CiteULike: Author Leisch

Interaction between serotonin 5-HT2A receptor gene and dopamine transporter (DAT1) gene polymorphisms influences personality trait of persistence in Austrian Caucasians.

Alexandra Schosser — 2008-07-22T20:45:58-00:00

The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry (13 February 2008), pp. 1-8.

We examined 89 normal volunteers using Cloninger's Temperament and Character Inventory (TCI). Genotyping the 102T/C polymorphism of the serotonin 5HT2A receptor gene and the ser9gly polymorphism in exon 1 of the dopamine D3 receptor (DRD3) gene was performed using PCR-RFLP, whereas the dopamine transporter (DAT1) gene variable number of tandem repeats (VNTR) polymorphism was investigated using PCR amplification followed by electrophoresis in an 8% acrylamide gel with a set of size markers. We found a nominally significant association between gender and harm avoidance (P=0.017; women showing higher scores). There was no association of either DAT1, DRD3 or 5HT2A alleles or genotypes with any dimension of the TCI applying Kruskal-Wallis rank-sum tests. Comparing homozygote and heterozygote DAT1 genotypes, we found higher novelty seeking scores in homozygotes (P=0.054). We further found a nominally significant interaction between DAT1 and 5HT2A homo-/heterozygous gene variants (P=0.0071; DAT1 and 5HT2A genotypes P value of 0.05), performing multivariate analysis of variance (MANOVA). Examining the temperamental TCI subscales, this interaction was associated with persistence (genotypes: P=0.004; homo-/heterozygous gene variants: P=0.0004). We conclude that an interaction between DAT1 and 5HT2A genes might influence the temperamental personality trait persistence.

Bioconductor: open software development for computational biology and bioinformatics.

RC Gentleman — 2005-04-21T13:38:17-00:00

Genome Biol, Vol. 5, No. 10. (2004)

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.

Stroking of different body regions by a human: Effects on behaviour and heart rate of dairy cows

Claudia Schmied — 2008-07-15T18:22:14-00:00

Applied Animal Behaviour Science, Vol. 109, No. 1. (January 2008), pp. 25-38.

From observations of intra-specific social grooming in cattle and studies on human stroking in other species, we hypothesised that cows' reactions to human stroking differ depending on the body regions being stroked. Moreover, we tested, whether cows [`]reactions to stroking change with the animals' experience of stroking. Sixty dairy cows were stroked in three different body regions, i.e. the withers, W, neck ventral, NV (both licked often in social grooming) and the lateral chest, LC (licked rarely), in a balanced order during 10-min sessions. Behavioural reactions and heart rate during stroking as well as reactions to the human just after stroking were recorded. Two test sessions were carried out with 3 weeks of treatment in-between. During this period, the cows were randomly allocated to four treatment groups: three groups received 5 min of daily stroking in either W, NV or LC and the last one (control group) was exposed to simple human presence. During stroking W and NV, cows showed longer neck stretching and ear hanging than during stroking LC (P < 0.001). Moreover, ear hanging was shown longer when W was stroked as compared to NV (P < 0.001), but neck stretching was observed longer during stroking NV as compared to W only after the treatment period (P < 0.01). In the first test session, more animals showed head shaking and head throwing during stroking W and NV than LC (P < 0.01), whereas in the second test session these behaviours were observed only in few animals. In the first test session heart rate was higher during stroking W than the other body regions (P <= 0.01). In the second test session, the lowest heart rate was found during stroking NV (P < 0.05). Finally, contact with the experimenter following stroking differed for the three body regions stroked in both test sessions (first: P = 0.06, second: P < 0.01); contact was shortest for LC. When comparing both test sessions, stretching the neck and ear hanging increased (P < 0.001), while head shaking and head throwing decreased (P < 0.05); there was no difference for heart rate and contact with the experimenter. The four treatments had no influence on reactions to stroking. To conclude, stroking of body regions often licked during social grooming led to more responses than stroking the one licked rarely. Some reactions, such as stretching the neck, are also observed during social licking. This suggests that cows may in part perceive human stroking of body regions often licked similarly to social licking. This knowledge could be of interest for an improvement in quality of human-cattle interactions.

The support vector machine under test

David Meyer — 2008-05-09T19:40:26-00:00

Neurocomputing, Vol. 55, No. 1-2. (September 2003), pp. 169-186.

Support vector machines (SVMs) are rarely benchmarked against other classification or regression methods. We compare a popular SVM implementation (libsvm) to 16 classification methods and 9 regression methods--all accessible through the software --by the means of standard performance measures (classification error and mean squared error) which are also analyzed by the means of bias-variance decompositions. SVMs showed mostly good performances both on classification and regression tasks, but other methods proved to be very competitive.

StatDataML: An XML Format for Statistical Data

David Meyer — 2008-04-14T18:46:36-00:00

In order to circumvent common di#culties in exchanging statistical data between heterogeneous applications (format incompatibilities, technocentric data representation), we introduce an XML-based markup language for statistical data, called StatDataML. After comparing StatDataML to other data concepts, we detail the design which borrows from the language S, such that data objects are basically organized as recursive and nonrecursive structures, and may also be supplemented with meta-information.

Fitting finite mixtures of generalized linear regressions in R

Bettina Grun — 2007-09-06T14:17:05-00:00

Computational Statistics & Data Analysis, Vol. 51, No. 11. (15 July 2007), pp. 5247-5252.

R package flexmix provides flexible modelling of finite mixtures of regression models using the EM algorithm. Several new features of the software such as fixed and nested varying effects for mixtures of generalized linear models and multinomial regression for a priori probabilities given concomitant variables are introduced. The use of the software in addition to model selection is demonstrated on a logistic regression example.

Routine upstream initiation vs deferred selective use of glycoprotein IIb/IIIa inhibitors in acute coronary syndromes: the ACUITY Timing trial.

GW Stone — 2007-03-10T16:24:23-00:00

JAMA, Vol. 297, No. 6. (14 February 2007), pp. 591-602.

CONTEXT: In patients with moderate- and high-risk acute coronary syndromes (ACS) who undergo an early, invasive treatment strategy, current guidelines recommend administration of platelet glycoprotein IIb/IIIa (Gp IIb/IIIa) inhibitors, either upstream to all patients prior to angiography or deferred for selective use in the catheterization laboratory just prior to angioplasty. The preferred approach is undetermined. OBJECTIVE: To determine the optimal strategy for the use of Gp IIb/IIIa inhibitors in patients with moderate- and high-risk ACS undergoing an early, invasive treatment strategy. DESIGN: Prospective, randomized, open-label trial with 30-day clinical follow-up. SETTING: Four hundred fifty academic and community-based institutions in 17 countries. PATIENTS: A total of 9207 patients with moderate- and high-risk ACS undergoing an invasive treatment strategy. INTERVENTIONS: Patients were randomly assigned to receive either routine upstream (n=4605) or deferred selective (n=4602) Gp IIb/IIIa inhibitor administration, respectively. MAIN OUTCOME MEASURES: The primary outcome was assessment of noninferiority of deferred Gp IIb/IIIa inhibitor use compared with upstream administration for the prevention of composite ischemic events (death, myocardial infarction, or unplanned revascularization for ischemia) at 30 days, using a 1-sided alpha level of .025. Major secondary end points included noninferiority or superiority of major bleeding and net clinical outcomes (composite ischemia or major bleeding). RESULTS: Glycoprotein IIb/IIIa inhibitors were used more frequently (98.3% vs 55.7%, respectively) and for a significantly longer duration (median, 18.3 vs 13.1 hours; P<.001) in patients in the upstream group compared with the deferred group. Composite ischemia at 30 days occurred in 7.9% of patients assigned to deferred use compared with 7.1% of patients assigned to upstream administration (relative risk, 1.12; 95% confidence interval, 0.97-1.29; P = .044 for noninferiority; P = .13 for superiority); as such, the criterion for noninferiority was not met. Deferred use compared with upstream use resulted in reduced 30-day rates of major bleeding (4.9% vs 6.1%, respectively; P<.001 for noninferiority; P = .009 for superiority) and similar rates of net clinical outcomes (11.7% vs 11.7%; P<.001 for noninferiority; P = .93 for superiority). CONCLUSIONS: Among patients with moderate- and high-risk ACS undergoing an invasive treatment strategy, deferring the routine upstream use of Gp IIb/IIIa inhibitors for selective administration in the cardiac catheterization laboratory only to patients undergoing percutaneous coronary intervention resulted in a numerical increase in composite ischemia that, while not statistically significant, did not meet the criterion for noninferiority. This finding was offset by a significant reduction in major bleeding. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT00093158.

Sweave: Dynamic Generation of Statistical Reports Using Literate Data Analysis

Friedrich Leisch — 2005-02-01T04:38:39-00:00

Sweave combines typesetting with L T E X and data anlysis with S into integrated statistical documents. When run through R or Splus, all data analysis output (tables, graphs, . . . ) is created on the fly and inserted into a final L T E X document. Options control which parts of the original S code are shown to or hidden from the reader, respectively. Many S users are also L T E X users, hence no new software has to be learned. The report can be automatically updated if data or...