Beyond representing orthology relations by trees

Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple relations on a set of sequences called orthology relations may be employed. In addition to being interesting from a practical point of view they are also attractive from a theoretical perspective in that e.\,g.\,a characterization is known for when such a relation is representable by a certain type of phylogenetic tree. For an orthology relation inferred from real biological data it is however generally too much to hope for that it satisfies that characterization. Rather than trying to correct the data in some way or another which has its own drawbacks, as an alternative, we propose to represent an orthology relation $\delta$ in terms of a structure more general than a phylogenetic tree called a phylogenetic network. To compute such a network in the form of a level-1 representation for $\delta$, we formalize an orthology relation in terms of the novel concept of a symbolic 3- dissimilarity which is motivated by the biological concept of a ``cluster of orthologous groups'', or COG for short. For such maps which assign symbols rather that real values to elements, we introduce the novel {\sc Network-Popping} algorithm which has several attractive properties. In addition, we characterize an orthology relation $\delta$ on some set $X$ that has a level-1 representation in terms of eight natural properties for $\delta$ as well as in terms of level-1 representations of orthology relations on certain subsets of $X$

Understanding potential career changers’ experience of career confidence following a positive psychology based coaching programme

Changes in the labour market over the last decades have led to an increase in the number of career and job changes individuals are likely to face in their working lives. Previous research indicates that a high level of confidence can help individuals to make positive career changes, yet an agreed definition of confidence is not widely accepted, and the literature provides a limited evidence base for practice. This research involved five female participants who were contemplating a career change. They took part in a coaching programme which consisted of four positive psychology interventions based on a proposal of core confidence as a higher order construct composed of self-efficacy, hope, optimism and resilience. Data were gathered through semi-structured interviews and written reflections and an interpretative phenomenological analysis showed that participants perceived their career confidence before the programme as low, incorporating negative affect and self-doubt. After the programme, participants demonstrated increased career engagement, self-awareness and a positive and optimistic outlook. The analysis revealed that change was effected through the development of hope, change in cognitive processes and coaching as a catalyst. Implications for the definition of career confidence, and for positive psychology and career coaching practice are considered

Type-Ia Supernova Rates to Redshift 2.4 from Clash: The Cluster Lensing and Supernova Survey with Hubble

We present the supernova (SN) sample and Type-Ia SN (SN Ia) rates from the Cluster Lensing And Supernova survey with Hubble (CLASH). Using the Advanced Camera for Surveys and the Wide Field Camera 3 on the Hubble Space Telescope (HST), we have imaged 25 galaxy-cluster fields and parallel fields of non-cluster galaxies. We report a sample of 27 SNe discovered in the parallel fields. Of these SNe, approximately 13 are classified as SN Ia candidates, including four SN Ia candidates at redshifts z greater than 1.2.We measure volumetric SN Ia rates to redshift 1.8 and add the first upper limit on the SN Ia rate in the range z greater than 1.8 and less than 2.4. The results are consistent with the rates measured by the HST/ GOODS and Subaru Deep Field SN surveys.We model these results together with previous measurements at z less than 1 from the literature. The best-fitting SN Ia delay-time distribution (DTD; the distribution of times that elapse between a short burst of star formation and subsequent SN Ia explosions) is a power law with an index of 1.00 (+0.06(0.09))/(-0.06(0.10)) (statistical) (+0.12/0.08) (systematic), where the statistical uncertainty is a result of the 68% and 95% (in parentheses) statistical uncertainties reported for the various SN Ia rates (from this work and from the literature), and the systematic uncertainty reflects the range of possible cosmic star-formation histories. We also test DTD models produced by an assortment of published binary population synthesis (BPS) simulations. The shapes of all BPS double-degenerate DTDs are consistent with the volumetric SN Ia measurements, when the DTD models are scaled up by factors of 3-9. In contrast, all BPS single-degenerate DTDs are ruled out by the measurements at greater than 99% significance level

Review for the generalist: evaluation of pediatric hip pain

Hip pathology may cause groin pain, referred thigh or knee pain, refusal to bear weight or altered gait in the absence of pain. A young child with an irritable hip poses a diagnostic challenge. Transient synovitis, one of the most common causes of hip pain in children, must be differentiated from septic arthritis. Hip pain may be caused by conditions unique to the growing pediatric skeleton including Perthes disease, slipped capital femoral epiphysis and apophyseal avulsion fractures of the pelvis. Hip pain may also be referred from low back or pelvic pathology. Evaluation and management requires a thorough history and physical exam, and understanding of the pediatric skeleton. This article will review common causes of hip and pelvic musculoskeletal pain in the pediatric population

Serum S100B levels after meningioma surgery: A comparison of two laboratory assays

<p>Abstract</p> <p>Background</p> <p>S100B protein is a potential biomarker of central nervous system insult. This study quantitatively compared two methods for assessing serum concentration of S100B.</p> <p>Methods</p> <p>A prospective, observational study performed in a single tertiary medical center. Included were fifty two consecutive adult patients undergoing surgery for meningioma that provided blood samples for determination of S100B concentrations. Eighty samples (40 pre-operative and 40 postoperative) were randomly selected for batch testing. Each sample was divided into two aliquots. These were analyzed by ELISA (Sangtec) and a commercial kit (Roche Elecsys^®) for S100B concentrations. Statistical analysis included regression modelling and Bland-Altman analysis.</p> <p>Results</p> <p>A parsimonious linear model best described the prediction of commercial kit values by those determined by ELISA (y = 0.045 + 0.277*x, x = ELISA value, R²= 0.732). ELISA measurements tended to be higher than commercial kit measurements. This discrepancy increased linearly with increasing S100B concentrations. At concentrations above 0.7 μg/L the paired measurements were consistently outside the limits of agreement in the Bland-Altman display. Similar to other studies that used alternative measurement methods, sex and age related differences in serum S100B levels were not detected using the Elecsys^®(p = 0.643 and 0.728 respectively).</p> <p>Conclusion</p> <p>Although a generally linear relationship exists between serum S100B concentrations measured by ELISA and a commercially available kit, ELISA values tended to be higher than commercial kit measurements particularly at concentrations over 0.7 μg/L, which are suggestive of brain injury. International standardization of commercial kits is required before the predictive validity of S100B for brain damage can be effectively assessed in clinical practice.</p

A strong conditional mutualism limits and enhances seed dispersal and germination of a tropical palm

Seed predation and seed dispersal can have strong effects on early life history stages of plants. These processes have often been studied as individual effects, but the degree to which their relative importance co-varies with seed predator abundance and how this influences seed germination rates is poorly understood. Therefore, we used a combination of observations and field experiments to determine the degree to which germination rates of the palm Astrocaryum mexicanum varied with abundance of a small mammal seed predator/disperser, Heteromysdesmarestianus, in a lowland tropical forest. Patterns of abundance of the two species were strongly related; density of H. desmarestianus was low in sites with low density of A. mexicanum and vice versa. Rates of predation and dispersal of A. mexicanum seeds depended on abundance of H. desmarestianus; sites with high densities of H. desmarestianus had the highest rates of seed predation and lowest rates of seed germination, but a greater total number of seeds were dispersed and there was greater density of seedlings, saplings, and adults of A. mexicanum in these sites. When abundance of H. desmarestianus was experimentally reduced, rates of seed predation decreased, but so did dispersal of A. mexicanum seeds. Critically, rates of germination of dispersed seeds were 5 times greater than undispersed seeds. The results suggest that the relationship between A. mexicanum and H. desmarestianus is a conditional mutualism that results in a strong local effect on the abundance of each species. However, the magnitude and direction of these effects are determined by the relative strength of opposing, but related, mechanisms. A. mexicanum nuts provide H. desmarestianus with a critical food resource, and while seed predation on A. mexicanum nuts by H. desmarestianus is very intense, A. mexicanum ultimately benefits because of the relatively high germination rates of its seeds that are dispersed by H. desmarestianus

Early Presymptomatic and Long-Term Changes of Rest Activity Cycles and Cognitive Behavior in a MPTP-Monkey Model of Parkinson's Disease

It is increasingly recognized that non-motor symptoms are a prominent feature of Parkinson's disease and in the case of cognitive deficits can precede onset of the characteristic motor symptoms. Here, we examine in 4 monkeys chronically treated with low doses of the neurotoxin MPTP the early and long-term alterations of rest-activity rhythms in relationship to the appearance of motor and cognitive symptoms.Behavioral activity recordings as well as motor and cognitive assessments were carried out continuously and in parallel before, during and for several months following MPTP-treatment (12–56 weeks). Cognitive abilities were assessed using a task that is dependent on the functional integrity of the fronto-striatal axis. Rest-activity cycles were monitored continuously using infrared movement detectors of locomotor activity. Motor impairment was evaluated using standardized scales for primates. Results show that MPTP treatment led to an immediate alteration (within one week) of rest-activity cycles and cognitive deficits. Parkinsonian motor deficits only became apparent 3 to 5 weeks after initiating chronic MPTP administration. In three of the four animals studied, clinical scores returned to control levels 5–7 weeks following cessation of MPTP treatment. In contrast, both cognitive deficits and chronobiological alterations persisted for many months. Levodopa treatment led to an improvement of cognitive performance but did not affect rest-activity rhythms in the two cases tested.Present results show that i) changes in the rest activity cycles constituted early detectable consequences of MPTP treatment and, along with cognitive alterations, characterize the presymptomatic stage; ii) following motor recovery there is a long-term persistence of non-motor symptoms that could reflect differential underlying compensatory mechanisms in these domains; iii) the progressive MPTP-monkey model of presymptomatic ongoing parkinsonism offers possibilities for in-depth studies of early non-motor symptoms including sleep alterations and cognitive deficits

Sin Nombre Virus and Rodent Species Diversity: A Test of the Dilution and Amplification Hypotheses

BACKGROUND:Species diversity is proposed to greatly impact the prevalence of pathogens. Two predominant hypotheses, the "Dilution Effect" and the "Amplification Effect", predict divergent outcomes with respect to the impact of species diversity. The Dilution Effect predicts that pathogen prevalence will be negatively correlated with increased species diversity, while the Amplification Effect predicts that pathogen prevalence will be positively correlated with diversity. For many host-pathogen systems, the relationship between diversity and pathogen prevalence has not be empirically examined. METHODOLOGY/PRINCIPAL FINDINGS:We tested the Dilution and Amplification Effect hypotheses by examining the prevalence of Sin Nombre virus (SNV) with respect to diversity of the nocturnal rodent community. SNV is directly transmitted primarily between deer mice (Peromyscus maniculatus). Using mark-recapture sampling in the Spring and Fall of 2003-2005, we measured SNV prevalence in deer mice at 16 landscape level sites (3.1 hectares each) that varied in rodent species diversity. We explored several mechanisms by which species diversity may affect SNV prevalence, including reduced host density, reduced host persistence, the presence of secondary reservoirs and community composition. We found a negative relationship between species diversity and SNV prevalence in deer mice, thereby supporting the Dilution Effect hypothesis. Deer mouse density and persistence were lower at sites with greater species diversity; however, only deer mouse persistence was positively correlated with SNV prevalence. Pinyon mice (P. truei) may serve as dilution agents, having a negative effect on prevalence, while kangaroo rats (Dipodomys ordii), may have a positive effect on the prevalence of SNV, perhaps through effects on deer mouse behavior. CONCLUSIONS/SIGNIFICANCE:While previous studies on host-pathogen systems have found patterns of diversity consistent with either the Dilution or Amplification Effects, the mechanisms by which species diversity influences prevalence have not been investigated. Our study indicates that changes in host persistence, coupled with interspecific interactions, are important mechanisms through which diversity may influence patterns of pathogens. Our results reveal the complexity of rodent community interactions with respect to SNV dynamics