results, the World Health Organization, the Pan American Health Organization, Institut Pasteur, the networks of Fiocruz, the Consortia for the Standardization of Influenza Seroepidemiology (CONSISE and the International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC have generated six standardized clinical and epidemiological research protocols and questionnaires to address key public health questions on ZIKV.We conducted a systematic search of ongoing study protocols related to ZIKV research. We analyzed the content of protocols of 32 cohort studies and 13 case control studies for systematic bias that could produce erroneous results. Additionally we aimed to characterize the risks of bias and confounding in observational studies related to ZIKV and to propose ways to minimize them, including the use of six newly standardized research protocols.Observational studies of ZIKV face an array of challenges, including measurement of exposure and outcomes (microcephaly and Guillain-Barré Syndrome. Potential confounders need to be measured where known and controlled for in the analysis. Selection bias due to non-random selection is a significant issue, particularly in the case-control design, and losses to follow-up is equally important for the cohort design.Observational research seeking to answer key questions on the ZIKV should consider these restrictions and take precautions to minimize bias in an effort to provide reliable and valid results. Utilization of the standardized research protocols developed by the WHO, PAHO, Institut Pasteur, and CONSISE will harmonize the key methodological aspects of each study design to

Minimum Bias Trigger in ATLAS

International Nuclear Information System (INIS)

Kwee, Regina

2010-01-01

Since the restart of the LHC in November 2009, ATLAS has collected inelastic pp collisions to perform first measurements on charged particle densities. These measurements will help to constrain various models describing phenomenologically soft parton interactions. Understanding the trigger efficiencies for different event types are therefore crucial to minimize any possible bias in the event selection. ATLAS uses two main minimum bias triggers, featuring complementary detector components and trigger levels. While a hardware based first trigger level situated in the forward regions with 2.2 < |η| < 3.8 has been proven to select pp-collisions very efficiently, the Inner Detector based minimum bias trigger uses a random seed on filled bunches and central tracking detectors for the event selection. Both triggers were essential for the analysis of kinematic spectra of charged particles. Their performance and trigger efficiency measurements as well as studies on possible bias sources will be presented. We also highlight the advantage of these triggers for particle correlation analyses. (author)

Cluster-randomized Studies in Educational Research: Principles and Methodological Aspects

Directory of Open Access Journals (Sweden)

Dreyhaupt, Jens

2017-05-01

Full Text Available An increasing number of studies are being performed in educational research to evaluate new teaching methods and approaches. These studies could be performed more efficiently and deliver more convincing results if they more strictly applied and complied with recognized standards of scientific studies. Such an approach could substantially increase the quality in particular of prospective, two-arm (intervention studies that aim to compare two different teaching methods. A key standard in such studies is randomization, which can minimize systematic bias in study findings; such bias may result if the two study arms are not structurally equivalent. If possible, educational research studies should also achieve this standard, although this is not yet generally the case. Some difficulties and concerns exist, particularly regarding organizational and methodological aspects. An important point to consider in educational research studies is that usually individuals cannot be randomized, because of the teaching situation, and instead whole groups have to be randomized (so-called “cluster randomization”. Compared with studies with individual randomization, studies with cluster randomization normally require (significantly larger sample sizes and more complex methods for calculating sample size. Furthermore, cluster-randomized studies require more complex methods for statistical analysis. The consequence of the above is that a competent expert with respective special knowledge needs to be involved in all phases of cluster-randomized studies.Studies to evaluate new teaching methods need to make greater use of randomization in order to achieve scientifically convincing results. Therefore, in this article we describe the general principles of cluster randomization and how to implement these principles, and we also outline practical aspects of using cluster randomization in prospective, two-arm comparative educational research studies.

Illustrating, Quantifying, and Correcting for Bias in Post-hoc Analysis of Gene-Based Rare Variant Tests of Association

Science.gov (United States)

Grinde, Kelsey E.; Arbet, Jaron; Green, Alden; O'Connell, Michael; Valcarcel, Alessandra; Westra, Jason; Tintle, Nathan

2017-01-01

To date, gene-based rare variant testing approaches have focused on aggregating information across sets of variants to maximize statistical power in identifying genes showing significant association with diseases. Beyond identifying genes that are associated with diseases, the identification of causal variant(s) in those genes and estimation of their effect is crucial for planning replication studies and characterizing the genetic architecture of the locus. However, we illustrate that straightforward single-marker association statistics can suffer from substantial bias introduced by conditioning on gene-based test significance, due to the phenomenon often referred to as “winner's curse.” We illustrate the ramifications of this bias on variant effect size estimation and variant prioritization/ranking approaches, outline parameters of genetic architecture that affect this bias, and propose a bootstrap resampling method to correct for this bias. We find that our correction method significantly reduces the bias due to winner's curse (average two-fold decrease in bias, p bias and improve inference in post-hoc analysis of gene-based tests under a wide variety of genetic architectures. PMID:28959274

The effect of framing on surrogate optimism bias: A simulation study.

Science.gov (United States)

Patel, Dev; Cohen, Elan D; Barnato, Amber E

2016-04-01

To explore the effect of emotion priming and physician communication behaviors on optimism bias. We conducted a 5 × 2 between-subject randomized factorial experiment using a Web-based interactive video designed to simulate a family meeting for a critically ill spouse/parent. Eligibility included age at least 35 years and self-identifying as the surrogate for a spouse/parent. The primary outcome was the surrogate's election of code status. We defined optimism bias as the surrogate's estimate of prognosis with cardiopulmonary resuscitation (CPR) > their recollection of the physician's estimate. Of 373 respondents, 256 (69%) logged in and were randomized and 220 (86%) had nonmissing data for prognosis. Sixty-seven (30%) of 220 overall and 56 of (32%) 173 with an accurate recollection of the physician's estimate had optimism bias. Optimism bias correlated with choosing CPR (P optimism bias. Framing the decision as the patient's vs the surrogate's (25% vs 36%, P = .066) and describing the alternative to CPR as "allow natural death" instead of "do not resuscitate" (25% vs 37%, P = .035) decreased optimism bias. Framing of CPR choice during code status conversations may influence surrogates' optimism bias. Copyright © 2015 Elsevier Inc. All rights reserved.

A bias-reducing pathway enrichment analysis of genome-wide association data confirmed association of the MHC region with schizophrenia.

LENUS (Irish Health Repository)

Jia, Peilin

2012-02-01

After the recent successes of genome-wide association studies (GWAS), one key challenge is to identify genetic variants that might have a significant joint effect on complex diseases but have failed to be identified individually due to weak to moderate marginal effect. One popular and effective approach is gene set based analysis, which investigates the joint effect of multiple functionally related genes (eg, pathways). However, a typical gene set analysis method is biased towards long genes, a problem that is especially severe in psychiatric diseases.

Gender bias in teaching evaluations

NARCIS (Netherlands)

Mengel, Friederike; Sauermann, Jan; Zölitz, Ulf Zoelitz

2017-01-01

This paper provides new evidence on gender bias in teaching evaluations. We exploit a quasi-experimental dataset of 19,952 student evaluations of university faculty in a context where students are randomly allocated to female or male instructors. Despite the fact that neither students’ grades nor

A father effect explains sex-ratio bias.

Science.gov (United States)

Malo, Aurelio F; Martinez-Pastor, Felipe; Garcia-Gonzalez, Francisco; Garde, Julián; Ballou, Jonathan D; Lacy, Robert C

2017-08-30

Sex ratio allocation has important fitness consequences, and theory predicts that parents should adjust offspring sex ratio in cases where the fitness returns of producing male and female offspring vary. The ability of fathers to bias offspring sex ratios has traditionally been dismissed given the expectation of an equal proportion of X- and Y-chromosome-bearing sperm (CBS) in ejaculates due to segregation of sex chromosomes at meiosis. This expectation has been recently refuted. Here we used Peromyscus leucopus to demonstrate that sex ratio is explained by an exclusive effect of the father, and suggest a likely mechanism by which male-driven sex-ratio bias is attained. We identified a male sperm morphological marker that is associated with the mechanism leading to sex ratio bias; differences among males in the sperm nucleus area (a proxy for the sex chromosome that the sperm contains) explain 22% variation in litter sex ratio. We further show the role played by the sperm nucleus area as a mediator in the relationship between individual genetic variation and sex-ratio bias. Fathers with high levels of genetic variation had ejaculates with a higher proportion of sperm with small nuclei area. This, in turn, led to siring a higher proportion of sons (25% increase in sons per 0.1 decrease in the inbreeding coefficient). Our results reveal a plausible mechanism underlying unexplored male-driven sex-ratio biases. We also discuss why this pattern of paternal bias can be adaptive. This research puts to rest the idea that father contribution to sex ratio variation should be disregarded in vertebrates, and will stimulate research on evolutionary constraints to sex ratios-for example, whether fathers and mothers have divergent, coinciding, or neutral sex allocation interests. Finally, these results offer a potential explanation for those intriguing cases in which there are sex ratio biases, such as in humans. © 2017 The Author(s).

Priming psychic and conjuring abilities of a magic demonstration influences event interpretation and random number generation biases

Science.gov (United States)

Mohr, Christine; Koutrakis, Nikolaos; Kuhn, Gustav

2015-01-01

Magical ideation and belief in the paranormal is considered to represent a trait-like character; people either believe in it or not. Yet, anecdotes indicate that exposure to an anomalous event can turn skeptics into believers. This transformation is likely to be accompanied by altered cognitive functioning such as impaired judgments of event likelihood. Here, we investigated whether the exposure to an anomalous event changes individuals’ explicit traditional (religious) and non-traditional (e.g., paranormal) beliefs as well as cognitive biases that have previously been associated with non-traditional beliefs, e.g., repetition avoidance when producing random numbers in a mental dice task. In a classroom, 91 students saw a magic demonstration after their psychology lecture. Before the demonstration, half of the students were told that the performance was done respectively by a conjuror (magician group) or a psychic (psychic group). The instruction influenced participants’ explanations of the anomalous event. Participants in the magician, as compared to the psychic group, were more likely to explain the event through conjuring abilities while the reverse was true for psychic abilities. Moreover, these explanations correlated positively with their prior traditional and non-traditional beliefs. Finally, we observed that the psychic group showed more repetition avoidance than the magician group, and this effect remained the same regardless of whether assessed before or after the magic demonstration. We conclude that pre-existing beliefs and contextual suggestions both influence people’s interpretations of anomalous events and associated cognitive biases. Beliefs and associated cognitive biases are likely flexible well into adulthood and change with actual life events. PMID:25653626

Priming psychic and conjuring abilities of a magic demonstration influences event interpretation and random number generation biases

Directory of Open Access Journals (Sweden)

Christine eMohr

2015-01-01

Full Text Available Magical ideation and belief in the paranormal is considered to represent a trait-like character; people either believe in it or not. Yet, anecdotes indicate that exposure to an anomalous event can turn sceptics into believers. This transformation is likely to be accompanied by altered cognitive functioning such as impaired judgements of event likelihood. Here, we investigated whether the exposure to an anomalous event changes individuals’ explicit traditional (religious and non-traditional (e.g. paranormal beliefs as well as cognitive biases that have previously been associated with non-traditional beliefs, e.g. repetition avoidance when producing random numbers in a mental dice task. In a classroom, 91 students saw a magic demonstration after their psychology lecture. Before the demonstration, half of the students were told that the performance was done respectively by a conjuror (magician group or a psychic (psychic group. The instruction influenced participants’ explanations of the anomalous event. Participants in the magician, as compared to the psychic group, were more likely to explain the event through conjuring abilities while the reverse was true for psychic abilities. Moreover, these explanations correlated positively with their prior traditional and non-traditional beliefs. Finally, we observed that the psychic group showed more repetition avoidance than the magician group, and this effect remained the same regardless of whether assessed before or after the magic demonstration. We conclude that pre-existing beliefs and contextual suggestions both influence people’s interpretations of anomalous events and associated cognitive biases. Beliefs and associated cognitive biases are likely flexible well into adulthood and change with actual life events.

The cosmic microwave background radiation power spectrum as a random bit generator for symmetric- and asymmetric-key cryptography

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Jeffrey S. Lee

2017-10-01

Full Text Available In this note, the Cosmic Microwave Background (CMB Radiation is shown to be capable of functioning as a Random Bit Generator, and constitutes an effectively infinite supply of truly random one-time pad values of arbitrary length. It is further argued that the CMB power spectrum potentially conforms to the FIPS 140-2 standard. Additionally, its applicability to the generation of a (n × n random key matrix for a Vernam cipher is established. Keywords: Particle physics, Computer science, Mathematics, Astrophysics

A Systematic Review of Genetic Testing and Lifestyle Behaviour Change: Are We Using High-Quality Genetic Interventions and Considering Behaviour Change Theory?

Science.gov (United States)

Horne, Justine; Madill, Janet; O'Connor, Colleen; Shelley, Jacob; Gilliland, Jason

2018-04-10

Studying the impact of genetic testing interventions on lifestyle behaviour change has been a priority area of research in recent years. Substantial heterogeneity exists in the results and conclusions of this literature, which has yet to be explained using validated behaviour change theory and an assessment of the quality of genetic interventions. The theory of planned behaviour (TPB) helps to explain key contributors to behaviour change. It has been hypothesized that personalization could be added to this theory to help predict changes in health behaviours. This systematic review provides a detailed, comprehensive identification, assessment, and summary of primary research articles pertaining to lifestyle behaviour change (nutrition, physical activity, sleep, and smoking) resulting from genetic testing interventions. The present review further aims to provide in-depth analyses of studies conducted to date within the context of the TPB and the quality of genetic interventions provided to participants while aiming to determine whether or not genetic testing facilitates changes in lifestyle habits. This review is timely in light of a recently published "call-to-action" paper, highlighting the need to incorporate the TPB into personalized healthcare behaviour change research. Three bibliographic databases, one key website, and article reference lists were searched for relevant primary research articles. The PRISMA Flow Diagram and PRISMA Checklist were used to guide the search strategy and manuscript preparation. Out of 32,783 titles retrieved, 26 studies met the inclusion criteria. Three quality assessments were conducted and included: (1) risk of bias, (2) quality of genetic interventions, and (3) consideration of theoretical underpinnings - primarily the TPB. Risk of bias in studies was overall rated to be "fair." Consideration of the TPB was "poor," with no study making reference to this validated theory. While some studies (n = 11; 42%) made reference to other

Are Anti-Stigma Films a Useful Strategy for Reducing Weight Bias Among Trainee Healthcare Professionals? Results of a Pilot Randomized Control Trial

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Judy Anne Swift

2013-03-01

Full Text Available Background: Weight bias is an important clinical issue that the educators of tomorrow's healthcare professionals cannot afford to ignore. This study, therefore, aimed to pilot a randomized controlled trial of the effects of educational films designed to reduce weight stigmatization toward obese patients on trainee dietitians' and doctors' attitudes. Methods: A pre-post experimental design with a 6-week follow-up, which consisted of an intervention group (n = 22 and a control group (n = 21, was conducted to assess the efficacy of brief anti-stigma films in reducing weight bias, and to test whether future, larger-scale studies among trainee healthcare professionals are feasible. Results: Participants at baseline demonstrated weight bias, on both implicit and explicit attitude measures, as well as strong beliefs that obesity is under a person's control. The intervention films significantly improved explicit attitudes and beliefs toward obese people, and participant evaluation was very positive. The intervention did not significantly improve implicit anti-fat bias. Conclusion: The current study suggests both that it is possible to conduct a substantive trial of the effects of educational films designed to reduce weight stigma on a larger cohort of trainee healthcare professionals, and that brief educational interventions may be effective in reducing stigmatizing attitudes in this population.

Nonresponse bias in randomized controlled experiments in criminology: Putting the Queensland Community Engagement Trial (QCET) under a microscope.

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Antrobus, Emma; Elffers, Henk; White, Gentry; Mazerolle, Lorraine

2013-01-01

The goal of this article is to examine whether or not the results of the Queensland Community Engagement Trial (QCET)-a randomized controlled trial that tested the impact of procedural justice policing on citizen attitudes toward police-were affected by different types of nonresponse bias. We use two methods (Cochrane and Elffers methods) to explore nonresponse bias: First, we assess the impact of the low response rate by examining the effects of nonresponse group differences between the experimental and control conditions and pooled variance under different scenarios. Second, we assess the degree to which item response rates are influenced by the control and experimental conditions. Our analysis of the QCET data suggests that our substantive findings are not influenced by the low response rate in the trial. The results are robust even under extreme conditions, and statistical significance of the results would only be compromised in cases where the pooled variance was much larger for the nonresponse group and the difference between experimental and control conditions was greatly diminished. We also find that there were no biases in the item response rates across the experimental and control conditions. RCTs that involve field survey responses-like QCET-are potentially compromised by low response rates and how item response rates might be influenced by the control or experimental conditions. Our results show that the QCET results were not sensitive to the overall low response rate across the experimental and control conditions and the item response rates were not significantly different across the experimental and control groups. Overall, our analysis suggests that the results of QCET are robust and any biases in the survey responses do not significantly influence the main experimental findings.

Peak-locking centroid bias in Shack-Hartmann wavefront sensing

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Anugu, Narsireddy; Garcia, Paulo J. V.; Correia, Carlos M.

2018-05-01

Shack-Hartmann wavefront sensing relies on accurate spot centre measurement. Several algorithms were developed with this aim, mostly focused on precision, i.e. minimizing random errors. In the solar and extended scene community, the importance of the accuracy (bias error due to peak-locking, quantization, or sampling) of the centroid determination was identified and solutions proposed. But these solutions only allow partial bias corrections. To date, no systematic study of the bias error was conducted. This article bridges the gap by quantifying the bias error for different correlation peak-finding algorithms and types of sub-aperture images and by proposing a practical solution to minimize its effects. Four classes of sub-aperture images (point source, elongated laser guide star, crowded field, and solar extended scene) together with five types of peak-finding algorithms (1D parabola, the centre of gravity, Gaussian, 2D quadratic polynomial, and pyramid) are considered, in a variety of signal-to-noise conditions. The best performing peak-finding algorithm depends on the sub-aperture image type, but none is satisfactory to both bias and random errors. A practical solution is proposed that relies on the antisymmetric response of the bias to the sub-pixel position of the true centre. The solution decreases the bias by a factor of ˜7 to values of ≲ 0.02 pix. The computational cost is typically twice of current cross-correlation algorithms.

Genetic Analysis of Daily Maximum Milking Speed by a Random Walk Model in Dairy Cows

DEFF Research Database (Denmark)

Karacaören, Burak; Janss, Luc; Kadarmideen, Haja

Data were obtained from dairy cows stationed at research farm ETH Zurich for maximum milking speed. The main aims of this paper are a) to evaluate if the Wood curve is suitable to model mean lactation curve b) to predict longitudinal breeding values by random regression and random walk models of ...... filter applications: random walk model could give online prediction of breeding values. Hence without waiting for whole lactation records, genetic evaluation could be made when the daily or monthly data is available......Data were obtained from dairy cows stationed at research farm ETH Zurich for maximum milking speed. The main aims of this paper are a) to evaluate if the Wood curve is suitable to model mean lactation curve b) to predict longitudinal breeding values by random regression and random walk models...... of maximum milking speed. Wood curve did not provide a good fit to the data set. Quadratic random regressions gave better predictions compared with the random walk model. However random walk model does not need to be evaluated for different orders of regression coefficients. In addition with the Kalman...

Mouse forward genetics in the study of the peripheral nervous system and human peripheral neuropathy

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Douglas, Darlene S.; Popko, Brian

2009-01-01

Forward genetics, the phenotype-driven approach to investigating gene identity and function, has a long history in mouse genetics. Random mutations in the mouse transcend bias about gene function and provide avenues towards unique discoveries. The study of the peripheral nervous system is no exception; from historical strains such as the trembler mouse, which led to the identification of PMP22 as a human disease gene causing multiple forms of peripheral neuropathy, to the more recent identification of the claw paw and sprawling mutations, forward genetics has long been a tool for probing the physiology, pathogenesis, and genetics of the PNS. Even as spontaneous and mutagenized mice continue to enable the identification of novel genes, provide allelic series for detailed functional studies, and generate models useful for clinical research, new methods, such as the piggyBac transposon, are being developed to further harness the power of forward genetics. PMID:18481175

Eliminating Survivor Bias in Two-stage Instrumental Variable Estimators.

Science.gov (United States)

Vansteelandt, Stijn; Walter, Stefan; Tchetgen Tchetgen, Eric

2018-07-01

Mendelian randomization studies commonly focus on elderly populations. This makes the instrumental variables analysis of such studies sensitive to survivor bias, a type of selection bias. A particular concern is that the instrumental variable conditions, even when valid for the source population, may be violated for the selective population of individuals who survive the onset of the study. This is potentially very damaging because Mendelian randomization studies are known to be sensitive to bias due to even minor violations of the instrumental variable conditions. Interestingly, the instrumental variable conditions continue to hold within certain risk sets of individuals who are still alive at a given age when the instrument and unmeasured confounders exert additive effects on the exposure, and moreover, the exposure and unmeasured confounders exert additive effects on the hazard of death. In this article, we will exploit this property to derive a two-stage instrumental variable estimator for the effect of exposure on mortality, which is insulated against the above described selection bias under these additivity assumptions.

Non-random temporary emigration and the robust design: Conditions for bias at the end of a time series: Section VIII

Science.gov (United States)

Langtimm, Catherine A.

2008-01-01

Deviations from model assumptions in the application of capture–recapture models to real life situations can introduce unknown bias. Understanding the type and magnitude of bias under these conditions is important to interpreting model results. In a robust design analysis of long-term photo-documented sighting histories of the endangered Florida manatee, I found high survival rates, high rates of non-random temporary emigration, significant time-dependence, and a diversity of factors affecting temporary emigration that made it difficult to model emigration in any meaningful fashion. Examination of the time-dependent survival estimates indicated a suspicious drop in survival rates near the end of the time series that persisted when the original capture histories were truncated and reanalyzed under a shorter time frame. Given the wide swings in manatee emigration estimates from year to year, a likely source of bias in survival was the convention to resolve confounding of the last survival probability in a time-dependent model with the last emigration probabilities by setting the last unmeasurable emigration probability equal to the previous year’s probability when the equality was actually false. Results of a series of simulations demonstrated that if the unmeasurable temporary emigration probabilities in the last time period were not accurately modeled, an estimation model with significant annual variation in survival probabilities and emigration probabilities produced bias in survival estimates at the end of the study or time series being explored. Furthermore, the bias propagated back in time beyond the last two time periods and the number of years affected varied positively with survival and emigration probabilities. Truncating the data to a shorter time frame and reanalyzing demonstrated that with additional years of data surviving temporary emigrants eventually return and are detected, thus in subsequent analysis unbiased estimates are eventually realized.

Interwell radiative recombination in the presence of random potential fluctuations in GaAs/AlGaAs biased double quantum wells

DEFF Research Database (Denmark)

Timofeev, V.B.; Larionov, A.V.; Ioselevich, A.S.

1998-01-01

narrowing with temperature increase from 4.5 to 30 K. A theoretical model is presented which explains the observed narrowing in terms of lateral thermally activated tunneling of spatially separated e-h pairs localized by random potential fluctuations in the quantum wells. (C) 1998 American Institute......The interwell radiative recombination from biased double quantum wells (DQW) in pin GaAs/AlGaAs heterostructures is investigated at different temperatures and external electrical fields. The luminescence line of interwell recombination of spatially separated electron-hole pairs exhibits systematic...

Transcription regulation of sex-biased genes during ontogeny in the malaria vector Anopheles gambiae.

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Kalle Magnusson

Full Text Available In Anopheles gambiae, sex-regulated genes are responsible for controlling gender dimorphism and are therefore crucial in determining the ability of female mosquitoes to transmit human malaria. The identification and functional characterization of these genes will shed light on the sexual development and maturation of mosquitoes and provide useful targets for genetic control measures aimed at reducing mosquito fertility and/or distorting the sex ratio.We conducted a genome wide transcriptional analysis of sex-regulated genes from early developmental stages through adulthood combined with functional screening of novel gonadal genes. Our results demonstrate that the male-biased genes undergo a major transcription turnover starting from larval stages to adulthood. The male biased genes at the adult stage include a significant high number of unique sequences compared to the rest of the genome. This is in contrast to female-biased genes that are much more conserved and are mainly activated during late developmental stages.The high frequency of unique sequences would indicate that male-biased genes evolve more rapidly than the rest of the genome. This finding is particularly intriguing because A. gambiae is a strictly female monogamous species suggesting that driving forces in addition to sperm competition must account for the rapid evolution of male-biased genes. We have also identified and functionally characterized a number of previously unknown A. gambiae testis- and ovary-specific genes. Two of these genes, zero population growth and a suppressor of defective silencing 3 domain of the histone deacetylase co-repressor complex, were shown to play a key role in gonad development.

Genetic test feedback with weight control advice: study protocol for a randomized controlled trial

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Meisel Susanne F

2012-12-01

Full Text Available Abstract Background Genetic testing for risk of weight gain is already available over the internet despite uncertain benefits and concerns about adverse emotional or behavioral effects. Few studies have assessed the effect of adding genetic test feedback to weight control advice, even though one of the proposed applications of genetic testing is to stimulate preventive action. This study will investigate the motivational effect of adding genetic test feedback to simple weight control advice in a situation where weight gain is relatively common. Methods/design First-year university students (n = 800 will be randomized to receive either 1 their personal genetic test result for a gene (FTO related to weight gain susceptibility in addition to a leaflet with simple weight control advice (‘Feedback + Advice’ group, FA, or 2 only the leaflet containing simple weight control advice (‘Advice Only’ group, AO. Motivation to avoid weight gain and active use of weight control strategies will be assessed one month after receipt of the leaflet with or without genetic test feedback. Weight and body fat will be measured at baseline and eight months follow-up. We will also assess short-term psychological reactions to the genetic test result. In addition, we will explore interactions between feedback condition and gene test status. Discussion We hope to provide a first indication of the clinical utility of weight-related genetic test feedback in the prevention context. Trial registration Current controlled trials ISRCTN91178663

Genetic dissection of a key reproductive barrier between nascent species of house mice.

Science.gov (United States)

White, Michael A; Steffy, Brian; Wiltshire, Tim; Payseur, Bret A

2011-09-01

Reproductive isolation between species is often caused by deleterious interactions among loci in hybrids. Finding the genes involved in these incompatibilities provides insight into the mechanisms of speciation. With recently diverged subspecies, house mice provide a powerful system for understanding the genetics of reproductive isolation early in the speciation process. Although previous studies have yielded important clues about the genetics of hybrid male sterility in house mice, they have been restricted to F1 sterility or incompatibilities involving the X chromosome. To provide a more complete characterization of this key reproductive barrier, we conducted an F2 intercross between wild-derived inbred strains from two subspecies of house mice, Mus musculus musculus and Mus musculus domesticus. We identified a suite of autosomal and X-linked QTL that underlie measures of hybrid male sterility, including testis weight, sperm density, and sperm morphology. In many cases, the autosomal loci were unique to a specific sterility trait and exhibited an effect only when homozygous, underscoring the importance of examining reproductive barriers beyond the F1 generation. We also found novel two-locus incompatibilities between the M. m. musculus X chromosome and M. m. domesticus autosomal alleles. Our results reveal a complex genetic architecture for hybrid male sterility and suggest a prominent role for reproductive barriers in advanced generations in maintaining subspecies integrity in house mice.

Genetic Dissection of a Key Reproductive Barrier Between Nascent Species of House Mice

Science.gov (United States)

White, Michael A.; Steffy, Brian; Wiltshire, Tim; Payseur, Bret A.

2011-01-01

Reproductive isolation between species is often caused by deleterious interactions among loci in hybrids. Finding the genes involved in these incompatibilities provides insight into the mechanisms of speciation. With recently diverged subspecies, house mice provide a powerful system for understanding the genetics of reproductive isolation early in the speciation process. Although previous studies have yielded important clues about the genetics of hybrid male sterility in house mice, they have been restricted to F1 sterility or incompatibilities involving the X chromosome. To provide a more complete characterization of this key reproductive barrier, we conducted an F2 intercross between wild-derived inbred strains from two subspecies of house mice, Mus musculus musculus and Mus musculus domesticus. We identified a suite of autosomal and X-linked QTL that underlie measures of hybrid male sterility, including testis weight, sperm density, and sperm morphology. In many cases, the autosomal loci were unique to a specific sterility trait and exhibited an effect only when homozygous, underscoring the importance of examining reproductive barriers beyond the F1 generation. We also found novel two-locus incompatibilities between the M. m. musculus X chromosome and M. m. domesticus autosomal alleles. Our results reveal a complex genetic architecture for hybrid male sterility and suggest a prominent role for reproductive barriers in advanced generations in maintaining subspecies integrity in house mice. PMID:21750261

Denoising of genetic switches based on Parrondo's paradox

Science.gov (United States)

Fotoohinasab, Atiyeh; Fatemizadeh, Emad; Pezeshk, Hamid; Sadeghi, Mehdi

2018-03-01

Random decision making in genetic switches can be modeled as tossing a biased coin. In other word, each genetic switch can be considered as a game in which the reactive elements compete with each other to increase their molecular concentrations. The existence of a very small number of reactive element molecules has caused the neglect of effects of noise to be inevitable. Noise can lead to undesirable cell fate in cellular differentiation processes. In this paper, we study the robustness to noise in genetic switches by considering another switch to have a new gene regulatory network (GRN) in which both switches have been affected by the same noise and for this purpose, we will use Parrondo's paradox. We introduce two networks of games based on possible regulatory relations between genes. Our results show that the robustness to noise can increase by combining these noisy switches. We also describe how one of the switches in network II can model lysis/lysogeny decision making of bacteriophage lambda in Escherichia coli and we change its fate by another switch.

Bias in emerging biomarkers for bipolar disorder

DEFF Research Database (Denmark)

Carvalho, A F; Köhler, C A; Fernandes, B S

2016-01-01

BACKGROUND: To date no comprehensive evaluation has appraised the likelihood of bias or the strength of the evidence of peripheral biomarkers for bipolar disorder (BD). Here we performed an umbrella review of meta-analyses of peripheral non-genetic biomarkers for BD. METHOD: The Pubmed/Medline, E...

A Stress-Induced Bias in the Reading of the Genetic Code in Escherichia coli

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Adi Oron-Gottesman

2016-11-01

Full Text Available Escherichia coli mazEF is an extensively studied stress-induced toxin-antitoxin (TA system. The toxin MazF is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress, the induced MazF generates a stress-induced translation machinery (STM, composed of MazF-processed mRNAs and selective ribosomes that specifically translate the processed mRNAs. Here, we further characterized the STM system, finding that MazF cleaves only ACA sites located in the open reading frames of processed mRNAs, while out-of-frame ACAs are resistant. This in-frame ACA cleavage of MazF seems to depend on MazF binding to an extracellular-death-factor (EDF-like element in ribosomal protein bS1 (bacterial S1, apparently causing MazF to be part of STM ribosomes. Furthermore, due to the in-frame MazF cleavage of ACAs under stress, a bias occurs in the reading of the genetic code causing the amino acid threonine to be encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA.

Effects of Bias Modification Training in Binge Eating Disorder.

Science.gov (United States)

Schmitz, Florian; Svaldi, Jennifer

2017-09-01

Food-related attentional biases have been identified as maintaining factors in binge eating disorder (BED) as they can trigger a binge episode. Bias modification training may reduce symptoms, as it has been shown to be successful in other appetitive disorders. The aim of this study was to assess and modify food-related biases in BED. It was tested whether biases could be increased and decreased by means of a modified dot-probe paradigm, how long such bias modification persisted, and whether this affected subjective food craving. Participants were randomly assigned to a bias enhancement (attend to food stimulus) group or to a bias reduction (avoid food stimulus) group. Food-related attentional bias was found to be successfully reduced in the bias-reduction group, and effects persisted briefly. Additionally, subjective craving for food was influenced by the intervention, and possible mechanisms are discussed. Given these promising initial results, future research should investigate boundary conditions of the experimental intervention to understand how it could complement treatment of BED. Copyright © 2017. Published by Elsevier Ltd.

The evolution of social learning rules: payoff-biased and frequency-dependent biased transmission.

Science.gov (United States)

Kendal, Jeremy; Giraldeau, Luc-Alain; Laland, Kevin

2009-09-21

Humans and other animals do not use social learning indiscriminately, rather, natural selection has favoured the evolution of social learning rules that make selective use of social learning to acquire relevant information in a changing environment. We present a gene-culture coevolutionary analysis of a small selection of such rules (unbiased social learning, payoff-biased social learning and frequency-dependent biased social learning, including conformism and anti-conformism) in a population of asocial learners where the environment is subject to a constant probability of change to a novel state. We define conditions under which each rule evolves to a genetically polymorphic equilibrium. We find that payoff-biased social learning may evolve under high levels of environmental variation if the fitness benefit associated with the acquired behaviour is either high or low but not of intermediate value. In contrast, both conformist and anti-conformist biases can become fixed when environment variation is low, whereupon the mean fitness in the population is higher than for a population of asocial learners. Our examination of the population dynamics reveals stable limit cycles under conformist and anti-conformist biases and some highly complex dynamics including chaos. Anti-conformists can out-compete conformists when conditions favour a low equilibrium frequency of the learned behaviour. We conclude that evolution, punctuated by the repeated successful invasion of different social learning rules, should continuously favour a reduction in the equilibrium frequency of asocial learning, and propose that, among competing social learning rules, the dominant rule will be the one that can persist with the lowest frequency of asocial learning.

Ethnic bias and clinical decision-making among New Zealand medical students: an observational study.

Science.gov (United States)

Harris, Ricci; Cormack, Donna; Stanley, James; Curtis, Elana; Jones, Rhys; Lacey, Cameron

2018-01-23

Health professional racial/ethnic bias may impact on clinical decision-making and contribute to subsequent ethnic health inequities. However, limited research has been undertaken among medical students. This paper presents findings from the Bias and Decision-Making in Medicine (BDMM) study, which sought to examine ethnic bias (Māori (indigenous peoples) compared with New Zealand European) among medical students and associations with clinical decision-making. All final year New Zealand (NZ) medical students in 2014 and 2015 (n = 888) were invited to participate in a cross-sectional online study. Key components included: two chronic disease vignettes (cardiovascular disease (CVD) and depression) with randomized patient ethnicity (Māori or NZ European) and questions on patient management; implicit bias measures (an ethnicity preference Implicit Association Test (IAT) and an ethnicity and compliant patient IAT); and, explicit ethnic bias questions. Associations between ethnic bias and clinical decision-making responses to vignettes were tested using linear regression. Three hundred and two students participated (34% response rate). Implicit and explicit ethnic bias favoring NZ Europeans was apparent among medical students. In the CVD vignette, no significant differences in clinical decision-making by patient ethnicity were observed. There were also no differential associations by patient ethnicity between any measures of ethnic bias (implicit or explicit) and patient management responses in the CVD vignette. In the depression vignette, some differences in the ranking of recommended treatment options were observed by patient ethnicity and explicit preference for NZ Europeans was associated with increased reporting that NZ European patients would benefit from treatment but not Māori (slope difference 0.34, 95% CI 0.08, 0.60; p = 0.011), although this was the only significant finding in these analyses. NZ medical students demonstrated ethnic bias, although

"Fair Play": A Videogame Designed to Address Implicit Race Bias Through Active Perspective Taking.

Science.gov (United States)

Gutierrez, Belinda; Kaatz, Anna; Chu, Sarah; Ramirez, Dennis; Samson-Samuel, Clem; Carnes, Molly

2014-12-01

Having diverse faculty in academic health centers will help diversify the healthcare workforce and reduce health disparities. Implicit race bias is one factor that contributes to the underrepresentation of Black faculty. We designed the videogame "Fair Play" in which players assume the role of a Black graduate student named Jamal Davis. As Jamal, players experience subtle race bias while completing "quests" to obtain a science degree. We hypothesized that participants randomly assigned to play the game would have greater empathy for Jamal and lower implicit race bias than participants randomized to read narrative text describing Jamal's experience. University of Wisconsin-Madison graduate students were recruited via e-mail and randomly assigned to play "Fair Play" or read narrative text through an online link. Upon completion, participants took an Implicit Association Test to measure implicit bias and answered survey questions assessing empathy toward Jamal and awareness of bias. As hypothesized, gameplayers showed the least implicit bias but only when they also showed high empathy for Jamal (P=0.013). Gameplayers did not show greater empathy than text readers, and women in the text condition reported the greatest empathy for Jamal (P=0.008). However, high empathy only predicted lower levels of implicit bias among those who actively took Jamal's perspective through gameplay (P=0.014). A videogame in which players experience subtle race bias as a Black graduate student has the potential to reduce implicit bias, possibly because of a game's ability to foster empathy through active perspective taking.

Dual-electrode biasing experiments in KT-5C device

International Nuclear Information System (INIS)

Yu Yi; Lu Ronghua; Wang Chen; Pan Geshen; Wen Yizhi; Yu Changxuan; Ma Jinxiu; Wan Shude; Liu Wandong

2005-01-01

Based on the single biasing electrode experiments to optimize the confinement of plasma in the device of KT-5C tokamak, dual-biasing electrodes were inserted into the KT5C plasma for the first time to explore the enhancement of the effects of biasing and the mechanisms of the biasing. By means of applying different combinations of biasing voltages to the dual electrodes, the changes in E r , which is the key factor for boosting up the Er x B flow shear, were observed. The time evolution showed the inner electrode played a major role in dual-biasing, for it always drew a larger current than the outer one. The outer electrode made little influence. It turned out that the dual-biasing electrodes were as effective as a single one, in improving plasma confinement, for the mechanism of biasing was essentially an edge effect. (author)

Analysis of random number generators in abnormal usage conditions

International Nuclear Information System (INIS)

Soucarros, M.

2012-01-01

Random numbers have been used through the ages for games of chance, more recently for secret codes and today they are necessary to the execution of computer programs. Random number generators have now evolved from simple dices to electronic circuits and algorithms. Accordingly, the ability to distinguish between random and non-random numbers has become more difficult. Furthermore, whereas in the past dices were loaded in order to increase winning chances, it is now possible to influence the outcome of random number generators. In consequence, this subject is still very much an issue and has recently made the headlines. Indeed, there was talks about the PS3 game console which generates constant random numbers and redundant distribution of secret keys on the internet. This thesis presents a study of several generators as well as different means to perturb them. It shows the inherent defects of their conceptions and possible consequences of their failure when they are embedded inside security components. Moreover, this work highlights problems yet to be solved concerning the testing of random numbers and the post-processing eliminating bias in these numbers distribution. (author) [fr

Bias and Causation Models and Judgment for Valid Comparisons

CERN Document Server

Weisberg, Herbert I

2010-01-01

A one-of-a-kind resource on identifying and dealing with bias in statistical research on causal effects. Do cell phones cause cancer? Can a new curriculum increase student achievement? Determining what the real causes of such problems are, and how powerful their effects may be, are central issues in research across various fields of study. Some researchers are highly skeptical of drawing causal conclusions except in tightly controlled randomized experiments, while others discount the threats posed by different sources of bias, even in less rigorous observational studies. Bias and Causation pre

Key interactions by conserved polar amino acids located at the transmembrane helical boundaries in Class B GPCRs modulate activation, effector specificity and biased signalling in the glucagon-like peptide-1 receptor

OpenAIRE

Wootten, Denise; Reynolds, Christopher A.; Smith, Kevin J.; Mobarec, Juan C.; Furness, Sebastian G.B.; Miller, Laurence J.; Christopoulos, Arthur; Sexton, Patrick M.

2016-01-01

Class B GPCRs can activate multiple signalling effectors with the potential to exhibit biased agonism in response to ligand stimulation. Previously, we highlighted key TM domain polar amino acids that were crucial for the function of the GLP-1 receptor, a key therapeutic target for diabetes and obesity. Using a combination of mutagenesis, pharmacological characterisation, mathematical and computational molecular modelling, this study identifies additional highly conserved polar residues locat...

Accounting for unknown foster dams in the genetic evaluation of embryo transfer progeny.

Science.gov (United States)

Suárez, M J; Munilla, S; Cantet, R J C

2015-02-01

Animals born by embryo transfer (ET) are usually not included in the genetic evaluation of beef cattle for preweaning growth if the recipient dam is unknown. This is primarily to avoid potential bias in the estimation of the unknown age of dam. We present a method that allows including records of calves with unknown age of dam. Assumptions are as follows: (i) foster cows belong to the same breed being evaluated, (ii) there is no correlation between the breeding value (BV) of the calf and the maternal BV of the recipient cow, and (iii) cows of all ages are used as recipients. We examine the issue of bias for the fixed level of unknown age of dam (AOD) and propose an estimator of the effect based on classical measurement error theory (MEM) and a Bayesian approach. Using stochastic simulation under random mating or selection, the MEM estimating equations were compared with BLUP in two situations as follows: (i) full information (FI); (ii) missing AOD information on some dams. Predictions of breeding value (PBV) from the FI situation had the smallest empirical average bias followed by PBV obtained without taking measurement error into account. In turn, MEM displayed the highest bias, although the differences were small. On the other hand, MEM showed the smallest MSEP, for either random mating or selection, followed by FI, whereas ignoring measurement error produced the largest MSEP. As a consequence from the smallest MSEP with a relatively small bias, empirical accuracies of PBV were larger for MEM than those for full information, which in turn showed larger accuracies than the situation ignoring measurement error. It is concluded that MEM equations are a useful alternative for analysing weaning weight data when recipient cows are unknown, as it mitigates the effects of bias in AOD by decreasing MSEP. © 2014 Blackwell Verlag GmbH.

The Effectiveness of Cognitive Bias Modification Interventions for Substance Addictions: A Meta-Analysis

DEFF Research Database (Denmark)

Cristea, Ioana; Kok, Robin; Cuijpers, Pim

2016-01-01

Background and Aims Cognitive bias modification (CBM) interventions, presumably targeting automatic processes, are considered particularly promising for addictions. We conducted a meta-analysis examining randomized controlled trials (RCTs) of CBM for substance addiction outcomes. Methods Studies...... were identified through systematic searches in bibliographical databases. We included RCTs of CBM interventions, alone or in combination with other treatments, for any type of addiction. We examined trial risk of bias, publication bias and possible moderators. Effects sizes were computed for post......-test and follow-up, using a random-effects model. We grouped outcome measures and reported results for addiction (all related measures), craving and cognitive bias. Results We identified 25 trials, 18 for alcohol problems, and 7 for smoking. At post-test, there was no significant effect of CBM for addiction, g...

Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems

Science.gov (United States)

Medford, June; Prasad, Ashok

2014-01-01

Biological protein interactions networks such as signal transduction or gene transcription networks are often treated as modular, allowing motifs to be analyzed in isolation from the rest of the network. Modularity is also a key assumption in synthetic biology, where it is similarly expected that when network motifs are combined together, they do not lose their essential characteristics. However, the interactions that a network module has with downstream elements change the dynamical equations describing the upstream module and thus may change the dynamic and static properties of the upstream circuit even without explicit feedback. In this work we analyze the behavior of a ubiquitous motif in gene transcription and signal transduction circuits: the switch. We show that adding an additional downstream component to the simple genetic toggle switch changes its dynamical properties by changing the underlying potential energy landscape, and skewing it in favor of the unloaded side, and in some situations adding loads to the genetic switch can also abrogate bistable behavior. We find that an additional positive feedback motif found in naturally occurring toggle switches could tune the potential energy landscape in a desirable manner. We also analyze autocatalytic signal transduction switches and show that a ubiquitous positive feedback switch can lose its switch-like properties when connected to a downstream load. Our analysis underscores the necessity of incorporating the effects of downstream components when understanding the physics of biochemical network motifs, and raises the question as to how these effects are managed in real biological systems. This analysis is particularly important when scaling synthetic networks to more complex organisms. PMID:24676102

The Analysis of Polyploid Genetic Data.

Science.gov (United States)

Meirmans, Patrick G; Liu, Shenglin; van Tienderen, Peter H

2018-03-16

Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has seriously lagged behind that of diploids. This is unfortunate since the analysis of polyploid genetic data-and the interpretation of the results-requires even more scrutiny than with diploid data. This is because of several polyploidy-specific complications in segregation and genotyping such as tetrasomy, double reduction, and missing dosage information. Here, we review the theoretical and statistical aspects of the population genetics of polyploids. We discuss several widely used types of inferences, including genetic diversity, Hardy-Weinberg equilibrium, population differentiation, genetic distance, and detecting population structure. For each, we point out how the statistical approach, expected result, and interpretation differ between different ploidy levels. We also discuss for each type of inference what biases may arise from the polyploid-specific complications and how these biases can be overcome. From our overview, it is clear that the statistical toolbox that is available for the analysis of genetic data is flexible and still expanding. Modern sequencing techniques will soon be able to overcome some of the current limitations to the analysis of polyploid data, though the techniques are lagging behind those available for diploids. Furthermore, the availability of more data may aggravate the biases that can arise, and increase the risk of false inferences. Therefore, simulations such as we used throughout this review are an important tool to verify the results of analyses of polyploid genetic data.

Significant biases affecting abundance determinations

Science.gov (United States)

Wesson, Roger

2015-08-01

I have developed two highly efficient codes to automate analyses of emission line nebulae. The tools place particular emphasis on the propagation of uncertainties. The first tool, ALFA, uses a genetic algorithm to rapidly optimise the parameters of gaussian fits to line profiles. It can fit emission line spectra of arbitrary resolution, wavelength range and depth, with no user input at all. It is well suited to highly multiplexed spectroscopy such as that now being carried out with instruments such as MUSE at the VLT. The second tool, NEAT, carries out a full analysis of emission line fluxes, robustly propagating uncertainties using a Monte Carlo technique.Using these tools, I have found that considerable biases can be introduced into abundance determinations if the uncertainty distribution of emission lines is not well characterised. For weak lines, normally distributed uncertainties are generally assumed, though it is incorrect to do so, and significant biases can result. I discuss observational evidence of these biases. The two new codes contain routines to correctly characterise the probability distributions, giving more reliable results in analyses of emission line nebulae.

Genetic Analysis of Milk Yield Using Random Regression Test Day Model in Tehran Province Holstein Dairy Cow

Directory of Open Access Journals (Sweden)

A. Seyeddokht

2012-09-01

Full Text Available In this research a random regression test day model was used to estimate heritability values and calculation genetic correlations between test day milk records. a total of 140357 monthly test day milk records belonging to 28292 first lactation Holstein cattle(trice time a day milking distributed in 165 herd and calved from 2001 to 2010 belonging to the herds of Tehran province were used. The fixed effects of herd-year-month of calving as contemporary group and age at calving and Holstein gene percentage as covariate were fitted. Orthogonal legendre polynomial with a 4th-order was implemented to take account of genetic and environmental aspects of milk production over the course of lactation. RRM using Legendre polynomials as base functions appears to be the most adequate to describe the covariance structure of the data. The results showed that the average of heritability for the second half of lactation period was higher than that of the first half. The heritability value for the first month was lowest (0.117 and for the eighth month of the lactation was highest (0.230 compared to the other months of lactation. Because of genetic variation was increased gradually, and residual variance was high in the first months of lactation, heritabilities were different over the course of lactation. The RRMs with a higher number of parameters were more useful to describe the genetic variation of test-day milk yield throughout the lactation. In this research estimation of genetic parameters, and calculation genetic correlations were implemented by random regression test day model, therefore using this method is the exact way to take account of parameters rather than the other ways.

The self-attribution bias and paranormal beliefs.

Science.gov (United States)

van Elk, Michiel

2017-03-01

The present study investigated the relation between paranormal beliefs, illusory control and the self-attribution bias, i.e., the motivated tendency to attribute positive outcomes to oneself while negative outcomes are externalized. Visitors of a psychic fair played a card guessing game and indicated their perceived control over randomly selected cards as a function of the congruency and valence of the card. A stronger self-attribution bias was observed for paranormal believers compared to skeptics and this bias was specifically related to traditional religious beliefs and belief in superstition. No relation between paranormal beliefs and illusory control was found. Self-report measures indicated that paranormal beliefs were associated to being raised in a spiritual family and to anomalous experiences during childhood. Thereby this study suggests that paranormal beliefs are related to specific cognitive biases that in turn are shaped by socio-cultural factors. Copyright © 2017 Elsevier Inc. All rights reserved.

Role-playing is an effective instructional strategy for genetic counseling training: an investigation and comparative study.

Science.gov (United States)

Xu, Xiao-Feng; Wang, Yan; Wang, Yan-Yan; Song, Ming; Xiao, Wen-Gang; Bai, Yun

2016-09-02

Genetic diseases represent a significant public health challenge in China that will need to be addressed by a correspondingly large number of professional genetic counselors. However, neither an official training program for genetic counseling, nor formal board certification, was available in China before 2015. In 2009, a genetic counseling training program based on role-playing was implemented as a pilot study at the Third Military Medical University to train third-year medical students. Questionnaires on participant attitudes to the program and role-playing were randomly administered to 324 students after they had finished their training. Pre- and post-training instructional tests, focusing on 42 key components of genetic counseling, were administered randomly to 200 participants to assess mastery of each component. Finally, scores in final examinations of 578 participants from 2009 to 2011 were compared to scores obtained by 614 non-participating students from 2006 to 2008 to further assess program efficacy. Both the training program and the instructional strategy of role-playing were accepted by most participants. Students believed that role-playing improved their practice of genetic counseling and medical genetics, enhanced their communication skills, and would likely contribute to future professional performance. The average understanding of 40 of the key points in genetic counseling was significantly improved, and most students approached excellent levels of mastery. Scores in final examinations and the percentages of students scoring above 90 were also significantly elevated. Role-playing is a feasible and effective instructional strategy for training genetic counselors in China as well as in other developing countries.

Bias against research on gender bias.

Science.gov (United States)

Cislak, Aleksandra; Formanowicz, Magdalena; Saguy, Tamar

2018-01-01

The bias against women in academia is a documented phenomenon that has had detrimental consequences, not only for women, but also for the quality of science. First, gender bias in academia affects female scientists, resulting in their underrepresentation in academic institutions, particularly in higher ranks. The second type of gender bias in science relates to some findings applying only to male participants, which produces biased knowledge. Here, we identify a third potentially powerful source of gender bias in academia: the bias against research on gender bias. In a bibliometric investigation covering a broad range of social sciences, we analyzed published articles on gender bias and race bias and established that articles on gender bias are funded less often and published in journals with a lower Impact Factor than articles on comparable instances of social discrimination. This result suggests the possibility of an underappreciation of the phenomenon of gender bias and related research within the academic community. Addressing this meta-bias is crucial for the further examination of gender inequality, which severely affects many women across the world.

Patterns of Cancer Genetic Testing: A Randomized Survey of Oregon Clinicians

International Nuclear Information System (INIS)

Cox, S. L.; Zlot, A. I.; Silvey, S. K.; Silvey, S. K.

2012-01-01

Introduction. Appropriate use of genetic tests for population-based cancer screening, diagnosis of inherited cancers, and guidance of cancer treatment can improve health outcomes. We investigated clinicians’ use and knowledge of eight breast, ovarian, and colorectal cancer genetic tests. Methods. We conducted a randomized survey of 2,191 Oregon providers, asking about their experience with fecal DNA, OncoVue, BRCA, MMR, CYP2D6, tumor gene expression profiling, UGT1A1, and KRAS. Results. Clinicians reported low confidence in their knowledge of medical genetics; most confident were OB-GYNs and specialists. Clinicians were more likely to have ordered/recommended BRCA and MMR than the other tests, and OB-GYNs were twice as likely to have ordered/recommended BRCA testing than primary care providers. Less than 10% of providers ordered/recommended OncoVue, fecal DNA, CYP2D6, or UGT1A1; less than 30% ordered/recommended tumor gene expression profiles or KRAS. The most common reason for not ordering/recommending these tests was lack of familiarity. Conclusions. Use of appropriate, evidence-based testing can help reduce incidence and mortality of certain cancers, but these tests need to be better integrated into clinical practice. Continued evaluation of emerging technologies, dissemination of findings, and an increase in provider confidence and knowledge are necessary to achieve this end.

Imagine the bright side of life: A randomized controlled trial of two types of interpretation bias modification procedure targeting adolescent anxiety and depression.

Directory of Open Access Journals (Sweden)

E L de Voogd

Full Text Available Anxiety and depression are highly prevalent during adolescence and characterized by negative interpretation biases. Cognitive bias modification of interpretations (CBM-I may reduce such biases and improve emotional functioning. However, as findings have been mixed and the traditional scenario training is experienced as relatively boring, a picture-based type of training might be more engaging and effective.The current study investigated short- and long-term effects (up to 6 months and users' experience of two types of CBM-I procedure in adolescents with heightened symptoms of anxiety or depression (N = 119, aged 12-18 year. Participants were randomized to eight online sessions of text-based scenario training, picture-word imagery training, or neutral control training.No significant group differences were observed on primary or secondary emotional outcomes. A decrease in anxiety and depressive symptoms, and improvements in emotional resilience were observed, irrespective of condition. Scenario training marginally reduced negative interpretation bias on a closely matched assessment task, while no such effects were found on a different task, nor for the picture-word or control group. Subjective evaluations of all training paradigms were relatively negative and the imagery component appeared particularly difficult for adolescents with higher symptom levels.The current results question the preventive efficacy and feasibility of both CBM-I procedures as implemented here in adolescents.

A Note on the Correlated Random Coefficient Model

DEFF Research Database (Denmark)

Kolodziejczyk, Christophe

In this note we derive the bias of the OLS estimator for a correlated random coefficient model with one random coefficient, but which is correlated with a binary variable. We provide set-identification to the parameters of interest of the model. We also show how to reduce the bias of the estimator...

A test of genetic association among male nuptial coloration, female mating preference, and male aggression bias within a polymorphic population of cichlid fish

Directory of Open Access Journals (Sweden)

Inke van der SLUIJS, Peter D. DIJKSTRA, Charlotte M. LINDEYER et al.

2013-04-01

Full Text Available Both inter- and intrasexual selection have been implicated in the origin and maintenance of species-rich taxa with diverse sexual traits. Simultaneous disruptive selection by female mate choice and male-male competition can, in theory, lead to speciation without geographical isolation if both act on the same male trait. Female mate choice can generate discontinuities in gene flow, while male-male competition can generate negative frequency-dependent selection stabilizing the male trait polymorphism. Speciation may be facilitated when mating preference and/or aggression bias are physically linked to the trait they operate on. We tested for genetic associations among female mating preference, male aggression bias and male coloration in the Lake Victoria cichlid Pundamilia. We crossed females from a phenotypically variable population with males from both extreme ends of the phenotype distribution in the same population (blue or red. Male offspring of a red sire were significantly redder than males of a blue sire, indicating that intra-population variation in male coloration is heritable. We tested mating preferences of female offspring and aggression biases of male offspring using binary choice tests. There was no evidence for associations at the family level between female mating preferences and coloration of sires, but dam identity had a significant effect on female mate preference. Sons of the red sire directed significantly more aggression to red than blue males, whereas sons of the blue sire did not show any bias. There was a positive correlation among individuals between male aggression bias and body coloration, possibly due to pleiotropy or physical linkage, which could facilitate the maintenance of color polymorphism [Current Zoology 59 (2: 221-229, 2013].

A machine learning model with human cognitive biases capable of learning from small and biased datasets.

Science.gov (United States)

Taniguchi, Hidetaka; Sato, Hiroshi; Shirakawa, Tomohiro

2018-05-09

Human learners can generalize a new concept from a small number of samples. In contrast, conventional machine learning methods require large amounts of data to address the same types of problems. Humans have cognitive biases that promote fast learning. Here, we developed a method to reduce the gap between human beings and machines in this type of inference by utilizing cognitive biases. We implemented a human cognitive model into machine learning algorithms and compared their performance with the currently most popular methods, naïve Bayes, support vector machine, neural networks, logistic regression and random forests. We focused on the task of spam classification, which has been studied for a long time in the field of machine learning and often requires a large amount of data to obtain high accuracy. Our models achieved superior performance with small and biased samples in comparison with other representative machine learning methods.

Correcting Biases in a lower resolution global circulation model with data assimilation

Science.gov (United States)

Canter, Martin; Barth, Alexander

2016-04-01

With this work, we aim at developping a new method of bias correction using data assimilation. This method is based on the stochastic forcing of a model to correct bias. First, through a preliminary run, we estimate the bias of the model and its possible sources. Then, we establish a forcing term which is directly added inside the model's equations. We create an ensemble of runs and consider the forcing term as a control variable during the assimilation of observations. We then use this analysed forcing term to correct the bias of the model. Since the forcing is added inside the model, it acts as a source term, unlike external forcings such as wind. This procedure has been developed and successfully tested with a twin experiment on a Lorenz 95 model. It is currently being applied and tested on the sea ice ocean NEMO LIM model, which is used in the PredAntar project. NEMO LIM is a global and low resolution (2 degrees) coupled model (hydrodynamic model and sea ice model) with long time steps allowing simulations over several decades. Due to its low resolution, the model is subject to bias in area where strong currents are present. We aim at correcting this bias by using perturbed current fields from higher resolution models and randomly generated perturbations. The random perturbations need to be constrained in order to respect the physical properties of the ocean, and not create unwanted phenomena. To construct those random perturbations, we first create a random field with the Diva tool (Data-Interpolating Variational Analysis). Using a cost function, this tool penalizes abrupt variations in the field, while using a custom correlation length. It also decouples disconnected areas based on topography. Then, we filter the field to smoothen it and remove small scale variations. We use this field as a random stream function, and take its derivatives to get zonal and meridional velocity fields. We also constrain the stream function along the coasts in order not to have

Attentional bias modification encourages healthy eating.

Science.gov (United States)

Kakoschke, Naomi; Kemps, Eva; Tiggemann, Marika

2014-01-01

The continual exposure to unhealthy food cues in the environment encourages poor dietary habits, in particular consuming too much fat and sugar, and not enough fruit and vegetables. According to Berridge's (2009) model of food reward, unhealthy eating is a behavioural response to biased attentional processing. The present study used an established attentional bias modification paradigm to discourage the consumption of unhealthy food and instead promote healthy eating. Participants were 146 undergraduate women who were randomly assigned to two groups: one was trained to direct their attention toward pictures of healthy food ('attend healthy' group) and the other toward unhealthy food ('attend unhealthy' group). It was found that participants trained to attend to healthy food cues demonstrated an increased attentional bias for such cues and ate relatively more of the healthy than unhealthy snacks compared to the 'attend unhealthy' group. Theoretically, the results support the postulated link between biased attentional processing and consumption (Berridge, 2009). At a practical level, they offer potential scope for interventions that focus on eating well. Copyright © 2013 Elsevier Ltd. All rights reserved.

MycoKey round table discussions of future directions in research on chemical detection methods, genetics and biodiversity of mycotoxins

Science.gov (United States)

MycoKey, an EU-funded Horizon 2020 project, includes a series of “Roundtable Discussions” to gather information on trending research areas in the field of mycotoxicology. This presentation includes summaries of the Roundtable Discussions on the role of Genetics and Biodiversity in mycotoxin product...

Quantum Hash function and its application to privacy amplification in quantum key distribution, pseudo-random number generation and image encryption

Science.gov (United States)

Yang, Yu-Guang; Xu, Peng; Yang, Rui; Zhou, Yi-Hua; Shi, Wei-Min

2016-01-01

Quantum information and quantum computation have achieved a huge success during the last years. In this paper, we investigate the capability of quantum Hash function, which can be constructed by subtly modifying quantum walks, a famous quantum computation model. It is found that quantum Hash function can act as a hash function for the privacy amplification process of quantum key distribution systems with higher security. As a byproduct, quantum Hash function can also be used for pseudo-random number generation due to its inherent chaotic dynamics. Further we discuss the application of quantum Hash function to image encryption and propose a novel image encryption algorithm. Numerical simulations and performance comparisons show that quantum Hash function is eligible for privacy amplification in quantum key distribution, pseudo-random number generation and image encryption in terms of various hash tests and randomness tests. It extends the scope of application of quantum computation and quantum information.

Quantum Hash function and its application to privacy amplification in quantum key distribution, pseudo-random number generation and image encryption

Science.gov (United States)

Yang, Yu-Guang; Xu, Peng; Yang, Rui; Zhou, Yi-Hua; Shi, Wei-Min

2016-01-01

Quantum information and quantum computation have achieved a huge success during the last years. In this paper, we investigate the capability of quantum Hash function, which can be constructed by subtly modifying quantum walks, a famous quantum computation model. It is found that quantum Hash function can act as a hash function for the privacy amplification process of quantum key distribution systems with higher security. As a byproduct, quantum Hash function can also be used for pseudo-random number generation due to its inherent chaotic dynamics. Further we discuss the application of quantum Hash function to image encryption and propose a novel image encryption algorithm. Numerical simulations and performance comparisons show that quantum Hash function is eligible for privacy amplification in quantum key distribution, pseudo-random number generation and image encryption in terms of various hash tests and randomness tests. It extends the scope of application of quantum computation and quantum information. PMID:26823196

Strategies for MCMC computation in quantitative genetics

DEFF Research Database (Denmark)

Waagepetersen, Rasmus; Ibanez, Noelia; Sorensen, Daniel

2006-01-01

Given observations of a trait and a pedigree for a group of animals, the basic model in quantitative genetics is a linear mixed model with genetic random effects. The correlation matrix of the genetic random effects is determined by the pedigree and is typically very highdimensional but with a sp......Given observations of a trait and a pedigree for a group of animals, the basic model in quantitative genetics is a linear mixed model with genetic random effects. The correlation matrix of the genetic random effects is determined by the pedigree and is typically very highdimensional...

Perils of parsimony: properties of reduced-rank estimates of genetic covariance matrices.

Science.gov (United States)

Meyer, Karin; Kirkpatrick, Mark

2008-10-01

Eigenvalues and eigenvectors of covariance matrices are important statistics for multivariate problems in many applications, including quantitative genetics. Estimates of these quantities are subject to different types of bias. This article reviews and extends the existing theory on these biases, considering a balanced one-way classification and restricted maximum-likelihood estimation. Biases are due to the spread of sample roots and arise from ignoring selected principal components when imposing constraints on the parameter space, to ensure positive semidefinite estimates or to estimate covariance matrices of chosen, reduced rank. In addition, it is shown that reduced-rank estimators that consider only the leading eigenvalues and -vectors of the "between-group" covariance matrix may be biased due to selecting the wrong subset of principal components. In a genetic context, with groups representing families, this bias is inverse proportional to the degree of genetic relationship among family members, but is independent of sample size. Theoretical results are supplemented by a simulation study, demonstrating close agreement between predicted and observed bias for large samples. It is emphasized that the rank of the genetic covariance matrix should be chosen sufficiently large to accommodate all important genetic principal components, even though, paradoxically, this may require including a number of components with negligible eigenvalues. A strategy for rank selection in practical analyses is outlined.

Bias of genetic trend of genomic predictions based on both real dairy cattle and simulated data

DEFF Research Database (Denmark)

Ma, Peipei; Lund, Mogens Sandø; Nielsen, Ulrik Sander

This study investigated the phenomenon of bias in the trend of genomic predictions and attempted to find the reason and solution for this bias. The data used in this study include Danish Jersey data and simulation data. In Jersey data, the bias was reduced when cows were included in the reference...... population. In simulated data, there was no bias when the test animals were unselected cows. When the G matrix was derived from genotypes of causal genes, the bias was reduced. The results suggest that the main reasons for causing the bias of the prediction trends are the selection of bulls and bull dams...

Implicit Messages:A Review of "Bias in Mental Testing."

Science.gov (United States)

Scarr, Sandra

1981-01-01

Reviews Arthur Jensen's "Bias in Mental Testing" in terms of its implications for racial genetic inferiority, and offers alternate explanations for racial differences in testing based on data from studies on Black socialization and cultural differences in child rearing. (CM)

Potential genetic anticipation in hereditary leiomyomatosis-renal cell cancer (HLRCC).

Science.gov (United States)

Wong, Mei Hua; Tan, Chuen Seng; Lee, Soo Chin; Yong, Yvonne; Ooi, Aik Seng; Ngeow, Joanne; Tan, Min Han

2014-06-01

Hereditary leiomyomatosis-renal cell cancer (HLRCC) is an autosomal dominant disorder characterised by cutaneous leiomyomas, symptomatic uterine leiomyomas and aggressive type II papillary renal cell carcinoma. It is caused by heterozygous mutations in the fumarate hydratase (FH) gene on chromosome 1q43. We present evidence of genetic anticipation in HLRCC syndrome. A comprehensive literature review was performed to determine the potential for genetic anticipation in HLRCC syndrome. The normal random effects model was used to evaluate for genetic anticipation to ensure reduction in bias. A total of 11 FH kindreds with available multi-generational data were identified for analysis. The mean difference in age at diagnosis of RCC between the first and second generation was -18.6 years (95 % CI -26.6 to -10.6, p anticipation for uterine leiomyomas was observed (p = 0.349). We report preliminary evidence of genetic anticipation of RCC in HLRCC syndrome. Additional clinical validation is important to confirm this observation, which may have practical implications on counseling and timing of surveillance initiation. Exploration of the underlying mechanisms of anticipation in HLRCC would be of considerable biological interest.

The use of random amplified polymorphic DNA to evaluate the genetic variability of Ponkan mandarin (Citrus reticulata Blanco accessions

Directory of Open Access Journals (Sweden)

Coletta Filho Helvécio Della

2000-01-01

Full Text Available RAPD analysis of 19 Ponkan mandarin accessions was performed using 25 random primers. Of 112 amplification products selected, only 32 were polymorphic across five accessions. The absence of genetic variability among the other 14 accessions suggested that they were either clonal propagations with different local names, or that they had undetectable genetic variability, such as point mutations which cannot be detected by RAPD.

Internet-based attentional bias modification training as add-on to regular treatment in alcohol and cannabis dependent outpatients: a study protocol of a randomized control trial.

Science.gov (United States)

Heitmann, Janika; van Hemel-Ruiter, Madelon E; Vermeulen, Karin M; Ostafin, Brian D; MacLeod, Colin; Wiers, Reinout W; DeFuentes-Merillas, Laura; Fledderus, Martine; Markus, Wiebren; de Jong, Peter J

2017-05-23

The automatic tendency to attend to and focus on substance-related cues in the environment (attentional bias), has been found to contribute to the persistence of addiction. Attentional bias modification (ABM) interventions might, therefore, contribute to treatment outcome and the reduction of relapse rates. Based on some promising research findings, we designed a study to test the clinical relevance of ABM as an add-on component of regular intervention for alcohol and cannabis patients. The current protocol describes a study which will investigate the effectiveness and cost-effectiveness of a newly developed home-delivered, multi-session, internet-based ABM (iABM) intervention as an add-on to treatment as usual (TAU). TAU consists of cognitive behavioural therapy-based treatment according to the Dutch guidelines for the treatment of addiction. Participants (N = 213) will be outpatients from specialized addiction care institutions diagnosed with alcohol or cannabis dependency who will be randomly assigned to one of three conditions: TAU + iABM; TAU + placebo condition; TAU-only. Primary outcome measures are substance use, craving, and rates of relapse. Changes in attentional bias will be measured to investigate whether changes in primary outcome measures can be attributed to the modification of attentional bias. Indices of cost-effectiveness and secondary physical and psychological complaints (depression, anxiety, and stress) are assessed as secondary outcome measures. This randomized control trial will be the first to investigate whether a home-delivered, multi-session iABM intervention is (cost-) effective in reducing relapse rates in alcohol and cannabis dependency as an add-on to TAU, compared with an active and a waiting list control group. If proven effective, this ABM intervention could be easily implemented as a home-delivered component of current TAU. Netherlands Trial Register, NTR5497 , registered on 18th September 2015.

Surprisingly rational: probability theory plus noise explains biases in judgment.

Science.gov (United States)

Costello, Fintan; Watts, Paul

2014-07-01

The systematic biases seen in people's probability judgments are typically taken as evidence that people do not use the rules of probability theory when reasoning about probability but instead use heuristics, which sometimes yield reasonable judgments and sometimes yield systematic biases. This view has had a major impact in economics, law, medicine, and other fields; indeed, the idea that people cannot reason with probabilities has become a truism. We present a simple alternative to this view, where people reason about probability according to probability theory but are subject to random variation or noise in the reasoning process. In this account the effect of noise is canceled for some probabilistic expressions. Analyzing data from 2 experiments, we find that, for these expressions, people's probability judgments are strikingly close to those required by probability theory. For other expressions, this account produces systematic deviations in probability estimates. These deviations explain 4 reliable biases in human probabilistic reasoning (conservatism, subadditivity, conjunction, and disjunction fallacies). These results suggest that people's probability judgments embody the rules of probability theory and that biases in those judgments are due to the effects of random noise. (c) 2014 APA, all rights reserved.

Avoiding bias in safety testing design

DEFF Research Database (Denmark)

Calow, Peter

2011-01-01

All scientists are biased, no matter what their backgrounds or affiliations, so what is it about the scientific method that overcomes this and which makes science so successful? Key features are transparency and critical peer scrutiny. These general issues will be will be considered in terms...

The key elements for genetic response in Finnish dairy cattle breeding

Directory of Open Access Journals (Sweden)

Jarmo Juga

1998-01-01

Full Text Available This paper reviews some key elements of Finnish animal breeding research contributing to the Finnish dairy cattle breeding programme and discusses the possibilities and problems in collecting data for genetic evaluation, prediction of breeding values both within and across countries, estimation of the economic value of important traits, and selection of bulls and cows. Economic values are calculated for fertility, udder health and production traits when one genetic standard deviation unit (gen. sd. is changed in each trait independently and the financial returns from selection response in the Finnish dairy cattle breeding programme are estimated. The following components were used to calculate the economic value of mastitis treatments: 1 cost of mastitis including discarded milk and treatment costs, 2 reduction in milk price due to higher somatic cell count, 3 replacement costs and 4 lower production level of the herd due to involuntary culling of cows because of udder problems. A high somatic cell count lowers the price of milk and eventually leads to involuntary culling. For treatments for fertility disorders the following costs were included: 1 treatment costs 2 higher replacement costs and 3 decreased milk production in the herd. Days open included the following costs: 1 extra insemination, 2 reduced annual milk yield and 3 fewer calves born. Animal breeding was found to be a very cost effective investment, yielding returns of FIM 876.9 per cow from one round of selection when the gene flow was followed for over 25 years in the Finnish dairy cattle breeding programme.

Genetic Essentialism: On the Deceptive Determinism of DNA

OpenAIRE

Dar-Nimrod, Ilan; Heine, Steven J.

2011-01-01

This paper introduces the notion of genetic essentialist biases: cognitive biases associated with essentialist thinking that are elicited when people encounter arguments that genes are relevant for a behavior, condition, or social group. Learning about genetic attributions for various human conditions leads to a particular set of thoughts regarding those conditions: they are more likely to be perceived as a) immutable and determined, b) having a specific etiology, c) homogeneous and discrete,...

The male handicap: male-biased mortality explains skewed sex ratios in brown trout embryos.

Science.gov (United States)

Morán, P; Labbé, L; Garcia de Leaniz, C

2016-12-01

Juvenile sex ratios are often assumed to be equal for many species with genetic sex determination, but this has rarely been tested in fish embryos due to their small size and absence of sex-specific markers. We artificially crossed three populations of brown trout and used a recently developed genetic marker for sexing the offspring of both pure and hybrid crosses. Sex ratios (SR = proportion of males) varied widely one month after hatching ranging from 0.15 to 0.90 (mean = 0.39 ± 0.03). Families with high survival tended to produce balanced or male-biased sex ratios, but SR was significantly female-biased when survival was low, suggesting that males sustain higher mortality during development. No difference in SR was found between pure and hybrid families, but the existence of sire × dam interactions suggests that genetic incompatibility may play a role in determining sex ratios. Our findings have implications for animal breeding and conservation because skewed sex ratios will tend to reduce effective population size and bias selection estimates. © 2016 The Authors.

Human X-chromosome inactivation pattern distributions fit a model of genetically influenced choice better than models of completely random choice

Science.gov (United States)

Renault, Nisa K E; Pritchett, Sonja M; Howell, Robin E; Greer, Wenda L; Sapienza, Carmen; Ørstavik, Karen Helene; Hamilton, David C

2013-01-01

In eutherian mammals, one X-chromosome in every XX somatic cell is transcriptionally silenced through the process of X-chromosome inactivation (XCI). Females are thus functional mosaics, where some cells express genes from the paternal X, and the others from the maternal X. The relative abundance of the two cell populations (X-inactivation pattern, XIP) can have significant medical implications for some females. In mice, the ‘choice' of which X to inactivate, maternal or paternal, in each cell of the early embryo is genetically influenced. In humans, the timing of XCI choice and whether choice occurs completely randomly or under a genetic influence is debated. Here, we explore these questions by analysing the distribution of XIPs in large populations of normal females. Models were generated to predict XIP distributions resulting from completely random or genetically influenced choice. Each model describes the discrete primary distribution at the onset of XCI, and the continuous secondary distribution accounting for changes to the XIP as a result of development and ageing. Statistical methods are used to compare models with empirical data from Danish and Utah populations. A rigorous data treatment strategy maximises information content and allows for unbiased use of unphased XIP data. The Anderson–Darling goodness-of-fit statistics and likelihood ratio tests indicate that a model of genetically influenced XCI choice better fits the empirical data than models of completely random choice. PMID:23652377

Scaling of the first-passage time of biased diffusion on hierarchical comb structures

International Nuclear Information System (INIS)

Lin Zhifang; Tao Ruibao.

1989-12-01

Biased diffusion on hierarchical comb structures is studied within an exact renormalization group scheme. The scaling exponents of the moments of the first-passage time for random walks are obtained. It is found that the scaling properties of the diffusion depend only on the direction of bias. In this particular case, the presence of bias may give rise to a new multifractality. (author). 7 refs, 2 figs

A simple bias correction in linear regression for quantitative trait association under two-tail extreme selection.

Science.gov (United States)

Kwan, Johnny S H; Kung, Annie W C; Sham, Pak C

2011-09-01

Selective genotyping can increase power in quantitative trait association. One example of selective genotyping is two-tail extreme selection, but simple linear regression analysis gives a biased genetic effect estimate. Here, we present a simple correction for the bias.

Children's Attentional Biases and "5-HTTLPR" Genotype: Potential Mechanisms Linking Mother and Child Depression

Science.gov (United States)

Gibb, Brandon E.; Benas, Jessica S.; Grassia, Marie; McGeary, John

2009-01-01

In this study, we examined the roles of specific cognitive (attentional bias) and genetic ("5-HTTLPR") risk factors in the intergenerational transmission of depression. Focusing first on the link between maternal history of major depressive disorder (MDD) and children's attentional biases, we found that children of mothers with a history…

Towards understanding the known-key security of block ciphers

DEFF Research Database (Denmark)

Andreeva, Elena; Bogdanov, Andrey; Mennink, Bart

2014-01-01

ciphers based on ideal components such as random permutations and random functions as well as propose new generic known-key attacks on generalized Feistel ciphers. We introduce the notion of known-key indifferentiability to capture the security of such block ciphers under a known key. To show its...... meaningfulness, we prove that the known-key attacks on block ciphers with ideal primitives to date violate security under known-key indifferentiability. On the other hand, to demonstrate its constructiveness, we prove the balanced Feistel cipher with random functions and the multiple Even-Mansour cipher...... with random permutations known-key indifferentiable for a sufficient number of rounds. We note that known-key indifferentiability is more quickly and tightly attained by multiple Even-Mansour which puts it forward as a construction provably secure against known-key attacks....

Continual training of attentional bias in social anxiety.

Science.gov (United States)

Li, Songwei; Tan, Jieqing; Qian, Mingyi; Liu, Xinghua

2008-08-01

Using the dot-probe paradigm, it has been shown that high social anxiety is associated with an attentional bias toward negative information. In the present study, individuals with high social anxiety were divided into two groups randomly. One group was the attentional bias training group (Group T), and the other was the control group (Group C). For Group T, 7 days' continuous training of attentional bias was conducted using the dot-probe paradigm to make socially anxious individuals focus more on positive face pictures. The results showed that the training was effective in changing attentional bias in Group T. Scores of the Social Interaction Anxiety Scale (SIAS) in Group T were reduced compared to Group C, while the scores of Social Phobia Scale (SPS) and scores of Negative Evaluation Scale (FNE) showed no difference between the two groups, which suggested a limited reduction of social anxiety.

EVOLUTION OF THE MERGER-INDUCED HYDROSTATIC MASS BIAS IN GALAXY CLUSTERS

International Nuclear Information System (INIS)

Nelson, Kaylea; Nagai, Daisuke; Rudd, Douglas H.; Shaw, Laurie

2012-01-01

In this work, we examine the effects of mergers on the hydrostatic mass estimate of galaxy clusters using high-resolution Eulerian cosmological simulations. We utilize merger trees to isolate the last merger for each cluster in our sample and follow the time evolution of the hydrostatic mass bias as the systems relax. We find that during a merger, a shock propagates outward from the parent cluster, resulting in an overestimate in the hydrostatic mass bias. After the merger, as a cluster relaxes, the bias in hydrostatic mass estimate decreases but remains at a level of –5%-10% with 15%-20% scatter within r 500 . We also investigate the post-merger evolution of the pressure support from bulk motions, a dominant cause of this residual mass bias. At r 500 , the contribution from random motions peaks at 30% of the total pressure during the merger and quickly decays to ∼10%-15% as a cluster relaxes. Additionally, we use a measure of the random motion pressure to correct the hydrostatic mass estimate. We discover that 4 Gyr after mergers, the direct effects of the merger event on the hydrostatic mass bias have become negligible. Thereafter, the mass bias is primarily due to residual bulk motions in the gas which are not accounted for in the hydrostatic equilibrium equation. We present a hydrostatic mass bias correction method that can recover the unbiased cluster mass for relaxed clusters with 9% scatter at r 500 and 11% scatter in the outskirts, within r 200 .

Genetic alterations of hepatocellular carcinoma by random amplified polymorphic DNA analysis and cloning sequencing of tumor differential DNA fragment

Science.gov (United States)

Xian, Zhi-Hong; Cong, Wen-Ming; Zhang, Shu-Hui; Wu, Meng-Chao

2005-01-01

AIM: To study the genetic alterations and their association with clinicopathological characteristics of hepatocellular carcinoma (HCC), and to find the tumor related DNA fragments. METHODS: DNA isolated from tumors and corresponding noncancerous liver tissues of 56 HCC patients was amplified by random amplified polymorphic DNA (RAPD) with 10 random 10-mer arbitrary primers. The RAPD bands showing obvious differences in tumor tissue DNA corresponding to that of normal tissue were separated, purified, cloned and sequenced. DNA sequences were analyzed and compared with GenBank data. RESULTS: A total of 56 cases of HCC were demonstrated to have genetic alterations, which were detected by at least one primer. The detestability of genetic alterations ranged from 20% to 70% in each case, and 17.9% to 50% in each primer. Serum HBV infection, tumor size, histological grade, tumor capsule, as well as tumor intrahepatic metastasis, might be correlated with genetic alterations on certain primers. A band with a higher intensity of 480 bp or so amplified fragments in tumor DNA relative to normal DNA could be seen in 27 of 56 tumor samples using primer 4. Sequence analysis of these fragments showed 91% homology with Homo sapiens double homeobox protein DUX10 gene. CONCLUSION: Genetic alterations are a frequent event in HCC, and tumor related DNA fragments have been found in this study, which may be associated with hepatocarcin-ogenesis. RAPD is an effective method for the identification and analysis of genetic alterations in HCC, and may provide new information for further evaluating the molecular mechanism of hepatocarcinogenesis. PMID:15996039

Implementation of linear bias corrections for calorimeters at Mound

International Nuclear Information System (INIS)

Barnett, T.M.

1993-01-01

In the past, Mound has generally made relative bias corrections as part of the calibration of individual calorimeters. The correction made was the same over the entire operating range of the calorimeter, regardless of the magnitude of the range. Recently, an investigation was performed to check the relevancy of using linear bias corrections to calibrate the calorimeters. The bias is obtained by measuring calibrated plutonium and/or electrical heat standards over the operating range of the calorimeter. The bias correction is then calculated using a simple least squares fit (y = mx + b) of the bias in milliwatts over the operating range of the calorimeter in watts. The equation used is B i = B 0 + (B w * W m ), where B i is the bias at any given power in milliwatts, B 0 is the intercept (absolute bias in milliwatts), B w is the slope (relative bias in milliwatts per watt), and W m is the measured power in watts. The results of the study showed a decrease in the random error of bias corrected data for most of the calorimeters which are operated over a large wattage range (greater than an order of magnitude). The linear technique for bias correction has been fully implemented at Mound and has been included in the Technical Manual, ''A Measurement Control Program for Radiometric Calorimeters at Mound'' (MD-21900)

Stochastic dynamics of genetic broadcasting networks

Science.gov (United States)

Potoyan, Davit A.; Wolynes, Peter G.

2017-11-01

The complex genetic programs of eukaryotic cells are often regulated by key transcription factors occupying or clearing out of a large number of genomic locations. Orchestrating the residence times of these factors is therefore important for the well organized functioning of a large network. The classic models of genetic switches sidestep this timing issue by assuming the binding of transcription factors to be governed entirely by thermodynamic protein-DNA affinities. Here we show that relying on passive thermodynamics and random release times can lead to a "time-scale crisis" for master genes that broadcast their signals to a large number of binding sites. We demonstrate that this time-scale crisis for clearance in a large broadcasting network can be resolved by actively regulating residence times through molecular stripping. We illustrate these ideas by studying a model of the stochastic dynamics of the genetic network of the central eukaryotic master regulator NFκ B which broadcasts its signals to many downstream genes that regulate immune response, apoptosis, etc.

Genetic Parameters for Body condition score, Body weigth, Milk yield and Fertility estimated using random regression models

NARCIS (Netherlands)

Berry, D.P.; Buckley, F.; Dillon, P.; Evans, R.D.; Rath, M.; Veerkamp, R.F.

2003-01-01

Genetic (co)variances between body condition score (BCS), body weight (BW), milk yield, and fertility were estimated using a random regression animal model extended to multivariate analysis. The data analyzed included 81,313 BCS observations, 91,937 BW observations, and 100,458 milk test-day yields

Influence of the impurity-scattering on zero-bias conductance peak in ferromagnet/insulator/d-wave superconductor junctions

CERN Document Server

Yoshida, N; Itoh, H; Tanaka, Y; Inoue, J I; Kashiwaya, S

2003-01-01

Effects of impurity-scattering on a zero-bias conductance peak in ferromagnet/insulator/d-wave superconductor junctions are theoretically studied. The impurities are introduced through the random potential in ferromagnets near the junction interface. As in the case of normal-metal/insulator/d-wave superconductor junctions, the magnitude of zero-bias conductance peak decreases with increasing the degree of disorder. However, when the magnitude of the exchange potential in ferromagnet is sufficiently large, the random potential can enhance the zero-bias conductance peak in ferromagnetic junctions. (author)

Undesirable Choice Biases with Small Differences in the Spatial Structure of Chance Stimulus Sequences.

Directory of Open Access Journals (Sweden)

David Herrera

Full Text Available In two-alternative discrimination tasks, experimenters usually randomize the location of the rewarded stimulus so that systematic behavior with respect to irrelevant stimuli can only produce chance performance on the learning curves. One way to achieve this is to use random numbers derived from a discrete binomial distribution to create a 'full random training schedule' (FRS. When using FRS, however, sporadic but long laterally-biased training sequences occur by chance and such 'input biases' are thought to promote the generation of laterally-biased choices (i.e., 'output biases'. As an alternative, a 'Gellerman-like training schedule' (GLS can be used. It removes most input biases by prohibiting the reward from appearing on the same location for more than three consecutive trials. The sequence of past rewards obtained from choosing a particular discriminative stimulus influences the probability of choosing that same stimulus on subsequent trials. Assuming that the long-term average ratio of choices matches the long-term average ratio of reinforcers, we hypothesized that a reduced amount of input biases in GLS compared to FRS should lead to a reduced production of output biases. We compared the choice patterns produced by a 'Rational Decision Maker' (RDM in response to computer-generated FRS and GLS training sequences. To create a virtual RDM, we implemented an algorithm that generated choices based on past rewards. Our simulations revealed that, although the GLS presented fewer input biases than the FRS, the virtual RDM produced more output biases with GLS than with FRS under a variety of test conditions. Our results reveal that the statistical and temporal properties of training sequences interacted with the RDM to influence the production of output biases. Thus, discrete changes in the training paradigms did not translate linearly into modifications in the pattern of choices generated by a RDM. Virtual RDMs could be further employed to guide

Undesirable Choice Biases with Small Differences in the Spatial Structure of Chance Stimulus Sequences.

Science.gov (United States)

Herrera, David; Treviño, Mario

2015-01-01

In two-alternative discrimination tasks, experimenters usually randomize the location of the rewarded stimulus so that systematic behavior with respect to irrelevant stimuli can only produce chance performance on the learning curves. One way to achieve this is to use random numbers derived from a discrete binomial distribution to create a 'full random training schedule' (FRS). When using FRS, however, sporadic but long laterally-biased training sequences occur by chance and such 'input biases' are thought to promote the generation of laterally-biased choices (i.e., 'output biases'). As an alternative, a 'Gellerman-like training schedule' (GLS) can be used. It removes most input biases by prohibiting the reward from appearing on the same location for more than three consecutive trials. The sequence of past rewards obtained from choosing a particular discriminative stimulus influences the probability of choosing that same stimulus on subsequent trials. Assuming that the long-term average ratio of choices matches the long-term average ratio of reinforcers, we hypothesized that a reduced amount of input biases in GLS compared to FRS should lead to a reduced production of output biases. We compared the choice patterns produced by a 'Rational Decision Maker' (RDM) in response to computer-generated FRS and GLS training sequences. To create a virtual RDM, we implemented an algorithm that generated choices based on past rewards. Our simulations revealed that, although the GLS presented fewer input biases than the FRS, the virtual RDM produced more output biases with GLS than with FRS under a variety of test conditions. Our results reveal that the statistical and temporal properties of training sequences interacted with the RDM to influence the production of output biases. Thus, discrete changes in the training paradigms did not translate linearly into modifications in the pattern of choices generated by a RDM. Virtual RDMs could be further employed to guide the selection of

Biased sampling, over-identified parameter problems and beyond

CERN Document Server

Qin, Jing

2017-01-01

This book is devoted to biased sampling problems (also called choice-based sampling in Econometrics parlance) and over-identified parameter estimation problems. Biased sampling problems appear in many areas of research, including Medicine, Epidemiology and Public Health, the Social Sciences and Economics. The book addresses a range of important topics, including case and control studies, causal inference, missing data problems, meta-analysis, renewal process and length biased sampling problems, capture and recapture problems, case cohort studies, exponential tilting genetic mixture models etc. The goal of this book is to make it easier for Ph. D students and new researchers to get started in this research area. It will be of interest to all those who work in the health, biological, social and physical sciences, as well as those who are interested in survey methodology and other areas of statistical science, among others. .

STACCATO: a novel solution to supernova photometric classification with biased training sets

Science.gov (United States)

Revsbech, E. A.; Trotta, R.; van Dyk, D. A.

2018-01-01

We present a new solution to the problem of classifying Type Ia supernovae from their light curves alone given a spectroscopically confirmed but biased training set, circumventing the need to obtain an observationally expensive unbiased training set. We use Gaussian processes (GPs) to model the supernovae's (SN's) light curves, and demonstrate that the choice of covariance function has only a small influence on the GPs ability to accurately classify SNe. We extend and improve the approach of Richards et al. - a diffusion map combined with a random forest classifier - to deal specifically with the case of biased training sets. We propose a novel method called Synthetically Augmented Light Curve Classification (STACCATO) that synthetically augments a biased training set by generating additional training data from the fitted GPs. Key to the success of the method is the partitioning of the observations into subgroups based on their propensity score of being included in the training set. Using simulated light curve data, we show that STACCATO increases performance, as measured by the area under the Receiver Operating Characteristic curve (AUC), from 0.93 to 0.96, close to the AUC of 0.977 obtained using the 'gold standard' of an unbiased training set and significantly improving on the previous best result of 0.88. STACCATO also increases the true positive rate for SNIa classification by up to a factor of 50 for high-redshift/low-brightness SNe.

Apparent directional selection by biased pleiotropic mutation.

Science.gov (United States)

Tanaka, Yoshinari

2010-07-01

Pleiotropic effects of deleterious mutations are considered to be among the factors responsible for genetic constraints on evolution by long-term directional selection acting on a quantitative trait. If pleiotropic phenotypic effects are biased in a particular direction, mutations generate apparent directional selection, which refers to the covariance between fitness and the trait owing to a linear association between the number of mutations possessed by individuals and the genotypic values of the trait. The present analysis has shown how the equilibrium mean value of the trait is determined by a balance between directional selection and biased pleiotropic mutations. Assuming that genes act additively both on the trait and on fitness, the total variance-standardized directional selection gradient was decomposed into apparent and true components. Experimental data on mutation bias from the bristle traits of Drosophila and life history traits of Daphnia suggest that apparent selection explains a small but significant fraction of directional selection pressure that is observed in nature; the data suggest that changes induced in a trait by biased pleiotropic mutation (i.e., by apparent directional selection) are easily compensated for by (true) directional selection.

Effect of Duplicate Genes on Mouse Genetic Robustness: An Update

Directory of Open Access Journals (Sweden)

Zhixi Su

2014-01-01

Full Text Available In contrast to S. cerevisiae and C. elegans, analyses based on the current knockout (KO mouse phenotypes led to the conclusion that duplicate genes had almost no role in mouse genetic robustness. It has been suggested that the bias of mouse KO database toward ancient duplicates may possibly cause this knockout duplicate puzzle, that is, a very similar proportion of essential genes (PE between duplicate genes and singletons. In this paper, we conducted an extensive and careful analysis for the mouse KO phenotype data and corroborated a strong effect of duplicate genes on mouse genetics robustness. Moreover, the effect of duplicate genes on mouse genetic robustness is duplication-age dependent, which holds after ruling out the potential confounding effect from coding-sequence conservation, protein-protein connectivity, functional bias, or the bias of duplicates generated by whole genome duplication (WGD. Our findings suggest that two factors, the sampling bias toward ancient duplicates and very ancient duplicates with a proportion of essential genes higher than that of singletons, have caused the mouse knockout duplicate puzzle; meanwhile, the effect of genetic buffering may be correlated with sequence conservation as well as protein-protein interactivity.

No sex-biased dispersal in a primate with an uncommon social system—cooperative polyandry

Directory of Open Access Journals (Sweden)

Samuel L. Díaz-Muñoz

2014-10-01

Full Text Available An influential hypothesis proposed by Greenwood (1980 suggests that different mating systems result in female and male-biased dispersal, respectively, in birds and mammals. However, other aspects of social structure and behavior can also shape sex-biased dispersal. Although sex-specific patterns of kin cooperation are expected to affect the benefits of philopatry and dispersal patterns, empirical evidence is scarce. Unlike many mammals, Saguinus geoffroyi (Geoffroy’s tamarin has a breeding system in which typically multiple males mate with a single breeding female. Males typically form cooperative reproductive partnerships between relatives, whereas females generally compete for reproductive opportunities. This system of cooperative polyandry is predicted to result in female-biased dispersal, providing an opportunity to test the current hypotheses of sex-biased dispersal. Here we test for evidence of sex-biased dispersal in S. geoffroyi using demographic and genetic data from three populations. We find no sex bias in natal dispersal, contrary to the prediction based on the mating patterns. This pattern was consistent after controlling for the effects of historical population structure. Limited breeding opportunities within social groups likely drive both males and females to disperse, suggesting that dispersal is intimately related to the social context. The integration of genetic and field data revealed that tamarins are another exception to the presumed pattern of male-biased dispersal in mammals. A shift in focus from mating systems to social behavior, which plays a role in most all processes expected to influence sex-bias in dispersal, will be a fruitful target for research both within species and across taxa.

Detecting and correcting for publication bias in meta-analysis - A truncated normal distribution approach.

Science.gov (United States)

Zhu, Qiaohao; Carriere, K C

2016-01-01

Publication bias can significantly limit the validity of meta-analysis when trying to draw conclusion about a research question from independent studies. Most research on detection and correction for publication bias in meta-analysis focus mainly on funnel plot-based methodologies or selection models. In this paper, we formulate publication bias as a truncated distribution problem, and propose new parametric solutions. We develop methodologies of estimating the underlying overall effect size and the severity of publication bias. We distinguish the two major situations, in which publication bias may be induced by: (1) small effect size or (2) large p-value. We consider both fixed and random effects models, and derive estimators for the overall mean and the truncation proportion. These estimators will be obtained using maximum likelihood estimation and method of moments under fixed- and random-effects models, respectively. We carried out extensive simulation studies to evaluate the performance of our methodology, and to compare with the non-parametric Trim and Fill method based on funnel plot. We find that our methods based on truncated normal distribution perform consistently well, both in detecting and correcting publication bias under various situations.

Genetic variability of Amorphophallus muelleri Blume in Java based on Random Amplified Polymorphic DNA

Directory of Open Access Journals (Sweden)

DIYAH MARTANTI

2008-10-01

Full Text Available Amorphophallus muelleri Blume (Araceae is valued for its glucomanan content for use in food industry (healthy diet food, paper industry, pharmacy and cosmetics. The species is triploid (2n=3x=39 and the seed is developed apomictically. The present research is aimed to identify genetic variability of six population of A. muelleri from Java (consisted of 50 accessions using random amplified polymorphic DNA (RAPD. The six populations of the species are: East Java: (1 Silo-Jember, (2 Saradan-Madiun, (3 IPB (cultivated, from Saradan-Madiun, (4 Panti-Jember, (5 Probolinggo; and Central Java: (6 Cilacap. The results showed that five RAPD primers generated 42 scorable bands of which 29 (69.05% were polymorphic. Size of the bands varied from 300bp to 1.5kbp. The 50 accessions of A. muelleri were divided into two main clusters, some of them were grouped based on their populations, and some others were not. The range of individual genetic dissimilarity was from 0.02 to 0.36. The results showed that among six populations investigated, Saradan population showed the highest levels of genetic variation with mean values of na = 1.500+ 0.5061, ne = 1.3174 + 0.3841, PLP = 50% and He = 0, 0.1832+0.2054, whereas Silo-Jember population showed the lowest levels of genetic variation with mean values na = 1.2619+ 0.4450, ne = 1.1890 + 0.3507, PLP = 26.19% and He = 0.1048+0.1887. Efforts to conserve, domesticate, cultivate and improve genetically should be based on the genetic properties of each population and individual within population, especially Saradan population which has the highest levels of genetic variation, need more attention for its conservation.

Revealing the Cosmic Web-dependent Halo Bias

Science.gov (United States)

Yang, Xiaohu; Zhang, Youcai; Lu, Tianhuan; Wang, Huiyuan; Shi, Feng; Tweed, Dylan; Li, Shijie; Luo, Wentao; Lu, Yi; Yang, Lei

2017-10-01

Halo bias is the one of the key ingredients of the halo models. It was shown at a given redshift to be only dependent, to the first order, on the halo mass. In this study, four types of cosmic web environments—clusters, filaments, sheets, and voids—are defined within a state-of-the-art high-resolution N-body simulation. Within these environments, we use both halo-dark matter cross correlation and halo-halo autocorrelation functions to probe the clustering properties of halos. The nature of the halo bias differs strongly between the four different cosmic web environments described here. With respect to the overall population, halos in clusters have significantly lower biases in the {10}11.0˜ {10}13.5 {h}-1 {M}⊙ mass range. In other environments, however, halos show extremely enhanced biases up to a factor 10 in voids for halos of mass ˜ {10}12.0 {h}-1 {M}⊙ . Such a strong cosmic web environment dependence in the halo bias may play an important role in future cosmological and galaxy formation studies. Within this cosmic web framework, the age dependency of halo bias is found to be only significant in clusters and filaments for relatively small halos ≲ {10}12.5 {h}-1 {M}⊙ .

Weak randomness in device independent quantum key distribution and the advantage of using high dimensional entanglement

OpenAIRE

Huber, Marcus; Pawlowski, Marcin

2013-01-01

We show that in device independent quantum key distribution protocols the privacy of randomness is of crucial importance. For sublinear test sample sizes even the slightest guessing probability by an eavesdropper will completely compromise security. We show that a combined attack exploiting test sample and measurement choices compromises the security even with a linear size test sample and otherwise device independent security considerations. We explicitly derive the sample size needed to ret...

Randomized trial of proactive rapid genetic counseling versus usual care for newly diagnosed breast cancer patients.

Science.gov (United States)

Schwartz, Marc D; Peshkin, Beth N; Isaacs, Claudine; Willey, Shawna; Valdimarsdottir, Heiddis B; Nusbaum, Rachel; Hooker, Gillian; O'Neill, Suzanne; Jandorf, Lina; Kelly, Scott P; Heinzmann, Jessica; Zidell, Aliza; Khoury, Katia

2018-04-02

Breast cancer patients who carry BRCA1/BRCA2 gene mutations may consider bilateral mastectomy. Having bilateral mastectomy at the time of diagnosis not only reduces risk of a contralateral breast cancer, but can eliminate the need for radiation therapy and yield improved reconstruction options. However, most patients do not receive genetic counseling or testing at the time of their diagnosis. In this trial, we tested proactive rapid genetic counseling and testing (RGCT) in newly diagnosed breast cancer patients in order to facilitate pre-surgical genetic counseling and testing. We recruited newly diagnosed breast cancer patients at increased risk for carrying a BRCA1/2 mutation. Of 379 eligible patients who completed a baseline survey, 330 agreed to randomization in a 2:1 ratio to RGCT (n = 220) versus UC (n = 108). Primary outcomes were genetic counseling and testing uptake and breast cancer surgical decisions. RGCT led to higher overall (83.8% vs. 54.6%; p genetic counseling uptake compared to UC. Despite higher rates of genetic counseling, RGCT did not differ from UC in overall (54.1% vs. 49.1%, p > 0.10) or pre-surgical (30.6% vs. 27.4%, p > 0.10) receipt of genetic test results nor did they differ in uptake of bilateral mastectomy (26.6% vs. 21.8%, p > 0.10). Although RGCT yielded increased genetic counseling participation, this did not result in increased rates of pre-surgical genetic testing or impact surgical decisions. These data suggest that those patients most likely to opt for genetic testing at the time of diagnosis are being effectively identified by their surgeons.

Study books on ADHD genetics : balanced or biased?

NARCIS (Netherlands)

te Meerman, Sanne; Batstra, Laura; Hoekstra, Rink; Grietens, Hans

2017-01-01

Academic study books are essential assets for disseminating knowledge about ADHD to future healthcare professionals. This study examined if they are balanced with regard to genetics. We selected and analyzed study books (N=43) used in (pre) master's programmes at 10 universities in the Netherlands.

Non-fragile observer design for discrete-time genetic regulatory networks with randomly occurring uncertainties

International Nuclear Information System (INIS)

Banu, L Jarina; Balasubramaniam, P

2015-01-01

This paper investigates the problem of non-fragile observer design for a class of discrete-time genetic regulatory networks (DGRNs) with time-varying delays and randomly occurring uncertainties. A non-fragile observer is designed, for estimating the true concentration of mRNAs and proteins from available measurement outputs. One important feature of the results obtained that are reported here is that the parameter uncertainties are assumed to be random and their probabilities of occurrence are known a priori. On the basis of the Lyapunov–Krasovskii functional approach and using a convex combination technique, a delay-dependent estimation criterion is established for DGRNs in terms of linear matrix inequalities (LMIs) that can be efficiently solved using any available LMI solver. Finally numerical examples are provided to substantiate the theoretical results. (paper)

Genetic moderation of the association between regulatory focus and reward responsiveness: a proof-of-concept study.

Science.gov (United States)

Goetz, Elena L; Hariri, Ahmad R; Pizzagalli, Diego A; Strauman, Timothy J

2013-02-01

Recent studies implicate individual differences in regulatory focus as contributing to self-regulatory dysfunction, particularly not responding to positive outcomes. How such individual differences emerge, however, is unclear. We conducted a proof-of-concept study to examine the moderating effects of genetically driven variation in dopamine signaling, a key modulator of neural reward circuits, on the association between regulatory focus and reward cue responsiveness. Healthy Caucasians (N=59) completed a measure of chronic regulatory focus and a probabilistic reward task. A common functional genetic polymorphism impacting prefrontal dopamine signaling (COMT rs4680) was evaluated. Response bias, the participants' propensity to modulate behavior as a function of reward, was predicted by an interaction of regulatory focus and COMT genotype. Specifically, self-perceived success at achieving promotion goals predicted total response bias, but only for individuals with the COMT genotype (Val/Val) associated with relatively increased phasic dopamine signaling and cognitive flexibility. The combination of success in promotion goal pursuit and Val/Val genotype appears to facilitate responding to reward opportunities in the environment. This study is among the first to integrate an assessment of self-regulatory style with an examination of genetic variability that underlies responsiveness to positive outcomes in goal pursuit.

A simple bias correction in linear regression for quantitative trait association under two-tail extreme selection

OpenAIRE

Kwan, Johnny S. H.; Kung, Annie W. C.; Sham, Pak C.

2011-01-01

Selective genotyping can increase power in quantitative trait association. One example of selective genotyping is two-tail extreme selection, but simple linear regression analysis gives a biased genetic effect estimate. Here, we present a simple correction for the bias. © The Author(s) 2011.

Application of random number generators in genetic algorithms to improve rainfall-runoff modelling

Czech Academy of Sciences Publication Activity Database

Chlumecký, M.; Buchtele, Josef; Richta, K.

2017-01-01

Roč. 553, October (2017), s. 350-355 ISSN 0022-1694 Institutional support: RVO:67985874 Keywords : genetic algorithm * optimisation * rainfall-runoff modeling * random generator Subject RIV: DA - Hydrology ; Limnology OBOR OECD: Hydrology Impact factor: 3.483, year: 2016 https://ac.els-cdn.com/S0022169417305516/1-s2.0-S0022169417305516-main.pdf?_tid=fa1bad8a-bd6a-11e7-8567-00000aab0f27&acdnat=1509365462_a1335d3d997e9eab19e23b1eee977705

Blinding in randomized clinical trials: imposed impartiality

DEFF Research Database (Denmark)

Hróbjartsson, A; Boutron, I

2011-01-01

Blinding, or "masking," is a crucial method for reducing bias in randomized clinical trials. In this paper, we review important methodological aspects of blinding, emphasizing terminology, reporting, bias mechanisms, empirical evidence, and the risk of unblinding. Theoretical considerations...

Genetic predisposition to increased blood cholesterol and triglyceride lipid levels and risk of Alzheimer disease: a Mendelian randomization analysis.

Directory of Open Access Journals (Sweden)

Petroula Proitsi

2014-09-01

Full Text Available Although altered lipid metabolism has been extensively implicated in the pathogenesis of Alzheimer disease (AD through cell biological, epidemiological, and genetic studies, the molecular mechanisms linking cholesterol and AD pathology are still not well understood and contradictory results have been reported. We have used a Mendelian randomization approach to dissect the causal nature of the association between circulating lipid levels and late onset AD (LOAD and test the hypothesis that genetically raised lipid levels increase the risk of LOAD.We included 3,914 patients with LOAD, 1,675 older individuals without LOAD, and 4,989 individuals from the general population from six genome wide studies drawn from a white population (total n=10,578. We constructed weighted genotype risk scores (GRSs for four blood lipid phenotypes (high-density lipoprotein cholesterol [HDL-c], low-density lipoprotein cholesterol [LDL-c], triglycerides, and total cholesterol using well-established SNPs in 157 loci for blood lipids reported by Willer and colleagues (2013. Both full GRSs using all SNPs associated with each trait at p<5×10-8 and trait specific scores using SNPs associated exclusively with each trait at p<5 × 10-8 were developed. We used logistic regression to investigate whether the GRSs were associated with LOAD in each study and results were combined together by meta-analysis. We found no association between any of the full GRSs and LOAD (meta-analysis results: odds ratio [OR]=1.005, 95% CI 0.82-1.24, p = 0.962 per 1 unit increase in HDL-c; OR=0.901, 95% CI 0.65-1.25, p=0.530 per 1 unit increase in LDL-c; OR=1.104, 95% CI 0.89-1.37, p=0.362 per 1 unit increase in triglycerides; and OR=0.954, 95% CI 0.76-1.21, p=0.688 per 1 unit increase in total cholesterol. Results for the trait specific scores were similar; however, the trait specific scores explained much smaller phenotypic variance.Genetic predisposition to increased blood cholesterol and

Information bias and lifetime mortality risks of radiation-induced cancer: Low LET radiation

International Nuclear Information System (INIS)

Peterson, L.E.; Schull, W.J.; Davis, B.R.; Buffler, P.A.

1994-04-01

Additive and multiplicative models of relative risk were used to measure the effect of cancer misclassification and DS86 random errors on lifetime risk projections in the Life Span Study (LSS) of Hiroshima and Nagasaki atomic bomb survivors. The true number of cancer deaths in each stratum of the cancer mortality cross-classification was estimated using sufficient statistics from the EM algorithm. Average survivor doses in the strata were corrected for DS86 random error (σ=0.45) by use of reduction factors. Poisson regression was used to model the corrected and uncorrected mortality rates with risks in RERF Report 11 (Part 2) and the BEIR-V Report. Bias due to DS86 random error typically ranged from -15% to -30% for both sexes, and all sites and models. The total bias, including diagnostic misclassification, of excess risk of nonleukemia for exposure to 1 Sv from age 18 to 65 under the non-constant relative project model was -37.1% for males and -23.3% for females. Total excess risks of leukemia under the relative projection model were biased -27.1% for males and -43.4% for females. Thus, nonleukemia risks for 1 Sv from ages 18 to 65 (DRREF=2) increased from 1.91%/Sv to 2.68%/Sv among males and from 3.23%/Sv to 4.92%/Sv among females. Leukemia excess risk increased from 0.87%/Sv to 1.10/Sv among males and from 0.73%/Sv to 1.04/Sv among females. Bias was dependent on the gender, site, correction method, exposure profile and projection model considered. Future studies that use LSS data for US nuclear workers may be downwardly biased if lifetime risk projections are not adjusted for random and systematic errors

Information bias and lifetime mortality risks of radiation-induced cancer: Low LET radiation

Energy Technology Data Exchange (ETDEWEB)

Peterson, L.E.; Schull, W.J.; Davis, B.R. [Texas Univ., Houston, TX (United States). Health Science Center; Buffler, P.A. [California Univ., Berkeley, CA (United States). School of Public Health

1994-04-01

Additive and multiplicative models of relative risk were used to measure the effect of cancer misclassification and DS86 random errors on lifetime risk projections in the Life Span Study (LSS) of Hiroshima and Nagasaki atomic bomb survivors. The true number of cancer deaths in each stratum of the cancer mortality cross-classification was estimated using sufficient statistics from the EM algorithm. Average survivor doses in the strata were corrected for DS86 random error ({sigma}=0.45) by use of reduction factors. Poisson regression was used to model the corrected and uncorrected mortality rates with risks in RERF Report 11 (Part 2) and the BEIR-V Report. Bias due to DS86 random error typically ranged from {minus}15% to {minus}30% for both sexes, and all sites and models. The total bias, including diagnostic misclassification, of excess risk of nonleukemia for exposure to 1 Sv from age 18 to 65 under the non-constant relative project model was {minus}37.1% for males and {minus}23.3% for females. Total excess risks of leukemia under the relative projection model were biased {minus}27.1% for males and {minus}43.4% for females. Thus, nonleukemia risks for 1 Sv from ages 18 to 65 (DRREF=2) increased from 1.91%/Sv to 2.68%/Sv among males and from 3.23%/Sv to 4.92%/Sv among females. Leukemia excess risk increased from 0.87%/Sv to 1.10/Sv among males and from 0.73%/Sv to 1.04/Sv among females. Bias was dependent on the gender, site, correction method, exposure profile and projection model considered. Future studies that use LSS data for US nuclear workers may be downwardly biased if lifetime risk projections are not adjusted for random and systematic errors.

Effectiveness of oncogenetics training on general practitioners' consultation skills: a randomized controlled trial.

Science.gov (United States)

Houwink, Elisa J F; Muijtjens, Arno M M; van Teeffelen, Sarah R; Henneman, Lidewij; Rethans, Jan Joost; van der Jagt, Liesbeth E J; van Luijk, Scheltus J; Dinant, Geert Jan; van der Vleuten, Cees; Cornel, Martina C

2014-01-01

General practitioners are increasingly called upon to deliver genetic services and could play a key role in translating potentially life-saving advancements in oncogenetic technologies to patient care. If general practitioners are to make an effective contribution in this area, their genetics competencies need to be upgraded. The aim of this study was to investigate whether oncogenetics training for general practitioners improves their genetic consultation skills. In this pragmatic, blinded, randomized controlled trial, the intervention consisted of a 4-h training (December 2011 and April 2012), covering oncogenetic consultation skills (family history, familial risk assessment, and efficient referral), attitude (medical ethical issues), and clinical knowledge required in primary-care consultations. Outcomes were measured using observation checklists by unannounced standardized patients and self-reported questionnaires. Of 88 randomized general practitioners who initially agreed to participate, 56 completed all measurements. Key consultation skills significantly and substantially improved; regression coefficients after intervention were equivalent to 0.34 and 0.28 at 3-month follow-up, indicating a moderate effect size. Satisfaction and perceived applicability of newly learned skills were highly scored. The general practitioner-specific training proved to be a feasible, satisfactory, and clinically applicable method to improve oncogenetics consultation skills and could be used as an educational framework to inform future training activities with the ultimate aim of improving medical care.

Genetic analysis of partial egg production records in Japanese quail using random regression models.

Science.gov (United States)

Abou Khadiga, G; Mahmoud, B Y F; Farahat, G S; Emam, A M; El-Full, E A

2017-08-01

The main objectives of this study were to detect the most appropriate random regression model (RRM) to fit the data of monthly egg production in 2 lines (selected and control) of Japanese quail and to test the consistency of different criteria of model choice. Data from 1,200 female Japanese quails for the first 5 months of egg production from 4 consecutive generations of an egg line selected for egg production in the first month (EP1) was analyzed. Eight RRMs with different orders of Legendre polynomials were compared to determine the proper model for analysis. All criteria of model choice suggested that the adequate model included the second-order Legendre polynomials for fixed effects, and the third-order for additive genetic effects and permanent environmental effects. Predictive ability of the best model was the highest among all models (ρ = 0.987). According to the best model fitted to the data, estimates of heritability were relatively low to moderate (0.10 to 0.17) showed a descending pattern from the first to the fifth month of production. A similar pattern was observed for permanent environmental effects with greater estimates in the first (0.36) and second (0.23) months of production than heritability estimates. Genetic correlations between separate production periods were higher (0.18 to 0.93) than their phenotypic counterparts (0.15 to 0.87). The superiority of the selected line over the control was observed through significant (P egg production in earlier ages (first and second months) than later ones. A methodology based on random regression animal models can be recommended for genetic evaluation of egg production in Japanese quail. © 2017 Poultry Science Association Inc.

Illustrating, Quantifying, and Correcting for Bias in Post-hoc Analysis of Gene-Based Rare Variant Tests of Association

Directory of Open Access Journals (Sweden)

Kelsey E. Grinde

2017-09-01

Full Text Available To date, gene-based rare variant testing approaches have focused on aggregating information across sets of variants to maximize statistical power in identifying genes showing significant association with diseases. Beyond identifying genes that are associated with diseases, the identification of causal variant(s in those genes and estimation of their effect is crucial for planning replication studies and characterizing the genetic architecture of the locus. However, we illustrate that straightforward single-marker association statistics can suffer from substantial bias introduced by conditioning on gene-based test significance, due to the phenomenon often referred to as “winner's curse.” We illustrate the ramifications of this bias on variant effect size estimation and variant prioritization/ranking approaches, outline parameters of genetic architecture that affect this bias, and propose a bootstrap resampling method to correct for this bias. We find that our correction method significantly reduces the bias due to winner's curse (average two-fold decrease in bias, p < 2.2 × 10−6 and, consequently, substantially improves mean squared error and variant prioritization/ranking. The method is particularly helpful in adjustment for winner's curse effects when the initial gene-based test has low power and for relatively more common, non-causal variants. Adjustment for winner's curse is recommended for all post-hoc estimation and ranking of variants after a gene-based test. Further work is necessary to continue seeking ways to reduce bias and improve inference in post-hoc analysis of gene-based tests under a wide variety of genetic architectures.

Mitochondrial DNA sequence characteristics modulate the size of the genetic bottleneck.

Science.gov (United States)

Wilson, Ian J; Carling, Phillipa J; Alston, Charlotte L; Floros, Vasileios I; Pyle, Angela; Hudson, Gavin; Sallevelt, Suzanne C E H; Lamperti, Costanza; Carelli, Valerio; Bindoff, Laurence A; Samuels, David C; Wonnapinij, Passorn; Zeviani, Massimo; Taylor, Robert W; Smeets, Hubert J M; Horvath, Rita; Chinnery, Patrick F

2016-03-01

With a combined carrier frequency of 1:200, heteroplasmic mitochondrial DNA (mtDNA) mutations cause human disease in ∼1:5000 of the population. Rapid shifts in the level of heteroplasmy seen within a single generation contribute to the wide range in the severity of clinical phenotypes seen in families transmitting mtDNA disease, consistent with a genetic bottleneck during transmission. Although preliminary evidence from human pedigrees points towards a random drift process underlying the shifting heteroplasmy, some reports describe differences in segregation pattern between different mtDNA mutations. However, based on limited observations and with no direct comparisons, it is not clear whether these observations simply reflect pedigree ascertainment and publication bias. To address this issue, we studied 577 mother-child pairs transmitting the m.11778G>A, m.3460G>A, m.8344A>G, m.8993T>G/C and m.3243A>G mtDNA mutations. Our analysis controlled for inter-assay differences, inter-laboratory variation and ascertainment bias. We found no evidence of selection during transmission but show that different mtDNA mutations segregate at different rates in human pedigrees. m.8993T>G/C segregated significantly faster than m.11778G>A, m.8344A>G and m.3243A>G, consistent with a tighter mtDNA genetic bottleneck in m.8993T>G/C pedigrees. Our observations support the existence of different genetic bottlenecks primarily determined by the underlying mtDNA mutation, explaining the different inheritance patterns observed in human pedigrees transmitting pathogenic mtDNA mutations. © The Author 2016. Published by Oxford University Press.

The generation of 68 Gbps quantum random number by measuring laser phase fluctuations

International Nuclear Information System (INIS)

Nie, You-Qi; Liu, Yang; Zhang, Jun; Pan, Jian-Wei; Huang, Leilei; Payne, Frank

2015-01-01

The speed of a quantum random number generator is essential for practical applications, such as high-speed quantum key distribution systems. Here, we push the speed of a quantum random number generator to 68 Gbps by operating a laser around its threshold level. To achieve the rate, not only high-speed photodetector and high sampling rate are needed but also a very stable interferometer is required. A practical interferometer with active feedback instead of common temperature control is developed to meet the requirement of stability. Phase fluctuations of the laser are measured by the interferometer with a photodetector and then digitalized to raw random numbers with a rate of 80 Gbps. The min-entropy of the raw data is evaluated by modeling the system and is used to quantify the quantum randomness of the raw data. The bias of the raw data caused by other signals, such as classical and detection noises, can be removed by Toeplitz-matrix hashing randomness extraction. The final random numbers can pass through the standard randomness tests. Our demonstration shows that high-speed quantum random number generators are ready for practical usage

A simple algorithm to estimate genetic variance in an animal threshold model using Bayesian inference Genetics Selection Evolution 2010, 42:29

DEFF Research Database (Denmark)

Ødegård, Jørgen; Meuwissen, Theo HE; Heringstad, Bjørg

2010-01-01

Background In the genetic analysis of binary traits with one observation per animal, animal threshold models frequently give biased heritability estimates. In some cases, this problem can be circumvented by fitting sire- or sire-dam models. However, these models are not appropriate in cases where...... records exist for the parents). Furthermore, the new algorithm showed much faster Markov chain mixing properties for genetic parameters (similar to the sire-dam model). Conclusions The new algorithm to estimate genetic parameters via Gibbs sampling solves the bias problems typically occurring in animal...... individual records exist on parents. Therefore, the aim of our study was to develop a new Gibbs sampling algorithm for a proper estimation of genetic (co)variance components within an animal threshold model framework. Methods In the proposed algorithm, individuals are classified as either "informative...

Security of BB84 with weak randomness and imperfect qubit encoding

Science.gov (United States)

Zhao, Liang-Yuan; Yin, Zhen-Qiang; Li, Hong-Wei; Chen, Wei; Fang, Xi; Han, Zheng-Fu; Huang, Wei

2018-03-01

The main threats for the well-known Bennett-Brassard 1984 (BB84) practical quantum key distribution (QKD) systems are that its encoding is inaccurate and measurement device may be vulnerable to particular attacks. Thus, a general physical model or security proof to tackle these loopholes simultaneously and quantitatively is highly desired. Here we give a framework on the security of BB84 when imperfect qubit encoding and vulnerability of measurement device are both considered. In our analysis, the potential attacks to measurement device are generalized by the recently proposed weak randomness model which assumes the input random numbers are partially biased depending on a hidden variable planted by an eavesdropper. And the inevitable encoding inaccuracy is also introduced here. From a fundamental view, our work reveals the potential information leakage due to encoding inaccuracy and weak randomness input. For applications, our result can be viewed as a useful tool to quantitatively evaluate the security of a practical QKD system.

Effect of Risk of Bias on the Effect Size of Meta-Analytic Estimates in Randomized Controlled Trials in Periodontology and Implant Dentistry

Science.gov (United States)

Faggion, Clovis Mariano; Wu, Yun-Chun; Scheidgen, Moritz; Tu, Yu-Kang

2015-01-01

Background Risk of bias (ROB) may threaten the internal validity of a clinical trial by distorting the magnitude of treatment effect estimates, although some conflicting information on this assumption exists. Objective The objective of this study was evaluate the effect of ROB on the magnitude of treatment effect estimates in randomized controlled trials (RCTs) in periodontology and implant dentistry. Methods A search for Cochrane systematic reviews (SRs), including meta-analyses of RCTs published in periodontology and implant dentistry fields, was performed in the Cochrane Library in September 2014. Random-effect meta-analyses were performed by grouping RCTs with different levels of ROBs in three domains (sequence generation, allocation concealment, and blinding of outcome assessment). To increase power and precision, only SRs with meta-analyses including at least 10 RCTs were included. Meta-regression was performed to investigate the association between ROB characteristics and the magnitudes of intervention effects in the meta-analyses. Results Of the 24 initially screened SRs, 21 SRs were excluded because they did not include at least 10 RCTs in the meta-analyses. Three SRs (two from periodontology field) generated information for conducting 27 meta-analyses. Meta-regression did not reveal significant differences in the relationship of the ROB level with the size of treatment effect estimates, although a trend for inflated estimates was observed in domains with unclear ROBs. Conclusion In this sample of RCTs, high and (mainly) unclear risks of selection and detection biases did not seem to influence the size of treatment effect estimates, although several confounders might have influenced the strength of the association. PMID:26422698

Quantum random walks using quantum accelerator modes

International Nuclear Information System (INIS)

Ma, Z.-Y.; Burnett, K.; D'Arcy, M. B.; Gardiner, S. A.

2006-01-01

We discuss the use of high-order quantum accelerator modes to achieve an atom optical realization of a biased quantum random walk. We first discuss how one can create coexistent quantum accelerator modes, and hence how momentum transfer that depends on the atoms' internal state can be achieved. When combined with microwave driving of the transition between the states, a different type of atomic beam splitter results. This permits the realization of a biased quantum random walk through quantum accelerator modes

Accelerating foreign-key joins using asymmetric memory channels

NARCIS (Netherlands)

Pirk, H.; Manegold, S.; Kersten, M.

2011-01-01

Indexed Foreign-Key Joins expose a very asymmetric access pattern: the Foreign-Key Index is sequentially scanned whilst the Primary-Key table is target of many quasi-random lookups which is the dominant cost factor. To reduce the costs of the random lookups the fact-table can be (re-) partitioned at

Body image related negative interpretation bias in anorexia nervosa.

Science.gov (United States)

Brockmeyer, Timo; Anderle, Alisa; Schmidt, Hagen; Febry, Stephanie; Wünsch-Leiteritz, Wally; Leiteritz, Andreas; Friederich, Hans-Christoph

2018-05-01

A distorted body image and pronounced body dissatisfaction are hallmarks of anorexia nervosa (AN) that typically result in dietary restraint and compensatory behaviours. Cognitive biases such as negative interpretation bias are considered key maintaining factors of these maladaptive cognitions and behaviours. However, little attention has been paid to empirical tests whether negative interpretation bias exists in AN and to what degree it is associated with symptom severity. Participants in the present study were 40 women with AN and 40 healthy women with no history of an eating disorder. Body-related negative interpretation bias (i.e., a tendency to interpret ambiguous information about the own body in a negative way) was measured by a Scrambled Sentences Task. Patients with AN showed a stronger body-related negative interpretation bias than healthy controls. Within both groups, negative interpretation bias correlated strongly and positively with AN symptom severity and these effects were not moderated by levels of depressive symptoms. The findings support the idea that biased interpretation of body-related information is associated with the specific psychopathology of AN. Targeted, computerised interventions (e.g. interpretation bias modification) may help to alter these dysfunctional cognitive schemas that lie at the heart of AN. Copyright © 2018 Elsevier Ltd. All rights reserved.

Examinations of Home Economics Textbooks for Sex Bias.

Science.gov (United States)

Weis, Susan F.

1979-01-01

Four analyses were conducted on a sample of 100 randomly selected, secondary home economics textbooks published between 1964 and 1974. Results indicated that the contents presented sex bias in language usage, in pictures portraying male and female role environments, and in role behaviors and expectations emphasized. (Author/JH)

Sex-biased gene flow among elk in the greater Yellowstone ecosystem

Science.gov (United States)

Hand, Brian K.; Chen, Shanyuan; Anderson, Neil; Beja-Pereira, Albano; Cross, Paul C.; Ebinger, Michael R.; Edwards, Hank; Garrott, Robert A.; Kardos, Marty D.; Kauffman, Matthew J.; Landguth, Erin L.; Middleton, Arthur; Scurlock, Brandon M.; White, P.J.; Zager, Pete; Schwartz, Michael K.; Luikart, Gordon

2014-01-01

We quantified patterns of population genetic structure to help understand gene flow among elk populations across the Greater Yellowstone Ecosystem. We sequenced 596 base pairs of the mitochondrial control region of 380 elk from eight populations. Analysis revealed high mitochondrial DNA variation within populations, averaging 13.0 haplotypes with high mean gene diversity (0.85). The genetic differentiation among populations for mitochondrial DNA was relatively high (FST  =  0.161; P  =  0.001) compared to genetic differentiation for nuclear microsatellite data (FST  =  0.002; P  =  0.332), which suggested relatively low female gene flow among populations. The estimated ratio of male to female gene flow (mm/mf  =  46) was among the highest we have seen reported for large mammals. Genetic distance (for mitochondrial DNA pairwise FST) was not significantly correlated with geographic (Euclidean) distance between populations (Mantel's r  =  0.274, P  =  0.168). Large mitochondrial DNA genetic distances (e.g., FST > 0.2) between some of the geographically closest populations (<65 km) suggested behavioral factors and/or landscape features might shape female gene flow patterns. Given the strong sex-biased gene flow, future research and conservation efforts should consider the sexes separately when modeling corridors of gene flow or predicting spread of maternally transmitted diseases. The growing availability of genetic data to compare male vs. female gene flow provides many exciting opportunities to explore the magnitude, causes, and implications of sex-biased gene flow likely to occur in many species.

Opposing Forces of A/T-Biased Mutations and G/C-Biased Gene Conversions Shape the Genome of the Nematode Pristionchus pacificus

Science.gov (United States)

Weller, Andreas M.; Rödelsperger, Christian; Eberhardt, Gabi; Molnar, Ruxandra I.; Sommer, Ralf J.

2014-01-01

Base substitution mutations are a major source of genetic novelty and mutation accumulation line (MAL) studies revealed a nearly universal AT bias in de novo mutation spectra. While a comparison of de novo mutation spectra with the actual nucleotide composition in the genome suggests the existence of general counterbalancing mechanisms, little is known about the evolutionary and historical details of these opposing forces. Here, we correlate MAL-derived mutation spectra with patterns observed from population resequencing. Variation observed in natural populations has already been subject to evolutionary forces. Distinction between rare and common alleles, the latter of which are close to fixation and of presumably older age, can provide insight into mutational processes and their influence on genome evolution. We provide a genome-wide analysis of de novo mutations in 22 MALs of the nematode Pristionchus pacificus and compare the spectra with natural variants observed in resequencing of 104 natural isolates. MALs show an AT bias of 5.3, one of the highest values observed to date. In contrast, the AT bias in natural variants is much lower. Specifically, rare derived alleles show an AT bias of 2.4, whereas common derived alleles close to fixation show no AT bias at all. These results indicate the existence of a strong opposing force and they suggest that the GC content of the P. pacificus genome is in equilibrium. We discuss GC-biased gene conversion as a potential mechanism acting against AT-biased mutations. This study provides insight into genome evolution by combining MAL studies with natural variation. PMID:24414549

Improved Anonymity for Key-trees

NARCIS (Netherlands)

Veugen, P.J.M.; Beye, M.

2013-01-01

Randomized hash-lock protocols for Radio Frequency IDentification (RFID) tags offer forward untraceability, but incur heavy search on the server. Key trees have been proposed as a way to reduce search times, but because partial keys in such trees are shared, key compromise affects several tags.

Lifestyle Advice Combined with Personalized Estimates of Genetic or Phenotypic Risk of Type 2 Diabetes, and Objectively Measured Physical Activity: A Randomized Controlled Trial.

Directory of Open Access Journals (Sweden)

Job G Godino

2016-11-01

Full Text Available Information about genetic and phenotypic risk of type 2 diabetes is now widely available and is being incorporated into disease prevention programs. Whether such information motivates behavior change or has adverse effects is uncertain. We examined the effect of communicating an estimate of genetic or phenotypic risk of type 2 diabetes in a parallel group, open, randomized controlled trial.We recruited 569 healthy middle-aged adults from the Fenland Study, an ongoing population-based, observational study in the east of England (Cambridgeshire, UK. We used a computer-generated random list to assign participants in blocks of six to receive either standard lifestyle advice alone (control group, n = 190 or in combination with a genetic (n = 189 or a phenotypic (n = 190 risk estimate for type 2 diabetes (intervention groups. After 8 wk, we measured the primary outcome, objectively measured physical activity (kJ/kg/day, and also measured several secondary outcomes (including self-reported diet, self-reported weight, worry, anxiety, and perceived risk. The study was powered to detect a between-group difference of 4.1 kJ/kg/d at follow-up. 557 (98% participants completed the trial. There were no significant intervention effects on physical activity (difference in adjusted mean change from baseline: genetic risk group versus control group 0.85 kJ/kg/d (95% CI -2.07 to 3.77, p = 0.57; phenotypic risk group versus control group 1.32 (95% CI -1.61 to 4.25, p = 0.38; and genetic risk group versus phenotypic risk group -0.47 (95% CI -3.40 to 2.46, p = 0.75. No significant differences in self-reported diet, self-reported weight, worry, and anxiety were observed between trial groups. Estimates of perceived risk were significantly more accurate among those who received risk information than among those who did not. Key limitations include the recruitment of a sample that may not be representative of the UK population, use of self-reported secondary outcome

Inferring genetic parameters of lactation in Tropical Milking Criollo cattle with random regression test-day models.

Science.gov (United States)

Santellano-Estrada, E; Becerril-Pérez, C M; de Alba, J; Chang, Y M; Gianola, D; Torres-Hernández, G; Ramírez-Valverde, R

2008-11-01

This study inferred genetic and permanent environmental variation of milk yield in Tropical Milking Criollo cattle and compared 5 random regression test-day models using Wilmink's function and Legendre polynomials. Data consisted of 15,377 test-day records from 467 Tropical Milking Criollo cows that calved between 1974 and 2006 in the tropical lowlands of the Gulf Coast of Mexico and in southern Nicaragua. Estimated heritabilities of test-day milk yields ranged from 0.18 to 0.45, and repeatabilities ranged from 0.35 to 0.68 for the period spanning from 6 to 400 d in milk. Genetic correlation between days in milk 10 and 400 was around 0.50 but greater than 0.90 for most pairs of test days. The model that used first-order Legendre polynomials for additive genetic effects and second-order Legendre polynomials for permanent environmental effects gave the smallest residual variance and was also favored by the Akaike information criterion and likelihood ratio tests.

Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus

Directory of Open Access Journals (Sweden)

Zhitao Niu

2017-11-01

Full Text Available The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization. However, the reason for this variation is still an open question. Different kinds of hypotheses have been proposed to explain the variation of GC content during genome evolution. However, these hypotheses have not been explicitly investigated in whole plastome sequences. Dendrobium is one of the largest genera in the orchid species. Evolutionary studies of the plastomic organization and base composition are limited in this genus. In this study, we obtained the high-quality plastome sequences of D. loddigesii and D. devonianum. The comparison results showed a nearly identical organization in Dendrobium plastomes, indicating that the plastomic organization is highly conserved in Dendrobium genus. Furthermore, the impact of three evolutionary forces—selection, mutational biases, and GC-biased gene conversion (gBGC—on the variation of GC content in Dendrobium plastomes was evaluated. Our results revealed: (1 consistent GC content evolution trends and mutational biases in single-copy (SC and inverted repeats (IRs regions; and (2 that gBGC has influenced the plastome-wide GC content evolution. These results suggest that both mutational biases and gBGC affect GC content in the plastomes of Dendrobium genus.

Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus

Science.gov (United States)

Niu, Zhitao; Xue, Qingyun; Wang, Hui; Xie, Xuezhu; Zhu, Shuying; Liu, Wei; Ding, Xiaoyu

2017-01-01

The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization. However, the reason for this variation is still an open question. Different kinds of hypotheses have been proposed to explain the variation of GC content during genome evolution. However, these hypotheses have not been explicitly investigated in whole plastome sequences. Dendrobium is one of the largest genera in the orchid species. Evolutionary studies of the plastomic organization and base composition are limited in this genus. In this study, we obtained the high-quality plastome sequences of D. loddigesii and D. devonianum. The comparison results showed a nearly identical organization in Dendrobium plastomes, indicating that the plastomic organization is highly conserved in Dendrobium genus. Furthermore, the impact of three evolutionary forces—selection, mutational biases, and GC-biased gene conversion (gBGC)—on the variation of GC content in Dendrobium plastomes was evaluated. Our results revealed: (1) consistent GC content evolution trends and mutational biases in single-copy (SC) and inverted repeats (IRs) regions; and (2) that gBGC has influenced the plastome-wide GC content evolution. These results suggest that both mutational biases and gBGC affect GC content in the plastomes of Dendrobium genus. PMID:29099062

Dose-rate effects of low-dropout voltage regulator at various biases

International Nuclear Information System (INIS)

Wang Yiyuan; Zheng Yuzhan; Gao Bo; Chen Rui; Fei Wuxiong; Lu Wu; Ren Diyuan

2010-01-01

A low-dropout voltage regulator, LM2941, was irradiated by 60 Co γ-rays at various dose rates and biases for investigating the total dose and dose rate effects. The radiation responses show that the key electrical parameters, including its output and dropout voltage, and the maximum output current, are sensitive to total dose and dose rates, and are significantly degraded at low dose rate and zero bias. The integrated circuits damage change with the dose rates and biases, and the dose-rate effects are relative to its electric field. (authors)

Regression dilution bias: tools for correction methods and sample size calculation.

Science.gov (United States)

Berglund, Lars

2012-08-01

Random errors in measurement of a risk factor will introduce downward bias of an estimated association to a disease or a disease marker. This phenomenon is called regression dilution bias. A bias correction may be made with data from a validity study or a reliability study. In this article we give a non-technical description of designs of reliability studies with emphasis on selection of individuals for a repeated measurement, assumptions of measurement error models, and correction methods for the slope in a simple linear regression model where the dependent variable is a continuous variable. Also, we describe situations where correction for regression dilution bias is not appropriate. The methods are illustrated with the association between insulin sensitivity measured with the euglycaemic insulin clamp technique and fasting insulin, where measurement of the latter variable carries noticeable random error. We provide software tools for estimation of a corrected slope in a simple linear regression model assuming data for a continuous dependent variable and a continuous risk factor from a main study and an additional measurement of the risk factor in a reliability study. Also, we supply programs for estimation of the number of individuals needed in the reliability study and for choice of its design. Our conclusion is that correction for regression dilution bias is seldom applied in epidemiological studies. This may cause important effects of risk factors with large measurement errors to be neglected.

Addressing weight bias and discrimination: moving beyond raising awareness to creating change.

Science.gov (United States)

Ramos Salas, X; Alberga, A S; Cameron, E; Estey, L; Forhan, M; Kirk, S F L; Russell-Mayhew, S; Sharma, A M

2017-11-01

Weight discrimination is the unjust treatment of individuals because of their weight. There have been very few interventions to address weight discrimination, due in part to the lack of consensus on key messages and strategies. The objective of the third Canadian Weight Bias Summit was to review current evidence and move towards consensus on key weight bias and obesity discrimination reduction messages and strategies. Using a modified brokered dialogue approach, participants, including researchers, health professionals, policy makers and people living with obesity, reviewed the evidence and moved towards consensus on key messages and strategies for future interventions. Participants agreed to these key messages: (1) Weight bias and obesity discrimination should not be tolerated in education, health care and public policy sectors; (2) obesity should be recognized and treated as a chronic disease in health care and policy sectors; and (3) in the education sector, weight and health need to be decoupled. Consensus on future strategies included (1) creating resources to support policy makers, (2) using personal narratives from people living with obesity to engage audiences and communicate anti-discrimination messages and (3) developing a better clinical definition for obesity. Messages and strategies should be implemented and evaluated using consistent theoretical frameworks and methodologies. © 2017 World Obesity Federation.

Genetic correlations among body condition score, yield, and fertility in first-parity cows estimated by random regression models.

Science.gov (United States)

Veerkamp, R F; Koenen, E P; De Jong, G

2001-10-01

Twenty type classifiers scored body condition (BCS) of 91,738 first-parity cows from 601 sires and 5518 maternal grandsires. Fertility data during first lactation were extracted for 177,220 cows, of which 67,278 also had a BCS observation, and first-lactation 305-d milk, fat, and protein yields were added for 180,631 cows. Heritabilities and genetic correlations were estimated using a sire-maternal grandsire model. Heritability of BCS was 0.38. Heritabilities for fertility traits were low (0.01 to 0.07), but genetic standard deviations were substantial, 9 d for days to first service and calving interval, 0.25 for number of services, and 5% for first-service conception. Phenotypic correlations between fertility and yield or BCS were small (-0.15 to 0.20). Genetic correlations between yield and all fertility traits were unfavorable (0.37 to 0.74). Genetic correlations with BCS were between -0.4 and -0.6 for calving interval and days to first service. Random regression analysis (RR) showed that correlations changed with days in milk for BCS. Little agreement was found between variances and correlations from RR, and analysis including a single month (mo 1 to 10) of data for BCS, especially during early and late lactation. However, this was due to excluding data from the conventional analysis, rather than due to the polynomials used. RR and a conventional five-traits model where BCS in mo 1, 4, 7, and 10 was treated as a separate traits (plus yield or fertility) gave similar results. Thus a parsimonious random regression model gave more realistic estimates for the (co)variances than a series of bivariate analysis on subsets of the data for BCS. A higher genetic merit for yield has unfavorable effects on fertility, but the genetic correlation suggests that BCS (at some stages of lactation) might help to alleviate the unfavorable effect of selection for higher yield on fertility.

Effects of Cognitive Bias Modification Training via Smartphones

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Ranming Yang

2017-08-01

Full Text Available Background and Objectives: Negative cognitive biases have been linked to anxiety and mood problems. Accumulated data from laboratory studies show that positive and negative interpretation styles with accompanying changes in mood can be induced through cognitive bias modification (CBM paradigms. Despite the therapeutic potential of positive training effects, few studies have explored training paradigms administered via smartphones. The current study aimed to compare the effectiveness of three different types of training programmes (cognitive bias modification-attention, CBM-A; cognitive bias modification-interpretation, CBM-I; attention and interpretation modification, AIM administered via smart-phones by using a control condition (CC.Methods:Seventy-six undergraduate participants with high social anxiety (Liebowitz Social Anxiety Scale, LSAS ≥ 30 were randomly assigned to four groups: CBM-A (n = 20, CBM-I (n = 20, AIM (n = 16, and CC (n = 20.Results: The results showed that the effects of CBM training, CBM-I training, or AIM training vs. CC for attention yielded no significant differences in dot-probe attention bias scores. The CBM-I group showed significantly less threat interpretation and more benign interpretation than the CC group on interpretation bias scores.Conclusions: The present results supported the feasibility of delivering CBM-I via smartphones, but the effectiveness of CBM-A and AIM training via smartphones was limited.

Role of the antiferromagnetic bulk spins in exchange bias

Energy Technology Data Exchange (ETDEWEB)

Schuller, Ivan K. [Center for Advanced Nanoscience and Physics Department, University of California San Diego, La Jolla, CA 92093 (United States); Morales, Rafael, E-mail: rafael.morales@ehu.es [Department of Chemical-Physics & BCMaterials, University of the Basque Country UPV/EHU (Spain); IKERBASQUE, Basque Foundation for Science, 48011 Bilbao (Spain); Batlle, Xavier [Departament Física Fonamental and Institut de Nanociència i Nanotecnologia, Universitat de Barcelona, c/ Martí i Franqués s/n, 08028 Barcelona, Catalonia (Spain); Nowak, Ulrich [Department of Physics, University of Konstanz, 78464 Konstanz (Germany); Güntherodt, Gernot [Physics Institute (IIA), RWTH Aachen University, Campus RWTH-Melaten, 52074 Aachen (Germany)

2016-10-15

This “Critical Focused Issue” presents a brief review of experiments and models which describe the origin of exchange bias in epitaxial or textured ferromagnetic/antiferromagnetic bilayers. Evidence is presented which clearly indicates that inner, uncompensated, pinned moments in the bulk of the antiferromagnet (AFM) play a very important role in setting the magnitude of the exchange bias. A critical evaluation of the extensive literature in the field indicates that it is useful to think of this bulk, pinned uncompensated moments as a new type of a ferromagnet which has a low total moment, an ordering temperature given by the AFM Néel temperature, with parallel aligned moments randomly distributed on the regular AFM lattice. - Highlights: • We address the role of bulk antiferromagnetic spins in the exchange bias phenomenon. • Significant experiments on how bulk AFM spins determine exchange bias are highlighted. • We explain the model that accounts for experimental results.

Role of the antiferromagnetic bulk spins in exchange bias

International Nuclear Information System (INIS)

Schuller, Ivan K.; Morales, Rafael; Batlle, Xavier; Nowak, Ulrich; Güntherodt, Gernot

2016-01-01

This “Critical Focused Issue” presents a brief review of experiments and models which describe the origin of exchange bias in epitaxial or textured ferromagnetic/antiferromagnetic bilayers. Evidence is presented which clearly indicates that inner, uncompensated, pinned moments in the bulk of the antiferromagnet (AFM) play a very important role in setting the magnitude of the exchange bias. A critical evaluation of the extensive literature in the field indicates that it is useful to think of this bulk, pinned uncompensated moments as a new type of a ferromagnet which has a low total moment, an ordering temperature given by the AFM Néel temperature, with parallel aligned moments randomly distributed on the regular AFM lattice. - Highlights: • We address the role of bulk antiferromagnetic spins in the exchange bias phenomenon. • Significant experiments on how bulk AFM spins determine exchange bias are highlighted. • We explain the model that accounts for experimental results.

Low Genetic Quality Alters Key Dimensions of the Mutational Spectrum.

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Nathaniel P Sharp

2016-03-01

Full Text Available Mutations affect individual health, population persistence, adaptation, diversification, and genome evolution. There is evidence that the mutation rate varies among genotypes, but the causes of this variation are poorly understood. Here, we link differences in genetic quality with variation in spontaneous mutation in a Drosophila mutation accumulation experiment. We find that chromosomes maintained in low-quality genetic backgrounds experience a higher rate of indel mutation and a lower rate of gene conversion in a manner consistent with condition-based differences in the mechanisms used to repair DNA double strand breaks. These aspects of the mutational spectrum were also associated with body mass, suggesting that the effect of genetic quality on DNA repair was mediated by overall condition, and providing a mechanistic explanation for the differences in mutational fitness decline among these genotypes. The rate and spectrum of substitutions was unaffected by genetic quality, but we find variation in the probability of substitutions and indels with respect to several aspects of local sequence context, particularly GC content, with implications for models of molecular evolution and genome scans for signs of selection. Our finding that the chances of mutation depend on genetic context and overall condition has important implications for how sequences evolve, the risk of extinction, and human health.

Disentangling the effects of selection and loss bias on gene dynamics

NARCIS (Netherlands)

Iranzo, J.; Cuesta, J.A.; Manrubia, S.; Katsnelson, M.I.; Koonin, E.V.

2017-01-01

We combine mathematical modeling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the

Evaluation of biases present in the cohort multiple randomised controlled trial design: a simulation study

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Jane Candlish

2017-01-01

Full Text Available Abstract Background The cohort multiple randomised controlled trial (cmRCT design provides an opportunity to incorporate the benefits of randomisation within clinical practice; thus reducing costs, integrating electronic healthcare records, and improving external validity. This study aims to address a key concern of the cmRCT design: refusal to treatment is only present in the intervention arm, and this may lead to bias and reduce statistical power. Methods We used simulation studies to assess the effect of this refusal, both random and related to event risk, on bias of the effect estimator and statistical power. A series of simulations were undertaken that represent a cmRCT trial with time-to-event endpoint. Intention-to-treat (ITT, per protocol (PP, and instrumental variable (IV analysis methods, two stage predictor substitution and two stage residual inclusion, were compared for various refusal scenarios. Results We found the IV methods provide a less biased estimator for the causal effect when refusal is present in the intervention arm, with the two stage residual inclusion method performing best with regards to minimum bias and sufficient power. We demonstrate that sample sizes should be adapted based on expected and actual refusal rates in order to be sufficiently powered for IV analysis. Conclusion We recommend running both an IV and ITT analyses in an individually randomised cmRCT as it is expected that the effect size of interest, or the effect we would observe in clinical practice, would lie somewhere between that estimated with ITT and IV analyses. The optimum (in terms of bias and power instrumental variable method was the two stage residual inclusion method. We recommend using adaptive power calculations, updating them as refusal rates are collected in the trial recruitment phase in order to be sufficiently powered for IV analysis.

Quantifying selective reporting and the Proteus phenomenon for multiple datasets with similar bias.

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Thomas Pfeiffer

2011-03-01

Full Text Available Meta-analyses play an important role in synthesizing evidence from diverse studies and datasets that address similar questions. A major obstacle for meta-analyses arises from biases in reporting. In particular, it is speculated that findings which do not achieve formal statistical significance are less likely reported than statistically significant findings. Moreover, the patterns of bias can be complex and may also depend on the timing of the research results and their relationship with previously published work. In this paper, we present an approach that is specifically designed to analyze large-scale datasets on published results. Such datasets are currently emerging in diverse research fields, particularly in molecular medicine. We use our approach to investigate a dataset on Alzheimer's disease (AD that covers 1167 results from case-control studies on 102 genetic markers. We observe that initial studies on a genetic marker tend to be substantially more biased than subsequent replications. The chances for initial, statistically non-significant results to be published are estimated to be about 44% (95% CI, 32% to 63% relative to statistically significant results, while statistically non-significant replications have almost the same chance to be published as statistically significant replications (84%; 95% CI, 66% to 107%. Early replications tend to be biased against initial findings, an observation previously termed Proteus phenomenon: The chances for non-significant studies going in the same direction as the initial result are estimated to be lower than the chances for non-significant studies opposing the initial result (73%; 95% CI, 55% to 96%. Such dynamic patterns in bias are difficult to capture by conventional methods, where typically simple publication bias is assumed to operate. Our approach captures and corrects for complex dynamic patterns of bias, and thereby helps generating conclusions from published results that are more robust

The Effectiveness of Cognitive Bias Modification Interventions for Substance Addictions: A Meta-Analysis.

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Ioana A Cristea

Full Text Available Cognitive bias modification (CBM interventions, presumably targeting automatic processes, are considered particularly promising for addictions. We conducted a meta-analysis examining randomized controlled trials (RCTs of CBM for substance addiction outcomes.Studies were identified through systematic searches in bibliographical databases. We included RCTs of CBM interventions, alone or in combination with other treatments, for any type of addiction. We examined trial risk of bias, publication bias and possible moderators. Effects sizes were computed for post-test and follow-up, using a random-effects model. We grouped outcome measures and reported results for addiction (all related measures, craving and cognitive bias.We identified 25 trials, 18 for alcohol problems, and 7 for smoking. At post-test, there was no significant effect of CBM for addiction, g = 0.08 (95% CI -0.02 to 0.18 or craving, g = 0.05 (95% CI -0.06 to 0.16, but there was a significant, moderate effect on cognitive bias, g = 0.60 (95% CI 0.39 to 0.79. Results were similar for alcohol and smoking outcomes taken separately. Follow-up addiction outcomes were reported in 7 trials, resulting in a small but significant effect of CBM, g = 0.18 (95% CI 0.03 to 0.32. Results for addiction and craving did not differ by substance type, sample type, delivery setting, bias targeted or number of sessions. Risk of bias was high or uncertain in most trials, for most criteria considered. Meta-regression analyses revealed significant inverse relationships between risk of bias and effect sizes for addiction outcomes and craving. The relationship between cognitive bias and respectively addiction ESs was not significant. There was consistent evidence of publication bias in the form of funnel plot asymmetry.Our results cast serious doubts on the clinical utility of CBM interventions for addiction problems, but sounder methodological trials are necessary before this issue can be settled. We found no

Flexibility of the genetic code with respect to DNA structure

DEFF Research Database (Denmark)

Baisnée, P. F.; Baldi, Pierre; Brunak, Søren

2001-01-01

Motivation. The primary function of DNA is to carry genetic information through the genetic code. DNA, however, contains a variety of other signals related, for instance, to reading frame, codon bias, pairwise codon bias, splice sites and transcription regulation, nucleosome positioning and DNA...... structure. Here we study the relationship between the genetic code and DNA structure and address two questions. First, to which degree does the degeneracy of the genetic code and the acceptable amino acid substitution patterns allow for the superimposition of DNA structural signals to protein coding...... sequences? Second, is the origin or evolution of the genetic code likely to have been constrained by DNA structure? Results. We develop an index for code flexibility with respect to DNA structure. Using five different di- or tri-nucleotide models of sequence-dependent DNA structure, we show...

Genetic programming in microorganisms

Energy Technology Data Exchange (ETDEWEB)

Hopwood, D A

1981-11-01

Formerly, when microbiologists had only existing organisms at their disposal whose characteristics could only be changed randomly by genetic experiments, they used to dream of programmed genetic changes. This dream has come true with modern genetic engineering.

Effective size of density-dependent two-sex populations: the effect of mating systems.

Science.gov (United States)

Myhre, A M; Engen, S; SAEther, B-E

2017-08-01

Density dependence in vital rates is a key feature affecting temporal fluctuations of natural populations. This has important implications for the rate of random genetic drift. Mating systems also greatly affect effective population sizes, but knowledge of how mating system and density regulation interact to affect random genetic drift is poor. Using theoretical models and simulations, we compare N e in short-lived, density-dependent animal populations with different mating systems. We study the impact of a fluctuating, density-dependent sex ratio and consider both a stable and a fluctuating environment. We find a negative relationship between annual N e /N and adult population size N due to density dependence, suggesting that loss of genetic variation is reduced at small densities. The magnitude of this decrease was affected by mating system and life history. A male-biased, density-dependent sex ratio reduces the rate of genetic drift compared to an equal, density-independent sex ratio, but a stochastic change towards male bias reduces the N e /N ratio. Environmental stochasticity amplifies temporal fluctuations in population size and is thus vital to consider in estimation of effective population sizes over longer time periods. Our results on the reduced loss of genetic variation at small densities, particularly in polygamous populations, indicate that density regulation may facilitate adaptive evolution at small population sizes. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Dynamic Load Balanced Clustering using Elitism based Random Immigrant Genetic Approach for Wireless Sensor Networks

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K. Mohaideen Pitchai

2017-07-01

Full Text Available Wireless Sensor Network (WSN consists of a large number of small sensors with restricted energy. Prolonged network lifespan, scalability, node mobility and load balancing are important needs for several WSN applications. Clustering the sensor nodes is an efficient technique to reach these goals. WSN have the characteristics of topology dynamics because of factors like energy conservation and node movement that leads to Dynamic Load Balanced Clustering Problem (DLBCP. In this paper, Elitism based Random Immigrant Genetic Approach (ERIGA is proposed to solve DLBCP which adapts to topology dynamics. ERIGA uses the dynamic Genetic Algorithm (GA components for solving the DLBCP. The performance of load balanced clustering process is enhanced with the help of this dynamic GA. As a result, the ERIGA achieves to elect suitable cluster heads which balances the network load and increases the lifespan of the network.

The 'whys' and 'whens' of individual differences in thinking biases.

Science.gov (United States)

De Neys, Wim; Bonnefon, Jean-François

2013-04-01

Although human thinking is often biased, some individuals are less susceptible to biases than others. These individual differences have been at the forefront of thinking research for more than a decade. We organize the literature in three key accounts (storage, monitoring, and inhibition failure) and propose that a critical but overlooked question concerns the time point at which individual variance arises: do biased and unbiased reasoners take different paths early on in the reasoning process or is the observed variance late to arise? We discuss how this focus on the 'whens' suggests that individual differences in thinking biases are less profound than traditionally assumed, in the sense that they might typically arise at a later stage of the reasoning process. Copyright © 2013 Elsevier Ltd. All rights reserved.

Genetic variation of seedling traits in a random mating population of sunflower

International Nuclear Information System (INIS)

Habib, S.

2004-01-01

Forty S/sub 1/ families obtained from a random mating population of sunflower were evaluated in the laboratory for various seedling traits. The objectives of this study were to investigate the extent and nature of genetic variability and to determine the estimates of genotypic and phenotypic correlations among ten seedling traits prevailing in a random mating population of sunflower. The results indicated that significant differences existed among the 40 S/sub 1/ families for all the traits evaluated. Genotypic and phenotypic coefficients of variation were comparatively high for emergence rate index, root/shoot ratio, dry root weight, fresh root weight and fresh shoot weight. The estimates of broad-sense heritability were high and significant for all the traits. The study of genotypic and phenotypic correlations among these traits revealed that generally, the seedlings which took more time to emerge were vigorous for most of the traits except fresh shoot length. However, rapidly emerging seedlings had higher emergence percentage. The root traits appeared to be better indicators of seedling vigour compared to other traits as these traits exhibited strong and positive genotypic and phenotypic correlations among them. (author)

Longitudinal changes in telomere length and associated genetic parameters in dairy cattle analysed using random regression models.

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Luise A Seeker

Full Text Available Telomeres cap the ends of linear chromosomes and shorten with age in many organisms. In humans short telomeres have been linked to morbidity and mortality. With the accumulation of longitudinal datasets the focus shifts from investigating telomere length (TL to exploring TL change within individuals over time. Some studies indicate that the speed of telomere attrition is predictive of future disease. The objectives of the present study were to 1 characterize the change in bovine relative leukocyte TL (RLTL across the lifetime in Holstein Friesian dairy cattle, 2 estimate genetic parameters of RLTL over time and 3 investigate the association of differences in individual RLTL profiles with productive lifespan. RLTL measurements were analysed using Legendre polynomials in a random regression model to describe TL profiles and genetic variance over age. The analyses were based on 1,328 repeated RLTL measurements of 308 female Holstein Friesian dairy cattle. A quadratic Legendre polynomial was fitted to the fixed effect of age in months and to the random effect of the animal identity. Changes in RLTL, heritability and within-trait genetic correlation along the age trajectory were calculated and illustrated. At a population level, the relationship between RLTL and age was described by a positive quadratic function. Individuals varied significantly regarding the direction and amount of RLTL change over life. The heritability of RLTL ranged from 0.36 to 0.47 (SE = 0.05-0.08 and remained statistically unchanged over time. The genetic correlation of RLTL at birth with measurements later in life decreased with the time interval between samplings from near unity to 0.69, indicating that TL later in life might be regulated by different genes than TL early in life. Even though animals differed in their RLTL profiles significantly, those differences were not correlated with productive lifespan (p = 0.954.

Genetic evidence for landscape effects on dispersal in the army ant Eciton burchellii.

Science.gov (United States)

Soare, Thomas W; Kumar, Anjali; Naish, Kerry A; O'Donnell, Sean

2014-01-01

Inhibited dispersal, leading to reduced gene flow, threatens populations with inbreeding depression and local extinction. Fragmentation may be especially detrimental to social insects because inhibited gene flow has important consequences for cooperation and competition within and among colonies. Army ants have winged males and permanently wingless queens; these traits imply male-biased dispersal. However, army ant colonies are obligately nomadic and have the potential to traverse landscapes. Eciton burchellii, the most regularly nomadic army ant, is a forest interior species: colony raiding activities are limited in the absence of forest cover. To examine whether nomadism and landscape (forest clearing and elevation) affect population genetic structure in a montane E. burchellii population, we reconstructed queen and male genotypes from 25 colonies at seven polymorphic microsatellite loci. Pairwise genetic distances among individuals were compared to pairwise geographical and resistance distances using regressions with permutations, partial Mantel tests and random forests analyses. Although there was no significant spatial genetic structure in queens or males in montane forest, dispersal may be male-biased. We found significant isolation by landscape resistance for queens based on land cover (forest clearing), but not on elevation. Summed colony emigrations over the lifetime of the queen may contribute to gene flow in this species and forest clearing impedes these movements and subsequent gene dispersal. Further forest cover removal may increasingly inhibit Eciton burchellii colony dispersal. We recommend maintaining habitat connectivity in tropical forests to promote population persistence for this keystone species. © 2013 John Wiley & Sons Ltd.

Strategies for MCMC computation in quantitative genetics

DEFF Research Database (Denmark)

Waagepetersen, Rasmus; Ibánez, N.; Sorensen, Daniel

2006-01-01

Given observations of a trait and a pedigree for a group of animals, the basic model in quantitative genetics is a linear mixed model with genetic random effects. The correlation matrix of the genetic random effects is determined by the pedigree and is typically very highdimensional but with a sp...

Exploring the repetition bias in voluntary task switching.

Science.gov (United States)

Mittelstädt, Victor; Dignath, David; Schmidt-Ott, Magdalena; Kiesel, Andrea

2018-01-01

In the voluntary task-switching paradigm, participants are required to randomly select tasks. We reasoned that the consistent finding of a repetition bias (i.e., participants repeat tasks more often than expected by chance) reflects reasonable adaptive task selection behavior to balance the goal of random task selection with the goals to minimize the time and effort for task performance. We conducted two experiments in which participants were provided with variable amount of preview for the non-chosen task stimuli (i.e., potential switch stimuli). We assumed that switch stimuli would initiate some pre-processing resulting in improved performance in switch trials. Results showed that reduced switch costs due to extra-preview in advance of each trial were accompanied by more task switches. This finding is in line with the characteristics of rational adaptive behavior. However, participants were not biased to switch tasks more often than chance despite large switch benefits. We suggest that participants might avoid effortful additional control processes that modulate the effects of preview on task performance and task choice.

Estimation of Genetic Parameters for First Lactation Monthly Test-day Milk Yields using Random Regression Test Day Model in Karan Fries Cattle

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Ajay Singh

2016-06-01

Full Text Available A single trait linear mixed random regression test-day model was applied for the first time for analyzing the first lactation monthly test-day milk yield records in Karan Fries cattle. The test-day milk yield data was modeled using a random regression model (RRM considering different order of Legendre polynomial for the additive genetic effect (4th order and the permanent environmental effect (5th order. Data pertaining to 1,583 lactation records spread over a period of 30 years were recorded and analyzed in the study. The variance component, heritability and genetic correlations among test-day milk yields were estimated using RRM. RRM heritability estimates of test-day milk yield varied from 0.11 to 0.22 in different test-day records. The estimates of genetic correlations between different test-day milk yields ranged 0.01 (test-day 1 [TD-1] and TD-11 to 0.99 (TD-4 and TD-5. The magnitudes of genetic correlations between test-day milk yields decreased as the interval between test-days increased and adjacent test-day had higher correlations. Additive genetic and permanent environment variances were higher for test-day milk yields at both ends of lactation. The residual variance was observed to be lower than the permanent environment variance for all the test-day milk yields.

Cognitive bias in forensic anthropology: visual assessment of skeletal remains is susceptible to confirmation bias.

Science.gov (United States)

Nakhaeizadeh, Sherry; Dror, Itiel E; Morgan, Ruth M

2014-05-01

An experimental study was designed to examine cognitive biases within forensic anthropological non-metric methods in assessing sex, ancestry and age at death. To investigate examiner interpretation, forty-one non-novice participants were semi randomly divided into three groups. Prior to conducting the assessment of the skeletal remains, two of the groups were given different extraneous contextual information regarding the sex, ancestry and age at death of the individual. The third group acted as a control group with no extraneous contextual information. The experiment was designed to investigate if the interpretation and conclusions of the skeletal remains would differ amongst participants within the three groups, and to assess whether the examiners would confirm or disagree with the given extraneous context when establishing a biological profile. The results revealed a significant biasing effect within the three groups, demonstrating a strong confirmation bias in the assessment of sex, ancestry and age at death. In assessment of sex, 31% of the participants in the control group concluded that the skeleton remains were male. In contrast, in the group that received contextual information that the remains were male, 72% concluded that the remains were male, and in the participant group where the context was that the remains were of a female, 0% of the participants concluded that the remains were male. Comparable results showing bias were found in assessing ancestry and age at death. These data demonstrate that cognitive bias can impact forensic anthropological non-metric methods on skeletal remains and affects the interpretation and conclusions of the forensic scientists. This empirical study is a step in establishing an evidence base approach for dealing with cognitive issues in forensic anthropological assessments, so as to enhance this valuable forensic science discipline. Copyright © 2013 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights

Errors in causal inference: an organizational schema for systematic error and random error.

Science.gov (United States)

Suzuki, Etsuji; Tsuda, Toshihide; Mitsuhashi, Toshiharu; Mansournia, Mohammad Ali; Yamamoto, Eiji

2016-11-01

To provide an organizational schema for systematic error and random error in estimating causal measures, aimed at clarifying the concept of errors from the perspective of causal inference. We propose to divide systematic error into structural error and analytic error. With regard to random error, our schema shows its four major sources: nondeterministic counterfactuals, sampling variability, a mechanism that generates exposure events and measurement variability. Structural error is defined from the perspective of counterfactual reasoning and divided into nonexchangeability bias (which comprises confounding bias and selection bias) and measurement bias. Directed acyclic graphs are useful to illustrate this kind of error. Nonexchangeability bias implies a lack of "exchangeability" between the selected exposed and unexposed groups. A lack of exchangeability is not a primary concern of measurement bias, justifying its separation from confounding bias and selection bias. Many forms of analytic errors result from the small-sample properties of the estimator used and vanish asymptotically. Analytic error also results from wrong (misspecified) statistical models and inappropriate statistical methods. Our organizational schema is helpful for understanding the relationship between systematic error and random error from a previously less investigated aspect, enabling us to better understand the relationship between accuracy, validity, and precision. Copyright © 2016 Elsevier Inc. All rights reserved.

Lifting the Curtain on the Wizard of Oz: Biased Voice-Based Impressions of Speaker Size

Science.gov (United States)

Rendall, Drew; Vokey, John R.; Nemeth, Christie

2007-01-01

The consistent, but often wrong, impressions people form of the size of unseen speakers are not random but rather point to a consistent misattribution bias, one that the advertising, broadcasting, and entertainment industries also routinely exploit. The authors report 3 experiments examining the perceptual basis of this bias. The results indicate…

Disclosure of genetic information and change in dietary intake: a randomized controlled trial.

Directory of Open Access Journals (Sweden)

Daiva E Nielsen

Full Text Available Proponents of consumer genetic tests claim that the information can positively impact health behaviors and aid in chronic disease prevention. However, the effects of disclosing genetic information on dietary intake behavior are not clear.A double-blinded, parallel group, 2:1 online randomized controlled trial was conducted to determine the short- and long-term effects of disclosing nutrition-related genetic information for personalized nutrition on dietary intakes of caffeine, vitamin C, added sugars, and sodium. Participants were healthy men and women aged 20-35 years (n = 138. The intervention group (n = 92 received personalized DNA-based dietary advice for 12-months and the control group (n = 46 received general dietary recommendations with no genetic information for 12-months. Food frequency questionnaires were collected at baseline and 3- and 12-months after the intervention to assess dietary intakes. General linear models were used to compare changes in intakes between those receiving general dietary advice and those receiving DNA-based dietary advice.Compared to the control group, no significant changes to dietary intakes of the nutrients were observed at 3-months. At 12-months, participants in the intervention group who possessed a risk version of the ACE gene, and were advised to limit their sodium intake, significantly reduced their sodium intake (mg/day compared to the control group (-287.3 ± 114.1 vs. 129.8 ± 118.2, p = 0.008. Those who had the non-risk version of ACE did not significantly change their sodium intake compared to the control group (12-months: -244.2 ± 150.2, p = 0.11. Among those with the risk version of the ACE gene, the proportion who met the targeted recommendation of 1500 mg/day increased from 19% at baseline to 34% after 12 months (p = 0.06.These findings demonstrate that disclosing genetic information for personalized nutrition results in greater changes in intake for some dietary components compared to

Simulation of a directed random-walk model: the effect of pseudo-random-number correlations

OpenAIRE

Shchur, L. N.; Heringa, J. R.; Blöte, H. W. J.

1996-01-01

We investigate the mechanism that leads to systematic deviations in cluster Monte Carlo simulations when correlated pseudo-random numbers are used. We present a simple model, which enables an analysis of the effects due to correlations in several types of pseudo-random-number sequences. This model provides qualitative understanding of the bias mechanism in a class of cluster Monte Carlo algorithms.

KeyPathwayMiner 4.0

DEFF Research Database (Denmark)

Alcaraz, Nicolas; Pauling, Josch; Batra, Richa

2014-01-01

release of KeyPathwayMiner (version 4.0) that is not limited to analyses of single omics data sets, e.g. gene expression, but is able to directly combine several different omics data types. Version 4.0 can further integrate existing knowledge by adding a search bias towards sub-networks that contain...... (avoid) genes provided in a positive (negative) list. Finally the new release now also provides a set of novel visualization features and has been implemented as an app for the standard bioinformatics network analysis tool: Cytoscape. CONCLUSION: With KeyPathwayMiner 4.0, we publish a Cytoscape app...

Rationality and emotionality: serotonin transporter genotype influences reasoning bias.

Science.gov (United States)

Stollstorff, Melanie; Bean, Stephanie E; Anderson, Lindsay M; Devaney, Joseph M; Vaidya, Chandan J

2013-04-01

Reasoning often occurs under emotionally charged, opinion-laden circumstances. The belief-bias effect indexes the extent to which reasoning is based upon beliefs rather than logical structure. We examined whether emotional content increases this effect, particularly for adults genetically predisposed to be more emotionally reactive. SS/SL(G) carriers of the serotonin transporter genotype (5-HTTLPR) were less accurate selectively for evaluating emotional relational reasoning problems with belief-logic conflict relative to L(A)L(A) carriers. Trait anxiety was positively associated with emotional belief-bias, and the 5-HTTLPR genotype significantly accounted for the variance in this association. Thus, deductive reasoning, a higher cognitive ability, is sensitive to differences in emotionality rooted in serotonin neurotransmitter function.

Highly aligned carbon nanotube arrays fabricated by bias sputtering

International Nuclear Information System (INIS)

Hayashi, Nobuyuki; Honda, Shin-ichi; Tsuji, Keita; Lee, Kuei-Yi; Ikuno, Takashi; Fujimoto, Keiichi; Ohkura, Shigeharu; Katayama, Mitsuhiro; Oura, Kenjiro; Hirao, Takashi

2003-01-01

Vertically aligned carbon nanotube (CNT) arrays have been successfully grown on Si substrates by dc bias sputtering. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observations revealed that the resultant arrays consisted of dense CNTs with diameters of 40-60 nm and lengths of 300-400 nm. The CNTs were found to have a bamboo-like structure at the end of which metallic nanoparticle was formed, indicating tip growth mechanism. The energy enhancement of carbon particles is a key factor for synthesis of CNTs using dc bias sputtering system

A Framework for Integrating Implicit Bias Recognition Into Health Professions Education.

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Sukhera, Javeed; Watling, Chris

2018-01-01

Existing literature on implicit bias is fragmented and comes from a variety of fields like cognitive psychology, business ethics, and higher education, but implicit-bias-informed educational approaches have been underexplored in health professions education and are difficult to evaluate using existing tools. Despite increasing attention to implicit bias recognition and management in health professions education, many programs struggle to meaningfully integrate these topics into curricula. The authors propose a six-point actionable framework for integrating implicit bias recognition and management into health professions education that draws on the work of previous researchers and includes practical tools to guide curriculum developers. The six key features of this framework are creating a safe and nonthreatening learning context, increasing knowledge about the science of implicit bias, emphasizing how implicit bias influences behaviors and patient outcomes, increasing self-awareness of existing implicit biases, improving conscious efforts to overcome implicit bias, and enhancing awareness of how implicit bias influences others. Important considerations for designing implicit-bias-informed curricula-such as individual and contextual variables, as well as formal and informal cultural influences-are discussed. The authors also outline assessment and evaluation approaches that consider outcomes at individual, organizational, community, and societal levels. The proposed framework may facilitate future research and exploration regarding the use of implicit bias in health professions education.

A simple method for analyzing data from a randomized trial with a missing binary outcome

Directory of Open Access Journals (Sweden)

Freedman Laurence S

2003-05-01

Full Text Available Abstract Background Many randomized trials involve missing binary outcomes. Although many previous adjustments for missing binary outcomes have been proposed, none of these makes explicit use of randomization to bound the bias when the data are not missing at random. Methods We propose a novel approach that uses the randomization distribution to compute the anticipated maximum bias when missing at random does not hold due to an unobserved binary covariate (implying that missingness depends on outcome and treatment group. The anticipated maximum bias equals the product of two factors: (a the anticipated maximum bias if there were complete confounding of the unobserved covariate with treatment group among subjects with an observed outcome and (b an upper bound factor that depends only on the fraction missing in each randomization group. If less than 15% of subjects are missing in each group, the upper bound factor is less than .18. Results We illustrated the methodology using data from the Polyp Prevention Trial. We anticipated a maximum bias under complete confounding of .25. With only 7% and 9% missing in each arm, the upper bound factor, after adjusting for age and sex, was .10. The anticipated maximum bias of .25 × .10 =.025 would not have affected the conclusion of no treatment effect. Conclusion This approach is easy to implement and is particularly informative when less than 15% of subjects are missing in each arm.

Direct random insertion mutagenesis of Helicobacter pylori

NARCIS (Netherlands)

de Jonge, Ramon; Bakker, Dennis; van Vliet, Arnoud H. M.; Kuipers, Ernst J.; Vandenbroucke-Grauls, Christina M. J. E.; Kusters, Johannes G.

2003-01-01

Random insertion mutagenesis is a widely used technique for the identification of bacterial virulence genes. Most strategies for random mutagenesis involve cloning in Escherichia coli for passage of plasmids or for phenotypic selection. This can result in biased selection due to restriction or

Direct random insertion mutagenesis of Helicobacter pylori.

NARCIS (Netherlands)

Jonge, de R.; Bakker, D.; Vliet, van AH; Kuipers, E.J.; Vandenbroucke-Grauls, C.M.J.E.; Kusters, J.G.

2003-01-01

Random insertion mutagenesis is a widely used technique for the identification of bacterial virulence genes. Most strategies for random mutagenesis involve cloning in Escherichia coli for passage of plasmids or for phenotypic selection. This can result in biased selection due to restriction or

Obesity bias among health and non-health students attending an Australian university and their perceived obesity education.

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Robinson, Emma L; Ball, Lauren E; Leveritt, Michael D

2014-01-01

This study compared the level of prejudice against obese individuals (obesity bias) among final-year health and non-health students, and associated obesity education. Cross-sectional online survey of 479 final-year students (292 health and 187 non-health) from Griffith University, Australia. Implicit and explicit obesity bias was measured using validated tools, and perceived obesity education ranked from "none" to "excellent." Data were analyzed quantitatively using analysis of variance and independent sample t tests. Statistical significance was set at P Students' mean age was 26.2 ± 7.6 years and body mass index was 23.2 ± 4.7 kg/m(2). Health and non-health students exhibited significant levels of obesity bias. Non-health students were more likely to suggest that obese individuals lacked willpower (P = .03). Students' self-reported obesity education varied considerably. Those who reported a higher level of genetics-related obesity education were less likely to believe that obese individuals were "bad" (P = .002) or to show concern about putting on weight (P = .01). Obesity bias exists in health students in Australia and is similar to non-health students' obesity bias levels. Students' self-reported genetics-related obesity education may be associated with obesity bias. Modifications to existing health curricula should be considered to reduce obesity bias among future health professionals. Copyright © 2014 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

On the motion of a Brownian particle with an asymmetric bias

International Nuclear Information System (INIS)

Kim, K.S.

1981-01-01

On the infinite three dimensional cubic lattice, the transport process of a Brownian particle biased on the direction (in the case of nearest-neighbor jumping) is discussed. The Brownian particle is considered as a walker of the random process. By introducing the theorem that the probability density P(l,t) becomes Gaussian for large t, P(l,t) is completely specified when the first and second moments of P(l,t) become known. The respective values for the transprot averaged velocity and dispersion of a biased Brownian particle are obtained. Finally as t becomes large we find Gaussian packets of a biased Brownian particle which propagate with a constant velocity and have a dispersion proportional to time t. (KAERI)

Occupation times and ergodicity breaking in biased continuous time random walks

International Nuclear Information System (INIS)

Bel, Golan; Barkai, Eli

2005-01-01

Continuous time random walk (CTRW) models are widely used to model diffusion in condensed matter. There are two classes of such models, distinguished by the convergence or divergence of the mean waiting time. Systems with finite average sojourn time are ergodic and thus Boltzmann-Gibbs statistics can be applied. We investigate the statistical properties of CTRW models with infinite average sojourn time; in particular, the occupation time probability density function is obtained. It is shown that in the non-ergodic phase the distribution of the occupation time of the particle on a given lattice point exhibits bimodal U or trimodal W shape, related to the arcsine law. The key points are as follows. (a) In a CTRW with finite or infinite mean waiting time, the distribution of the number of visits on a lattice point is determined by the probability that a member of an ensemble of particles in equilibrium occupies the lattice point. (b) The asymmetry parameter of the probability distribution function of occupation times is related to the Boltzmann probability and to the partition function. (c) The ensemble average is given by Boltzmann-Gibbs statistics for either finite or infinite mean sojourn time, when detailed balance conditions hold. (d) A non-ergodic generalization of the Boltzmann-Gibbs statistical mechanics for systems with infinite mean sojourn time is found

The genealogy and genetic viability of reintroduced Yellowstone grey wolves.

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Vonholdt, Bridgett M; Stahler, Daniel R; Smith, Douglas W; Earl, Dent A; Pollinger, John P; Wayne, Robert K

2008-01-01

The recovery of the grey wolf in Yellowstone National Park is an outstanding example of a successful reintroduction. A general question concerning reintroduction is the degree to which genetic variation has been preserved and the specific behavioural mechanisms that enhance the preservation of genetic diversity and reduce inbreeding. We have analysed 200 Yellowstone wolves, including all 31 founders, for variation in 26 microsatellite loci over the 10-year reintroduction period (1995-2004). The population maintained high levels of variation (1995 H(0) = 0.69; 2004 H(0) = 0.73) with low levels of inbreeding (1995 F(IS) = -0.063; 2004 F(IS) = -0.051) and throughout, the population expanded rapidly (N(1995) = 21; N(2004) = 169). Pedigree-based effective population size ratios did not vary appreciably over the duration of population expansion (1995 N(e)/N(g) = 0.29; 2000 N(e)/N(g) = 0.26; 2004 N(e)/N(g) = 0.33). We estimated kinship and found only two of 30 natural breeding pairs showed evidence of being related (average r = -0.026, SE = 0.03). We reconstructed the genealogy of 200 wolves based on genetic and field data and discovered that they avoid inbreeding through a wide variety of behavioural mechanisms including absolute avoidance of breeding with related pack members, male-biased dispersal to packs where they breed with nonrelatives, and female-biased subordinate breeding. We documented a greater diversity of such population assembly patterns in Yellowstone than previously observed in any other natural wolf population. Inbreeding avoidance is nearly absolute despite the high probability of within-pack inbreeding opportunities and extensive interpack kinship ties between adjacent packs. Simulations showed that the Yellowstone population has levels of genetic variation similar to that of a population managed for high variation and low inbreeding, and greater than that expected for random breeding within packs or across the entire breeding pool. Although short

Double random phase spread spectrum spread space technique for secure parallel optical multiplexing with individual encryption key

Science.gov (United States)

Hennelly, B. M.; Javidi, B.; Sheridan, J. T.

2005-09-01

A number of methods have been recently proposed in the literature for the encryption of 2-D information using linear optical systems. In particular the double random phase encoding system has received widespread attention. This system uses two Random Phase Keys (RPK) positioned in the input spatial domain and the spatial frequency domain and if these random phases are described by statistically independent white noises then the encrypted image can be shown to be a white noise. Decryption only requires knowledge of the RPK in the frequency domain. The RPK may be implemented using a Spatial Light Modulators (SLM). In this paper we propose and investigate the use of SLMs for secure optical multiplexing. We show that in this case it is possible to encrypt multiple images in parallel and multiplex them for transmission or storage. The signal energy is effectively spread in the spatial frequency domain. As expected the number of images that can be multiplexed together and recovered without loss is proportional to the ratio of the input image and the SLM resolution. Many more images may be multiplexed with some loss in recovery. Furthermore each individual encryption is more robust than traditional double random phase encoding since decryption requires knowledge of both RPK and a lowpass filter in order to despread the spectrum and decrypt the image. Numerical simulations are presented and discussed.

The genetic consequences of selection in natural populations.

Science.gov (United States)

Thurman, Timothy J; Barrett, Rowan D H

2016-04-01

The selection coefficient, s, quantifies the strength of selection acting on a genetic variant. Despite this parameter's central importance to population genetic models, until recently we have known relatively little about the value of s in natural populations. With the development of molecular genetic techniques in the late 20th century and the sequencing technologies that followed, biologists are now able to identify genetic variants and directly relate them to organismal fitness. We reviewed the literature for published estimates of natural selection acting at the genetic level and found over 3000 estimates of selection coefficients from 79 studies. Selection coefficients were roughly exponentially distributed, suggesting that the impact of selection at the genetic level is generally weak but can occasionally be quite strong. We used both nonparametric statistics and formal random-effects meta-analysis to determine how selection varies across biological and methodological categories. Selection was stronger when measured over shorter timescales, with the mean magnitude of s greatest for studies that measured selection within a single generation. Our analyses found conflicting trends when considering how selection varies with the genetic scale (e.g., SNPs or haplotypes) at which it is measured, suggesting a need for further research. Besides these quantitative conclusions, we highlight key issues in the calculation, interpretation, and reporting of selection coefficients and provide recommendations for future research. © 2016 John Wiley & Sons Ltd.

Correction of stream quality trends for the effects of laboratory measurement bias

Science.gov (United States)

Alexander, Richard B.; Smith, Richard A.; Schwarz, Gregory E.

1993-01-01

We present a statistical model relating measurements of water quality to associated errors in laboratory methods. Estimation of the model allows us to correct trends in water quality for long-term and short-term variations in laboratory measurement errors. An illustration of the bias correction method for a large national set of stream water quality and quality assurance data shows that reductions in the bias of estimates of water quality trend slopes are achieved at the expense of increases in the variance of these estimates. Slight improvements occur in the precision of estimates of trend in bias by using correlative information on bias and water quality to estimate random variations in measurement bias. The results of this investigation stress the need for reliable, long-term quality assurance data and efficient statistical methods to assess the effects of measurement errors on the detection of water quality trends.

A review of cognitive biases in youth depression: attention, interpretation and memory.

Science.gov (United States)

Platt, Belinda; Waters, Allison M; Schulte-Koerne, Gerd; Engelmann, Lina; Salemink, Elske

2017-04-01

Depression is one of the most common mental health problems in childhood and adolescence. Although data consistently show it is associated with self-reported negative cognitive styles, less is known about the mechanisms underlying this relationship. Cognitive biases in attention, interpretation and memory represent plausible mechanisms and are known to characterise adult depression. We provide the first structured review of studies investigating the nature and causal role of cognitive biases in youth depression. Key questions are (i) do cognitive biases characterise youth depression? (ii) are cognitive biases a vulnerability factor for youth depression? and (iii) do cognitive biases play a causal role in youth depression? We find consistent evidence for positive associations between attention and interpretation biases and youth depression. Stronger biases in youth with an elevated risk of depression support cognitive-vulnerability models. Preliminary evidence from cognitive bias modification paradigms supports a causal role of attention and interpretation biases in youth depression but these paradigms require testing in clinical samples before they can be considered treatment tools. Studies of memory biases in youth samples have produced mixed findings and none have investigated the causal role of memory bias. We identify numerous areas for future research in this emerging field.

A practical introduction to Random Forest for genetic association studies in ecology and evolution.

Science.gov (United States)

Brieuc, Marine S O; Waters, Charles D; Drinan, Daniel P; Naish, Kerry A

2018-03-05

Large genomic studies are becoming increasingly common with advances in sequencing technology, and our ability to understand how genomic variation influences phenotypic variation between individuals has never been greater. The exploration of such relationships first requires the identification of associations between molecular markers and phenotypes. Here, we explore the use of Random Forest (RF), a powerful machine-learning algorithm, in genomic studies to discern loci underlying both discrete and quantitative traits, particularly when studying wild or nonmodel organisms. RF is becoming increasingly used in ecological and population genetics because, unlike traditional methods, it can efficiently analyse thousands of loci simultaneously and account for nonadditive interactions. However, understanding both the power and limitations of Random Forest is important for its proper implementation and the interpretation of results. We therefore provide a practical introduction to the algorithm and its use for identifying associations between molecular markers and phenotypes, discussing such topics as data limitations, algorithm initiation and optimization, as well as interpretation. We also provide short R tutorials as examples, with the aim of providing a guide to the implementation of the algorithm. Topics discussed here are intended to serve as an entry point for molecular ecologists interested in employing Random Forest to identify trait associations in genomic data sets. © 2018 John Wiley & Sons Ltd.

ESTIMATION OF GENETIC PARAMETERS IN TROPICARNE CATTLE WITH RANDOM REGRESSION MODELS USING B-SPLINES

Directory of Open Access Journals (Sweden)

Joel Domínguez Viveros

2015-04-01

Full Text Available The objectives were to estimate variance components, and direct (h2 and maternal (m2 heritability in the growth of Tropicarne cattle based on a random regression model using B-Splines for random effects modeling. Information from 12 890 monthly weightings of 1787 calves, from birth to 24 months old, was analyzed. The pedigree included 2504 animals. The random effects model included genetic and permanent environmental (direct and maternal of cubic order, and residuals. The fixed effects included contemporaneous groups (year – season of weighed, sex and the covariate age of the cow (linear and quadratic. The B-Splines were defined in four knots through the growth period analyzed. Analyses were performed with the software Wombat. The variances (phenotypic and residual presented a similar behavior; of 7 to 12 months of age had a negative trend; from birth to 6 months and 13 to 18 months had positive trend; after 19 months were maintained constant. The m2 were low and near to zero, with an average of 0.06 in an interval of 0.04 to 0.11; the h2 also were close to zero, with an average of 0.10 in an interval of 0.03 to 0.23.

Random Assignment: Practical Considerations from Field Experiments.

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Dunford, Franklyn W.

1990-01-01

Seven qualitative issues associated with randomization that have the potential to weaken or destroy otherwise sound experimental designs are reviewed and illustrated via actual field experiments. Issue areas include ethics and legality, liability risks, manipulation of randomized outcomes, hidden bias, design intrusiveness, case flow, and…

Addressing Unconscious Bias: Steps toward an Inclusive Scientific Culture

Science.gov (United States)

Stewart, Abigail

2011-01-01

In this talk I will outline the nature of unconscious bias, as it operates to exclude or marginalize some participants in the scientific community. I will show how bias results from non-conscious expectations about certain groups of people, including scientists and astronomers. I will outline scientific research in psychology, sociology and economics that has identified the impact these expectations have on interpersonal judgments that are at the heart of assessment of individuals' qualifications. This research helps us understand not only how bias operates within a single instance of evaluation, but how evaluation bias can accumulate over a career if not checked, creating an appearance of confirmation of biased expectations. Some research has focused on how best to interrupt and mitigate unconscious bias, and many institutions--including the University of Michigan--have identified strategic interventions at key points of institutional decision-making (particularly hiring, annual review, and promotion) that can make a difference. The NSF ADVANCE Institutional Transformation program encouraged institutions to draw on the social science literature to create experimental approaches to addressing unconscious bias. I will outline four approaches to intervention that have arisen through the ADVANCE program: (1) systematic education that increases awareness among decisionmakers of how evaluation bias operates; (2) development of practices that mitigate the operation of bias even when it is out of conscious awareness; (3) creation of institutional policies that routinize and sanction these practices; and (4) holding leaders accountable for these implementation of these new practices and policies. Although I will focus on ways to address unconscious bias within scientific institutions (colleges and universities, laboratories and research centers, etc.), I will close by considering how scientific organizations can address unconscious bias and contribute to creating an

The efficacy of a standardized questionnaire in facilitating personalized communication about problems encountered in cancer genetic counseling: design of a randomized controlled trial.

Science.gov (United States)

Eijzenga, Willem; Aaronson, Neil K; Kluijt, Irma; Sidharta, Grace N; Hahn, Daniela Ee; Ausems, Margreet Gem; Bleiker, Eveline Ma

2014-01-15

Individuals with a personal or family history of cancer, can opt for genetic counseling and DNA-testing. Approximately 25% of these individuals experience clinically relevant levels of psychosocial distress, depression and/or anxiety after counseling. These problems are frequently left undetected by genetic counselors. The aim of this study is to evaluate the efficacy of a cancer genetics-specific screening questionnaire for psychosocial problems, the 'Psychosocial Aspects of Hereditary Cancer (PAHC) questionnaire' together with the Distress Thermometer, in: (1) facilitating personalized counselor-counselee communication; (2) increasing counselors' awareness of their counselees' psychosocial problems; and (3) facilitating the management of psychosocial problems during and after genetic counseling. This multicenter, randomized controlled trial will include 264 individuals undergoing cancer genetic counseling in two family cancer clinics in the Netherlands. Participants will be randomized to either: (1) an intervention group that completes the PAHC questionnaire, the results of which are made available to the genetic counselor prior to the counseling session; or (2) a control group that completes the PAHC questionnaire, but without feedback being given to the genetic counselor. The genetic counseling sessions will be audiotaped for content analysis. Additionally, study participants will be asked to complete questionnaires at baseline, three weeks after the initial counseling session, and four months after a telephone follow-up counseling session. The genetic counselors will be asked to complete questionnaires at the start of and at completion of the study, as well as a checklist directly after each counseling session. The questionnaires/checklists of the study include items on communication during genetic counseling, counselor awareness of their clients' psychosocial problems, the (perceived) need for professional psychosocial support, cancer worries, general

Compositional Bias in Naïve and Chemically-modified Phage-Displayed Libraries uncovered by Paired-end Deep Sequencing.

Science.gov (United States)

He, Bifang; Tjhung, Katrina F; Bennett, Nicholas J; Chou, Ying; Rau, Andrea; Huang, Jian; Derda, Ratmir

2018-01-19

Understanding the composition of a genetically-encoded (GE) library is instrumental to the success of ligand discovery. In this manuscript, we investigate the bias in GE-libraries of linear, macrocyclic and chemically post-translationally modified (cPTM) tetrapeptides displayed on the M13KE platform, which are produced via trinucleotide cassette synthesis (19 codons) and NNK-randomized codon. Differential enrichment of synthetic DNA {S}, ligated vector {L} (extension and ligation of synthetic DNA into the vector), naïve libraries {N} (transformation of the ligated vector into the bacteria followed by expression of the library for 4.5 hours to yield a "naïve" library), and libraries chemically modified by aldehyde ligation and cysteine macrocyclization {M} characterized by paired-end deep sequencing, detected a significant drop in diversity in {L} → {N}, but only a minor compositional difference in {S} → {L} and {N} → {M}. Libraries expressed at the N-terminus of phage protein pIII censored positively charged amino acids Arg and Lys; libraries expressed between pIII domains N1 and N2 overcame Arg/Lys-censorship but introduced new bias towards Gly and Ser. Interrogation of biases arising from cPTM by aldehyde ligation and cysteine macrocyclization unveiled censorship of sequences with Ser/Phe. Analogous analysis can be used to explore library diversity in new display platforms and optimize cPTM of these libraries.

Assessing the risk of bias in randomized controlled trials in the field of dentistry indexed in the Lilacs (Literatura Latino-Americana e do Caribe em Ciências da Saúde) database.

Science.gov (United States)

Ferreira, Christiane Alves; Loureiro, Carlos Alfredo Salles; Saconato, Humberto; Atallah, Alvaro Nagib

2011-03-01

Well-conducted randomized controlled trials (RCTs) represent the highest level of evidence when the research question relates to the effect of therapeutic or preventive interventions. However, the degree of control over bias between RCTs presents great variability between studies. For this reason, with the increasing interest in and production of systematic reviews and meta-analyses, it has been necessary to develop methodology supported by empirical evidence, so as to encourage and enhance the production of valid RCTs with low risk of bias. The aim here was to conduct a methodological analysis within the field of dentistry, regarding the risk of bias in open-access RCTs available in the Lilacs (Literatura Latino-Americana e do Caribe em Ciências da Saúde) database. This was a methodology study conducted at Universidade Federal de São Paulo (Unifesp) that assessed the risk of bias in RCTs, using the following dimensions: allocation sequence generation, allocation concealment, blinding, and data on incomplete outcomes. Out of the 4,503 articles classified, only 10 studies (0.22%) were considered to be true RCTs and, of these, only a single study was classified as presenting low risk of bias. The items that the authors of these RCTs most frequently controlled for were blinding and data on incomplete outcomes. The effective presence of bias seriously weakened the reliability of the results from the dental studies evaluated, such that they would be of little use for clinicians and administrators as support for decision-making processes.

Genetic counselors’ implicit racial attitudes and their relationship to communication

Science.gov (United States)

Schaa, Kendra L; Roter, Debra L; Biesecker, Barbara B; Cooper, Lisa A; Erby, Lori H

2015-01-01

Objective Implicit racial attitudes are thought to shape interpersonal interactions and may contribute to health care disparities. This study explored the relationship between genetic counselors’ implicit racial attitudes and their communication during simulated genetic counseling sessions. Methods A nationally representative sample of genetic counselors completed a web-based survey that included the Race Implicit Association Test (IAT). A subset of these counselors (n=67) had participated in an earlier study in which they were video recorded counseling Black, Hispanic and non-Hispanic White simulated clients (SC) about their prenatal or cancer risks. The counselors’ IAT scores were related to their session communication through robust regression modeling. Results Genetic counselors showed a moderate to strong pro-White bias on the Race IAT (M=0.41, SD=0.35). Counselors with stronger pro-White bias were rated as displaying lower levels of positive affect (pcommunication (pcommunication in minority client sessions and may contribute to racial disparities in processes of care related to genetic services. PMID:25622081

Random regression analysis for body weights and main morphological traits in genetically improved farmed tilapia (Oreochromis niloticus).

Science.gov (United States)

He, Jie; Zhao, Yunfeng; Zhao, Jingli; Gao, Jin; Xu, Pao; Yang, Runqing

2018-02-01

To genetically analyse growth traits in genetically improved farmed tilapia (GIFT), the body weight (BWE) and main morphological traits, including body length (BL), body depth (BD), body width (BWI), head length (HL) and length of the caudal peduncle (CPL), were measured six times in growth duration on 1451 fish from 45 mixed families of full and half sibs. A random regression model (RRM) was used to model genetic changes of the growth traits with days of age and estimate the heritability for any growth point and genetic correlations between pairwise growth points. Using the covariance function based on optimal RRMs, the heritabilities were estimated to be from 0.102 to 0.662 for BWE, 0.157 to 0.591 for BL, 0.047 to 0.621 for BD, 0.018 to 0.577 for BWI, 0.075 to 0.597 for HL and 0.032 to 0.610 for CPL between 60 and 140 days of age. All genetic correlations exceeded 0.5 between pairwise growth points. Moreover, the traits at initial days of age showed less correlation with those at later days of age. With phenotypes observed repeatedly, the model choice showed that the optimal RRMs could more precisely predict breeding values at a specific growth time than repeatability models or multiple trait animal models, which enhanced the efficiency of selection for the BWE and main morphological traits.

Subjective and objective outcomes in randomized clinical trials

DEFF Research Database (Denmark)

Moustgaard, Helene; Bello, Segun; Miller, Franklin G

2014-01-01

explicitly defined the terms. CONCLUSION: The terms "subjective" and "objective" are ambiguous when used to describe outcomes in randomized clinical trials. We suggest that the terms should be defined explicitly when used in connection with the assessment of risk of bias in a clinical trial......OBJECTIVES: The degree of bias in randomized clinical trials varies depending on whether the outcome is subjective or objective. Assessment of the risk of bias in a clinical trial will therefore often involve categorization of the type of outcome. Our primary aim was to examine how the concepts...... "subjective outcome" and "objective outcome" are defined in methodological publications and clinical trial reports. To put this examination into perspective, we also provide an overview of how outcomes are classified more broadly. STUDY DESIGN AND SETTING: A systematic review of methodological publications...

The Selective Advantage of Synonymous Codon Usage Bias in Salmonella.

Directory of Open Access Journals (Sweden)

Gerrit Brandis

2016-03-01

Full Text Available The genetic code in mRNA is redundant, with 61 sense codons translated into 20 different amino acids. Individual amino acids are encoded by up to six different codons but within codon families some are used more frequently than others. This phenomenon is referred to as synonymous codon usage bias. The genomes of free-living unicellular organisms such as bacteria have an extreme codon usage bias and the degree of bias differs between genes within the same genome. The strong positive correlation between codon usage bias and gene expression levels in many microorganisms is attributed to selection for translational efficiency. However, this putative selective advantage has never been measured in bacteria and theoretical estimates vary widely. By systematically exchanging optimal codons for synonymous codons in the tuf genes we quantified the selective advantage of biased codon usage in highly expressed genes to be in the range 0.2-4.2 x 10-4 per codon per generation. These data quantify for the first time the potential for selection on synonymous codon choice to drive genome-wide sequence evolution in bacteria, and in particular to optimize the sequences of highly expressed genes. This quantification may have predictive applications in the design of synthetic genes and for heterologous gene expression in biotechnology.

Rationality and emotionality: serotonin transporter genotype influences reasoning bias

OpenAIRE

Stollstorff, Melanie; Bean, Stephanie E.; Anderson, Lindsay M.; Devaney, Joseph M.; Vaidya, Chandan J.

2012-01-01

Reasoning often occurs under emotionally charged, opinion-laden circumstances. The belief-bias effect indexes the extent to which reasoning is based upon beliefs rather than logical structure. We examined whether emotional content increases this effect, particularly for adults genetically predisposed to be more emotionally reactive. SS/SLG carriers of the serotonin transporter genotype (5-HTTLPR) were less accurate selectively for evaluating emotional relational reasoning problems with belief...

Molecular doping for control of gate bias stress in organic thin film transistors

Energy Technology Data Exchange (ETDEWEB)

Hein, Moritz P., E-mail: hein@iapp.de; Lüssem, Björn; Jankowski, Jens; Tietze, Max L.; Riede, Moritz K. [Institut für Angewandte Photophysik, Technische Universität Dresden, George-Bähr-Straße 1, 01069 Dresden (Germany); Zakhidov, Alexander A. [Fraunhofer COMEDD, Maria-Reiche-Str. 2, 01109 Dresden (Germany); Leo, Karl [Institut für Angewandte Photophysik, Technische Universität Dresden, George-Bähr-Straße 1, 01069 Dresden (Germany); Fraunhofer COMEDD, Maria-Reiche-Str. 2, 01109 Dresden (Germany)

2014-01-06

The key active devices of future organic electronic circuits are organic thin film transistors (OTFTs). Reliability of OTFTs remains one of the most challenging obstacles to be overcome for broad commercial applications. In particular, bias stress was identified as the key instability under operation for numerous OTFT devices and interfaces. Despite a multitude of experimental observations, a comprehensive mechanism describing this behavior is still missing. Furthermore, controlled methods to overcome these instabilities are so far lacking. Here, we present the approach to control and significantly alleviate the bias stress effect by using molecular doping at low concentrations. For pentacene and silicon oxide as gate oxide, we are able to reduce the time constant of degradation by three orders of magnitude. The effect of molecular doping on the bias stress behavior is explained in terms of the shift of Fermi Level and, thus, exponentially reduced proton generation at the pentacene/oxide interface.

Molecular doping for control of gate bias stress in organic thin film transistors

International Nuclear Information System (INIS)

Hein, Moritz P.; Lüssem, Björn; Jankowski, Jens; Tietze, Max L.; Riede, Moritz K.; Zakhidov, Alexander A.; Leo, Karl

2014-01-01

The key active devices of future organic electronic circuits are organic thin film transistors (OTFTs). Reliability of OTFTs remains one of the most challenging obstacles to be overcome for broad commercial applications. In particular, bias stress was identified as the key instability under operation for numerous OTFT devices and interfaces. Despite a multitude of experimental observations, a comprehensive mechanism describing this behavior is still missing. Furthermore, controlled methods to overcome these instabilities are so far lacking. Here, we present the approach to control and significantly alleviate the bias stress effect by using molecular doping at low concentrations. For pentacene and silicon oxide as gate oxide, we are able to reduce the time constant of degradation by three orders of magnitude. The effect of molecular doping on the bias stress behavior is explained in terms of the shift of Fermi Level and, thus, exponentially reduced proton generation at the pentacene/oxide interface

Altering attentional control settings causes persistent biases of visual attention.

Science.gov (United States)

Knight, Helen C; Smith, Daniel T; Knight, David C; Ellison, Amanda

2016-01-01

Attentional control settings have an important role in guiding visual behaviour. Previous work within cognitive psychology has found that the deployment of general attentional control settings can be modulated by training. However, research has not yet established whether long-term modifications of one particular type of attentional control setting can be induced. To address this, we investigated persistent alterations to feature search mode, also known as an attentional bias, towards an arbitrary stimulus in healthy participants. Subjects were biased towards the colour green by an information sheet. Attentional bias was assessed using a change detection task. After an interval of either 1 or 2 weeks, participants were then retested on the same change detection task, tested on a different change detection task where colour was irrelevant, or were biased towards an alternative colour. One experiment included trials in which the distractor stimuli (but never the target stimuli) were green. The key finding was that green stimuli in the second task attracted attention, despite this impairing task performance. Furthermore, inducing a second attentional bias did not override the initial bias toward green objects. The attentional bias also persisted for at least two weeks. It is argued that this persistent attentional bias is mediated by a chronic change to participants' attentional control settings, which is aided by long-term representations involving contextual cueing. We speculate that similar changes to attentional control settings and continuous cueing may relate to attentional biases observed in psychopathologies. Targeting these biases may be a productive approach to treatment.

An unbiased estimator of the variance of simple random sampling using mixed random-systematic sampling

OpenAIRE

Padilla, Alberto

2009-01-01

Systematic sampling is a commonly used technique due to its simplicity and ease of implementation. The drawback of this simplicity is that it is not possible to estimate the design variance without bias. There are several ways to circumvent this problem. One method is to suppose that the variable of interest has a random order in the population, so the sample variance of simple random sampling without replacement is used. By means of a mixed random - systematic sample, an unbiased estimator o...

DNA Cryptography and Deep Learning using Genetic Algorithm with NW algorithm for Key Generation.

Science.gov (United States)

Kalsi, Shruti; Kaur, Harleen; Chang, Victor

2017-12-05

Cryptography is not only a science of applying complex mathematics and logic to design strong methods to hide data called as encryption, but also to retrieve the original data back, called decryption. The purpose of cryptography is to transmit a message between a sender and receiver such that an eavesdropper is unable to comprehend it. To accomplish this, not only we need a strong algorithm, but a strong key and a strong concept for encryption and decryption process. We have introduced a concept of DNA Deep Learning Cryptography which is defined as a technique of concealing data in terms of DNA sequence and deep learning. In the cryptographic technique, each alphabet of a letter is converted into a different combination of the four bases, namely; Adenine (A), Cytosine (C), Guanine (G) and Thymine (T), which make up the human deoxyribonucleic acid (DNA). Actual implementations with the DNA don't exceed laboratory level and are expensive. To bring DNA computing on a digital level, easy and effective algorithms are proposed in this paper. In proposed work we have introduced firstly, a method and its implementation for key generation based on the theory of natural selection using Genetic Algorithm with Needleman-Wunsch (NW) algorithm and Secondly, a method for implementation of encryption and decryption based on DNA computing using biological operations Transcription, Translation, DNA Sequencing and Deep Learning.

Asymmetrical transfer effects of cognitive bias modification: Modifying attention to threat influences interpretation of emotional ambiguity, but not vice versa

OpenAIRE

Bowler, J.O.; Hoppitt, L.; Illingworth, J.; Dalgleish, T.; Ononaiye, M.; Perez-Olivas, G.; Mackintosh, B.

2017-01-01

Background and objectives: It is well established that attention bias and interpretation bias each have a key role in the development and continuation of anxiety. How the biases may interact with one another in anxiety is, however, poorly understood. Using cognitive bias modification techniques, the present study examined whether training a more positive interpretation bias or attention bias resulted in transfer of effects to the untrained cognitive domain. Differences in anxiety reactivity t...

Bias in patient satisfaction surveys: a threat to measuring healthcare quality.

Science.gov (United States)

Dunsch, Felipe; Evans, David K; Macis, Mario; Wang, Qiao

2018-01-01

Patient satisfaction surveys are an increasingly common element of efforts to evaluate the quality of healthcare. Many patient satisfaction surveys in low/middle-income countries frame statements positively and invite patients to agree or disagree, so that positive responses may reflect either true satisfaction or bias induced by the positive framing. In an experiment with more than 2200 patients in Nigeria, we distinguish between actual satisfaction and survey biases. Patients randomly assigned to receive negatively framed statements expressed significantly lower levels of satisfaction (87%) than patients receiving the standard positively framed statements (95%-pquality of health services. Providers and policymakers wishing to gauge the quality of care will need to avoid framing that induces bias and to complement patient satisfaction measures with more objective measures of quality.

Application of random number generators in genetic algorithms to improve rainfall-runoff modelling

Science.gov (United States)

Chlumecký, Martin; Buchtele, Josef; Richta, Karel

2017-10-01

The efficient calibration of rainfall-runoff models is a difficult issue, even for experienced hydrologists. Therefore, fast and high-quality model calibration is a valuable improvement. This paper describes a novel methodology and software for the optimisation of a rainfall-runoff modelling using a genetic algorithm (GA) with a newly prepared concept of a random number generator (HRNG), which is the core of the optimisation. The GA estimates model parameters using evolutionary principles, which requires a quality number generator. The new HRNG generates random numbers based on hydrological information and it provides better numbers compared to pure software generators. The GA enhances the model calibration very well and the goal is to optimise the calibration of the model with a minimum of user interaction. This article focuses on improving the internal structure of the GA, which is shielded from the user. The results that we obtained indicate that the HRNG provides a stable trend in the output quality of the model, despite various configurations of the GA. In contrast to previous research, the HRNG speeds up the calibration of the model and offers an improvement of rainfall-runoff modelling.

Estimating Heritability from Nuclear Family and Pedigree Data.

Science.gov (United States)

Bochud, Murielle

2017-01-01

Heritability is a measure of familial resemblance. Estimating the heritability of a trait could be one of the first steps in the gene mapping process. This chapter describes how to estimate heritability for quantitative traits from nuclear and pedigree data using the ASSOC program in the Statistical Analysis in Genetic Epidemiology (S.A.G.E.) software package. Estimating heritability rests on the assumption that the total phenotypic variance of a quantitative trait can be partitioned into independent genetic and environmental components. In turn, the genetic variance can be divided into an additive (polygenic) genetic variance, a dominance variance (nonlinear interaction effects between alleles at the same locus) and an epistatic variance (interaction effects between alleles at different loci). The last two are often assumed to be zero. The additive genetic variance represents the average effects of individual alleles on the phenotype and reflects transmissible resemblance between relatives. Heritability in the narrow sense (h 2 ) refers to the ratio of the additive genetic variance to the total phenotypic variance. Heritability is a dimensionless population-specific parameter. ASSOC estimates association parameters (regression coefficients) and variance components from family data. ASSOC uses a linear regression model in which the total residual variance is partitioned, after regressing on covariates, into the sum of random components such as an additive polygenic component, a random sibship component, random nuclear family components, a random marital component, and an individual-specific random component. Assortative mating, nonrandom ascertainment of families, and failure to account for key confounding factors may bias heritability estimates.

Personalized Genetic Risk Counseling to Motivate Diabetes Prevention

OpenAIRE

Grant, Richard W.; O’Brien, Kelsey E.; Waxler, Jessica L.; Vassy, Jason L.; Delahanty, Linda M.; Bissett, Laurie G.; Green, Robert C.; Stember, Katherine G.; Guiducci, Candace; Park, Elyse R.; Florez, Jose C.; Meigs, James B.

2012-01-01

OBJECTIVE To examine whether diabetes genetic risk testing and counseling can improve diabetes prevention behaviors. RESEARCH DESIGN AND METHODS We conducted a randomized trial of diabetes genetic risk counseling among overweight patients at increased phenotypic risk for type 2 diabetes. Participants were randomly allocated to genetic testing versus no testing. Genetic risk was calculated by summing 36 single nucleotide polymorphisms associated with type 2 diabetes. Participants in the top an...

Population genetic analysis of ascertained SNP data

Directory of Open Access Journals (Sweden)

Nielsen Rasmus

2004-03-01

Full Text Available Abstract The large single nucleotide polymorphism (SNP typing projects have provided an invaluable data resource for human population geneticists. Almost all of the available SNP loci, however, have been identified through a SNP discovery protocol that will influence the allelic distributions in the sampled loci. Standard methods for population genetic analysis based on the available SNP data will, therefore, be biased. This paper discusses the effect of this ascertainment bias on allelic distributions and on methods for quantifying linkage disequilibrium and estimating demographic parameters. Several recently developed methods for correcting for the ascertainment bias will also be discussed.

Target selection biases from recent experience transfer across effectors.

Science.gov (United States)

Moher, Jeff; Song, Joo-Hyun

2016-02-01

Target selection is often biased by an observer's recent experiences. However, not much is known about whether these selection biases influence behavior across different effectors. For example, does looking at a red object make it easier to subsequently reach towards another red object? In the current study, we asked observers to find the uniquely colored target object on each trial. Randomly intermixed pre-trial cues indicated the mode of action: either an eye movement or a visually guided reach movement to the target. In Experiment 1, we found that priming of popout, reflected in faster responses following repetition of the target color on consecutive trials, occurred regardless of whether the effector was repeated from the previous trial or not. In Experiment 2, we examined whether an inhibitory selection bias away from a feature could transfer across effectors. While priming of popout reflects both enhancement of the repeated target features and suppression of the repeated distractor features, the distractor previewing effect isolates a purely inhibitory component of target selection in which a previewed color is presented in a homogenous display and subsequently inhibited. Much like priming of popout, intertrial suppression biases in the distractor previewing effect transferred across effectors. Together, these results suggest that biases for target selection driven by recent trial history transfer across effectors. This indicates that representations in memory that bias attention towards or away from specific features are largely independent from their associated actions.

Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process

DEFF Research Database (Denmark)

Ramírez-Soriano, Anna; Nielsen, Rasmus

2009-01-01

Most single-nucleotide polymorphism (SNP) data suffer from an ascertainment bias caused by the process of SNP discovery followed by SNP genotyping. The final genotyped data are biased toward an excess of common alleles compared to directly sequenced data, making standard genetic methods of analysis...... the variances and covariances of these estimators and provide a corrected version of Tajima's D statistic. We reanalyze a human genomewide SNP data set and find substantial differences in the results with or without ascertainment bias correction....

Correcting Classifiers for Sample Selection Bias in Two-Phase Case-Control Studies

Science.gov (United States)

Theis, Fabian J.

2017-01-01

Epidemiological studies often utilize stratified data in which rare outcomes or exposures are artificially enriched. This design can increase precision in association tests but distorts predictions when applying classifiers on nonstratified data. Several methods correct for this so-called sample selection bias, but their performance remains unclear especially for machine learning classifiers. With an emphasis on two-phase case-control studies, we aim to assess which corrections to perform in which setting and to obtain methods suitable for machine learning techniques, especially the random forest. We propose two new resampling-based methods to resemble the original data and covariance structure: stochastic inverse-probability oversampling and parametric inverse-probability bagging. We compare all techniques for the random forest and other classifiers, both theoretically and on simulated and real data. Empirical results show that the random forest profits from only the parametric inverse-probability bagging proposed by us. For other classifiers, correction is mostly advantageous, and methods perform uniformly. We discuss consequences of inappropriate distribution assumptions and reason for different behaviors between the random forest and other classifiers. In conclusion, we provide guidance for choosing correction methods when training classifiers on biased samples. For random forests, our method outperforms state-of-the-art procedures if distribution assumptions are roughly fulfilled. We provide our implementation in the R package sambia. PMID:29312464

social desirability bias and possible implications for HIV-prevention ...

African Journals Online (AJOL)

Evaluations of the safety, effectiveness, and feasibility of HIV prevention interventions rely on self-reported sexual behaviour data. The accuracy of such data has sometimes been questioned. The absence of a so-called objective measure of sexual behaviour complicates this. Social desirability bias (SDB) is a key factor ...

A New Source Biasing Approach in ADVANTG

International Nuclear Information System (INIS)

Bevill, Aaron M.; Mosher, Scott W.

2012-01-01

The ADVANTG code has been developed at Oak Ridge National Laboratory to generate biased sources and weight window maps for MCNP using the CADIS and FW-CADIS methods. In preparation for an upcoming RSICC release, a new approach for generating a biased source has been developed. This improvement streamlines user input and improves reliability. Previous versions of ADVANTG generated the biased source from ADVANTG input, writing an entirely new general fixed-source definition (SDEF). Because volumetric sources were translated into SDEF-format as a finite set of points, the user had to perform a convergence study to determine whether the number of source points used accurately represented the source region. Further, the large number of points that must be written in SDEF-format made the MCNP input and output files excessively long and difficult to debug. ADVANTG now reads SDEF-format distributions and generates corresponding source biasing cards, eliminating the need for a convergence study. Many problems of interest use complicated source regions that are defined using cell rejection. In cell rejection, the source distribution in space is defined using an arbitrarily complex cell and a simple bounding region. Source positions are sampled within the bounding region but accepted only if they fall within the cell; otherwise, the position is resampled entirely. When biasing in space is applied to sources that use rejection sampling, current versions of MCNP do not account for the rejection in setting the source weight of histories, resulting in an 'unfair game'. This problem was circumvented in previous versions of ADVANTG by translating volumetric sources into a finite set of points, which does not alter the mean history weight ((bar w)). To use biasing parameters without otherwise modifying the original cell-rejection SDEF-format source, ADVANTG users now apply a correction factor for (bar w) in post-processing. A stratified-random sampling approach in ADVANTG is under

Visual search attentional bias modification reduced social phobia in adolescents.

Science.gov (United States)

De Voogd, E L; Wiers, R W; Prins, P J M; Salemink, E

2014-06-01

An attentional bias for negative information plays an important role in the development and maintenance of (social) anxiety and depression, which are highly prevalent in adolescence. Attention Bias Modification (ABM) might be an interesting tool in the prevention of emotional disorders. The current study investigated whether visual search ABM might affect attentional bias and emotional functioning in adolescents. A visual search task was used as a training paradigm; participants (n = 16 adolescents, aged 13-16) had to repeatedly identify the only smiling face in a 4 × 4 matrix of negative emotional faces, while participants in the control condition (n = 16) were randomly allocated to one of three placebo training versions. An assessment version of the task was developed to directly test whether attentional bias changed due to the training. Self-reported anxiety and depressive symptoms and self-esteem were measured pre- and post-training. After two sessions of training, the ABM group showed a significant decrease in attentional bias for negative information and self-reported social phobia, while the control group did not. There were no effects of training on depressive mood or self-esteem. No correlation between attentional bias and social phobia was found, which raises questions about the validity of the attentional bias assessment task. Also, the small sample size precludes strong conclusions. Visual search ABM might be beneficial in changing attentional bias and social phobia in adolescents, but further research with larger sample sizes and longer follow-up is needed. Copyright © 2013 Elsevier Ltd. All rights reserved.

The role of cognitive biases in short-term psychodynamic psychotherapy.

Science.gov (United States)

Kramer, Ueli; Ortega, Diana; Ambresin, Gilles; Despland, Jean-Nicolas; de Roten, Yves

2018-06-01

The concept of biased thinking - or cognitive biases - is relevant to psychotherapy research and clinical conceptualization, beyond cognitive theories. The present naturalistic study aimed to examine the changes in biased thinking over the course of a short-term dynamic psychotherapy (STDP) and to discover potential links between these changes and symptomatic improvement. This study focuses on 32 self-referred patients consulting for Adjustment Disorder according to DSM-IV-TR. The therapists were experienced psychodynamically oriented psychiatrists and psychotherapists. Coding of cognitive biases (using the Cognitive Errors Rating Scale; CERS) was made by external raters based on transcripts of interviews of psychotherapy; the reliability of these ratings on a randomly chosen 24% of all sessions was established. Based on the Symptom Check List SCL-90-R given before and after, the Reliable Change Index (RCI) was used. The assessment of cognitive errors was done at three time points: early (session 4-7), mid-treatment (session 12-17), and close to the end (after session 20) of the treatment. The results showed that the total frequency of cognitive biases was stable over time (p = .20), which was true both for positive and for negative cognitive biases. In exploring the three main subscales of the CERS, we found a decrease in selective abstraction (p = .02) and an increase in personalization (p = .05). A significant link between RCI scores (outcome) and frequency of positive cognitive biases was found, suggesting that biases towards the positive might have a protective function in psychotherapy. Therapists may be attentive to changes in biased thinking across short-term dynamic psychotherapy for adjustment disorder. Therapists may foster the emergence of positive cognitive biases at mid-treatment for adjustment disorder. © 2017 The British Psychological Society.

Capturing Dynamics of Biased Attention: Are New Attention Variability Measures the Way Forward?

Directory of Open Access Journals (Sweden)

Anne-Wil Kruijt

Full Text Available New indices, calculated on data from the widely used Dot Probe Task, were recently proposed to capture variability in biased attention allocation. We observed that it remains unclear which data pattern is meant to be indicative of dynamic bias and thus to be captured by these indices. Moreover, we hypothesized that the new indices are sensitive to SD differences at the response time (RT level in the absence of bias.Randomly generated datasets were analyzed to assess properties of the Attention Bias Variability (ABV and Trial Level Bias Score (TL-BS indices. Sensitivity to creating differences in 1 RT standard deviation, 2 mean RT, and 3 bias magnitude were assessed. In addition, two possible definitions of dynamic attention bias were explored by creating differences in 4 frequency of bias switching, and 5 bias magnitude in the presence of constant switching.ABV and TL-BS indices were found highly sensitive to increasing SD at the response time level, insensitive to increasing bias, linearly sensitive to increasing bias magnitude in the presence of bias switches, and non-linearly sensitive to increasing the frequency of bias switches. The ABV index was also found responsive to increasing mean response times in the absence of bias.Recently proposed DPT derived variability indices cannot uncouple measurement error from bias variability. Significant group differences may be observed even if there is no bias present in any individual dataset. This renders the new indices in their current form unfit for empirical purposes. Our discussion focuses on fostering debate and ideas for new research to validate the potentially very important notion of biased attention being dynamic.

Feto-maternal haemorrhage associated with genetic amniocentesis

DEFF Research Database (Denmark)

Tabor, A; Bang, J; Nørgaard-Pedersen, B

1987-01-01

Maternal serum alpha-fetoprotein (AFP) levels were determined before and after genetic amniocentesis (n = 283) or ultrasound scan (n = 268) in a group of women participating in a randomized trial of genetic amniocentesis. Increases in AFP levels were seen significantly more often after amniocente......Maternal serum alpha-fetoprotein (AFP) levels were determined before and after genetic amniocentesis (n = 283) or ultrasound scan (n = 268) in a group of women participating in a randomized trial of genetic amniocentesis. Increases in AFP levels were seen significantly more often after...

Moisture Forecast Bias Correction in GEOS DAS

Science.gov (United States)

Dee, D.

1999-01-01

Data assimilation methods rely on numerous assumptions about the errors involved in measuring and forecasting atmospheric fields. One of the more disturbing of these is that short-term model forecasts are assumed to be unbiased. In case of atmospheric moisture, for example, observational evidence shows that the systematic component of errors in forecasts and analyses is often of the same order of magnitude as the random component. we have implemented a sequential algorithm for estimating forecast moisture bias from rawinsonde data in the Goddard Earth Observing System Data Assimilation System (GEOS DAS). The algorithm is designed to remove the systematic component of analysis errors and can be easily incorporated in an existing statistical data assimilation system. We will present results of initial experiments that show a significant reduction of bias in the GEOS DAS moisture analyses.

Genetic relatedness of artichoke (Cynara scolymus L.) hybrids using random amplified polymorphic DNA (RAPD) fingerprinting.

Science.gov (United States)

Sharaf-Eldin, M A; Al-Tamimi, A; Alam, P; Elkholy, S F; Jordan, J R

2015-12-28

The artichoke (Cynara scolymus L.) is an important food and medicinal crop that is cultivated in Mediterranean countries. Morphological characteristics, such as head shape and diameter, leaf shape, and bract shape, are mainly affected by environmental conditions. A molecular marker approach was used to analyze the degree of polymorphism between artichoke hybrid lines. The degree of genetic difference among three artichoke hybrids was evaluated using random amplified polymorphic DNA-PCR (RAPD-PCR). In this study, the DNA fingerprints of three artichoke lines (A13-010, A11-018, and A12-179) were generated, and a total of 10 decamer primers were applied for RAPD-PCR analyses. Polymorphism  (16.66 to 62.50%) was identified using eight arbitrary decamers and total genomic DNA extracted from the hybrids. Of the 59 loci detected, there were 25 polymorphic and 34 monomorphic loci. Jaccard's similarity index (JSI) ranged between 1.0 and 0.84. Based on the unweighted pair group method with arithmetic mean (UPGMA) similarity matrix and dendrogram, the results indicated that two hybrids (A13-010 and A11-018) were closely related to each other, and the A12-179 line showed more divergence. When identifying correct accessions, consideration of the genetic variation and genetic relationships among the genotypes are required. The RAPD-PCR fingerprinting of artichoke lines clearly showed that it is possible to analyze the RAPD patterns for correlation between genetic means and differences or resemblance between close accessions (A13-010 and A11- 018) at the genomic level.

Gaze Bias in Preference Judgments by Younger and Older Adults

Directory of Open Access Journals (Sweden)

Toshiki Saito

2017-08-01

Full Text Available Individuals’ gaze behavior reflects the choice they will ultimately make. For example, people confronting a choice among multiple stimuli tend to look longer at stimuli that are subsequently chosen than at other stimuli. This tendency, called the gaze bias effect, is a key aspect of visual decision-making. Nevertheless, no study has examined the generality of the gaze bias effect in older adults. Here, we used a two-alternative forced-choice task (2AFC to compare the gaze behavior reflective of different stages of decision processes demonstrated by younger and older adults. Participants who had viewed two faces were instructed to choose the one that they liked/disliked or the one that they judged to be more/less similar to their own face. Their eye movements were tracked while they chose. The results show that the gaze bias effect occurred during the remaining time in both age groups irrespective of the decision type. However, no gaze bias effect was observed for the preference judgment during the first dwell time. Our study demonstrated that the gaze bias during the remaining time occurred regardless of decision-making task and age. Further study using diverse participants, such as clinic patients or infants, may help to generalize the gaze bias effect and to elucidate the mechanisms underlying the gaze bias.

The genetic signature of sex-biased migration in patrilocal chimpanzees and humans.

Directory of Open Access Journals (Sweden)

Kevin E Langergraber

Full Text Available A large body of theoretical work suggests that analyses of variation at the maternally inherited mitochondrial (mtDNA and the paternally inherited non-recombining portion of the Y chromosome (NRY are a potentially powerful way to reveal the differing migratory histories of men and women across human societies. However, the few empirical studies comparing mtDNA and NRY variation and known patterns of sex-biased migration have produced conflicting results. Here we review some methodological reasons for these inconsistencies, and take them into account to provide an unbiased characterization of mtDNA and NRY variation in chimpanzees, one of the few mammalian taxa where males routinely remain in and females typically disperse from their natal groups. We show that patterns of mtDNA and NRY variation are more strongly contrasting in patrilocal chimpanzees compared with patrilocal human societies. The chimpanzee data we present here thus provide a valuable comparative benchmark of the patterns of mtDNA and NRY variation to be expected in a society with extremely female-biased dispersal.

A Robust SRAM-PUF Key Generation Scheme Based on Polar Codes

OpenAIRE

Chen, Bin; Ignatenko, Tanya; Willems, Frans M. J.; Maes, Roel; van der Sluis, Erik; Selimis, Georgios

2017-01-01

Physical unclonable functions (PUFs) are relatively new security primitives used for device authentication and device-specific secret key generation. In this paper we focus on SRAM-PUFs. The SRAM-PUFs enjoy uniqueness and randomness properties stemming from the intrinsic randomness of SRAM memory cells, which is a result of manufacturing variations. This randomness can be translated into the cryptographic keys thus avoiding the need to store and manage the device cryptographic keys. Therefore...

Association between funding, risk of bias, and outcome of randomised controlled trials in oral and maxillofacial surgery

NARCIS (Netherlands)

Oomens, M.A.E.M.; Lazzari, S.; Heymans, M.W.; Forouzanfar, T.

2016-01-01

The influence of funding on the main outcome of a random control trial (RCT) is important, as it could potentially lead to bias towards industry, and results that are too optimistic. We investigated the association between funding, the published outcome, and the risk of bias in trials in oral and

Natural genetic engineering: intelligence & design in evolution?

DEFF Research Database (Denmark)

Ussery, David

2011-01-01

There are many things that I like about James Shapiro's new book "Evolution: A View from the 21st Century" (FT Press Science, 2011). He begins the book by saying that it is the creation of novelty, and not selection, that is important in the history of life. In the presence of heritable traits...... function. Shapiro argues that what we see in genomes is 'Natural Genetic Engineering', or designed evolution: "Thinking about genomes from an informatics perspective, it is apparent that systems engineering is a better metaphor for the evolutionary process than the conventional view of evolution...... as a select-biased random walk through limitless space of possible DNA configurations" (page 6). In this review, I will have a look at four topics: 1.) why I think genomics is not the whole story; 2.) my own perspective of E. coli genomics, and how I think it relates to this book; 3.) a brief discussion...

Finite-key analysis for quantum key distribution with weak coherent pulses based on Bernoulli sampling

Science.gov (United States)

Kawakami, Shun; Sasaki, Toshihiko; Koashi, Masato

2017-07-01

An essential step in quantum key distribution is the estimation of parameters related to the leaked amount of information, which is usually done by sampling of the communication data. When the data size is finite, the final key rate depends on how the estimation process handles statistical fluctuations. Many of the present security analyses are based on the method with simple random sampling, where hypergeometric distribution or its known bounds are used for the estimation. Here we propose a concise method based on Bernoulli sampling, which is related to binomial distribution. Our method is suitable for the Bennett-Brassard 1984 (BB84) protocol with weak coherent pulses [C. H. Bennett and G. Brassard, Proceedings of the IEEE Conference on Computers, Systems and Signal Processing (IEEE, New York, 1984), Vol. 175], reducing the number of estimated parameters to achieve a higher key generation rate compared to the method with simple random sampling. We also apply the method to prove the security of the differential-quadrature-phase-shift (DQPS) protocol in the finite-key regime. The result indicates that the advantage of the DQPS protocol over the phase-encoding BB84 protocol in terms of the key rate, which was previously confirmed in the asymptotic regime, persists in the finite-key regime.

The effect of selection on genetic parameter estimates

African Journals Online (AJOL)

Unknown

The South African Journal of Animal Science is available online at ... A simulation study was carried out to investigate the effect of selection on the estimation of genetic ... The model contained a fixed effect, random genetic and random.

Conceptual and methodological biases in network models.

Science.gov (United States)

Lamm, Ehud

2009-10-01

Many natural and biological phenomena can be depicted as networks. Theoretical and empirical analyses of networks have become prevalent. I discuss theoretical biases involved in the delineation of biological networks. The network perspective is shown to dissolve the distinction between regulatory architecture and regulatory state, consistent with the theoretical impossibility of distinguishing a priori between "program" and "data." The evolutionary significance of the dynamics of trans-generational and interorganism regulatory networks is explored and implications are presented for understanding the evolution of the biological categories development-heredity, plasticity-evolvability, and epigenetic-genetic.

Fundamentals of randomized clinical trials in wound care

DEFF Research Database (Denmark)

Eskes, Anne M; Brölmann, Fleur E; Sumpio, Bauer E

2012-01-01

randomization is a necessary feature of a robust comparative study, it is not sufficient to ensure a study at low risk of bias. Randomized clinical trials should also ensure adequate allocation concealment and blinding of outcome assessors, apply intention-to-treat analysis, and use patient-oriented outcomes...

Effects of nicotine and nicotine expectancy on attentional bias for emotional stimuli.

Science.gov (United States)

Adams, Sally; Attwood, Angela S; Munafò, Marcus R

2015-06-01

Nicotine's effects on mood are thought to enhance its addictive potential. However, the mechanisms underlying the effects of nicotine on affect regulation have not been reliably demonstrated in human laboratory studies. We investigated the effects of nicotine abstinence (Experiment 1), and nicotine challenge and expectancy (Experiment 2) on attentional bias towards facial emotional stimuli differing in emotional valence. In Experiment 1, 46 nicotine-deprived smokers were randomized to either continue to abstain from smoking or to smoke immediately before testing. In Experiment 2, 96 nicotine-deprived smokers were randomized to smoke a nicotinized or denicotinized cigarette and to be told that the cigarette did or did not contain nicotine. In both experiments participants completed a visual probe task, where positively valenced (happy) and negatively valenced (sad) facial expressions were presented, together with neutral facial expressions. In Experiment 1, there was evidence of an interaction between probe location and abstinence on reaction time, indicating that abstinent smokers showed an attentional bias for neutral stimuli. In Experiment 2, there was evidence of an interaction between probe location, nicotine challenge and expectation on reaction time, indicating that smokers receiving nicotine, but told that they did not receive nicotine, showed an attentional bias for emotional stimuli. Our data suggest that nicotine abstinence appears to disrupt attentional bias towards emotional facial stimuli. These data provide support for nicotine's modulation of attentional bias as a central mechanism for maintaining affect regulation in cigarette smoking. © The Author 2014. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Efficacy of attention bias modification using threat and appetitive stimuli: a meta-analytic review.

Science.gov (United States)

Beard, Courtney; Sawyer, Alice T; Hofmann, Stefan G

2012-12-01

Attention bias modification (ABM) protocols aim to modify attentional biases underlying many forms of pathology. Our objective was to conduct an effect size analysis of ABM across a wide range of samples and psychological problems. We conducted a literature search using PubMed, PsycInfo, and author searches to identify randomized studies that examined the effects of ABM on attention and subjective experiences. We identified 37 studies (41 experiments) totaling 2,135 participants who were randomized to training toward neutral, positive, threat, or appetitive stimuli or to a control condition. The effect size estimate for changes in attentional bias was large for the neutral versus threat comparisons (g=1.06), neutral versus appetitive (g=1.41), and neutral versus control comparisons (g=0.80), and small for positive versus control (g=0.24). The effects of ABM on attention bias were moderated by stimulus type (words vs. pictures) and sample characteristics (healthy vs. high symptomatology). Effect sizes of ABM on subjective experiences ranged from 0.03 to 0.60 for postchallenge outcomes, -0.31 to 0.51 for posttreatment, and were moderated by number of training sessions, stimulus type, and stimulus orientation (top/bottom vs. left/right). Fail-safe N calculations suggested that the effect size estimates were robust for the training effects on attentional biases, but not for the effect on subjective experiences. ABM studies using threat stimuli produced significant effects on attention bias across comparison conditions, whereas appetitive stimuli produced changes in attention only when comparing appetitive versus neutral conditions. ABM has a moderate and robust effect on attention bias when using threat stimuli. Further studies are needed to determine whether these effects are also robust when using appetitive stimuli and for affecting subjective experiences. Copyright © 2012. Published by Elsevier Ltd.

On theoretical models of gene expression evolution with random genetic drift and natural selection.

Directory of Open Access Journals (Sweden)

Osamu Ogasawara

2009-11-01

Full Text Available The relative contributions of natural selection and random genetic drift are a major source of debate in the study of gene expression evolution, which is hypothesized to serve as a bridge from molecular to phenotypic evolution. It has been suggested that the conflict between views is caused by the lack of a definite model of the neutral hypothesis, which can describe the long-run behavior of evolutionary change in mRNA abundance. Therefore previous studies have used inadequate analogies with the neutral prediction of other phenomena, such as amino acid or nucleotide sequence evolution, as the null hypothesis of their statistical inference.In this study, we introduced two novel theoretical models, one based on neutral drift and the other assuming natural selection, by focusing on a common property of the distribution of mRNA abundance among a variety of eukaryotic cells, which reflects the result of long-term evolution. Our results demonstrated that (1 our models can reproduce two independently found phenomena simultaneously: the time development of gene expression divergence and Zipf's law of the transcriptome; (2 cytological constraints can be explicitly formulated to describe long-term evolution; (3 the model assuming that natural selection optimized relative mRNA abundance was more consistent with previously published observations than the model of optimized absolute mRNA abundances.The models introduced in this study give a formulation of evolutionary change in the mRNA abundance of each gene as a stochastic process, on the basis of previously published observations. This model provides a foundation for interpreting observed data in studies of gene expression evolution, including identifying an adequate time scale for discriminating the effect of natural selection from that of random genetic drift of selectively neutral variations.

Sympathetic bias.

Science.gov (United States)

Levy, David M; Peart, Sandra J

2008-06-01

We wish to deal with investigator bias in a statistical context. We sketch how a textbook solution to the problem of "outliers" which avoids one sort of investigator bias, creates the temptation for another sort. We write down a model of the approbation seeking statistician who is tempted by sympathy for client to violate the disciplinary standards. We give a simple account of one context in which we might expect investigator bias to flourish. Finally, we offer tentative suggestions to deal with the problem of investigator bias which follow from our account. As we have given a very sparse and stylized account of investigator bias, we ask what might be done to overcome this limitation.

Angular Random Walk Estimation of a Time-Domain Switching Micromachined Gyroscope

Science.gov (United States)

2016-10-19

angular random walk (ARW), bias instability, and scale factor instability. While there are methods to address issues with bias and scale factor...effects. Thus, it is expected that it will have low bias and scale factor instabilities. Simulated ARW performance of a particular incarnation of the...1 2. PARAMETRIC SYSTEM IDENTIFICATION BASED ON TIME-DOMAIN SWITCHING ........ 2 3. FINITE ELEMENT MODELING OF RESONATOR

Genetics of complex diseases

DEFF Research Database (Denmark)

Mellerup, Erling; Møller, Gert Lykke; Koefoed, Pernille

2012-01-01

A complex disease with an inheritable component is polygenic, meaning that several different changes in DNA are the genetic basis for the disease. Such a disease may also be genetically heterogeneous, meaning that independent changes in DNA, i.e. various genotypes, can be the genetic basis...... for the disease. Each of these genotypes may be characterized by specific combinations of key genetic changes. It is suggested that even if all key changes are found in genes related to the biology of a certain disease, the number of combinations may be so large that the number of different genotypes may be close...... to the number of patients suffering from the disease. This hypothesis is based on a study of bipolar disorder....

Herd-specific random regression carcass profiles for beef cattle after adjustment for animal genetic merit.

Science.gov (United States)

Englishby, Tanya M; Moore, Kirsty L; Berry, Donagh P; Coffey, Mike P; Banos, Georgios

2017-07-01

Abattoir data are an important source of information for the genetic evaluation of carcass traits, but also for on-farm management purposes. The present study aimed to quantify the contribution of herd environment to beef carcass characteristics (weight, conformation score and fat score) with particular emphasis on generating finishing herd-specific profiles for these traits across different ages at slaughter. Abattoir records from 46,115 heifers and 78,790 steers aged between 360 and 900days, and from 22,971 young bulls aged between 360 and 720days, were analysed. Finishing herd-year and animal genetic (co)variance components for each trait were estimated using random regression models. Across slaughter age and gender, the ratio of finishing herd-year to total phenotypic variance ranged from 0.31 to 0.72 for carcass weight, 0.21 to 0.57 for carcass conformation and 0.11 to 0.44 for carcass fat score. These parameters indicate that the finishing herd environment is an important contributor to carcass trait variability and amenable to improvement with management practices. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evidence-based medicine, the research-practice gap, and biases in medical and surgical decision making in dermatology.

Science.gov (United States)

Eaglstein, William H

2010-10-01

The objectives of this article are to promote a better understanding of a group of biases that influence therapeutic decision making by physicians/dermatologists and to raise the awareness that these biases contribute to a research-practice gap that has an impact on physicians and treatment solutions. The literature included a wide range of peer-reviewed articles dealing with biases in decision making, evidence-based medicine, randomized controlled clinical trials, and the research-practice gap. Bias against new therapies, bias in favor of indirect harm or omission, and bias against change when multiple new choices are offered may unconsciously affect therapeutic decision making. Although there is no comprehensive understanding or theory as to how choices are made by physicians, recognition of certain cognition patterns and their associated biases will help narrow the research-practice gap and optimize decision making regarding therapeutic choices.

Combination of biased forecasts: Bias correction or bias based weights?

OpenAIRE

Wenzel, Thomas

1999-01-01

Most of the literature on combination of forecasts deals with the assumption of unbiased individual forecasts. Here, we consider the case of biased forecasts and discuss two different combination techniques resulting in an unbiased forecast. On the one hand we correct the individual forecasts, and on the other we calculate bias based weights. A simulation study gives some insight in the situations where we should use the different methods.

Genetic variation of wild and hatchery populations of the catla Indian major carp (Catla catla Hamilton 1822: Cypriniformes, Cyprinidae revealed by RAPD markers

Directory of Open Access Journals (Sweden)

S.M. Zakiur Rahman

2009-01-01

Full Text Available Genetic variation is a key component for improving a stock through selective breeding programs. Randomly amplified polymorphic DNA (RAPD markers were used to assess genetic variation in three wild population of the catla carp (Catla catla Hamilton 1822 in the Halda, Jamuna and Padma rivers and one hatchery population in Bangladesh. Five decamer random primers were used to amplify RAPD markers from 30 fish from each population. Thirty of the 55 scorable bands were polymorphic, indicating some degree of genetic variation in all the populations. The proportion of polymorphic loci and gene diversity values reflected a relatively higher level of genetic variation in the Halda population. Sixteen of the 30 polymorphic loci showed a significant (p < 0.05, p < 0.01, p < 0.001 departure from homogeneity and the F ST values in the different populations indicated some degree of genetic differentiation in the population pairs. Estimated genetic distances between populations were directly correlated with geographical distances. The unweighted pair group method with averages (UPGMA dendrogram showed two clusters, the Halda population forming one cluster and the other populations the second cluster. Genetic variation of C. catla is a useful trait for developing a good management strategy for maintaining genetic quality of the species.

Classification bias in commercial business lists for retail food stores in the U.S.

Science.gov (United States)

2012-01-01

Background Aspects of the food environment such as the availability of different types of food stores have recently emerged as key modifiable factors that may contribute to the increased prevalence of obesity. Given that many of these studies have derived their results based on secondary datasets and the relationship of food stores with individual weight outcomes has been reported to vary by store type, it is important to understand the extent to which often-used secondary data correctly classify food stores. We evaluated the classification bias of food stores in Dun & Bradstreet (D&B) and InfoUSA commercial business lists. Methods We performed a full census in 274 randomly selected census tracts in the Chicago metropolitan area and collected detailed store attributes inside stores for classification. Store attributes were compared by classification match status and store type. Systematic classification bias by census tract characteristics was assessed in multivariate regression. Results D&B had a higher classification match rate than InfoUSA for supermarkets and grocery stores, while InfoUSA was higher for convenience stores. Both lists were more likely to correctly classify large supermarkets, grocery stores, and convenience stores with more cash registers and different types of service counters (supermarkets and grocery stores only). The likelihood of a correct classification match for supermarkets and grocery stores did not vary systemically by tract characteristics whereas convenience stores were more likely to be misclassified in predominately Black tracts. Conclusion Researches can rely on classification of food stores in commercial datasets for supermarkets and grocery stores whereas classifications for convenience and specialty food stores are subject to some systematic bias by neighborhood racial/ethnic composition. PMID:22512874

Classification bias in commercial business lists for retail food stores in the U.S.

Directory of Open Access Journals (Sweden)

Han Euna

2012-04-01

Full Text Available Abstract Background Aspects of the food environment such as the availability of different types of food stores have recently emerged as key modifiable factors that may contribute to the increased prevalence of obesity. Given that many of these studies have derived their results based on secondary datasets and the relationship of food stores with individual weight outcomes has been reported to vary by store type, it is important to understand the extent to which often-used secondary data correctly classify food stores. We evaluated the classification bias of food stores in Dun & Bradstreet (D&B and InfoUSA commercial business lists. Methods We performed a full census in 274 randomly selected census tracts in the Chicago metropolitan area and collected detailed store attributes inside stores for classification. Store attributes were compared by classification match status and store type. Systematic classification bias by census tract characteristics was assessed in multivariate regression. Results D&B had a higher classification match rate than InfoUSA for supermarkets and grocery stores, while InfoUSA was higher for convenience stores. Both lists were more likely to correctly classify large supermarkets, grocery stores, and convenience stores with more cash registers and different types of service counters (supermarkets and grocery stores only. The likelihood of a correct classification match for supermarkets and grocery stores did not vary systemically by tract characteristics whereas convenience stores were more likely to be misclassified in predominately Black tracts. Conclusion Researches can rely on classification of food stores in commercial datasets for supermarkets and grocery stores whereas classifications for convenience and specialty food stores are subject to some systematic bias by neighborhood racial/ethnic composition.

Classification bias in commercial business lists for retail food stores in the U.S.

Science.gov (United States)

Han, Euna; Powell, Lisa M; Zenk, Shannon N; Rimkus, Leah; Ohri-Vachaspati, Punam; Chaloupka, Frank J

2012-04-18

Aspects of the food environment such as the availability of different types of food stores have recently emerged as key modifiable factors that may contribute to the increased prevalence of obesity. Given that many of these studies have derived their results based on secondary datasets and the relationship of food stores with individual weight outcomes has been reported to vary by store type, it is important to understand the extent to which often-used secondary data correctly classify food stores. We evaluated the classification bias of food stores in Dun & Bradstreet (D&B) and InfoUSA commercial business lists. We performed a full census in 274 randomly selected census tracts in the Chicago metropolitan area and collected detailed store attributes inside stores for classification. Store attributes were compared by classification match status and store type. Systematic classification bias by census tract characteristics was assessed in multivariate regression. D&B had a higher classification match rate than InfoUSA for supermarkets and grocery stores, while InfoUSA was higher for convenience stores. Both lists were more likely to correctly classify large supermarkets, grocery stores, and convenience stores with more cash registers and different types of service counters (supermarkets and grocery stores only). The likelihood of a correct classification match for supermarkets and grocery stores did not vary systemically by tract characteristics whereas convenience stores were more likely to be misclassified in predominately Black tracts. Researches can rely on classification of food stores in commercial datasets for supermarkets and grocery stores whereas classifications for convenience and specialty food stores are subject to some systematic bias by neighborhood racial/ethnic composition.

Citation bias of hepato-biliary randomized clinical trials

DEFF Research Database (Denmark)

Kjaergard, Lise L; Gluud, Christian

2002-01-01

-1996. From each trial, we extracted the statistical significance of the primary study outcome (positive or negative), the disease area, and methodological quality (randomization and double blinding). The number of citations during two calendar years after publication was obtained from Science Citation Index....... There was a significant positive association between a statistically significant study outcome and the citation frequency (beta, 0.55, 95% confidence interval, 0.39-0.72). The disease area and adequate generation of the allocation sequence were also significant predictors of the citation frequency. We concluded...

Estimation bias and bias correction in reduced rank autoregressions

DEFF Research Database (Denmark)

Nielsen, Heino Bohn

2017-01-01

This paper characterizes the finite-sample bias of the maximum likelihood estimator (MLE) in a reduced rank vector autoregression and suggests two simulation-based bias corrections. One is a simple bootstrap implementation that approximates the bias at the MLE. The other is an iterative root...

Pseudo Random Coins Show More Heads Than Tails

OpenAIRE

Bauke, Heiko; Mertens, Stephan

2003-01-01

Tossing a coin is the most elementary Monte Carlo experiment. In a computer the coin is replaced by a pseudo random number generator. It can be shown analytically and by exact enumerations that popular random number generators are not capable of imitating a fair coin: pseudo random coins show more heads than tails. This bias explains the empirically observed failure of some random number generators in random walk experiments. It can be traced down to the special role of the value zero in the ...

Securing information using optically generated biometric keys

Science.gov (United States)

Verma, Gaurav; Sinha, Aloka

2016-11-01

In this paper, we present a new technique to obtain biometric keys by using the fingerprint of a person for an optical image encryption system. The key generation scheme uses the fingerprint biometric information in terms of the amplitude mask (AM) and the phase mask (PM) of the reconstructed fingerprint image that is implemented using the digital holographic technique. Statistical tests have been conducted to check the randomness of the fingerprint PM key that enables its usage as an image encryption key. To explore the utility of the generated biometric keys, an optical image encryption system has been further demonstrated based on the phase retrieval algorithm and the double random phase encoding scheme in which keys for the encryption are used as the AM and the PM key. The advantage associated with the proposed scheme is that the biometric keys’ retrieval requires the simultaneous presence of the fingerprint hologram and the correct knowledge of the reconstruction parameters at the decryption stage, which not only verifies the authenticity of the person but also protects the valuable fingerprint biometric features of the keys. Numerical results are carried out to prove the feasibility and the effectiveness of the proposed encryption system.

Courting the future: cancer and genetics in Cuba.

Science.gov (United States)

2014-01-01

Describing this double issue of MEDICC Review could be an exercise for a first-year philosophy course in logic. It's not about "cancer and genetics" in Cuba. It's about cancer in Cuba and about genetics in Cuba, not about exploring relationships between them. Nevertheless, while the marriage of the two themes was fortuitous, in that the two had long been scheduled for the journal in 2014, there is a certain felicity to their sharing an issue. To date, the outstanding accomplishments of genetics have been most helpful for conditions occurring at the beginning of life and cancer is largely (though not exclusively) a disease related to aging. But the two are intrinsically connected: Although only a few of the more than 100 different diseases grouped under the term cancer are known to be hereditary, every cancer begins with a mutation in one or more genes, whether the mutation is inherited, due to an exposure, or is simply a random error in the millions of cell divisions that are part and parcel of cellular reproduction. Our cover image, a stained-glass window by Cuban artist Rosa María de la Terga at Cuba's National Medical Genetics Center, illustrates the elegance of the DNA molecule, the intricate key to life.

Chemosensory Communication of Gender Information: Masculinity Bias in Body Odor Perception and Femininity Bias Introduced by Chemosignals During Social Perception.

Science.gov (United States)

Mutic, Smiljana; Moellers, Eileen M; Wiesmann, Martin; Freiherr, Jessica

2015-01-01

Human body odor is a source of important social information. In this study, we explore whether the sex of an individual can be established based on smelling axillary odor and whether exposure to male and female odors biases chemosensory and social perception. In a double-blind, pseudo-randomized application, 31 healthy normosmic heterosexual male and female raters were exposed to male and female chemosignals (odor samples of 27 heterosexual donors collected during a cardio workout) and a no odor sample. Recipients rated chemosensory samples on a masculinity-femininity scale and provided intensity, familiarity and pleasantness ratings. Additionally, the modulation of social perception (gender-neutral faces and personality attributes) and affective introspection (mood) by male and female chemosignals was assessed. Male and female axillary odors were rated as rather masculine, regardless of the sex of the donor. As opposed to the masculinity bias in the odor perception, a femininity bias modulating social perception appeared. A facilitated femininity detection in gender-neutral faces and personality attributes in male and female chemosignals appeared. No chemosensory effect on mood of the rater was observed. The results are discussed with regards to the use of male and female chemosignals in affective and social communication.

Small private key MQPKS on an embedded microprocessor.

Science.gov (United States)

Seo, Hwajeong; Kim, Jihyun; Choi, Jongseok; Park, Taehwan; Liu, Zhe; Kim, Howon

2014-03-19

Multivariate quadratic (MQ) cryptography requires the use of long public and private keys to ensure a sufficient security level, but this is not favorable to embedded systems, which have limited system resources. Recently, various approaches to MQ cryptography using reduced public keys have been studied. As a result of this, at CHES2011 (Cryptographic Hardware and Embedded Systems, 2011), a small public key MQ scheme, was proposed, and its feasible implementation on an embedded microprocessor was reported at CHES2012. However, the implementation of a small private key MQ scheme was not reported. For efficient implementation, random number generators can contribute to reduce the key size, but the cost of using a random number generator is much more complex than computing MQ on modern microprocessors. Therefore, no feasible results have been reported on embedded microprocessors. In this paper, we propose a feasible implementation on embedded microprocessors for a small private key MQ scheme using a pseudo-random number generator and hash function based on a block-cipher exploiting a hardware Advanced Encryption Standard (AES) accelerator. To speed up the performance, we apply various implementation methods, including parallel computation, on-the-fly computation, optimized logarithm representation, vinegar monomials and assembly programming. The proposed method reduces the private key size by about 99.9% and boosts signature generation and verification by 5.78% and 12.19% than previous results in CHES2012.

Small Private Key PKS on an Embedded Microprocessor

Science.gov (United States)

Seo, Hwajeong; Kim, Jihyun; Choi, Jongseok; Park, Taehwan; Liu, Zhe; Kim, Howon

2014-01-01

Multivariate quadratic ( ) cryptography requires the use of long public and private keys to ensure a sufficient security level, but this is not favorable to embedded systems, which have limited system resources. Recently, various approaches to cryptography using reduced public keys have been studied. As a result of this, at CHES2011 (Cryptographic Hardware and Embedded Systems, 2011), a small public key scheme, was proposed, and its feasible implementation on an embedded microprocessor was reported at CHES2012. However, the implementation of a small private key scheme was not reported. For efficient implementation, random number generators can contribute to reduce the key size, but the cost of using a random number generator is much more complex than computing on modern microprocessors. Therefore, no feasible results have been reported on embedded microprocessors. In this paper, we propose a feasible implementation on embedded microprocessors for a small private key scheme using a pseudo-random number generator and hash function based on a block-cipher exploiting a hardware Advanced Encryption Standard (AES) accelerator. To speed up the performance, we apply various implementation methods, including parallel computation, on-the-fly computation, optimized logarithm representation, vinegar monomials and assembly programming. The proposed method reduces the private key size by about 99.9% and boosts signature generation and verification by 5.78% and 12.19% than previous results in CHES2012. PMID:24651722

Quantum random number generator

Science.gov (United States)

Pooser, Raphael C.

2016-05-10

A quantum random number generator (QRNG) and a photon generator for a QRNG are provided. The photon generator may be operated in a spontaneous mode below a lasing threshold to emit photons. Photons emitted from the photon generator may have at least one random characteristic, which may be monitored by the QRNG to generate a random number. In one embodiment, the photon generator may include a photon emitter and an amplifier coupled to the photon emitter. The amplifier may enable the photon generator to be used in the QRNG without introducing significant bias in the random number and may enable multiplexing of multiple random numbers. The amplifier may also desensitize the photon generator to fluctuations in power supplied thereto while operating in the spontaneous mode. In one embodiment, the photon emitter and amplifier may be a tapered diode amplifier.

Genetic variability in Asparagus racemosus (Willd.) from Madhya ...

African Journals Online (AJOL)

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Asparagus racemosus (Willd.) an important medicinal plant collected from 7 different locations covering Madhya Pradesh. High level of genetic similarity was observed in the collected accessions. 4 random primers generated a ...

Mental, psychomotor, neurologic, and behavioral outcomes of 2-year-old children born after preimplantation genetic screening : follow-up of a randomized controlled trial

NARCIS (Netherlands)

Middelburg, Karin J.; van der Heide, Maaike; Houtzager, Bregje; Pereboom, Marjolein; Fidler, Vaclav; Bos, Arend F.; Kok, Joke; Hadders-Algra, Mijna

Objective: To evaluate the effect of preimplantation genetic screening (PGS) on neurodevelopmental outcomes in children. Design: Prospective, assessor-blinded, follow-up study of children born to women randomly assigned to in vitro fertilization or intracytoplasmic sperm injection (IVF/ICSI) with or

Rapid Evolution of Ovarian-Biased Genes in the Yellow Fever Mosquito (Aedes aegypti).

Science.gov (United States)

Whittle, Carrie A; Extavour, Cassandra G

2017-08-01

Males and females exhibit highly dimorphic phenotypes, particularly in their gonads, which is believed to be driven largely by differential gene expression. Typically, the protein sequences of genes upregulated in males, or male-biased genes, evolve rapidly as compared to female-biased and unbiased genes. To date, the specific study of gonad-biased genes remains uncommon in metazoans. Here, we identified and studied a total of 2927, 2013, and 4449 coding sequences (CDS) with ovary-biased, testis-biased, and unbiased expression, respectively, in the yellow fever mosquito Aedes aegypti The results showed that ovary-biased and unbiased CDS had higher nonsynonymous to synonymous substitution rates (dN/dS) and lower optimal codon usage (those codons that promote efficient translation) than testis-biased genes. Further, we observed higher dN/dS in ovary-biased genes than in testis-biased genes, even for genes coexpressed in nonsexual (embryo) tissues. Ovary-specific genes evolved exceptionally fast, as compared to testis- or embryo-specific genes, and exhibited higher frequency of positive selection. Genes with ovary expression were preferentially involved in olfactory binding and reception. We hypothesize that at least two potential mechanisms could explain rapid evolution of ovary-biased genes in this mosquito: (1) the evolutionary rate of ovary-biased genes may be accelerated by sexual selection (including female-female competition or male-mate choice) affecting olfactory genes during female swarming by males, and/or by adaptive evolution of olfactory signaling within the female reproductive system ( e.g. , sperm-ovary signaling); and/or (2) testis-biased genes may exhibit decelerated evolutionary rates due to the formation of mating plugs in the female after copulation, which limits male-male sperm competition. Copyright © 2017 by the Genetics Society of America.

Forward-biased nanophotonic detector for ultralow-energy dissipation receiver

Science.gov (United States)

Nozaki, Kengo; Matsuo, Shinji; Fujii, Takuro; Takeda, Koji; Shinya, Akihiko; Kuramochi, Eiichi; Notomi, Masaya

2018-04-01

Generally, reverse-biased photodetectors (PDs) are used for high-speed optical receivers. The forward voltage region is only utilized in solar-cells, and this photovoltaic operation would not be concurrently obtained with high efficiency and high speed operation. Here we report that photonic-crystal waveguide PDs enable forward-biased high-speed operation at 40 Gbit/s with keeping high responsivity (0.88 A/W). Within our knowledge, this is the first demonstration of the forward-biased PDs with high responsivity. This achievement is attributed to the ultracompactness of our PD and the strong light confinement within the absorber and depleted regions, thereby enabling efficient photo-carrier generation and fast extraction. This result indicates that it is possible to construct a high-speed and ultracompact photo-receiver without an electrical amplifier nor an external bias circuit. Since there is no electrical energy required, our estimation shows that the consumption energy is just the optical energy of the injected signal pulse which is about 1 fJ/bit. Hence, it will lead to an ultimately efficient and highly integrable optical-to-electrical converter in a chip, which will be a key ingredient for dense nanophotonic communication and processors.

Forward-biased nanophotonic detector for ultralow-energy dissipation receiver

Directory of Open Access Journals (Sweden)

Kengo Nozaki

2018-04-01

Full Text Available Generally, reverse-biased photodetectors (PDs are used for high-speed optical receivers. The forward voltage region is only utilized in solar-cells, and this photovoltaic operation would not be concurrently obtained with high efficiency and high speed operation. Here we report that photonic-crystal waveguide PDs enable forward-biased high-speed operation at 40 Gbit/s with keeping high responsivity (0.88 A/W. Within our knowledge, this is the first demonstration of the forward-biased PDs with high responsivity. This achievement is attributed to the ultracompactness of our PD and the strong light confinement within the absorber and depleted regions, thereby enabling efficient photo-carrier generation and fast extraction. This result indicates that it is possible to construct a high-speed and ultracompact photo-receiver without an electrical amplifier nor an external bias circuit. Since there is no electrical energy required, our estimation shows that the consumption energy is just the optical energy of the injected signal pulse which is about 1 fJ/bit. Hence, it will lead to an ultimately efficient and highly integrable optical-to-electrical converter in a chip, which will be a key ingredient for dense nanophotonic communication and processors.

Looking on the bright side: biased attention and the human serotonin transporter gene.

Science.gov (United States)

Fox, Elaine; Ridgewell, Anna; Ashwin, Chris

2009-05-22

Humans differ in terms of biased attention for emotional stimuli and these biases can confer differential resilience and vulnerability to emotional disorders. Selective processing of positive emotional information, for example, is associated with enhanced sociability and well-being while a bias for negative material is associated with neuroticism and anxiety. A tendency to selectively avoid negative material might also be associated with mental health and well-being. The neurobiological mechanisms underlying these cognitive phenotypes are currently unknown. Here we show for the first time that allelic variation in the promotor region of the serotonin transporter gene (5-HTTLPR) is associated with differential biases for positive and negative affective pictures. Individuals homozygous for the long allele (LL) showed a marked bias to selectively process positive affective material alongside selective avoidance of negative affective material. This potentially protective pattern was absent among individuals carrying the short allele (S or SL). Thus, allelic variation on a common genetic polymorphism was associated with the tendency to selectively process positive or negative information. The current study is important in demonstrating a genotype-related alteration in a well-established processing bias, which is a known risk factor in determining both resilience and vulnerability to emotional disorders.

Effects of biases in domain wall network evolution. II. Quantitative analysis

Science.gov (United States)

Correia, J. R. C. C. C.; Leite, I. S. C. R.; Martins, C. J. A. P.

2018-04-01

Domain walls form at phase transitions which break discrete symmetries. In a cosmological context, they often overclose the Universe (contrary to observational evidence), although one may prevent this by introducing biases or forcing anisotropic evolution of the walls. In a previous work [Correia et al., Phys. Rev. D 90, 023521 (2014), 10.1103/PhysRevD.90.023521], we numerically studied the evolution of various types of biased domain wall networks in the early Universe, confirming that anisotropic networks ultimately reach scaling while those with a biased potential or biased initial conditions decay. We also found that the analytic decay law obtained by Hindmarsh was in good agreement with simulations of biased potentials, but not of biased initial conditions, and suggested that the difference was related to the Gaussian approximation underlying the analytic law. Here, we extend our previous work in several ways. For the cases of biased potential and biased initial conditions, we study in detail the field distributions in the simulations, confirming that the validity (or not) of the Gaussian approximation is the key difference between the two cases. For anisotropic walls, we carry out a more extensive set of numerical simulations and compare them to the canonical velocity-dependent one-scale model for domain walls, finding that the model accurately predicts the linear scaling regime after isotropization. Overall, our analysis provides a quantitative description of the cosmological evolution of these networks.

Evaluating Changes in Omega-3 Fatty Acid Intake after Receiving Personal FADS1 Genetic Information: A Randomized Nutrigenetic Intervention

Science.gov (United States)

Roke, Kaitlin; Walton, Kathryn; Klingel, Shannon L.; Harnett, Amber; Subedi, Sanjeena; Haines, Jess; Mutch, David M.

2017-01-01

Nutrigenetics research is anticipated to lay the foundation for personalized dietary recommendations; however, it remains unclear if providing individuals with their personal genetic information changes dietary behaviors. Our objective was to evaluate if providing information for a common variant in the fatty acid desaturase 1 (FADS1) gene changed omega-3 fatty acid (FA) intake and blood levels in young female adults (18–25 years). Participants were randomized into Genetic (intervention) and Non-Genetic (control) groups, with measurements taken at Baseline and Final (12 weeks). Dietary intake of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) was assessed using an omega-3 food frequency questionnaire. Red blood cell (RBC) FA content was quantified by gas chromatography. Implications of participation in a nutrigenetics study and awareness of omega-3 FAs were assessed with online questionnaires. Upon completion of the study, EPA and DHA intake increased significantly (p = 1.0 × 10−4) in all participants. This change was reflected by small increases in RBC %EPA. Participants in the Genetic group showed increased awareness of omega-3 terminology by the end of the study, reported that the dietary recommendations were more useful, and rated cost as a barrier to omega-3 consumption less often than those in the Non-Genetic group. Providing participants FADS1 genetic information did not appear to influence omega-3 intake during the 12 weeks, but did change perceptions and behaviors related to omega-3 FAs in this timeframe. PMID:28272299

Evaluating Changes in Omega-3 Fatty Acid Intake after Receiving Personal FADS1 Genetic Information: A Randomized Nutrigenetic Intervention

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Kaitlin Roke

2017-03-01

Full Text Available Nutrigenetics research is anticipated to lay the foundation for personalized dietary recommendations; however, it remains unclear if providing individuals with their personal genetic information changes dietary behaviors. Our objective was to evaluate if providing information for a common variant in the fatty acid desaturase 1 (FADS1 gene changed omega-3 fatty acid (FA intake and blood levels in young female adults (18–25 years. Participants were randomized into Genetic (intervention and Non-Genetic (control groups, with measurements taken at Baseline and Final (12 weeks. Dietary intake of eicosapentaenoic acid (EPA and docosahexaenoic acid (DHA was assessed using an omega-3 food frequency questionnaire. Red blood cell (RBC FA content was quantified by gas chromatography. Implications of participation in a nutrigenetics study and awareness of omega-3 FAs were assessed with online questionnaires. Upon completion of the study, EPA and DHA intake increased significantly (p = 1.0 × 10−4 in all participants. This change was reflected by small increases in RBC %EPA. Participants in the Genetic group showed increased awareness of omega-3 terminology by the end of the study, reported that the dietary recommendations were more useful, and rated cost as a barrier to omega-3 consumption less often than those in the Non-Genetic group. Providing participants FADS1 genetic information did not appear to influence omega-3 intake during the 12 weeks, but did change perceptions and behaviors related to omega-3 FAs in this timeframe.

Random Tagging Genotyping by Sequencing (rtGBS, an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome.

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Elena Hilario

Full Text Available Genotyping by sequencing (GBS is a restriction enzyme based targeted approach developed to reduce the genome complexity and discover genetic markers when a priori sequence information is unavailable. Sufficient coverage at each locus is essential to distinguish heterozygous from homozygous sites accurately. The number of GBS samples able to be pooled in one sequencing lane is limited by the number of restriction sites present in the genome and the read depth required at each site per sample for accurate calling of single-nucleotide polymorphisms. Loci bias was observed using a slight modification of the Elshire et al.some restriction enzyme sites were represented in higher proportions while others were poorly represented or absent. This bias could be due to the quality of genomic DNA, the endonuclease and ligase reaction efficiency, the distance between restriction sites, the preferential amplification of small library restriction fragments, or bias towards cluster formation of small amplicons during the sequencing process. To overcome these issues, we have developed a GBS method based on randomly tagging genomic DNA (rtGBS. By randomly landing on the genome, we can, with less bias, find restriction sites that are far apart, and undetected by the standard GBS (stdGBS method. The study comprises two types of biological replicates: six different kiwifruit plants and two independent DNA extractions per plant; and three types of technical replicates: four samples of each DNA extraction, stdGBS vs. rtGBS methods, and two independent library amplifications, each sequenced in separate lanes. A statistically significant unbiased distribution of restriction fragment size by rtGBS showed that this method targeted 49% (39,145 of BamH I sites shared with the reference genome, compared to only 14% (11,513 by stdGBS.

Transboundary Movements of Genetically Modified Organisms and the Cartagena Protocol: Key Issues and Concerns

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Odile J Lim Tung

2014-12-01

Full Text Available Biotechnology or the engineering of the genetic material of species can give way to avenues of possibilities for the benefit of people, fauna and flora but also has the potential of posing untold and undiscovered threats to human beings and other living organisms. One of the first attempts to legislate on international rules on biotechnology can be traced back to article 19 of the Convention on Biological Diversity (CBD in 1992. The CBD is indeed the first international legal instrument apart from the then European Community’s relevant directives to suggest that biotechnology is a matter of concern for the international community while providing a basis upon which more detailed procedures would be elaborated in the field of biosafety. While the CBD includes international rules on access to genetic resources, access to and the transfer of technology, the handling of biotechnology and the distribution of its benefits, it does not include a detailed regulation on genetically modified organisms (GMOs and their possible adverse effects on the environment, human and animal health. It was only with the coming into existence of the Cartagena Protocol on Biosafety (Cartagena Protocol to the CBD in 2000 that the safe transfer, handling and use of living modified organisms (LMOs such as genetically engineered plants, animals, and microbes were at last being catered for, albeit leaving aside the broader categories of GMOs. Due to the need for the negotiators of this protocol to make compromises, there were still key issues on the international biosafety framework pertaining mainly to the scope of the GMOs to be covered by this protocol and by the Advanced Informed Agreement procedure; identification and traceability issues; and liability and redress issues. Nine years after the entry into force of the Cartagena Protocol the transboundary movements of GMOs have clearly increased with new categories of GMOs and genetically modified products to regulate. The

Modification of cognitive biases related to posttraumatic stress: A systematic review and research agenda.

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Woud, Marcella L; Verwoerd, Johan; Krans, Julie

2017-06-01

Cognitive models of Posttraumatic Stress Disorder (PTSD) postulate that cognitive biases in attention, interpretation, and memory represent key factors involved in the onset and maintenance of PTSD. Developments in experimental research demonstrate that it may be possible to manipulate such biases by means of Cognitive Bias Modification (CBM). In the present paper, we summarize studies assessing cognitive biases in posttraumatic stress to serve as a theoretical and methodological background. However, our main aim was to provide an overview of the scientific literature on CBM in (analogue) posttraumatic stress. Results of our systematic literature review showed that most CBM studies targeted attentional and interpretation biases (attention: five studies; interpretation: three studies), and one study modified memory biases. Overall, results showed that CBM can indeed modify cognitive biases and affect (analog) trauma symptoms in a training congruent manner. Interpretation bias procedures seemed effective in analog samples, and memory bias training proved preliminary success in a clinical PTSD sample. Studies of attention bias modification provided more mixed results. This heterogeneous picture may be explained by differences in the type of population or variations in the CBM procedure. Therefore, we sketched a detailed research agenda targeting the challenges for CBM in posttraumatic stress. Copyright © 2017 Elsevier Ltd. All rights reserved.

Systematic bias in genomic classification due to contaminating non-neoplastic tissue in breast tumor samples.

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Elloumi, Fathi; Hu, Zhiyuan; Li, Yan; Parker, Joel S; Gulley, Margaret L; Amos, Keith D; Troester, Melissa A

2011-06-30

Genomic tests are available to predict breast cancer recurrence and to guide clinical decision making. These predictors provide recurrence risk scores along with a measure of uncertainty, usually a confidence interval. The confidence interval conveys random error and not systematic bias. Standard tumor sampling methods make this problematic, as it is common to have a substantial proportion (typically 30-50%) of a tumor sample comprised of histologically benign tissue. This "normal" tissue could represent a source of non-random error or systematic bias in genomic classification. To assess the performance characteristics of genomic classification to systematic error from normal contamination, we collected 55 tumor samples and paired tumor-adjacent normal tissue. Using genomic signatures from the tumor and paired normal, we evaluated how increasing normal contamination altered recurrence risk scores for various genomic predictors. Simulations of normal tissue contamination caused misclassification of tumors in all predictors evaluated, but different breast cancer predictors showed different types of vulnerability to normal tissue bias. While two predictors had unpredictable direction of bias (either higher or lower risk of relapse resulted from normal contamination), one signature showed predictable direction of normal tissue effects. Due to this predictable direction of effect, this signature (the PAM50) was adjusted for normal tissue contamination and these corrections improved sensitivity and negative predictive value. For all three assays quality control standards and/or appropriate bias adjustment strategies can be used to improve assay reliability. Normal tissue sampled concurrently with tumor is an important source of bias in breast genomic predictors. All genomic predictors show some sensitivity to normal tissue contamination and ideal strategies for mitigating this bias vary depending upon the particular genes and computational methods used in the predictor.

Models for Estimating Genetic Parameters of Milk Production Traits Using Random Regression Models in Korean Holstein Cattle

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C. I. Cho

2016-05-01

Full Text Available The objectives of the study were to estimate genetic parameters for milk production traits of Holstein cattle using random regression models (RRMs, and to compare the goodness of fit of various RRMs with homogeneous and heterogeneous residual variances. A total of 126,980 test-day milk production records of the first parity Holstein cows between 2007 and 2014 from the Dairy Cattle Improvement Center of National Agricultural Cooperative Federation in South Korea were used. These records included milk yield (MILK, fat yield (FAT, protein yield (PROT, and solids-not-fat yield (SNF. The statistical models included random effects of genetic and permanent environments using Legendre polynomials (LP of the third to fifth order (L3–L5, fixed effects of herd-test day, year-season at calving, and a fixed regression for the test-day record (third to fifth order. The residual variances in the models were either homogeneous (HOM or heterogeneous (15 classes, HET15; 60 classes, HET60. A total of nine models (3 orders of polynomials×3 types of residual variance including L3-HOM, L3-HET15, L3-HET60, L4-HOM, L4-HET15, L4-HET60, L5-HOM, L5-HET15, and L5-HET60 were compared using Akaike information criteria (AIC and/or Schwarz Bayesian information criteria (BIC statistics to identify the model(s of best fit for their respective traits. The lowest BIC value was observed for the models L5-HET15 (MILK; PROT; SNF and L4-HET15 (FAT, which fit the best. In general, the BIC values of HET15 models for a particular polynomial order was lower than that of the HET60 model in most cases. This implies that the orders of LP and types of residual variances affect the goodness of models. Also, the heterogeneity of residual variances should be considered for the test-day analysis. The heritability estimates of from the best fitted models ranged from 0.08 to 0.15 for MILK, 0.06 to 0.14 for FAT, 0.08 to 0.12 for PROT, and 0.07 to 0.13 for SNF according to days in milk of first

Comparison of Parametric and Nonparametric Methods for Analyzing the Bias of a Numerical Model

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Isaac Mugume

2016-01-01

Full Text Available Numerical models are presently applied in many fields for simulation and prediction, operation, or research. The output from these models normally has both systematic and random errors. The study compared January 2015 temperature data for Uganda as simulated using the Weather Research and Forecast model with actual observed station temperature data to analyze the bias using parametric (the root mean square error (RMSE, the mean absolute error (MAE, mean error (ME, skewness, and the bias easy estimate (BES and nonparametric (the sign test, STM methods. The RMSE normally overestimates the error compared to MAE. The RMSE and MAE are not sensitive to direction of bias. The ME gives both direction and magnitude of bias but can be distorted by extreme values while the BES is insensitive to extreme values. The STM is robust for giving the direction of bias; it is not sensitive to extreme values but it does not give the magnitude of bias. The graphical tools (such as time series and cumulative curves show the performance of the model with time. It is recommended to integrate parametric and nonparametric methods along with graphical methods for a comprehensive analysis of bias of a numerical model.

BONDI-97 A novel neutron energy spectrum unfolding tool using a genetic algorithm

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Mukherjee, B

1999-01-01

The neutron spectrum unfolding procedure using the count rate data obtained from a set of Bonner sphere neutron detectors requires the solution of the Fredholm integral equation of the first kind by using complex mathematical methods. This paper reports a new approach for the unfolding of neutron spectra using the Genetic Algorithm tool BONDI-97 (BOnner sphere Neutron DIfferentiation). The BONDI-97 was used as the input for Genetic Algorithm engine EVOLVER to search for a globally optimised solution vector from a population of randomly generated solutions. This solution vector corresponds to the unfolded neutron energy spectrum. The Genetic Algorithm engine emulates the Darwinian 'Survival of the Fittest' strategy, the key ingredient of the 'Theory of Evolution'. The spectra of sup 2 sup 4 sup 1 Am/Be (alpha,n) and sup 2 sup 3 sup 9 Pu/Be (alpha,n) neutron sources were unfolded using the BONDI-97 tool. (author)

Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates

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Roffler, Gretchen H.; Talbot, Sandra L.; Luikart, Gordon; Sage, George K.; Pilgrim, Kristy L.; Adams, Layne G.; Schwartz, Michael K.

2014-01-01

Identifying patterns of fine-scale genetic structure in natural populations can advance understanding of critical ecological processes such as dispersal and gene flow across heterogeneous landscapes. Alpine ungulates generally exhibit high levels of genetic structure due to female philopatry and patchy configuration of mountain habitats. We assessed the spatial scale of genetic structure and the amount of gene flow in 301 Dall’s sheep (Ovis dalli dalli) at the landscape level using 15 nuclear microsatellites and 473 base pairs of the mitochondrial (mtDNA) control region. Dall’s sheep exhibited significant genetic structure within contiguous mountain ranges, but mtDNA structure occurred at a broader geographic scale than nuclear DNA within the study area, and mtDNA structure for other North American mountain sheep populations. No evidence of male-mediated gene flow or greater philopatry of females was observed; there was little difference between markers with different modes of inheritance (pairwise nuclear DNA F ST = 0.004–0.325; mtDNA F ST = 0.009–0.544), and males were no more likely than females to be recent immigrants. Historical patterns based on mtDNA indicate separate northern and southern lineages and a pattern of expansion following regional glacial retreat. Boundaries of genetic clusters aligned geographically with prominent mountain ranges, icefields, and major river valleys based on Bayesian and hierarchical modeling of microsatellite and mtDNA data. Our results suggest that fine-scale genetic structure in Dall’s sheep is influenced by limited dispersal, and structure may be weaker in populations occurring near ancestral levels of density and distribution in continuous habitats compared to other alpine ungulates that have experienced declines and marked habitat fragmentation.

Endogenous Oxytocin Release Eliminates In-Group Bias in Monetary Transfers With Perspective-Taking

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Elizabeth T. Terris

2018-03-01

Full Text Available Oxytocin (OT has been shown to facilitate trust, empathy and other prosocial behaviors. At the same time, there is evidence that exogenous OT infusion may not result in prosocial behaviors in all contexts, increasing in-group biases in a number of studies. The current investigation seeks to resolve this inconsistency by examining if endogenous OT release is associated with in-group bias. We studied a large group of participants (N = 399 in existing groups and randomly formed groups. Participants provided two blood samples to measure the change in OT after a group salience task and then made computer-mediated monetary transfer decisions to in-group and out-group members. Our results show that participants with an increase in endogenous OT showed no bias in monetary offers in the ultimatum game (UG to out-group members compared to in-groups. There was also no bias in accepting UG offers, though in-group bias persisted for a unilateral monetary transfer. Our analysis shows that the strength of identification with one’s group diminished the effects that an increase in OT had on reducing bias, but bias only recurred when group identification reached 87% of its maximum value. Our results indicate that the endogenous OT system appears to reduce in-group bias in some contexts, particularly those that require perspective-taking.

Effects of interpretation training on hostile attribution bias and reactivity to interpersonal insult.

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Hawkins, Kirsten A; Cougle, Jesse R

2013-09-01

Research suggests that individuals high in anger have a bias for attributing hostile intentions to ambiguous situations. The current study tested whether this interpretation bias can be altered to influence anger reactivity to an interpersonal insult using a single-session cognitive bias modification program. One hundred thirty-five undergraduate students were randomized to receive positive training, negative training, or a control condition. Anger reactivity to insult was then assessed. Positive training led to significantly greater increases in positive interpretation bias relative to the negative group, though these increases were only marginally greater than the control group. Negative training led to increased negative interpretation bias relative to other groups. During the insult, participants in the positive condition reported less anger than those in the control condition. Observers rated participants in the positive condition as less irritated than those in the negative condition and more amused than the other two conditions. Though mediation of effects via bias modification was not demonstrated, among the positive condition posttraining interpretation bias was correlated with self-reported anger, suggesting that positive training reduced anger reactivity by influencing interpretation biases. Findings suggest that positive interpretation training may be a promising treatment for reducing anger. However, the current study was conducted with a non-treatment-seeking student sample; further research with a treatment-seeking sample with problematic anger is necessary. Copyright © 2013. Published by Elsevier Ltd.

Endogenous Oxytocin Release Eliminates In-Group Bias in Monetary Transfers With Perspective-Taking.

Science.gov (United States)

Terris, Elizabeth T; Beavin, Laura E; Barraza, Jorge A; Schloss, Jeff; Zak, Paul J

2018-01-01

Oxytocin (OT) has been shown to facilitate trust, empathy and other prosocial behaviors. At the same time, there is evidence that exogenous OT infusion may not result in prosocial behaviors in all contexts, increasing in-group biases in a number of studies. The current investigation seeks to resolve this inconsistency by examining if endogenous OT release is associated with in-group bias. We studied a large group of participants ( N = 399) in existing groups and randomly formed groups. Participants provided two blood samples to measure the change in OT after a group salience task and then made computer-mediated monetary transfer decisions to in-group and out-group members. Our results show that participants with an increase in endogenous OT showed no bias in monetary offers in the ultimatum game (UG) to out-group members compared to in-groups. There was also no bias in accepting UG offers, though in-group bias persisted for a unilateral monetary transfer. Our analysis shows that the strength of identification with one's group diminished the effects that an increase in OT had on reducing bias, but bias only recurred when group identification reached 87% of its maximum value. Our results indicate that the endogenous OT system appears to reduce in-group bias in some contexts, particularly those that require perspective-taking.

Mobile genetic elements, a key to microbial adaptation in extreme environments

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van Houdt, Rob; Mijnendonckx, Kristel; Provoost, Ann; Monsieurs, Pieter; Mergeay, Max; Leys, Natalie

hydrogenotrophy. Five transposons were identified in CH34. Two mercury transposons Tn4378 and Tn4380, respectively located on pMOL28 and pMOL30, were previously described. In addition, 3 novel transposons were identified. The large Tn6048 transposon contained 8 genes highly induced by zinc and lead. Transposon Tn6049 was found in twelve copies in the genome of strain CH34 and is seem-ingly often associated with genomic islands. Finally, Tn6050 was observed twice in the second chromosome with accessory genes not classically associated with transposons, namely a sulfate permease, a universal stress protein (UspA) and a DksA-like DnaK suppressor protein. The role of these genes is unclear but a functional association could be assumed. Finally, a set of 21 IS elements was found, counting in total for 57 copies dispersed over the genome. The number of copies ranged from 1 to 9 (IS1088 ) and 10 (ISRme3 ). The 21 IS elements could be divided into 10 different families. The elements ISRme5 and IS1071 were putatively involved in the recruitment of the genes for hydrogenotrophy and CO2 fixation, with mutants unable to grow on H2 and CO2 appeared to have lost these genes by IS1071 -mediated excision. These data clearly showed that the C. metallidurans CH34 model bacterium and some of it's Cupriavidus and Ralstonia relatives carry a multitude of tools that allowed them to genetically adapt to polluted and extreme soil environments, and that are a key in their success to adapt to the new anthropogenic spacecraft environments. Furthermore, these tools could be exploited to assess and measure genetic effects of spaceflight conditions. Acknowledgements This work was supported by the European Space Agency (ESA-PRODEX) and the Belgian Science Policy (Belspo) through the MISSEX and COMICS projects.

Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates

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Gretchen H. Roffler; Sandra L. Talbot; Gordon Luikart; George K. Sage; Kristy L. Pilgrim; Layne G. Adams; Michael K. Schwartz

2014-01-01

Identifying patterns of fine-scale genetic structure in natural populations can advance understanding of critical ecological processes such as dispersal and gene flow across heterogeneous landscapes. Alpine ungulates generally exhibit high levels of genetic structure due to female philopatry and patchy configuration of mountain habitats. We assessed the spatial scale...

Estimation of loss of genetic diversity in modern Japanese cultivars by comparison of diverse genetic resources in Asian pear (Pyrus spp.).

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Nishio, Sogo; Takada, Norio; Saito, Toshihiro; Yamamoto, Toshiya; Iketani, Hiroyuki

2016-06-14

Pears (Pyrus spp.) are one of the most important fruit crops in temperate regions. Japanese pear breeding has been carried out for over 100 years, working to release new cultivars that have good fruit quality and other desirable traits. Local cultivar 'Nijisseiki' and its relatives, which have excellent fruit texture, have been repeatedly used as parents in the breeding program. This strategy has led to inbreeding within recent cultivars and selections. To avoid inbreeding depression, we need to clarify the degree of inbreeding among crossbred cultivars and to introgress genetic resources that are genetically different from modern cultivars and selections. The objective of the present study was to clarify the genetic relatedness between modern Japanese pear cultivars and diverse Asian pear genetic resources. We genotyped 207 diverse accessions by using 19 simple sequence repeat (SSR) markers. The heterozygosity and allelic richness of modern cultivars was obviously decreased compared with that of wild individuals, Chinese pear cultivars, and local cultivars. In analyses using Structure software, the 207 accessions were classified into four clusters (K = 4): one consisting primarily of wild individuals, one of Chinese pear cultivars, one of local cultivars from outside the Kanto region, and one containing both local cultivars from the Kanto region and crossbred cultivars. The results of principal coordinate analysis (PCoA) were similar to those from the Structure analysis. Wild individuals and Chinese pears appeared to be distinct from other groups, and crossbred cultivars became closer to 'Nijisseiki' as the year of release became more recent. Both Structure and PCoA results suggest that the modern Japanese pear cultivars are genetically close to local cultivars that originated in the Kanto region, and that the genotypes of the modern cultivars were markedly biased toward 'Nijisseiki'. Introgression of germplasm from Chinese pear and wild individuals that are

Cognitive bias modification versus CBT in reducing adolescent social anxiety: a randomized controlled trial.

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Sportel, B Esther; de Hullu, Eva; de Jong, Peter J; Nauta, Maaike H

2013-01-01

Social anxiety is a common mental disorder among adolescents and is associated with detrimental long term outcomes. Therefore, this study investigated the efficacy of two possible early interventions for adolescent social anxiety and test anxiety. An internet-based cognitive bias modification (CBM; n = 86) was compared to a school-based cognitive behavioral group training (CBT; n = 84) and a control group (n = 70) in reducing symptoms of social and test anxiety in high socially and/or test anxious adolescents aged 13-15 years. Participants (n = 240) were randomized at school level over the three conditions. CBM consisted of a 20-session at home internet-delivered training; CBT was a 10-session at school group training with homework assignments; the control group received no training. Participants were assessed before and after the intervention and at 6 and 12 month follow-up. At 6 month follow-up CBT resulted in lower social anxiety than the control condition, while for CBM, this effect was only trend-significant. At 12 month follow-up this initial benefit was no longer present. Test anxiety decreased more in the CBT condition relative to the control condition in both short and long term. Interestingly, in the long term, participants in the CBM condition improved more with regard to automatic threat-related associations than both other conditions. The results indicate that the interventions resulted in a faster decline of social anxiety symptoms, whereas the eventual end point of social anxiety was not affected. Test anxiety was influenced in the long term by the CBT intervention, and CBM lead to increased positive automatic threat-related associations. TrialRegister.nl NTR965.