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1.  Effects of loss aversion on post-decision wagering: Implications for measures of awareness 
Consciousness and Cognition  2010;19(1):352-363.
Wagering contingent on a previous decision, or post-decision wagering, has recently been proposed to measure conscious awareness. Whilst intuitively appealing, it remains unclear whether economic context interacts with subjective confidence and how such interactions might impact on the measurement of awareness. Here we propose a signal detection model which predicts that advantageous wagers placed on the identity of preceding stimuli are affected by loss aversion, despite stimulus visibility remaining constant. This pattern of predicted results was evident in a psychophysical task where we independently manipulated perceptual and economic factors. Changes in wagering behaviour induced by changes in wager size were largely driven by changes in criterion, consistent with the model. However, for near-threshold stimuli, a reduction in wagering efficiency was also evident, consistent with an apparent but potentially illusory decrease in awareness of the stimulus. These findings challenge an assertion that post-decision wagering provides a direct index of subjective awareness.
doi:10.1016/j.concog.2009.11.002
PMCID: PMC2842936  PMID: 20005133
Post-decision wagering; Perception; Economics; Signal detection theory; Reward; Awareness; Metacognition; Psychophysics
2.  The evolution of superstitious and superstition-like behaviour 
Superstitious behaviours, which arise through the incorrect assignment of cause and effect, receive considerable attention in psychology and popular culture. Perhaps owing to their seeming irrationality, however, they receive little attention in evolutionary biology. Here we develop a simple model to define the condition under which natural selection will favour assigning causality between two events. This leads to an intuitive inequality—akin to an amalgam of Hamilton's rule and Pascal's wager—-that shows that natural selection can favour strategies that lead to frequent errors in assessment as long as the occasional correct response carries a large fitness benefit. It follows that incorrect responses are the most common when the probability that two events are really associated is low to moderate: very strong associations are rarely incorrect, while natural selection will rarely favour making very weak associations. Extending the model to include multiple events identifies conditions under which natural selection can favour associating events that are never causally related. Specifically, limitations on assigning causal probabilities to pairs of events can favour strategies that lump non-causal associations with causal ones. We conclude that behaviours which are, or appear, superstitious are an inevitable feature of adaptive behaviour in all organisms, including ourselves.
doi:10.1098/rspb.2008.0981
PMCID: PMC2615824  PMID: 18782752
optimality theory; behavioural ecology; animal behaviour
3.  Wagering on a large scale: Relationships between public gambling and game manipulations in two state lotteries 
Public wagering was examined in relation to game adjustments during the first 523 draws of Oregon's “Megabucks” lottery and the first 540 draws of Arizona's “The Pick” lottery. Oregon's lottery was modified five times during this period, and Arizona's lottery underwent four modifications. Public wagering was not related to decreases in the odds of winning in either state. Wagering increased in both states following the introduction of a minimum $1 million jackpot. Wagering also increased following a change in game frequency from weekly to semiweekly draws. Sales trends in both states suggest that over the period examined, larger jackpots were required to maintain previous levels of lottery play. These data suggest that public participation in gambling can be manipulated by state lottery commissions through adjustments in lottery contingencies.
doi:10.1901/jaba.1995.28-127
PMCID: PMC1279805  PMID: 16795861
wagering; state lotteries; game manipulations; naturalistic observation
4.  Human Wagering Behavior Depends on Opponents' Faces 
PLoS ONE  2010;5(7):e11663.
Research in competitive games has exclusively focused on how opponent models are developed through previous outcomes and how peoples' decisions relate to normative predictions. Little is known about how rapid impressions of opponents operate and influence behavior in competitive economic situations, although such subjective impressions have been shown to influence cooperative decision-making. This study investigates whether an opponent's face influences players' wagering decisions in a zero-sum game with hidden information. Participants made risky choices in a simplified poker task while being presented opponents whose faces differentially correlated with subjective impressions of trust. Surprisingly, we find that threatening face information has little influence on wagering behavior, but faces relaying positive emotional characteristics impact peoples' decisions. Thus, people took significantly longer and made more mistakes against emotionally positive opponents. Differences in reaction times and percent correct were greatest around the optimal decision boundary, indicating that face information is predominantly used when making decisions during medium-value gambles. Mistakes against emotionally positive opponents resulted from increased folding rates, suggesting that participants may have believed that these opponents were betting with hands of greater value than other opponents. According to these results, the best “poker face” for bluffing may not be a neutral face, but rather a face that contains emotional correlates of trustworthiness. Moreover, it suggests that rapid impressions of an opponent play an important role in competitive games, especially when people have little or no experience with an opponent.
doi:10.1371/journal.pone.0011663
PMCID: PMC2908123  PMID: 20657772
5.  The Effect of Recessions on Gambling Expenditures 
Journal of Gambling Studies  2011;28(4):703-717.
This article examines the influence of the business cycle on expenditures of three major types of legalized gambling activities: Casino gambling, lottery, and pari-mutuel wagering. Empirical results are obtained using monthly aggregated US per capita consumption time series for the period 1959.01–2010.08. Among the three gambling activities only lottery consumption appears to be recession-proof. This series is characterized by a vast and solid growth that exceeds the growth in income and the growth in other gambling sectors. Casino gambling expenditures show a positive growth during expansions and no growth during recessions. Hence, the loss in income during recessions affects casino gambling. However, income shocks which are not directly related to the business cycle do not influence casino gambling expenditures. Pari-mutuel wagering displays an overall negative trend and its average growth rate is smaller than the growth in income, especially during recessions. The findings of this article provide important implications for the gambling industry and for local governments.
doi:10.1007/s10899-011-9282-9
PMCID: PMC3501160  PMID: 22143980
Gambling; Business cycle; Time series analysis; Cointegration
6.  How do gamblers start gambling: identifying behavioural markers for high-risk internet gambling 
Background: The goal of this study is to identify betting patterns displayed during the first month of actual Internet gambling on a betting site that can serve as behavioural markers to predict the development of gambling-related problems. Methods: Using longitudinal data, k-means clustering analysis identified a small subgroup of high-risk gamblers. Results: Seventy-three percent of the members of this subgroup eventually closed their account due to gambling-related problems. The characteristics of this high-risk subgroup were as follows: (i) frequent and (ii) intensive betting combined with (iii) high variability across wager amount and (iv) an increasing wager size during the first month of betting. Conclusion: This analysis provides important information that can help to identify potentially problematic gamblers during the early stages of gambling-related problems. Public health workers can use these results to develop early interventions that target high-risk Internet gamblers for prevention efforts. However, one study limitation is that the results distinguish only a small proportion of the total sample; therefore, additional research will be necessary to identify markers that can classify larger segments of high-risk gamblers.
doi:10.1093/eurpub/ckp232
PMCID: PMC3324590  PMID: 20110273
7.  Impact of PPIs on patient focused symptomatology in GERD 
About half of patients with gastroesophageal reflux disease (GERD) have a normal endoscopy, so symptom assessment is the only appropriate outcome measure for these persons. Symptom assessment is also of great importance in persons with erosive esophagitis. There is currently no fully validated questionnaire to compare symptom response to treatment of patients with GERD. The aim of this review is to consider ReQuest™ assessment tool to evaluate esophageal, supra-esophageal, and infra-esophageal symptoms, as well as any modification of the patient’s quality of life. The ReQuest™ may be combined with the Los Angeles classification of esophagitis (LA A–D), to include the normal endoscopic finding in normal endoscopy reflux disease. The ReQuest™ score declines rapidly towards normal with patient treatment with a proton pump inhibitor. A proportion of patients need more than the usual 8 weeks of therapy. For example, in GERD patients with Los Angeles B–D, the ReQuest™ score falls more with pantoprazole 40 mg than with esomoprazole 40 mg after 12 weeks of therapy. Now that the simplified ReQuest in Practice™ is available, this validated brief questionnaire has potential as an instrument for use in GERD patients seen in everyday clinical practice.
PMCID: PMC2643100  PMID: 19337426
complete healing; dyspepsia; erosive esophagitis; GERD symptoms; pH; ReQuest™
8.  Climate of origin affects tick (Ixodes ricinus) host-seeking behavior in response to temperature: implications for resilience to climate change? 
Ecology and Evolution  2014;4(7):1186-1198.
Climate warming is changing distributions and phenologies of many organisms and may also impact on vectors of disease-causing pathogens. In Europe, the tick Ixodes ricinus is the primary vector of medically important pathogens (e.g., Borrelia burgdorferi sensu lato, the causative agent of Lyme borreliosis). How might climate change affect I. ricinus host-seeking behavior (questing)? We hypothesize that, in order to maximize survival, I. ricinus have adapted their questing in response to temperature in accordance with local climates. We predicted that ticks from cooler climates quest at cooler temperatures than those from warmer climates. This would suggest that I. ricinus can adapt and therefore have the potential to be resilient to climate change. I. ricinus were collected from a cline of climates using a latitudinal gradient (northeast Scotland, North Wales, South England, and central France). Under laboratory conditions, ticks were subjected to temperature increases of 1°C per day, from 6 to 15°C. The proportion of ticks questing was recorded five times per temperature (i.e., per day). The theoretical potential to quest was then estimated for each population over the year for future climate change projections. As predicted, more ticks from cooler climates quested at lower temperatures than did ticks from warmer climates. The proportion of ticks questing was strongly associated with key climate parameters from each location. Our projections, based on temperature alone, suggested that populations could advance their activity season by a month under climate change, which has implications for exposure periods of hosts to tick-borne pathogens. Our findings suggest that I. ricinus have adapted their behavior in response to climate, implying some potential to adapt to climate change. Predictive models of I. ricinus dynamics and disease risk over continental scales would benefit from knowledge of these differences between populations.
doi:10.1002/ece3.1014
PMCID: PMC3997332  PMID: 24772293
Adaptation; evolution; experiment; nymphs; phenotypic plasticity; questing
9.  Doctors' attitudes to risk in difficult clinical decisions: application of decision analysis in hepatobiliary disease. 
Twelve doctors with special training in hepatology independently reviewed two to five cases each from a group of seven cases of complicated hepatobiliary problems. A doctor's willingness to take risks to improve his patients' health was quantified by a wagering technique based on the probability of achieving a successful intervention. These probabilities were then used to calculate "utilities," which represented the average opinion of the doctors about the relative worth of each of six predefined states of health. The results showed that, in the context of risky decisions for severely ill patients, a year of life was considered by the doctors to be worth 44% of a full recovery; being mobile for that year increased this value to 57%. Survival for up to five years with restricted mobility was considered to be worth 70% of a full recovery and the ability to work during that period increased this value to 85%. It is concluded that in clinical decision making the uncertainty and preferences implicit in a course of action can be quantified and thus made explicit.
PMCID: PMC1442277  PMID: 6430413
10.  Brief Motivational Interventions for College Student Problem Gamblers 
Addiction (Abingdon, England)  2009;104(9):1569-1578.
Aims
College students experience high rates of problem and pathological gambling, yet little research has investigated methods for reducing gambling in this population. This study sought to examine the efficacy of brief intervention strategies.
Design
Randomized trial.
Setting
College campuses.
Participants
117 college student problem and pathological gamblers.
Interventions
Students were randomly assigned to: an assessment-only control, 10 minutes of Brief Advice, 1 session of motivational enhancement therapy (MET), or 1 session of MET plus 3 sessions of cognitive-behavioral therapy (CBT). The three interventions were designed to reduce gambling.
Measurements
Gambling was assessed at baseline, week 6, and month 9 using the Addiction Severity Index-Gambling (ASI-G) module, which also assesses days and dollars wagered.
Findings
Compared to the assessment-only condition, those receiving any intervention had significant decreases in ASI-G scores and days and dollars wagered over time. The MET condition significantly decreased ASI-G scores and dollars wagered over time, and it increased the odds of a clinically significant reduction in gambling at the 9-month follow-up relative to the assessment-only condition, even after controlling for baseline indices that could impact outcomes. The Brief Advice and MET+CBT conditions had benefits on some, but not all, indices of gambling. None of the interventions differed significantly from one another.
Conclusions
These results suggest the efficacy of brief interventions for reducing gambling problems in college students.
doi:10.1111/j.1360-0443.2009.02652.x
PMCID: PMC2758481  PMID: 19686527
gambling; brief interventions; motivational enhancement therapy; cognitive-behavioral therapy; treatment efficacy
11.  Consciousness of targets during the attentional blink: a gradual or all-or-none dimension? 
Models of consciousness differ in whether they predict a gradual change or a discontinuous transition between nonconscious and conscious perception. Sergent and Dehaene (Psychological Science, 15, 720–728, 2004) asked subjects to rate on a continuous scale the subjective visibility of target words presented during an attentional blink. They found that these words were either detected as well as targets outside the attentional-blink period or not detected at all, and interpreted these results as support for a discontinuous transition between nonconscious and conscious processing. We present results from 4 attentional-blink experiments showing that this all-or-none rating pattern disappears with the use of an alternative measure of consciousness (post-decision wagering) and a more difficult identification task. Instead, under these circumstances, subjects used the consciousness rating scales in a continuous fashion. These results are more consistent with models that assume a gradual change between nonconscious and conscious perception during the attentional blink.
Electronic supplementary material
The online version of this article (doi:10.3758/s13414-010-0026-1) contains supplementary material, which is available to authorized users.
doi:10.3758/s13414-010-0026-1
PMCID: PMC3037489  PMID: 21264738
Attentional blink; Consciousness; Post-decision wagering; Awareness; Subjective ratings
12.  Effects of Alcohol and Initial Gambling Outcomes on Within-Session Gambling Behavior 
Concurrent drinking and gambling is prevalent among young adults and may increase negative consequences associated with each behavior. The effects of alcohol, initial gambling outcomes, gambling-related cognitions, and impulsivity on gambling behavior were evaluated. Initial gambling outcomes, gambling-related cognitions, and impulsivity were also assessed as potential moderators of the relation between alcohol and gambling behavior. Participants (N = 130) were randomly assigned to receive active placebo or alcohol (0.84 g/kg and 0.76 g/kg for men and women, respectively) and were invited to wager on a simulated slot machine programmed to produce 1 of 3 initial outcomes (win, breakeven, or loss) before beginning a progressive loss schedule. Alcohol consumption was associated with larger average bets and more rapid loss of all available funds, though no evidence was found for predicted main effects and interactions for gambling persistence. The effect of impulsivity was moderated by beverage condition, such that higher levels of impulsivity were associated with larger average bets for participants in the placebo but not the alcohol group. Results have direct implications for individual-focused and public-health interventions.
doi:10.1037/a0019114
PMCID: PMC3039524  PMID: 20384426
alcohol; gambling; persistence; betting behavior; impulsivity
13.  Prize-based contingency management is efficacious in cocaine abusers with and without recent gambling participation 
Prize-based contingency management (CM) is efficacious in treating cocaine abuse, and the chance-based procedures of prize CM may be appealing to those who gamble. Using data from three randomized trials, we evaluated whether cocaine abusers who had wagered in the month before treatment (n = 62) responded more favorably to prize CM than those who had not (n = 278). Participants were randomized to standard care (SC) or SC plus prize CM. Although prize CM was related to better outcomes overall, recent gambling was not associated with outcomes across or within treatment conditions. Gambling participation before treatment entry was associated with reductions in gambling over time, and this effect was more pronounced among those assigned to CM. These data suggest that prize CM is equally efficacious for substance abusers who do and do not gamble, and they extend prior studies indicating that prize CM does not increase gambling.
doi:10.1016/j.jsat.2010.06.011
PMCID: PMC2937065  PMID: 20667679
treatment outcome; contingency management; cocaine dependence; gambling
14.  Searle’s wager 
AI & society  2011;26(4):363-369.
Nicholas Agar has recently argued that it would be irrational for future human beings to choose to radically enhance themselves by uploading their minds onto computers. Utilizing Searle’s argument that machines cannot think, he claims that uploading might entail death. He grants that Searle’s argument is controversial, but he claims, so long as there is a non-zero probability that uploading entails death, uploading is irrational. I argue that Agar’s argument, like Pascal’s wager on which it is modelled, fails, because the principle that we (or future agents) ought to avoid actions that might entail death is not action guiding. Too many actions fall under its scope for the principle to be plausible. I also argue that the probability that uploading entails death is likely to be lower than Agar recognizes.
doi:10.1007/s00146-011-0317-7
PMCID: PMC3303128  PMID: 22427723
Agar; Searle; Consciousness; Radical enhancement; Uploading; Probability
15.  A computational framework for the study of confidence in humans and animals 
Confidence judgements, self-assessments about the quality of a subject's knowledge, are considered a central example of metacognition. Prima facie, introspection and self-report appear the only way to access the subjective sense of confidence or uncertainty. Contrary to this notion, overt behavioural measures can be used to study confidence judgements by animals trained in decision-making tasks with perceptual or mnemonic uncertainty. Here, we suggest that a computational approach can clarify the issues involved in interpreting these tasks and provide a much needed springboard for advancing the scientific understanding of confidence. We first review relevant theories of probabilistic inference and decision-making. We then critically discuss behavioural tasks employed to measure confidence in animals and show how quantitative models can help to constrain the computational strategies underlying confidence-reporting behaviours. In our view, post-decision wagering tasks with continuous measures of confidence appear to offer the best available metrics of confidence. Since behavioural reports alone provide a limited window into mechanism, we argue that progress calls for measuring the neural representations and identifying the computations underlying confidence reports. We present a case study using such a computational approach to study the neural correlates of decision confidence in rats. This work shows that confidence assessments may be considered higher order, but can be generated using elementary neural computations that are available to a wide range of species. Finally, we discuss the relationship of confidence judgements to the wider behavioural uses of confidence and uncertainty.
doi:10.1098/rstb.2012.0037
PMCID: PMC3318772  PMID: 22492750
metacognition; uncertainty; Bayesian; psychophysics; model-based; post-decision wagering
16.  Discounting of probabilistic rewards is associated with gambling abstinence in treatment-seeking pathological gamblers 
Journal of abnormal psychology  2011;121(1):151-159.
Individuals with addictive disorders, including substance abusers and pathological gamblers, discount or devalue rewards delayed in time more than controls. Theoretically, preference for probabilistic rewards is directly related to gambling, but limited empirical research has examined probabilistic discounting in individuals with pathological gambling. This study evaluated probability and delay discounting in treatment-seeking pathological gamblers and their association with gambling treatment outcomes during and following treatment. At time of treatment entry, 226 pathological gamblers completed probability and delay discounting tasks. They were then randomized to one of three treatment conditions, and gambling behavior was measured throughout treatment and at a one-year follow-up assessment. After controlling for possibly confounding variables and treatment condition, more shallow probability discounting was associated with greater reductions in amounts wagered during treatment and likelihood of gambling abstinence at the end of treatment and throughout the follow-up period. No associations were noted between delay discounting and gambling treatment outcomes. These data suggest that probability discounting may be an important construct in understanding pathological gambling and its treatment.
doi:10.1037/a0024782
PMCID: PMC3773696  PMID: 21842965
probability discounting; pathological gambling; treatment
17.  A Meta-Analysis of Functional Neuroimaging Studies of Self and Other Judgments Reveals a Spatial Gradient for Mentalizing in Medial Prefrontal Cortex 
Journal of cognitive neuroscience  2012;24(8):1742-1752.
The distinction between processes used to perceive and understand the self and others has received considerable attention in psychology and neuroscience. Brain findings highlight a role for various regions, in particular the medial prefrontal cortex (mPFC), in supporting judgments about both the self and others. We performed a meta-analysis of 107 neuroimaging studies of self- and other-related judgments using Multilevel Kernel Density Analysis (MKDA; Kober & Wager, 2010). We sought to determine what brain regions are reliably involved in each judgment type, and in particular, what the spatial and functional organization of mPFC is with respect to them. Relative to non-mentalizing judgments, both self and other judgments were associated with activity in mPFC, ranging from ventral to dorsal extents, as well as common activation of the left temporoparietal junction (TPJ) and posterior cingulate. A direct comparison between self and other judgments revealed that ventral mPFC (vmPFC), as well as left ventrolateral PFC and left insula, were more frequently activated by self-related judgments, whereas dorsal mPFC (dmPFC), in addition to bilateral TPJ and cuneus, were more frequently activated by other-related judgments. Logistic regression analyses revealed that ventral and dorsal mPFC lay at opposite ends of a functional gradient: the z-coordinates reported in individual studies predicted whether the study involved self- or other-related judgments, which were associated with increasingly ventral or dorsal portions of mPFC, respectively. These results argue for a distributed rather than localizationist account of mPFC organization and support an emerging view on the functional heterogeneity of mPFC.
doi:10.1162/jocn_a_00233
PMCID: PMC3806720  PMID: 22452556
18.  Predicting the Match Outcome in One Day International Cricket Matches, while the Game is in Progress 
Millions of dollars are wagered on the outcome of one day international (ODI) cricket matches, with a large percentage of bets occurring after the game has commenced. Using match information gathered from all 2200 ODI matches played prior to January 2005, a range of variables that could independently explain statistically significant proportions of variation associated with the predicted run totals and match outcomes were created. Such variables include home ground advantage, past performances, match experience, performance at the specific venue, performance against the specific opposition, experience at the specific venue and current form. Using a multiple linear regression model, prediction variables were numerically weighted according to statistical significance and used to predict the match outcome. With the use of the Duckworth-Lewis method to determine resources remaining, at the end of each completed over, the predicted run total of the batting team could be updated to provide a more accurate prediction of the match outcome. By applying this prediction approach to a holdout sample of matches, the efficiency of the “in the run ”wagering market could be assessed. Preliminary results suggest that the market is prone to overreact to events occurring throughout the course of the match, thus creating brief inefficiencies in the wagering market.
Key PointsIn excess of 80% of monies wagered on the outcome of ODI matches are placed after the match has commenced.Using all past data from ODI matches, multiple linear regression models are constructed to predict team totals and margin of victory.By combining match information with prediction models, an ‘in the run’ prediction process is created for ODI matches.
PMCID: PMC3861745  PMID: 24357940
Linear regression; live prediction; market efficiency; betting
19.  A Comparative Study between Modified Bassini’s Repair and Lichtenstein Mesh Repair (LMR) of Inguinal Hernias in Rural Population 
Background: Bassini’s repair and the Lichtenstein’s tension free mesh hernioplasty are commonly used hernia repair techniques and yet there is no unison as to which is the best technique. Our hospital being in a rural setup and catering to majority of poor patients who are daily wagers, open hernia repairs are commonly done. This study was undertaken to compare the technique and post-operative course so as to determine the best suitable of the two procedures for them.
Materials and Methods: A comparative randomized study was conducted on a total of 70 patients with inguinal hernia and were operated upon by either of technique and followed up. Outcome of both the techniques were analyzed and compared with other similar studies.
Results: Study involved 35 each of Modified Bassini’s Repair (MBR) and Lichtenstein’s Mesh Repair (LMR), over a period of 18 months. MBR took more operating time than LMR. Commonest complication in both the groups was seroma formation. There were two recurrences in the MBR group and none in LMR group.
Conclusion: LMR was comparatively better than MBR due to its simplicity, less dissection and early ambulation in the post-operative period and with no recurrence, in our study.
doi:10.7860/JCDR/2014/7431.4016
PMCID: PMC3972608  PMID: 24701491
Inguinal hernia; Modified Bassini’s Repair; Lichtenstein Mesh Repair
20.  Searle’s wager 
Ai & Society  2011;26:363-369.
Nicholas Agar has recently argued that it would be irrational for future human beings to choose to radically enhance themselves by uploading their minds onto computers. Utilizing Searle’s argument that machines cannot think, he claims that uploading might entail death. He grants that Searle’s argument is controversial, but he claims, so long as there is a non-zero probability that uploading entails death, uploading is irrational. I argue that Agar’s argument, like Pascal’s wager on which it is modelled, fails, because the principle that we (or future agents) ought to avoid actions that might entail death is not action guiding. Too many actions fall under its scope for the principle to be plausible. I also argue that the probability that uploading entails death is likely to be lower than Agar recognizes.
doi:10.1007/s00146-011-0317-7
PMCID: PMC3303128  PMID: 22427723
Agar; Searle; Consciousness; Radical enhancement; Uploading; Probability
21.  A brain signature for acute pain 
Trends in cognitive sciences  2013;17(7):309-310.
Wager and colleagues developed an fMRI-based spatial and magnitude pattern for perception of acute pain, which seems to generalize across many task conditions and subjects. This is a strong demonstration of the existence of a pain signature and raises important questions regarding what pain and perception are.
doi:10.1016/j.tics.2013.05.001
PMCID: PMC3733463  PMID: 23747083
22.  IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis 
Nucleic Acids Research  2008;36(Web Server issue):W503-W508.
IMGT/V-QUEST is the highly customized and integrated system for the standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. IMGT/V-QUEST identifies the variable (V), diversity (D) and joining (J) genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. New functionalities were added through a complete rewrite in Java. IMGT/V-QUEST analyses batches of sequences (up to 50) in a single run. IMGT/V-QUEST describes the V-REGION mutations and identifies the hot spot positions in the closest germline V gene. IMGT/V-QUEST can detect insertions and deletions in the submitted sequences by reference to the IMGT unique numbering. IMGT/V-QUEST integrates IMGT/JunctionAnalysis for a detailed analysis of the V-J and V-D-J junctions, and IMGT/Automat for a full V-J- and V-D-J-REGION annotation. IMGT/V-QUEST displays, in ‘Detailed view’, the results and alignments for each submitted sequence individually and, in ‘Synthesis view’, the alignments of the sequences that, in a given run, express the same V gene and allele. The ‘Advanced parameters’ allow to modify default parameters used by IMGT/V-QUEST and IMGT/JunctionAnalysis according to the users’ interest. IMGT/V-QUEST is freely available for academic research at http://imgt.cines.fr
doi:10.1093/nar/gkn316
PMCID: PMC2447746  PMID: 18503082
23.  OntoQuest: A Physician Decision Support System based on Ontological Queries of the Hospital Database 
OntoQuest is a physician decision support system that mines the hospital data base for previous decisions made in cases similar to the current one. For example, OntoQuest displays a list of the medications prescribed to similar historical patients from which the physician may compare his choice of medication for the current patient. This information retrieval is accomplished using ontological queries. Unlike a regular database query, an ontological query is able to account for semantic similarity between patients. To implement the ontological query, we propose a method for computing the ontological similarity between patients represented by sets of ICD-9 diagnoses. We have tested the OntoQuest prototype on a pilot data set of 2077 patients. Finally, we compare the OntoQuest performance to conventional database queries. We believe that OntoQuest can be extended to compare services, quality and outcomes among patient and provider groups.
PMCID: PMC1839267  PMID: 17238419
24.  Variable Strength of Forest Stand Attributes and Weather Conditions on the Questing Activity of Ixodes ricinus Ticks over Years in Managed Forests 
PLoS ONE  2013;8(1):e55365.
Given the ever-increasing human impact through land use and climate change on the environment, we crucially need to achieve a better understanding of those factors that influence the questing activity of ixodid ticks, a major disease-transmitting vector in temperate forests. We investigated variation in the relative questing nymph densities of Ixodes ricinus in differently managed forest types for three years (2008–2010) in SW Germany by drag sampling. We used a hierarchical Bayesian modeling approach to examine the relative effects of habitat and weather and to consider possible nested structures of habitat and climate forces. The questing activity of nymphs was considerably larger in young forest successional stages of thicket compared with pole wood and timber stages. Questing nymph density increased markedly with milder winter temperatures. Generally, the relative strength of the various environmental forces on questing nymph density differed across years. In particular, winter temperature had a negative effect on tick activity across sites in 2008 in contrast to the overall effect of temperature across years. Our results suggest that forest management practices have important impacts on questing nymph density. Variable weather conditions, however, might override the effects of forest management practices on the fluctuations and dynamics of tick populations and activity over years, in particular, the preceding winter temperatures. Therefore, robust predictions and the detection of possible interactions and nested structures of habitat and climate forces can only be quantified through the collection of long-term data. Such data are particularly important with regard to future scenarios of forest management and climate warming.
doi:10.1371/journal.pone.0055365
PMCID: PMC3555926  PMID: 23372852
25.  Seasonality of Ixodes ricinus Ticks on Vegetation and on Rodents and Borrelia burgdorferi sensu lato Genospecies Diversity in Two Lyme Borreliosis–Endemic Areas in Switzerland 
Abstract
We compared Ixodes ricinus questing density, the infestation of rodents by immature stages, and the diversity of Borrelia burgdorferi sensu lato (sl) in questing ticks and ticks collected from rodents in two Lyme borreliosis (LB)-endemic areas in Switzerland (Portes-Rouges [PR] and Staatswald [SW]) from 2003 to 2005. There were variations in the seasonal pattern of questing tick densities among years. Questing nymphs were globally more abundant at PR than at SW, but the proportion of rodents infested by immature ticks was similar (59.4% and 61%, respectively). Questing tick activity lasted from February to November with a strong decline in June. The seasonal pattern of ticks infesting rodents was different. Ticks infested rodents without decline in summer, suggesting that the risk of being bitten by ticks remains high during the summer. Rodents from SW showed the highest infestation levels (10±21.6 for larvae and 0.54±1.65 for nymphs). The proportion of rodents infested simultaneously by larvae and nymphs (co-feeding ticks) was higher at SW (28%) than at PR (11%). Apodemus flavicollis was the species the most frequently infested by co-feeding ticks, and Myodes glareolus was the most infective rodent species as measured by xenodiagnosis. At PR, the prevalence of B. burgdorferi sl in questing ticks was higher (17.8% for nymphs and 32.4% for adults) than at SW (10.4% for nymphs and 24.8% for adults), with B. afzelii as the dominant species, but B. garinii, B. burgdorferi sensu stricto, and B. valaisiana were also detected. Rodents transmitted only B. afzelii (at PR and at SW) and B. bavariensis (at SW) to ticks, and no mixed infection by additional genospecies was observed in co-feeding ticks. This implies that co-feeding transmission does not contribute to genospecies diversity. However, persistent infections in rodents and co-feeding transmission contribute to the perpetuation of B. afzelii in nature.
doi:10.1089/vbz.2011.0763
PMCID: PMC3413890  PMID: 22607074
Borrelia burgdorferi sensu lato; Co-feeding transmission; Rodents

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