The role of geography and ecology in shaping repeated patterns of morphological and genetic differentiation between European minnows (Phoxinus phoxinus) from the Pyrenees and the Alps

Neutral and selective processes c an drive repeated patterns of evolu tion in dif ferent groups of populationsexp eriencing similar ecol ogica l gradients. In this paper, we used a combinat ion of nucl ear and mitochondrialDNA markers, as well as geometric morphometrics, to investigate repeated patterns of morphological andgenetic divergence of E uropean minnows in two mountain ranges : the Pyrenees and the Al ps. Europeanminnows (Phoxinus phoxinus) are cyprinid fish i nha bitin g most freshwater bodies in Europe, including those indifferent mountain r anges that could act as major geographical barriers to gene flow. We explored patterns ofP. phoxinus phenotypic and genetic di versi fication along a gradi ent of alti tude common to the two mountainranges, and tested for isolation by distance (IBD), isolation by environment (IBE) and isolation by adaptation(IBA). The results indicated that populations from the Pyr enees a nd the Alps bel ong to two well differentiated,reciprocally monophyletic mt DNA lineages. Substantial genetic differentiation due to geographical isolationwithin and between populations from the Pyrenees and the Alps was also found using rapidly evolving AFLPsmarkers (isolation by distance or IBD), as well as morphological differences between mountain ranges. Als o,morphology varied strong ly with elevation and so did genetic differentiation to a lower extent. Despitemoderate evidence for IBE and IBA, and therefore of repeated evolution, substantial population heterogeneitywas found at the genetic level, suggesting that selection and population specific genetic drift act in concert toaffect genetic divergence.

Life-time growth patterns of pumpkinseed Lepomis gibbosus introduced to Europe, relative to North American populations

The pumpkinseed Lepomis gibbosus, an omnivorous, nest guarding North American sunfish, was introduced into European waters about 100 years ago. To assess growth performance following introduction, we reviewed the available data for North American and European populations of pumpkinseed and compared the back-calculated age-specific growth for juveniles (standard length, SL, at age two) and adults (age two to five increment) as well as adult body size (SL at age five), von Bertalanffy growth model parameters and the index of growth (in length) performance (φ′). For continental comparisons of growth trajectory, mean growth curves for North American and Europe were calculated with the von Bertalanffy model using pooled data sets for each continent. Juvenile growth rate did not differ between European and North American pumpkinseed, but mean adult body size and adult growth rate were both significantly greater in North American than European populations. Adult body size decreased with increasing latitude (ANOVA) in North American populations, but this was not observed with adult growth rate. In contrast, adult body size tended to increase with latitude in European populations. Adult body size correlated significantly with φ′. The von Bertalanffy model described the overall growth patterns of North American and European populations reasonably well, but on the individual population level, length asymptotes were unrealistic (estimates that were > 20 % of the mean back-calculated size for the oldest age class) for a third of European populations and 80% of the North American populations. In contrast to North American pumpkinseed populations, somatic growth in European populations appears to be compromised by limited, but adequate, food resources, probably due to strong intraspecific interactions. This appears to be especially acute in adults, having potential ramifications for life span and reproductive allocation

New insight in the relationship between regional patterns of knee cartilage thickness, osteoarthritis disease severity, and gait mechanics.

To test if the relationship between knee kinetics during walking and regional patterns of cartilage thickness is influenced by disease severity we tested the following hypotheses in a cross-sectional study of medial compartment osteoarthritis (OA) subjects: (1) the peak knee flexion (KFM) and adduction moments (KAM) during walking are associated with regional cartilage thickness and medial-to-lateral cartilage thickness ratios, and (2) the associations between knee moments and cartilage thickness data are dependent on disease severity. Seventy individuals with medial compartment knee OA were studied. Gait analysis was used to determine the knee moments and cartilage thickness was measured from magnetic resonance imaging. Multiple linear regression analyses tested for associations between cartilage thickness and knee kinetics. Medial cartilage thickness and medial-to-lateral cartilage thickness ratios were lower in subjects with greater KAM for specific regions of the femoral condyle and tibial plateau with no associations for KFM in patients of all disease severities. When separated by severity, the association between KAM and cartilage thickness was found only in patients with more severe OA, and KFM was significantly associated with cartilage thickness only for the less severe OA subjects for specific tibial plateau regions. The results support the idea that the KAM is larger in patients with more severe disease and the KFM has greater influence early in the disease process, which may lessen as pain increases with disease severity. Each component influences different regions of cartilage. Thus the relative contributions of both KAM and KFM should be considered when evaluating gait mechanics and the influence of any intervention for knee OA.

Patterns of variability of retinol levels in a harbour porpoise population from an unpolluted environment

Organochlorine compounds (OC) are known to induce vitamin A (retinoids) deficiency in mammals, which may be associated with impairment of immunocompetence, reproduction and growth. This makes retinoids a potentially useful biomarker of organochlorine impact on marine mammals. However, use of retinoids as a biomarker requires knowledge about its intrapopulation patterns of variation in natural conditions, information which is not currently available. We investigated these patterns in a cetacean population living in an unpolluted environment. 100 harbour porpoises Phocoena phocoena from West Greenland were sampled during the 1995 hunting season. Sex, age, morphometrics, nutritive condition, and retinol (following saponification) and OC levels in blubber were determined for each individual. OC levels found were extremely low and therefore considered unlikely to affect the population adversely: mean blubber concentrations, expressed on an extractable basis, were 2.04 (SD = 1.1) ppm for PCBs and 2.76 (SD = 1.66) ppm for tDDT. The mean blubber retinol concentration for the overall population was 59.66 (SD = 45.26) mu g g(-1). Taking into account the high contribution of blubber to body mass, blubber constitutes a significant body site for retinoid deposition in harbour porpoises. Retinol concentrations did not differ significantly between geographical regions or sexes, but they did correlate significantly (p <0.001) with age. Body condition, measured by determining the lipid content of the blubber, did not have a significant effect on retinol levels but the individuals examined were considered to be in an overall good nutritive condition. It is concluded that measurement of retinol concentrations in blubber samples is feasible and has a potential for use as a biomarker of organochlorine exposure in cetaceans. However, in order to do so, biological information, particularly age, is critical for the correct assessment of physiological impact

Patterns of care in recurrent glioblastoma in Switzerland: a multicentre national approach based on diagnostic nodes.

Despite moderate improvements in outcome of glioblastoma after first-line treatment with chemoradiation recent clinical trials failed to improve the prognosis of recurrent glioblastoma. In the absence of a standard of care we aimed to investigate institutional treatment strategies to identify similarities and differences in the pattern of care for recurrent glioblastoma. We investigated re-treatment criteria and therapeutic pathways for recurrent glioblastoma of eight neuro-oncology centres in Switzerland having an established multidisciplinary tumour-board conference. Decision algorithms, differences and consensus were analysed using the objective consensus methodology. A total of 16 different treatment recommendations were identified based on combinations of eight different decision criteria. The set of criteria implemented as well as the set of treatments offered was different in each centre. For specific situations, up to 6 different treatment recommendations were provided by the eight centres. The only wide-range consensus identified was to offer best supportive care to unfit patients. A majority recommendation was identified for non-operable large early recurrence with unmethylated MGMT promoter status in the fit patients: here bevacizumab was offered. In fit patients with late recurrent non-operable MGMT promoter methylated glioblastoma temozolomide was recommended by most. No other majority recommendations were present. In the absence of strong evidence we identified few consensus recommendations in the treatment of recurrent glioblastoma. This contrasts the limited availability of single drugs and treatment modalities. Clinical situations of greatest heterogeneity may be suitable to be addressed in clinical trials and second opinion referrals are likely to yield diverging recommendations.

Temporal Patterns of Alcohol Consumption and Alcohol-Related Road Accidents in Young Swiss Men: Seasonal, Weekday and Public Holiday Effects.

AIMS: To assess seasonal, weekday, and public holiday effects on alcohol-related road accidents and drinking diaries among young Swiss men. METHODS: Federal road accident data (35,485 accidents) from Switzerland and drinking diary data from a large cohort of young Swiss men (11,930 subjects) were analysed for temporal effects by calendar week, weekday and public holiday (Christmas, New Years, National Day). Alcohol-related accidents were analysed using rate ratios for observed versus expected numbers of accidents and proportions of alcohol-related accidents relative to the total number. Drinking diaries were analysed for the proportion of drinkers, median number of drinks consumed, and the 90th percentile's number of drinks consumed. RESULTS: Several parallel peaks were identified in alcohol-related accidents and drinking diaries. These included increases on Fridays and Saturdays, with Saturday drinking extending until early Sunday morning, an increase during the summer on workdays but not weekends, an increase at the end of the year, and increases on public holidays and the evening before. CONCLUSIONS: Our results suggest specific time-windows that are associated with increases in drinking and alcohol-related harm. Established prevention measures should be enforced during these time-windows to reduce associated peaks.

Epidemiology and injury patterns of patients consulting following assault by nightclub security agents in a university hospital emergency service and an associated specialised forensic consultation

Introduction: The Violence Medical Unit (VMU), a specialised forensic medical consultation, was created at the Lausanne university Hospital in 2006. All patients consulting at the ED for interpersonal violencerelated injury are referred to the VMU, which provides forensic documentation of the injury and referral to the relevant community based victim-support organisations within 48 hours of the ED visit. This frees the ED medical staff from forensic injury documentation and legal/social referral, tasks for which they lack both time and training. Among community violence, assaults by nightclub security agents against patrons have increased from 6% to 10% between 2007 and 2009. We set out to characterise the demographics, assault mechanisms, subsequent injuries, prior alcohol intake and ED & VMU costs incurred by this group of patients. Methods: We retrospectively included all patients consulting at the VMU due to assault by nightclub security agents from January 2007 to December 2009. Data was obtained from ED & VMU medical, nursing and administrative records. Results: Our sample included 70 patients, of which 64 were referred by the CHUV ED. The victims were typically young (median age 29) males (93%). 77% of assaults occurred on the weekend between 12 PM and 4 AM, and 73% of the victims were under the influence of alcohol. 83% of the patients were punched, kicked and/or head-butted; 9% had been struck with a blunt instrument. 80% of the injuries were in the head and neck area and 19% of the victims sustained fractures. 21% of the victims were prescribed medical leave. Total ED & VMU costs averaged 1048 SFr. Conclusion: Medical staff treating this population of assault victims must be aware of the assault mechanisms and injury patterns, in particular the high probability of fractures, in order to provide adequate diagnosis and care. Associated inebriation mandates liberal use of radiology, as delayed or missed diagnosis may have medical, medicolegal and legal implications. Emergency medical services play an important role in detecting and reporting of such incidents. Centralised management of the forensic documentation facilitates referral to victim support organisations and epidemiological data collection. Magnitudes and trends of the different types of violence can be determined, and this information can be then impact public safety management policies.

Emergent patterns of social organization in captive Cercocebus torquatus: Testing the GrooFiWorld agent-based model

We empirically applied the GrooFiWorld agent-based model (Puga-González et al. 2009) in a group of captive mangabeys (Cercocebus torquatus). We analysed several measurements related to aggression and affiliative patterns. The group adopted a combination of despotic and egalitarian behaviours resulting from the behavioural flexibility observed in the Cercopithecinae subfamily. Our study also demonstrates that the GrooFiWorld agent-based model can be extended to other members of the Cercopithecinae subfamily generating parsimonious hypotheses related to the social organization.

Digital evidence, 'absence' of data and ambiguous patterns of reasoning

In this paper we discuss the use of digital data by the Swiss Federal Criminal Court in a recent case of attempted homicide. We use this case to examine drawbacks for the defense when the presentation of scientific evidence is partial, especially when the only perspective mentioned is that of the prosecution. We tackle this discussion at two distinct levels. First, we pursue an essentially non-technical presentation of the topic by drawing parallels between the court's summing up of the case and flawed patterns of reasoning commonly seen in other forensic disciplines, such as DNA and particle traces (e.g., gunshot residues). Then, we propose a formal analysis of the case, using elements of probability and graphical probability models, to justify our main claim that the partial presentation of digital evidence poses a risk to the administration of justice in that it keeps vital information from the defense. We will argue that such practice constitutes a violation of general principles of forensic interpretation as established by forensic science literature and current recommendations by forensic science interest groups (e.g., the European Network of Forensic Science Institutes). Finally, we posit that argument construction and analysis using formal methods can help replace digital evidence appropriately into context and thus support a sound evaluation of the evidence.

Complex patterns of global spread in invasive insects: eco-evolutionary and management consequences

The advent of simple and affordable tools for molecular identification of novel insect invaders and assessment of population diversity has changed the face of invasion biology in recent years. The widespread application of these tools has brought with it an emerging understanding that patterns in biogeography, introduction history and subsequent movement and spread of many invasive alien insects are far more complex than previously thought. We reviewed the literature and found that for a number of invasive insects, there is strong and growing evidence that multiple introductions, complex global movement, and population admixture in the invaded range are commonplace. Additionally, historical paradigms related to species and strain identities and origins of common invaders are in many cases being challenged. This has major consequences for our understanding of basic biology and ecology of invasive insects and impacts quarantine, management and biocontrol programs. In addition, we found that founder effects rarely limit fitness in invasive insects and may benefit populations (by purging harmful alleles or increasing additive genetic variance). Also, while phenotypic plasticity appears important post-establishment, genetic diversity in invasive insects is often higher than expected and increases over time via multiple introductions. Further, connectivity among disjunct regions of global invasive ranges is generally far higher than expected and is often asymmetric, with some populations contributing disproportionately to global spread. We argue that the role of connectivity in driving the ecology and evolution of introduced species with multiple invasive ranges has been historically underestimated and that such species are often best understood in a global context.

Identification of molecular subtypes and gene expression patterns of breast cancer analysing RNA-seq data

Breast cancer is the most common diagnosed cancer and the leading cause of cancer death among females worldwide. It is considered a highly heterogeneous disease and it must be classified into more homogeneous groups. Hence, the purpose of this study was to classify breast tumors based on variations in gene expression patterns derived from RNA sequencing by using different class discovery methods. 42 breast tumors paired-samples were sequenced by Illumine Genome Analyzer and the data was analyzed and prepared by TopHat2 and htseq-count. As reported previously, breast cancer could be grouped into five main groups known as basal epithelial-like group, HER2 group, normal breast-like group and two Luminal groups with a distinctive expression profile. Classifying breast tumor samples by using PAM50 method, the most common subtype was Luminal B and was significantly associated with ESR1 and ERBB2 high expression. Luminal A subtype had ESR1 and SLC39A6 significant high expression, whereas HER2 subtype had a high expression of ERBB2 and CNNE1 genes and low luminal epithelial gene expression. Basal-like and normal-like subtypes were associated with low expression of ESR1, PgR and HER2, and had significant high expression of cytokeratins 5 and 17. Our results were similar compared with TGCA breast cancer data results and with known studies related with breast cancer classification. Classifying breast tumors could add significant prognostic and predictive information to standard parameters, and moreover, identify marker genes for each subtype to find a better therapy for patients with breast cancer.

LSB Matching Steganalysis Based on Patterns of Pixel Differences and Random Embedding

Peer-reviewed

Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences

Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (~800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.