DIP-STR: Highly Sensitive Markers for the Analysis of Unbalanced Genomic Mixtures.

Samples containing highly unbalanced DNA mixtures from two individuals commonly occur both in forensic mixed stains and in peripheral blood DNA microchimerism induced by pregnancy or following organ transplant. Because of PCR amplification bias, the genetic identification of a DNA that contributes trace amounts to a mixed sample represents a tremendous challenge. This means that standard genetic markers, namely microsatellites, also referred as short tandem repeats (STR), and single-nucleotide polymorphism (SNP) have limited power in addressing common questions of forensic and medical genetics. To address this issue, we developed a molecular marker, named DIP-STR that relies on pairing deletion-insertion polymorphisms (DIP) with STR. This novel analytical approach allows for the unambiguous genotyping of a minor component in the presence of a major component, where DIP-STR genotypes of the minor were successfully procured at ratios up to 1:1,000. The compound nature of this marker generates a high level of polymorphism that is suitable for identity testing. Here, we demonstrate the power of the DIP-STR approach on an initial set of nine markers surveyed in a Swiss population. Finally, we discuss the limitations and potential applications of our new system including preliminary tests on clinical samples and estimates of their performance on simulated DNA mixtures.

Instrumental leadership: Measurement and extension of transformational-transactional leadership theory.

Leaders must scan the internal and external environment, chart strategic and task objectives, and provide performance feedback. These instrumental leadership (IL) functions go beyond the motivational and quid-pro quo leader behaviors that comprise the full-range-transformational, transactional, and laissez faire-leadership model. In four studies we examined the construct validity of IL. We found evidence for a four-factor IL model that was highly prototypical of good leadership. IL predicted top-level leader emergence controlling for the full-range factors, initiating structure, and consideration. It also explained unique variance in outcomes beyond the full-range factors; the effects of transformational leadership were vastly overstated when IL was omitted from the model. We discuss the importance of a "fuller full-range" leadership theory for theory and practice. We also showcase our methodological contributions regarding corrections for common method variance (i.e., endogeneity) bias using two-stage least squares (2SLS) regression and Monte Carlo split-sample designs.

Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test.

The application of DNA-based markers toward the task of discriminating among alternate salmon runs has evolved in accordance with ongoing genomic developments and increasingly has enabled resolution of which genetic markers associate with important life-history differences. Accurate and efficient identification of the most likely origin for salmon encountered during ocean fisheries, or at salvage from fresh water diversion and monitoring facilities, has far-reaching consequences for improving measures for management, restoration and conservation. Near-real-time provision of high-resolution identity information enables prompt response to changes in encounter rates. We thus continue to develop new tools to provide the greatest statistical power for run identification. As a proof of concept for genetic identification improvements, we conducted simulation and blind tests for 623 known-origin Chinook salmon (Oncorhynchus tshawytscha) to compare and contrast the accuracy of different population sampling baselines and microsatellite loci panels. This test included 35 microsatellite loci (1266 alleles), some known to be associated with specific coding regions of functional significance, such as the circadian rhythm cryptochrome genes, and others not known to be associated with any functional importance. The identification of fall run with unprecedented accuracy was demonstrated. Overall, the top performing panel and baseline (HMSC21) were predicted to have a success rate of 98%, but the blind-test success rate was 84%. Findings for bias or non-bias are discussed to target primary areas for further research and resolution.

Trends in overweight and obesity levels in Geneva: time for optimism?

Background/Introduction: ln Switzerland, most trends in overweight and obesity levels have been assessed using reported data, a methodology which is prone to reporting bias. ln this study, we aimed at assessing trends in overweight and obesity levels using objectively measured data. Methods: We used independent cross-sectional data collected between 2005 and 2011 by the Bus Santé study on representative samples of the Geneva population. Trends were assessed overall and according to different characteristics of the participants. Overweight and obesity were defined as a body mass index (BMI) between 25 and 29.9 kg/m2 and >=30 kg/m2, respectively. Results: Data from 4093 participants (2012 men) was assessed. Mean BMI was 25.2 ± 4.3 kg/m2 (mean ±standard deviation) in 2005 and 25.4 ± 4.3 in 2011 (p for trend using linear regression=0.98). For men, mean BMI was 26.3 ± 3.8 kg/m2 in 2005 and 26.1 ± 3.7 in 2011 (p for trend=0.37); for women, the corresponding values were 24.3 ± 4.6 and 24.7 ± 4.7 kg/m2 (p for trend=0.42). Overall prevalence of overweight and obesity was 32.2% and 13.3%, respectively, in 2005 and 33.6% and 13.7% in 2011 (p for trend using polytomous logistic regression adjusting for gender, age and smoking=0.49 and 0.94 for overweight and obesity, respectively). For men, prevalence of overweight and obesity was 45.9% and 12.2% in 2005 and 42.1 % and 14.6% in 2011 (P for trend=0.03 for overweight and 0.81 for obesity); for women, the corresponding values were 20.4% and 14.2% in 2005 and 25.4% and 12.9% in 2011 (p for trend=0.13 for overweight and 0.99 for obesity). Conclusion: Overweight and obesity levels appear to have levelled in Geneva, with a possible decrease in overweight levels in men. These favorable findings should be replicated in other geographical locations.

Biological embedding of early life exposures and disease risk in humans: a role for DNA methylation.

BACKGROUND: Following wider acceptance of "the thrifty phenotype" hypothesis and the convincing evidence that early life exposures can influence adult health even decades after the exposure, much interest has been placed on the mechanisms through which early life exposures become biologically embedded. METHODS: In this review, we summarize the current literature regarding biological embedding of early life experiences. To this end we conducted a literature search to identify studies investigating early life exposures in relation to DNA methylation changes. In addition, we summarize the challenges faced in investigations of epigenetic effects, stemming from the peculiarities of this emergent and complex field. A proper systematic review and meta-analyses were not feasible given the nature of the evidence. RESULTS: We identified 7 studies on early life socioeconomic circumstances, 10 studies on childhood obesity, and 6 studies on early life nutrition all relating to DNA methylation changes that met the stipulated inclusion criteria. The pool of evidence gathered, albeit small, favours a role of epigenetics and DNA methylation in biological embedding, but replication of findings, multiple comparison corrections, publication bias, and causality are concerns remaining to be addressed in future investigations. CONCLUSIONS: Based on these results, we hypothesize that epigenetics, in particular DNA methylation, is a plausible mechanism through which early life exposures are biologically embedded. This review describes the current status of the field and acts as a stepping stone for future, better designed investigations on how early life exposures might become biologically embedded through epigenetic effects. This article is protected by copyright. All rights reserved.

Estimation of time of death in relation to gastric contents

Introduction: Estimation of the time since death based on the gastric content is still a controversy subject. Many studies have been achieved leaving the same incertitude: the intra- and inter-individual variability. Aim: After a homicidal case where a specialized gastroenterologist was cited to estimate the time of death based on the gastric contents and his experience in clinical practice. Consequently we decided to make a review of the scientific literature to see if that method was more reliable nowadays. Material and methods: We chose articles from 1979 that describe the estimation of the gastric emptying rate according to several factors and the forensic articles about the estimation of the time of death in relation with the gastric content. Results: Most of the articles cited by the specialized gastroenterologist were studies about living healthy people and the effects of several factors (medication, supine versus upside-down position, body mass index or different type of food). Forensic articles frequently concluded that the estimation of the time since death by analyzing the gastric content can be used but not as the unique method. Conclusion: Estimation of the time since death by analyze of the gastric contents is a method that can be used nowadays. But it cannot be the only method as the inter- and intra-individual variability remains an important bias.

Could a satellite-based navigation system (GPS) be used to assess the physical activity of individuals on earth?

OBJECTIVES: To test whether the Global Positioning System (GPS) could be potentially useful to assess the velocity of walking and running in humans. SUBJECT: A young man was equipped with a GPS receptor while walking running and cycling at various velocity on an athletic track. The speed of displacement assessed by GPS, was compared to that directly measured by chronometry (76 tests). RESULTS: In walking and running conditions (from 2-20 km/h) as well as cycling conditions (from 20-40 km/h), there was a significant relationship between the speed assessed by GPS and that actually measured (r = 0.99, P < 0.0001) with little bias in the prediction of velocity. The overall error of prediction (s.d. of difference) averaged +/-0.8 km/h. CONCLUSION: The GPS technique appears very promising for speed assessment although the relative accuracy at walking speed is still insufficient for research purposes. It may be improved by using differential GPS measurement.

Variations régionales du recours aux soins: quelques problèmes méthodologiques. [Regional variations in health services: various methodological problems].

Many studies show strong variation of health consumption between regions, suggesting that theses variations are related to the uncertainty of medical practice or to other factors related to health services or patients attitude. However the statistical interpretation of these variations is far from easy: apart from usual and specific information bias, there are statistical problems when observing incidence of events like health care consumption: it is in fact a rare event, which is observed within small population, and among regions with unequal number of person. Therefore, most of the variation reported might be well explained by a purely statistical phenomenon. This paper presents some aspects of this variability for three common indicators of variation, and suggest the use of ad hoc simulation to get statistical criteria.

Tests for sex-biased dispersal using bi-parentally inherited genetic markers.

Understanding why dispersal is sex-biased in many taxa is still a major concern in evolutionary ecology. Dispersal tends to be male-biased in mammals and female-biased in birds, but counter-examples exist and little is known about sex bias in other taxa. Obtaining accurate measures of dispersal in the field remains a problem. Here we describe and compare several methods for detecting sex-biased dispersal using bi-parentally inherited, codominant genetic markers. If gene flow is restricted among populations, then the genotype of an individual tells something about its origin. Provided that dispersal occurs at the juvenile stage and that sampling is carried out on adults, genotypes sampled from the dispersing sex should on average be less likely (compared to genotypes from the philopatric sex) in the population in which they were sampled. The dispersing sex should be less genetically structured and should present a larger heterozygote deficit. In this study we use computer simulations and a permutation test on four statistics to investigate the conditions under which sex-biased dispersal can be detected. Two tests emerge as fairly powerful. We present results concerning the optimal sampling strategy (varying number of samples, individuals, loci per individual and level of polymorphism) under different amounts of dispersal for each sex. These tests for biases in dispersal are also appropriate for any attribute (e.g. size, colour, status) suspected to influence the probability of dispersal. A windows program carrying out these tests can be freely downloaded from http://www.unil.ch/izea/softwares/fstat.html

The predation cost of being a male: implications for sex-specific rates of ageing

Evolutionary theory predicts that the rate of extrinsic (i.e. age- and condition-independent) mortality should affect important life history traits such as the rate of ageing and maximum lifespan. Sex-specific differences in mortality rates due to predation may therefore result in the evolution of important differences in life history traits between males and females. However, quantifying the role of predators as a factor of extrinsic mortality is notoriously difficult in natural populations. We took advantage of the unusual prey caching behaviour of the barn owl Tyto alba and the tawny owl Strix aluco to estimate the sex ratio of their five most common preys. For all prey species, there was a significant bias in the sex ratio of remains found in nests of both these owls. A survey of literature revealed that sex-biased predation is a common phenomenon. These results demonstrate that predation, a chief source of extrinsic mortality, was strongly sex-biased. This may select for alternate life history strategies between males and females, and account for a male life span being frequently lower than female lifespan in many animal species.

Environnement et capacités cognitives chez le rat : compétition entre les facteurs qui influencent les stratégies spatiales

RESUME Ce travail se propose de discuter des résultats comportementaux observés chez des rats obtenus dans trois paradigmes expérimentaux différents : le bassin de Morris (Morris Water Maze, Morris, 1984) ; la table à trous (Homing Board, Schenk, 1989) et le labyrinthe radial (Radial Arm Maze, Olton et Samuelson, 1976). Les deux premières tâches sont spatiales et permettent un apprentissage de place en environnements contrôlés, et la troisième est une tâche comportementale qui différencie deux habiletés particulières, celle d'élimination (basée sur la mémoire de travail) et celle de sélection (basée sur la mémoire de référence). La discussion des résultats porte sur les stratégies de navigation utilisées par les animaux pour résoudre les tâches et plus précisément sur les facteurs qui peuvent influencer le choix de ces stratégies. Le facteur environnemental (environnement contrôlé) et le facteur cognitif (vieillissement) représentent les variables étudiées ici. C'est ainsi que certaines hypothèses communément acceptées ont été malmenées par nos résultats. Or si l'espace est habituellement supposé homogène (toutes les positions spatiales présentent le même degré de difficulté lors d'un apprentissage en champ ouvert), ce travail établit qu'une position associée -sans contiguïté - à l'un des trois indices visuels situés dans la périphérie de l'environnement est plus difficile à apprendre qu'une position située entre deux des trois indices. Deuxièmement, alors qu'il est admis que l'apprentissage d'une place dans un environnement riche requiert le même type d'information. dans la bassin de Morris (tâche nagée) que sur la table à trous (tâche marchée), nous avons montré que la discrimination spatiale en bassin ne peut être assurée par les trois indices visuels périphériques et nécessite la présence d'au moins un élément supplémentaire. Enfin, l'étude du vieillissement a souvent montré que l'âge réduit les capacités cognitives nécessaires à la navigation spatiale, conduisant à un déficit général des performances d'un animal sénescent, alors que dans notre travail, nous avons trouvé les animaux âgés plus performants et plus efficaces que les adultes dans une tâche particulière de collecte de nourriture. Ces expériences s'inscrivent dans une étude générale qui met à l'épreuve le modèle théorique proposé pax Schenk et Jacobs (2003), selon lequel l'encodage de la carte cognitive (Tolman, 1948 ; O'Keefe et Nadel, 1978) se ferait dans l'hippocampe par l'activité de deux modules complémentaires :d'une part le CA3 - Gyrus Denté pour le traitement d'une trame spatiale basée sur des éléments directionnels et Jou distribués en gradient (bearing map) et d'autre part le CAl - Subiculum pour le traitement des représentations locales basées sur les positions relatives des éléments fixes de l'environnement (sketch map). SUMMARY This work proposes to talk about behavioural results observed in three different experimental paradigms with rats: the Morris Water Maze (Morris, 1984); the Homing Board (Schenk, 1989) and the Radial Arm Maze (Olton and Samuelson, 1976). The two first tasks are spatial ones and allow place learning in controlled environments. The third one is a behavioural task which contrasts two particular skills, the elimination (based on working memory) and the selection one (based on reference memory). The topic of the discussion will be the navigation strategies used by animals to solve the different tasks, and more precisely the factors which can bias this strategies' choice. The environmental (controlled) and the cognitive (aging) factors are the variables studied here. Thus, some hypotheses usually accepted were manhandled by our results. Indeed, if space is habitually homogenously considered (all spatial positions present the same degree of difficulty in an open field learning), this work establishes that an associated position -without being adjacent - to one of the three visual cues localised in the environmental periphery is more difficult to learn than a configurationnel position (situated between two of the three cues). Secondly, if it is received that place learning in a rich environment requires the same information in the Morris water maze (swimming task) that on the Homing board (walking task), we showed that spatial discrimination in the water maze can't be provided by the three peripheral cue cards and needs the presence of a supplementary cue. At last, aging studies often showed that oldness decreases cognitive skills in spatial navigation, leading to a general deficit in performances. But, in our work, we found that senescent rats were more efficient than adult ones in a special food collecting task. These experiments come within the scope of a general study which tests the theoretical model proposed by Jacobs and Schenk (2003), according to which the cognitive map's encoding (Tolman, 1948, O'Keefe and Nadel, 1978) should take place in the hippocampus by two complementary modules, first the DG-CA3 should encode directional and/or gradients references (the bearing map), and secondly the Subiculum-CAl should process locale elements (the sketch map).

Pragmatic approach for interpreting antiretroviral drug concentrations based on a systematic review of population pharmacokinetic studies

Objectives: The study objective was to derive reference pharmacokinetic curves of antiretroviral drugs (ART) based on available population pharmacokinetic (Pop-PK) studies that can be used to optimize therapeutic drug monitoring guided dosage adjustment.¦Methods: A systematic search of Pop-PK studies of 8 ART in adults was performed in PubMed. To simulate reference PK curves, a summary of the PK parameters was obtained for each drug based on meta-analysis approach. Most models used one-compartment model, thus chosen as reference model. Models using bi-exponential disposition were simplified to one-compartment, since the first distribution phase was rapid and not determinant for the description of the terminal elimination phase, mostly relevant for this project. Different absorption were standardized for first-order absorption processes.¦Apparent clearance (CL), apparent volume of distribution of the terminal phase (Vz) and absorption rate constant (ka) and inter-individual variability were pooled into summary mean value, weighted by number of plasma levels; intra-individual variability was weighted by number of individuals in each study.¦Simulations based on summary PK parameters served to construct concentration PK percentiles (NONMEM®).¦Concordance between individual and summary parameters was assessed graphically using Forest-plots. To test robustness, difference in simulated curves based on published and summary parameters was calculated using efavirenz as probe drug.¦Results: CL was readily accessible from all studies. For studies with one-compartment, Vz was central volume of distribution; for two-compartment, Vz was CL/λz. ka was directly used or derived based on the mean absorption time (MAT) for more complicated absorption models, assuming MAT=1/ka.¦The value of CL for each drug was in excellent agreement throughout all Pop-PK models, suggesting that minimal concentration derived from summary models was adequately characterized. The comparison of the concentration vs. time profile for efavirenz between published and summary PK parameters revealed not more than 20% difference. Although our approach appears adequate for estimation of elimination phase, the simplification of absorption phase might lead to small bias shortly after drug intake.¦Conclusions: Simulated reference percentile curves based on such an approach represent a useful tool for interpretating drug concentrations. This Pop-PK meta-analysis approach should be further validated and could be extended to elaborate more sophisticated computerized tool for the Bayesian TDM of ART.

Non-pharmacological interventions for chronic pain in people with spinal cord injury.

BACKGROUND: Chronic pain is frequent in persons living with spinal cord injury (SCI). Conventionally, the pain is treated pharmacologically, yet long-term pain medication is often refractory and associated with side effects. Non-pharmacological interventions are frequently advocated, although the benefit and harm profiles of these treatments are not well established, in part because of methodological weaknesses of available studies. OBJECTIVES: To critically appraise and synthesise available research evidence on the effects of non-pharmacological interventions for the treatment of chronic neuropathic and nociceptive pain in people living with SCI. SEARCH METHODS: The search was run on the 1st March 2011. We searched the Cochrane Injuries Group's Specialised Register, the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE (OvidSP), Embase (OvidSP), PsycINFO (OvidSP), four other databases and clinical trials registers. In addition, we manually searched the proceedings of three major scientific conferences on SCI. We updated this search in November 2014 but these results have not yet been incorporated. SELECTION CRITERIA: Randomised controlled trials of any intervention not involving intake of medication or other active substances to treat chronic pain in people with SCI. DATA COLLECTION AND ANALYSIS: Two review authors independently extracted data and assessed risk of bias in the included studies. The primary outcome was any measure of pain intensity or pain relief. Secondary outcomes included adverse events, anxiety, depression and quality of life. When possible, meta-analyses were performed to calculate standardised mean differences for each type of intervention. MAIN RESULTS: We identified 16 trials involving a total of 616 participants. Eight different types of interventions were studied. Eight trials investigated the effects of electrical brain stimulation (transcranial direct current stimulation (tDCS) and cranial electrotherapy stimulation (CES); five trials) or repetitive transcranial magnetic stimulation (rTMS; three trials). Interventions in the remaining studies included exercise programmes (three trials); acupuncture (two trials); self-hypnosis (one trial); transcutaneous electrical nerve stimulation (TENS) (one trial); and a cognitive behavioural programme (one trial). None of the included trials were considered to have low overall risk of bias. Twelve studies had high overall risk of bias, and in four studies risk of bias was unclear. The overall quality of the included studies was weak. Their validity was impaired by methodological weaknesses such as inappropriate choice of control groups. An additional search in November 2014 identified more recent studies that will be included in an update of this review.For tDCS the pooled mean difference between intervention and control groups in pain scores on an 11-point visual analogue scale (VAS) (0-10) was a reduction of -1.90 units (95% confidence interval (CI) -3.48 to -0.33; P value 0.02) in the short term and of -1.87 (95% CI -3.30 to -0.45; P value 0.01) in the mid term. Exercise programmes led to mean reductions in chronic shoulder pain of -1.9 score points for the Short Form (SF)-36 item for pain experience (95% CI -3.4 to -0.4; P value 0.01) and -2.8 pain VAS units (95% CI -3.77 to -1.83; P value < 0.00001); this represented the largest observed treatment effects in the included studies. Trials using rTMS, CES, acupuncture, self-hypnosis, TENS or a cognitive behavioural programme provided no evidence that these interventions reduce chronic pain. Ten trials examined study endpoints other than pain, including anxiety, depression and quality of life, but available data were too scarce for firm conclusions to be drawn. In four trials no side effects were reported with study interventions. Five trials reported transient mild side effects. Overall, a paucity of evidence was found on any serious or long-lasting side effects of the interventions. AUTHORS' CONCLUSIONS: Evidence is insufficient to suggest that non-pharmacological treatments are effective in reducing chronic pain in people living with SCI. The benefits and harms of commonly used non-pharmacological pain treatments should be investigated in randomised controlled trials with adequate sample size and study methodology.

Critical review of cancer risk associated with angiotensin receptor blocker therapy.

The role of drugs in new cancer occurrence and cancer-related death is a major concern. Recently, a meta-analysis raised the possibility that angiotensin receptor blockers (ARBs) might have an adverse effect on patients. This generated a significant debate until the publication of two further meta-analyses, neither of which demonstrated an increased risk of new cancer occurrence or cancer-related death with the use of ARBs in patients with hypertension, heart failure, and/or nephropathy. This illustrates that the results of meta-analyses should be interpreted cautiously and critically as bias, such as selection bias, might lead to erroneous conclusions. Overall, the bulk of evidence today indicates that ARBs are not associated with increased cancer risk.

Role of surgery in the management of brain arteriovenous malformations: prospective cohort study.

BACKGROUND AND PURPOSE: Management of brain arteriovenous malformation (bAVM) is controversial. We have analyzed the largest surgical bAVM cohort for outcome. METHODS: Both operated and nonoperated cases were included for analysis. A total of 779 patients with bAVMs were consecutively enrolled between 1989 and 2014. Initial management recommendations were recorded before commencement of treatment. Surgical outcome was prospectively recorded and outcomes assigned at the last follow-up visit using modified Rankin Scale. First, a sensitivity analyses was performed to select a subset of the entire cohort for which the results of surgery could be generalized. Second, from this subset, variables were analyzed for risk of deficit or near miss (intraoperative hemorrhage requiring blood transfusion of ≥2.5 L, hemorrhage in resection bed requiring reoperation, and hemorrhage associated with either digital subtraction angiography or embolization). RESULTS: A total of 7.7% of patients with Spetzler-Ponce classes A and B bAVM had an adverse outcome from surgery leading to a modified Rankin Scale >1. Sensitivity analyses that demonstrated outcome results were not subject to selection bias for Spetzler-Ponce classes A and B bAVMs. Risk factors for adverse outcomes from surgery for these bAVMs include size, presence of deep venous drainage, and eloquent location. Preoperative embolization did not affect the risk of perioperative hemorrhage. CONCLUSIONS: Most of the ruptured and unruptured low and middle-grade bAVMs (Spetzler-Ponce A and B) can be surgically treated with a low risk of permanent morbidity and a high likelihood of preventing future hemorrhage. Our results do not apply to Spetzler-Ponce C bAVMs.