Origins and evolution of VNTR loci: The apolipoprotein B 3$\sp\prime$ VNTR

I studied the apolipoprotein (apo) B 3$\sp\prime$ variable number tandem repeat (VNTR) and did computer simulations of the stepwise mutation model to address four questions: (1) How did the apo B VNTR originate? (2) What is the mutational mechanism of repeat number change at the apo B VNTR? (3) To what extent are population and molecular level events responsible for the determination of the contemporary apo B allele frequency distribution? (4) Can VNTR allele frequency distributions be explained by a simple and conservative mutation-drift model? I used three general approaches to address these questions: (1) I characterized the apo B VNTR region in non-human primate species; (2) I constructed haplotypes of polymorphic markers flanking the apo B VNTR in a sample of individuals from Lorrain, France and studied the associations between the flanking-marker haplotypes and apo B VNTR size; (3) I did computer simulations of the one-step stepwise mutation model and compared the results to real data in terms of four allele frequency distribution characteristics.^ The results of this work have allowed me to conclude that the apo B VNTR originated after an initial duplication of a sequence which is still present as a single copy sequence in New World monkey species. I conclude that this locus did not originate by the transposition of an array of repeats from somewhere else in the genome. It is unlikely that recombination is the primary mutational mechanism. Furthermore, the clustered nature of these associations implicates a stepwise mutational mechanism. From the high frequencies of certain haplotype-allele size combinations, it is evident that population level events have also been important in the determination of the apo B VNTR allele frequency distribution. Results from computer simulations of the one-step stepwise mutation model have allowed me to conclude that bimodal and multimodal allele frequency distributions are not unexpected at loci evolving via stepwise mutation mechanisms. Short tandem repeat loci fit the stepwise mutation model best, followed by microsatellite loci. I therefore conclude that there are differences in the mutational mechanisms of VNTR loci as classed by repeat unit size. (Abstract shortened by UMI.) ^

Design and analysis for three level hierarchical structures with count response

In numerous intervention studies and education field trials, random assignment to treatment occurs in clusters rather than at the level of observation. This departure of random assignment of units may be due to logistics, political feasibility, or ecological validity. Data within the same cluster or grouping are often correlated. Application of traditional regression techniques, which assume independence between observations, to clustered data produce consistent parameter estimates. However such estimators are often inefficient as compared to methods which incorporate the clustered nature of the data into the estimation procedure (Neuhaus 1993).1 Multilevel models, also known as random effects or random components models, can be used to account for the clustering of data by estimating higher level, or group, as well as lower level, or individual variation. Designing a study, in which the unit of observation is nested within higher level groupings, requires the determination of sample sizes at each level. This study investigates the design and analysis of various sampling strategies for a 3-level repeated measures design on the parameter estimates when the outcome variable of interest follows a Poisson distribution. ^ Results study suggest that second order PQL estimation produces the least biased estimates in the 3-level multilevel Poisson model followed by first order PQL and then second and first order MQL. The MQL estimates of both fixed and random parameters are generally satisfactory when the level 2 and level 3 variation is less than 0.10. However, as the higher level error variance increases, the MQL estimates become increasingly biased. If convergence of the estimation algorithm is not obtained by PQL procedure and higher level error variance is large, the estimates may be significantly biased. In this case bias correction techniques such as bootstrapping should be considered as an alternative procedure. For larger sample sizes, those structures with 20 or more units sampled at levels with normally distributed random errors produced more stable estimates with less sampling variance than structures with an increased number of level 1 units. For small sample sizes, sampling fewer units at the level with Poisson variation produces less sampling variation, however this criterion is no longer important when sample sizes are large. ^ 1Neuhaus J (1993). “Estimation efficiency and Tests of Covariate Effects with Clustered Binary Data”. Biometrics , 49, 989–996^

The Hamburg-Model of Integrated Care for Patients with Psychosis: Part 2

Objective: Since the beginning of the integrated care model for severely ill patients with psychotic disorders ("Hamburg model") in 2007 different clinical parameters have been consecutively assessed within a naturalistic, observational, prospective study.Methods: Clinical outcome of the 2-year and 4-year follow-ups of n = 158 patients.Results: A significant and ongoing improvement of psychopathology, severity of illness, functional outcome, quality of life and satisfaction with care in this sample of severely ill and merely chronic patients with psychosis was shown. Moreover, medication adherence improved and quality and quantity of outpatient treatment increased.Conclusion: The ongoing psychosocial stabilisation of the patients most likely result from a combination of various factors: continuity of care, multimodal and individualized care, therapeutic specialisation and the multidisciplinary ACT team. Results provide clinical and scientific evidence for future implementations of the integrated care model "Hamburg Model" for the treatment of psychosis.

Projecting a relevant "next": Instruction sequences in driving lessons

Car interaction and the organisation of multi-activity in cars have become a fertile topic of research within CA and EM (Laurier 2005, Haddington & Keisanen 2009). While previous research has focused exclusively on everyday car rides, in this paper we will analyse a specific kind of car interaction, namely driving lessons. In addition to"driving" and"talking", as the two main parallel activities in everyday car rides (Mondada in press), in driving lessons a central activity is"instructing", that we understand to be a collaborative accomplishment (Sanchez Svensson et al. 2009). Drawing on a corpus of 7 video-recorded driving lessons, we will analyse the sequential organisation of"instruction sequences", i.e. of those actions that are initiated by the driving instructor with a turn projecting the next relevant action to be executed by the learner. Learners carry out next actions in two different ways: a) as"single" actions (e.g. using the indicator); b) as a complex series of overlapping or parallel actions. We will show that"single" actions occur as responses to instructions concerning the learner's command of the car, while complex actions occur when the instructors formulate direction indications. The aims of our analyses are twofold. Firstly, we will analyse how instruction sequences are fitted to the emerging contingencies of the car ride (movement in space, changing environment): we will show that a) the turn format of the instruction initiation displays the degree of"urgency" of the requested action; b) learners have the possibility to start the relevant"next" before the instruction initiation comes to completion. Secondly, we will focus on those"seconds" that the driving instructor treats as problematic by initiating a repair sequence (e.g. an improper use of the indicator). Our research contributes to the discussion about the multimodal resources that participants can employ to fulfil a projected action. In addition, it offers insights in a hitherto scarcely investigated topic, namely the organisation of instructions and the ecology of apprenticeship. References HADDINGTON, P. & KEISANEN, T. (2009) Location, mobility and the body as resources in selecting a route. Journal of Pragmatics 41 (10), 1938-1961. LAURIER, Eric (2005): Searching for a parking space. Intellectica 41-42/2-3: 101-116. MONDADA, Lorenza (in press). Talking and driving: multi-activity in the car. Semiotica. SANCHEZ SVENSSON, M. et al. (2009) "Embedding instruction in practice: contingency and collaboration during surgical training", Sociology of Health & Illness, 31/6: 889-906.

Optimal Workflow and Process-Based Performance Measures for Endovascular Therapy in Acute Ischemic Stroke: Analysis of the Solitaire FR Thrombectomy for Acute Revascularization Study.

BACKGROUND AND PURPOSE We report on workflow and process-based performance measures and their effect on clinical outcome in Solitaire FR Thrombectomy for Acute Revascularization (STAR), a multicenter, prospective, single-arm study of Solitaire FR thrombectomy in large vessel anterior circulation stroke patients. METHODS Two hundred two patients were enrolled across 14 centers in Europe, Canada, and Australia. The following time intervals were measured: stroke onset to hospital arrival, hospital arrival to baseline imaging, baseline imaging to groin puncture, groin puncture to first stent deployment, and first stent deployment to reperfusion. Effects of time of day, general anesthesia use, and multimodal imaging on workflow were evaluated. Patient characteristics and workflow processes associated with prolonged interval times and good clinical outcome (90-day modified Rankin score, 0-2) were analyzed. RESULTS Median times were onset of stroke to hospital arrival, 123 minutes (interquartile range, 163 minutes); hospital arrival to thrombolysis in cerebral infarction (TICI) 2b/3 or final digital subtraction angiography, 133 minutes (interquartile range, 99 minutes); and baseline imaging to groin puncture, 86 minutes (interquartile range, 24 minutes). Time from baseline imaging to puncture was prolonged in patients receiving intravenous tissue-type plasminogen activator (32-minute mean delay) and when magnetic resonance-based imaging at baseline was used (18-minute mean delay). Extracranial carotid disease delayed puncture to first stent deployment time on average by 25 minutes. For each 1-hour increase in stroke onset to final digital subtraction angiography (or TICI 2b/3) time, odds of good clinical outcome decreased by 38%. CONCLUSIONS Interval times in the STAR study reflect current intra-arterial therapy for patients with acute ischemic stroke. Improving workflow metrics can further improve clinical outcome. CLINICAL TRIAL REGISTRATION: URL http://www.clinicaltrials.gov. Unique identifier: NCT01327989.

Oxidative Stress in Hypobaric Hypoxia and Influence on Vessel-Tone Modifying Mediators

Increased pulmonary artery pressure is a well-known phenomenon of hypoxia and is seen in patients with chronic pulmonary diseases, and also in mountaineers on high altitude expedition. Different mediators are known to regulate pulmonary artery vessel tone. However, exact mechanisms are not fully understood and a multimodal process consisting of a whole panel of mediators is supposed to cause pulmonary artery vasoconstriction. We hypothesized that increased hypoxemia is associated with an increase in vasoconstrictive mediators and decrease of vasodilatators leading to a vasoconstrictive net effect. Furthermore, we suggested oxidative stress being partly involved in changement of these parameters. Oxygen saturation (Sao2) and clinical parameters were assessed in 34 volunteers before and during a Swiss research expedition to Mount Muztagh Ata (7549 m) in Western China. Blood samples were taken at four different sites up to an altitude of 6865 m. A mass spectrometry-based targeted metabolomic platform was used to detect multiple parameters, and revealed functional impairment of enzymes that require oxidation-sensitive cofactors. Specifically, the tetrahydrobiopterin (BH4)-dependent enzyme nitric oxide synthase (NOS) showed significantly lower activities (citrulline-to-arginine ratio decreased from baseline median 0.21 to 0.14 at 6265 m), indicating lower NO availability resulting in less vasodilatative activity. Correspondingly, an increase in systemic oxidative stress was found with a significant increase of the percentage of methionine sulfoxide from a median 6% under normoxic condition to a median level of 30% (p<0.001) in camp 1 at 5533 m. Furthermore, significant increase in vasoconstrictive mediators (e.g., tryptophan, serotonin, and peroxidation-sensitive lipids) were found. During ascent up to 6865 m, significant altitude-dependent changes in multiple vessel-tone modifying mediators with excess in vasoconstrictive metabolites could be demonstrated. These changes, as well as highly significant increase in systemic oxidative stress, may be predictive for increase in acute mountain sickness score and changes in Sao2.

Determination of genetic transferrin variants in human serum by high-resolution capillary zone electrophoresis(†)

High-resolution capillary zone electrophoresis in the routine arena with stringent quality assurance is employed for the determination of carbohydrate-deficient transferrin in human serum. The assay comprises mixing of human serum with a Fe(III) -containing solution prior to analysis of the iron-saturated mixture in a dynamically double-coated capillary using a commercial buffer at alkaline pH. In contrast to other assays, it provides sufficient resolution for proper recognition of genetic transferrin variants. Analysis of 7290 patient sera revealed 166 isoform patterns that could be assigned to genetic variants, namely, 109 BC, 53 CD, one BD and three CC variants. Several subtypes of transferrin D can be distinguished as they have large enough differences in pI values. Subtypes of transferrin C and B cannot be resolved. However, analysis of the detection time ratios of tetrasialo isoforms of transferrin BC and transferrin CD variants revealed multimodal frequency histograms, indicating the presence of subtypes of transferrin C, B and D. The data gathered over 11 years demonstrate the robustness of the high-resolution capillary zone electrophoresis assay. This is the first account of a capillary zone electrophoresis based carbohydrate-deficient transferrin assay with a broad overview on transferrin isoform patterns associated with genetic transferrin variants.

Robust meta-analytic-predictive priors in clinical trials with historical control information.

Historical information is always relevant for clinical trial design. Additionally, if incorporated in the analysis of a new trial, historical data allow to reduce the number of subjects. This decreases costs and trial duration, facilitates recruitment, and may be more ethical. Yet, under prior-data conflict, a too optimistic use of historical data may be inappropriate. We address this challenge by deriving a Bayesian meta-analytic-predictive prior from historical data, which is then combined with the new data. This prospective approach is equivalent to a meta-analytic-combined analysis of historical and new data if parameters are exchangeable across trials. The prospective Bayesian version requires a good approximation of the meta-analytic-predictive prior, which is not available analytically. We propose two- or three-component mixtures of standard priors, which allow for good approximations and, for the one-parameter exponential family, straightforward posterior calculations. Moreover, since one of the mixture components is usually vague, mixture priors will often be heavy-tailed and therefore robust. Further robustness and a more rapid reaction to prior-data conflicts can be achieved by adding an extra weakly-informative mixture component. Use of historical prior information is particularly attractive for adaptive trials, as the randomization ratio can then be changed in case of prior-data conflict. Both frequentist operating characteristics and posterior summaries for various data scenarios show that these designs have desirable properties. We illustrate the methodology for a phase II proof-of-concept trial with historical controls from four studies. Robust meta-analytic-predictive priors alleviate prior-data conflicts ' they should encourage better and more frequent use of historical data in clinical trials.

When the systems fail to communicate. Cerebral resting state networks in schizophrenia spectrum disorders.

There have been numerous attempts to reveal the neurobiological basis of schizophrenia spectrum disorders. Results however, remain as heterogeneous as the schizophrenia spectrum disorders itself. Therefore, one aim of this thesis was to divide patients affected by this disorder into subgroups in order to homogenize the results of future studies. In a first study it is suggested that psychopathological rating scales should focus on symptoms-clusters that may have a common neurophysiological background. The here presented Bern Psychopathology Scale (BPS) proposes that alterations in three wellknown brain systems (motor, language, and affective) are largely leading to the communication failures observable on a behavioral level, but also - as repeatedly hypothesized - to dysconnectivity within and between brain systems in schizophrenia spectrum disorders. The external validity of the motor domain in the BPS was tested against the objective measure of 24 hours wrist actigraphy, in a second study. The subjective, the quantitative, as well as the global rating of the degree of motor disorders in this patient group showed significant correlations to the acquired motor activity. This result confirmed in a first step the practicability of the motor domain of the BPS, but needs further validation regarding pathological brain alterations. Finally, in a third study (independent from the two other studies), two cerebral Resting State Networks frequently altered in schizophrenia were investigated for the first time using simultaneous EEG/fMRI: The well-known default mode network and the left working memory network. Besides the changes in these fMRI-based networks, there are well-documented findings that patients exhibit alterations in EEG spectra compared to healthy controls. However, only through the multimodal approach it was possible to discover that patients with schizophrenia spectrum disorders have a slower driving frequency of the Resting State Networks compared to the matched healthy controls. Such a dysfunctional coupling between neuronal frequency and functional brain organization could explain in a uni- or multifactorial way (dysfunctional cross-frequency coupling, maturational effects, vigilance fluctuations, task-related suppression), how the typical psychotic symptoms might occur. To conclude, the major contributions presented in this thesis were on one hand the development of a psychopathology rating scale that is based on the assumption of dysfunctional brain networks, as well as the new evidence of a dysfunctional triggering frequency of Resting State Networks from the simultaneous EEG/fMRI study in patients affected by a schizophrenia spectrum disorder.

Image registration for triggered and non-triggered DTI of the human kidney: Reduced variability of diffusion parameter estimation

BACKGROUND: To investigate if non-rigid image-registration reduces motion artifacts in triggered and non-triggered diffusion tensor imaging (DTI) of native kidneys. A secondary aim was to determine, if improvements through registration allow for omitting respiratory-triggering. METHODS: Twenty volunteers underwent coronal DTI of the kidneys with nine b-values (10-700 s/mm2 ) at 3 Tesla. Image-registration was performed using a multimodal nonrigid registration algorithm. Data processing yielded the apparent diffusion coefficient (ADC), the contribution of perfusion (FP ), and the fractional anisotropy (FA). For comparison of the data stability, the root mean square error (RMSE) of the fitting and the standard deviations within the regions of interest (SDROI ) were evaluated. RESULTS: RMSEs decreased significantly after registration for triggered and also for non-triggered scans (P < 0.05). SDROI for ADC, FA, and FP were significantly lower after registration in both medulla and cortex of triggered scans (P < 0.01). Similarly the SDROI of FA and FP decreased significantly in non-triggered scans after registration (P < 0.05). RMSEs were significantly lower in triggered than in non-triggered scans, both with and without registration (P < 0.05). CONCLUSION: Respiratory motion correction by registration of individual echo-planar images leads to clearly reduced signal variations in renal DTI for both triggered and particularly non-triggered scans. Secondarily, the results suggest that respiratory-triggering still seems advantageous.J. Magn. Reson. Imaging 2014. (c) 2014 Wiley Periodicals, Inc.

Patient-Specific Semi-Supervised Learning for Postoperative Brain Tumor Segmentation

In contrast to preoperative brain tumor segmentation, the problem of postoperative brain tumor segmentation has been rarely approached so far. We present a fully-automatic segmentation method using multimodal magnetic resonance image data and patient-specific semi-supervised learning. The idea behind our semi-supervised approach is to effectively fuse information from both pre- and postoperative image data of the same patient to improve segmentation of the postoperative image. We pose image segmentation as a classification problem and solve it by adopting a semi-supervised decision forest. The method is evaluated on a cohort of 10 high-grade glioma patients, with segmentation performance and computation time comparable or superior to a state-of-the-art brain tumor segmentation method. Moreover, our results confirm that the inclusion of preoperative MR images lead to a better performance regarding postoperative brain tumor segmentation.

State of the art of integrated therapy approaches in the treatment of schizophrenia: empirical evidence and clinical relevance

Objective: Integrated behavior therapy approaches are defined by the combination of behavioral and or cognitive interventions targeting neurocognition combined with other goal-oriented treatment targets such as social cognition, social skills, or educational issues. The Integrated Psychological Therapy Program (IPT) represents one of the very first behavior therapy approaches combining interventions of neurocognition, social cognition, and social competence. This comprehensive group-based bottom-up and top-down approach consists of five subprograms, each with incremental steps. IPT has been successfully implemented in several countries in Europe, America, Australia and in Asia. IPT worked as a model for some other approaches designed in the USA. IPT was undergone two further developments: based on the social competence part of IPT, the three specific therapy programs focusing residential, occupational or recreational topics were developed. Recently, the cognitive part of INT was rigorously expanded into the Integrated Neurocognitive Therapy (INT) designed exclusively for outpatient treatment: INT includes interventions targeting all neurocognitive and social cognitive domains defined by the NIMH-MATRICS initiative. These group and partially PC-based exercises are structured into four therapy modules, each starting with exercises on neurocognitive domains followed by social cognitive targets. Efficacy: The evidence of integrated therapy approaches and its advantage compared to of one-track interventions was becoming a discussion tool in therapy research as well as in mental health systems. Results of meta-analyses support superiority of integrated approaches compared to one-track interventions in more distal outcome areas such as social functioning. These results are in line with the large body of 37 independent IPT studies in 12 countries. Moreover, IPT research indicates the maintenance of therapy effects after the end of therapy and some evidence generalization effects. Additionally, the international randomized multi-center study on INT with 169 outpatients strongly supports the successful therapy of integrated therapy in proximal and distal outcome such as significant effects in cognition, functioning and negative symptoms. Clinical implication: therapy research as well as expert’s clinical experience recommends integrated therapy approaches such as IPT to be successful agents within multimodal psychiatric treatment concepts. Finally, integrated group therapy based on cognitive remediation seems to motivate and stimulate schizophrenia inpatients and outpatients to more successful and independent life also demanded by the recovery movement.

Facebook style: The use of non-standard features in virtual speech conditioned by the medium Facebook

Over the last few years Facebook has become a widespread and continuously expanding medium of communication. Being a new medium of social interaction, Facebook produces its own communication style. My focus of analysis is how Facebook users from the city of Malaga create this style by means of phonic features typical of the Andalusian variety and how the users reflect on the use of these phonic features. This project is based on a theoretical framework which combines variationist sociolinguistics with CMC to study the emergence of a style peculiar of the online social networks. In a corpus of Facebook users from three zones of Malaga, I have analysed the use of non-standard phonic features and then compared them with the same features in a reference corpus collected on three beaches of Malaga. From this comparison it can be deduced that the analysed social and linguistic factors work differently in real and virtual speech. Due to these different uses we can consider the peculiar electronic communication of Facebook as a style constrained by the electronic medium. It is a style which serves the users to create social meaning and to express their linguistic identities.

Nerve Stimulator–Guided Sciatic-Femoral Block in Pet Rabbits (Oryctolagus cuniculus) Undergoing Hind Limb Surgery: A Case Series

This article describes the clinical applicability of a nerve stimulator–guided technique, previously described in dogs, to block the sciatic and the femoral nerves in 4 pet rabbits (Oryctolagus cuniculus) undergoing hind limb surgeries. Preanesthetic intramuscular doses of medetomidine (0.08 mg/kg), ketamine (15 mg/kg), and buprenorphine (0.03 mg/kg) were administered to the rabbit patients. The rabbits were intubated and general anesthesia was maintained using isoflurane in oxygen. The sciatic-femoral nerve block was performed with 2% lidocaine at a volume of 0.05 mL/kg/nerve. Sciatic-femoral block was feasible in rabbits, and the motoric responses following electrical stimulation of both nerves were consistent with those reported in dogs after successful nerve location. Iatrogenic complications, namely nerve damage and local anesthetic toxicity, did not occur. Based on these results, the authors conclude that the sciatic-femoral nerve block described in dogs can be safely performed in rabbits. Clinical trials are required to assess the analgesic efficacy of the combined sciatic-femoral nerve block in rabbits as a part of multimodal pain management.