Genome-wide investigation reveals high evolutionary rates in annual model plants

Background: ;Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. In plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast;genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape (Vitis vinifera) and popular (Populus trichocarpa) for perennials.;Results: ;According to the cross-comparisons among the four species, 74-82% of the nuclear genes and 71-97% of the chloroplast genes suggested higher rates of molecular evolution in the two annuals than those in the two perennials. The significant heterogeneity in evolutionary rate between annuals and perennials was consistently found both in nonsynonymous sites and synonymous sites. While a linear correlation of evolutionary rates in orthologous genes between species was observed in nonsynonymous sites, the correlation was weak or invisible in synonymous sites. This tendency was clearer in nuclear genes than in chloroplast genes, in which the overall;evolutionary rate was small. The slope of the regression line was consistently lower than unity, further confirming the higher evolutionary rate in annuals at the genomic level.;Conclusions: ;The higher evolutionary rate in annuals than in perennials appears to be a universal phenomenon both in nuclear and chloroplast genomes in the four dicot model plants we investigated. Therefore, such heterogeneity in evolutionary rate should result from factors that have genome-wide influence, most likely those associated with annual/perennial life history. Although we acknowledge current limitations of this kind of study, mainly due to a small sample size available and a distant taxonomic relationship of the model organisms, our results indicate that the genome-wide survey is a promising approach toward further understanding of the;mechanism determining the molecular evolutionary rate at the genomic level.

The Lower Limb Functional Index: development and clinimetric properties

Background Existing lower-limb, region-specific, patient-reported outcome measures have clinimetric limitations, including limitations in psychometric characteristics (eg, lack of internal consistency, lack of responsiveness, measurement error) and the lack of reported practical and general characteristics. A new patient-reported outcome measure, the Lower Limb Functional Index (LLFI), was developed to address these limitations. Objective The purpose of this study was to overcome recognized deficiencies in existing lower-limb, region-specific, patient-reported outcome measures through: (1) development of a new lower-extremity outcome scale (ie, the LLFI) and (2) evaluation of the clinimetric properties of the LLFI using the Lower Extremity Functional Scale (LEFS) as a criterion measure. Design This was a prospective observational study. Methods The LLFI was developed in a 3-stage process of: (1) item generation, (2) item reduction with an expert panel, and (3) pilot field testing (n=18) for reliability, responsiveness, and sample size requirements for a larger study. The main study used a convenience sample (n=127) from 10 physical therapy clinics. Participants completed the LLFI and LEFS every 2 weeks for 6 weeks and then every 4 weeks until discharge. Data were used to assess the psychometric, practical, and general characteristics of the LLFI and the LEFS. The characteristics also were evaluated for overall performance using the Measurement of Outcome Measures and Bot clinimetric assessment scales. Results The LLFI and LEFS demonstrated a single-factor structure, comparable reliability (intraclass correlation coefficient [2,1]=.97), scale width, and high criterion validity (Pearson r=.88, with 95% confidence interval [CI]). Clinimetric performance was higher for the LLFI compared with the LEFS on the Measurement of Outcome Measures scale (96% and 95%, respectively) and the Bot scale (100% and 83%, respectively). The LLFI, compared with the LEFS, had improved responsiveness (standardized response mean=1.75 and 1.64, respectively), minimal detectable change with 90% CI (6.6% and 8.1%, respectively), and internal consistency (α=.91 and .95, respectively), as well as readability with reduced user error and completion and scoring times. Limitations Limitations of the study were that only participants recruited from outpatient physical therapy clinics were included and that no specific conditions or diagnostic subgroups were investigated. Conclusion The LLFI demonstrated sound clinimetric properties. There was lower response error, efficient completion and scoring, and improved responsiveness and overall performance compared with the LEFS. The LLFI is suitable for assessment of lower-limb function.

Role Stress and Job Outcomes in Public Accounting: Have the Gender Experiences Converged?

Using data collected from professionals in a large U.S. national public accounting firm, we explored gender differences in perceived levels of role stress and job outcomes as well as the effects of a healthy lifestyle as a coping mechanism for role stress, burnout and related job outcomes. Our large sample size (1,681) and equal participation by women (49.7%) and men (50.3%) allowed us to analyze the causal relationships of these variables using a previously tested multi-disciplinary research model (Jones, Norman, & Wier, 2010). We found that women and men perceive similar levels of role stress as defined by role ambiguity and role overload, and that women perceive less role conflict. Men and women perceive similar levels of job satisfaction and job performance. Contrary to earlier studies, women do not report higher levels of turnover intentions. Results show that efforts of the public accounting firms over the past decade may be somewhat successful in reducing the levels of role stress and turnover intentions among women. Another plausible explanation could be that an expansionist theory of gender, work and family (Barnett & Hyde, 2001) may now be responsible for improved well-being of females to the point where the genders have converged in their experience of role stress and job outcomes in public accounting.

Role of hepatitis C virus genotype 3 in liver fibrosis progression - a systematic review and meta-analysis

The progression of liver fibrosis in chronic hepatitis C has long been considered to be independent from viral genotypes. However, recent studies suggest an association between Hepatitis C virus (HCV) genotype 3 and accelerated liver disease progression. We completed a systematic review and meta-analysis of studies evaluating the association between HCV genotypes and fibrosis progression. PubMed, Embase and ISI Web of Knowledge databases were searched for cohort, cross-sectional and case-control studies on treatment-naïve HCV-infected adults in which liver fibrosis progression rate (FPR) was assessed by the ratio of fibrosis stage in one single biopsy to the duration of infection (single-biopsy studies) or from the change in fibrosis stage between two biopsies (paired biopsies studies). A random effect model was used to derive FPR among different HCV genotypes. Eight single-biopsy studies (3182 patients, mean/median duration of infection ranging from 9 to 21 years) and eight paired biopsies studies (mean interval between biopsies 2-12 years) met the selection criteria. The odds ratio for the association of genotype 3 with accelerated fibrosis progression was 1.52 (95% CI 1.12-2.07, P = 0.007) in single-biopsy studies and 1.37 (95% CI 0.87-2.17, P = 0.17) in paired biopsy studies. In conclusion, viral genotype 3 was associated with faster fibrosis progression in single-biopsy studies. This observation may have important consequences on the clinical management of genotype 3-infected patients. The association was not significant in paired biopsies studies, although the latter may be limited by important indication bias, short observation time and small sample size.

Viral genotype-specific role of PNPLA3, PPARG, MTTP, and IL28B in hepatitis C virus-associated steatosis

Steatosis is a prominent feature of hepatitis C, especially in patients infected with genotype 3. The analysis of genetic polymorphisms influencing steatosis in chronic hepatitis C has been limited by the studies' small sample size, and important single nucleotide polymorphisms (SNPs), such as those in the patatin-like phospholipase family 3 protein (PNPLA3), were never evaluated.

Bone dimensions in the posterior mandible: a retrospective radiographic study using cone beam computed tomography. Part 1--analysis of dentate sites

This retrospective radiographic study analyzed the dimensions of the alveolar bone in the posterior dentate mandible based on cone beam computed tomography (CBCT) images. A total of 56 CBCT images met the inclusion criteria, resulting in a sample size of 122 cross sections showing posterior mandibular teeth (premolars and molars). The thickness of the buccal and lingual bone walls was measured at two locations: 4 mm apical to the cementoenamel junction (measurement point 1, MP1) and at the middle of the root (measurement point 2, MP2). Further, alveolar bone width was assessed at the level of the most coronal buccal bone detectable (alveolar bone width 1, BW1) and at the superior border of the mandibular canal (alveolar bone width 2, BW2). The vertical distance between the two as well as the presence of a lingual undercut were also analyzed. There was a steady increase in buccal bone wall thickness from the first premolar to the second molar at both MP1 and MP2. BW1 at the level of the premolars was significantly thinner than that for molars. Alveolar bone height was constant for all teeth examined. For the selection of an appropriate postextraction treatment approach, analysis of the alveolar bone dimensions at the tooth to be extracted by means of CBCT can offer valuable information concerning bone volume and morphology at the future implant site.

Using scenario tree modelling for targeted herd sampling to substantiate freedom from disease

BACKGROUND: In order to optimise the cost-effectiveness of active surveillance to substantiate freedom from disease, a new approach using targeted sampling of farms was developed and applied on the example of infectious bovine rhinotracheitis (IBR) and enzootic bovine leucosis (EBL) in Switzerland. Relevant risk factors (RF) for the introduction of IBR and EBL into Swiss cattle farms were identified and their relative risks defined based on literature review and expert opinions. A quantitative model based on the scenario tree method was subsequently used to calculate the required sample size of a targeted sampling approach (TS) for a given sensitivity. We compared the sample size with that of a stratified random sample (sRS) with regard to efficiency. RESULTS: The required sample sizes to substantiate disease freedom were 1,241 farms for IBR and 1,750 farms for EBL to detect 0.2% herd prevalence with 99% sensitivity. Using conventional sRS, the required sample sizes were 2,259 farms for IBR and 2,243 for EBL. Considering the additional administrative expenses required for the planning of TS, the risk-based approach was still more cost-effective than a sRS (40% reduction on the full survey costs for IBR and 8% for EBL) due to the considerable reduction in sample size. CONCLUSIONS: As the model depends on RF selected through literature review and was parameterised with values estimated by experts, it is subject to some degree of uncertainty. Nevertheless, this approach provides the veterinary authorities with a promising tool for future cost-effective sampling designs.

Comparing the demonstration of freedom from Trichinella infection of domestic pigs by traditional and risk-based surveillance

Traditionally, the routine artificial digestion test is applied to assess the presence of Trichinella larvae in pigs. However, this diagnostic method has a low sensitivity compared to serological tests. The results from artificial digestion tests in Switzerland were evaluated over a time period of 15 years to determine by when freedom from infection based on these data could be confirmed. Freedom was defined as a 95% probability that the prevalence of infection was below 0.0001%. Freedom was demonstrated after 12 years at the latest. A new risk-based surveillance approach was then developed based on serology. Risk-based surveillance was also assessed over 15 years, starting in 2010. It was shown that by using this design, the sample size could be reduced by at least a factor of 4 when compared with the traditional testing regimen, without lowering the level of confidence in the Trichinella-free status of the pig population.

Seroprevalence of Taenia saginata cysticercosis in the federal state of Lower Saxony in Germany

Based on ELISA results from randomly selected serum samples taken from 128 cattle from different administrative and urban districts in the federal state of Lower Saxony in Germany a seroprevalence estimate of Taenia saginata cysticercosis in this area was derived. This estimate was subsequently used to calculate the sample size required in an epidemiological study to determine the actual prevalence of this infection in the cattle population (n = 2 604 767) in this federal state. The sample size was calculated as 1518 and the samples were collected according to the distribution of cattle among the 48 administrative and urban districts in Lower Saxony. The samples were tested with an evaluated antibody ELISA. The results showed a positive antibody titre rate of 8.83% from the total tested samples.

Tumor thrombus of inferior vena cava in patients with renal cell carcinoma - clinical and oncological outcome of 50 patients after surgery

Background To evaluate oncological and clinical outcome in patients with renal cell carcinoma (RCC) and tumor thrombus involving inferior vena cava (IVC) treated with nephrectomy and thrombectomy. Methods We identified 50 patients with a median age of 65 years, who underwent radical surgical treatment for RCC and tumor thrombus of the IVC between 1997 and 2010. The charts were reviewed for pathological and surgical parameters, as well as complications and oncological outcome. Results The median follow-up was 26 months. In 21 patients (42%) distant metastases were already present at the time of surgery. All patients underwent radical nephrectomy, thrombectomy and lymph node dissection through a flank (15 patients/30%), thoracoabdominal (14 patients/28%) or midline abdominal approach (21 patients/42%), depending upon surgeon preference and upon the characteristics of tumor and associated thrombus. Extracorporal circulation with cardiopulmonary bypass (CPB) was performed in 10 patients (20%) with supradiaphragmal thrombus of IVC. Cancer-specific survival for the whole cohort at 5 years was 33.1%. Survival for the patients without distant metastasis at 5 years was 50.7%, whereas survival rate in the metastatic group at 5 years was 7.4%. Median survival of patients with metastatic disease was 16.4 months. On multivariate analysis lymph node invasion, distant metastasis and grading were independent prognostic factors. There was no statistically significant influence of level of the tumor thrombus on survival rate. Indeed, patients with supradiaphragmal tumor thrombus (n = 10) even had a better outcome (overall survival at 5 years of 58.33%) than the entire cohort. Conclusions An aggressive surgical approach is the most effective therapeutic option in patients with RCC and any level of tumor thrombus and offers a reasonable longterm survival. Due to good clinical and oncological outcome we prefer the use of CPB with extracorporal circulation in patients with supradiaphragmal tumor thrombus. Cytoreductive surgery appears to be beneficial for patients with metastatic disease, especially when consecutive therapy is performed. Although sample size of our study cohort is limited consistent with some other studies lymph node invasion, distant metastasis and grading seem to have prognostic value.

Magnetic resonance imaging, ultrasonography and histology of the suspensory ligament origin: a comparative study of normal anatomy of warmblood horses

REASONS FOR PERFORMING STUDY: The diagnosis of lameness caused by proximal metacarpal and metatarsal pain can be challenging. Magnetic resonance imaging (MRI) offers the possibility for further diagnosis but there have been no studies on the normal MRI appearance of the origin of the suspensory ligament (OSL) in conjunction with ultrasonography and histology. OBJECTIVES: To describe the MRI appearance of the OSL in fore- and hindlimbs of sound horses and compare it to the ultrasonographic and histological appearance. The findings can be used as reference values to recognise pathology in the OSL. METHODS: The OSL in the fore- and hindlimbs of 6 sound horses was examined by ultrasonography prior to death, and MRI and histology post mortem. Qualitative evaluation and morphometry of the OSL were performed and results of all modalities compared. RESULTS: Muscular tissue, artefacts, variable SL size and shape complicated ultrasonographic interpretation. In MRI and histology the forelimb OSL consisted of 2 portions, the lateral being significantly thicker than medial. The hindlimb SL had a single large area of origin. In fore- and hindlimbs, the amount of muscular tissue was significantly larger laterally than medially. Overall SL measurements using MRI were significantly higher than using histology and ultrasonography and histological higher than ultrasonographic measurements. Morphologically, there was a good correlation between MRI and histology. CONCLUSIONS: MRI provides more detailed information than ultrasonography regarding muscle fibre detection and OSL dimension and correlates morphologically well with histology. Therefore, ultrasonographic results should be regarded with caution. POTENTIAL RELEVANCE: MRI may be a diagnostic aid when other modalities fail to identify clearly the cause of proximal metacarpal and metatarsal pain; and may improve selection of adequate therapy and prognosis for injuries in this region.

Association between sleep apnea severity and blood coagulability: Treatment effects of nasal continuous positive airway pressure

A prothrombotic state may contribute to the elevated cardiovascular risk in patients with obstructive sleep apnea (OSA). We investigated the relationship between apnea severity and hemostasis factors and effect of continuous positive airway pressure (CPAP) treatment on hemostatic activity. We performed full overnight polysomnography in 44 OSA patients (mean age 47+/-10 years), yielding apnea-hypopnea index (AHI) and mean nighttime oxyhemoglobin saturation (SpO2) as indices of apnea severity. For treatment, subjects were double-blind randomized to 2 weeks of either therapeutic CPAP (n = 18), 3 l/min supplemental nocturnal oxygen (n = 16) or placebo-CPAP (<1 cm H2O) (n = 10). Levels of von Willebrand factor antigen (VWF:Ag), soluble tissue factor (sTF), D-dimer, and plasminogen activator inhibitor (PAI)-1 antigen were measured in plasma pre- and posttreatment. Before treatment, PAI-1 was significantly correlated with AHI (r = 0.47, p = 0.001) and mean nighttime SpO2 (r = -0.32, p = 0.035), but these OSA measures were not significantly related with VWF:Ag, sTF, and D-dimer. AHI was a significant predictor of PAI-1 (R2 = 0.219, standardized beta = 0.47, p = 0.001), independent of mean nighttime SpO2, body mass index (BMI), and age. A weak time-by-treatment interaction for PAI-1 was observed (p = 0.041), even after adjusting for age, BMI, pre-treatment AHI, and mean SpO2 (p = 0.046). Post hoc analyses suggested that only CPAP treatment was associated with a decrease in PAI-1 (p = 0.039); there were no changes in VWF:Ag, sTF, and D-dimer associated with treatment with placebo-CPAP or with nocturnal oxygen. Apnea severity may be associated with impairment in the fibrinolytic capacity. To the extent that our sample size was limited, the observation that CPAP treatment led to a decrease in PAI-1 in OSA must be regarded as tentative.

Asymptotics for Marginal Generalized Linear Models With Sparse Correlations

Marginal generalized linear models can be used for clustered and longitudinal data by fitting a model as if the data were independent and using an empirical estimator of parameter standard errors. We extend this approach to data where the number of observations correlated with a given one grows with sample size and show that parameter estimates are consistent and asymptotically Normal with a slower convergence rate than for independent data, and that an information sandwich variance estimator is consistent. We present two problems that motivated this work, the modelling of patterns of HIV genetic variation and the behavior of clustered data estimators when clusters are large.

Magnetic resonance imaging features of orbital inflammation with intracranial extension in four dogs

This retrospective study describes the clinical and magnetic resonance (MR) imaging features of chronic orbital inflammation with intracranial extension in four dogs (two Dachshunds, one Labrador, one Swiss Mountain). Intracranial extension was observed through the optic canal (n=1), the orbital fissure (n=4), and the alar canal (n=1). On T1-weighted images structures within the affected skull foramina could not be clearly differentiated, but were all collectively isointense to hypointense compared with the contralateral, unaffected side, or compared with gray matter. On T2-, short tau inversion recovery (STIR)-, or fluid-attenuated inversion recovery (FLAIR)-weighted images structures within the affected skull foramina appeared hyperintense compared with gray matter, and extended with increased signal into the rostral cranial fossa (n=1) and middle cranial fossa (n=4). Contrast enhancement at the level of the affected skul foramina as well as at the skull base in continuity with the orbital fissure was observed in all patients. Brain edema or definite meningeal enhancement could not be observed, but a close anatomic relationship of the abnormal tissue to the cavernous sinus was seen in two patients. Diagnosis was confirmed in three dogs (one cytology, two biopsy, one necropsy) and was presumptive in one based on clinical improvement after treatment. This study is limited by its small sample size, but provides evidence for a potential risk of intracranial extension of chronic orbital inflammation. This condition can be identified best by abnormal signal increase at the orbital fissure on transverse T2-weighted images, on dorsal STIR images, or on postcontrast transverse or dorsal images.