Effects of Ponderosa Pine Ecological Restoration on Forest Soils and Understory Vegetation in Northern Arizona

The human exclusion of wildfire and overgrazing by livestock since settlement have caused dramatic changes in ponderosa pine (Pinus ponderosa Dougl ex Laws) forest ecosystems. These changes include increased numbers of tree stems, reduced understory cover and diversity, and the introduction of invasive, non-native understory species. This study evaluated the coverage and species composition of understory vegetation present in the “cool-season” (late spring and early summer) in a ponderosa pine forest on grazed and ungrazed plots that had undergone restoration treatments on three different soil/geologic parent material types near Flagstaff, Arizona, twelve years after tree thinning and grazing exclosure treatments were applied. Several measured soil properties, such as soil respiration and temperature, were also evaluated in this study. Species richness of “cool-season” vegetation was influenced more by grazing practices than restoration treatments. Differences could be less or greater when vegetation that is active later in the season is measured. Vegetative cover was significantly influenced by restoration treatments (9.3% cover under open canopies and 6.5% under dense canopies), probably due to differences in competition for light and other resources (i.e. soil moisture and nutrients). Unlike finding by Abella et al. (2015), who studied “warm-season” vegetation, “cool-season” understory cover was not influenced by soil parent material type in this study, which might suggest that differences in understory cover due to soil properties are only seen shortly after restoration treatments are applied, or the time of year vegetation is evaluated may play a role in the differences seen. Soil respiration was highest on limestone soil parent material type (3.3 g C-CO2 m-2 day-1), and soil temperature was lowest under closed canopy treatments (15°C)

Specialist or Nonspecialist Physical Education Teachers in Ontario Elementary Schools: Examining Differences in Opportunities for Physical Activity

Research supports the position that specialists are the preferred providers of physical education in elementary (primary) school settings. We examined whether specialists delivered more physical education lessons and provided greater opportunities for moderate and vigorous physical activity and whether barriers to curricular and extracurricular physical activity opportunities in Ontario elementary schools differed for specialist and nonspecialist teachers. Using a cross-sectional design, a questionnaire was mailed to key informants in 599 randomly selected elementary schools in Ontario, yielding an 85% response rate. Most physical education in Ontario elementary schools is delivered by nonspecialists (63%). No self-reported differences were found between specialists and generalist teachers in the number of physical education lessons delivered per week, the minutes per physical education class, or in the amount of reported moderate or vigorous physical activity in lessons. Compared with specialists, respondents in schools in which generalist teachers taught PE perceived lack of training as a greater barrier to delivering physical education. Given the importance of subject knowledge in teaching effectively, there is still need to advocate for specialist physical education teaching in elementary schools. However, concerns about teaching specialism may be secondary to broader and more complex factors surrounding the delivery of physical education in elementary schools.La recherche appuie le point de vue selon lequel les spécialistes sont les mieux placés pour enseigner l’éducation physique au primaire. Nous nous sommes penchés sur deux questions: (a) les spécialistes offrent-ils plus de cours d’éducation physique et d’occasions de pratiquer des activités physiques modérées ou vigoureuses ?, et (b) les obstacles à la participation aux activités physiques scolaires et extra-scolaires dans les écoles primaires de l’Ontario sont-ils les mêmes pour les enseignants spécialistes et les enseignants non-spécialistes ? Dans le contexte d’un modèle croisé, nous avons envoyé un questionnaire à des répondants clés dans 599 écoles primaires sélectionnées au hasard en Ontario. Notre taux de réponse a été de 85%. La majorité (63%) des cours d’éducation physique en Ontario sont offerts par des non spécialistes. Les résultats n’indiquent aucune différence entre les enseignants spécialistes et les enseignants non-spécialistes quant aux critères suivants: le nombre de cours d’éducation physique offerts par semaine, la durée des cours d’éducation physique et la mesure dans laquelle les cours impliquent de l’activité physique modérée ou vigoureuse. Par rapport aux répondants des écoles où les cours d’éducation physique se donnaient par des spécialistes, ceux des écoles où ces cours se donnaient par des généralistes ont indiqué que le manque de formation constituait un obstacle plus important à l’enseignement de l’éducation physique. Compte tenu du rôle important de la connaissance de la matière dans l’enseignement efficace, il faudrait continuer à promouvoir l’enseignement de l’éducation physique par des spécialistes dans les écoles primaires. Toutefois, les préoccupations portant sur l’enseignement par des spécialistes semblent secondaires face aux facteurs plus généraux et complexes en matière d’enseignement de l’éducation physique dans les écoles primaires

Treatment options for muscle-invasive urothelial cancer for patients who were not eligible for cystectomy or neoadjuvant chemotherapy with methotrexate, vinblastine, doxorubicin, and cisplatin

BACKGROUND. Many patients with invasive urothelial cell cancer are poor candidates for cisplatin-based chemotherapy, and many are high risk for cystectomy. Southwest Oncology Group Trial 8733 was designed to address treatment for such patients. METHODS. Eligible patients had primary or recurrent muscle-invasive disease with transitional cell or squamous cell histology, a performance status from 0 to 2, no extrapelvic disease, a life expectancy >3 months, and adequate hematologic function. The treating clinician assigned patients to operable or inoperable groups. All patients received 2 cycles of 5-fluorouracil (5-FU) at a dose of 1000mg/m 2 per day × 4 starting concurrently with radiation at a dose of 200 centigrays per day × 10 each cycle. After 2 cycles, operable patients with positive biopsies underwent cystectomy, and patients with negative biopsies received a third cycle of chemoradiotherapy. Patients in the inoperable group received 3 cycles without interim biopsy. RESULTS. Eighteen of 24 eligible patients in the operable group were evaluable for response. Five patients had a complete response (CR), 9 patients had stable disease, 1 patient had progressive disease, and 3 patients were not assessable. The median progression-free survival was 10 months (95% confidence interval [95% CI], 4–14 months), and the median overall survival was 18 months (95% CI, 7–28 months). In the inoperable group, 35 of 37 eligible patients were evaluable for response with 17 CRs (49%; 95% CI, 31%–66%). The median progression-free survival was 13 months (95% CI, 10–17 months), and the median overall survival was 20 months (95% CI, 11–53 months). There were no episodes of grade 4 toxicity. CONCLUSIONS. In the current study, the combination of 5-FU and radiation was found to be tolerated well by patients with numerous comorbidities who could not tolerate cisplatin-based therapy or cystectomy. Cancer 2008. © 2008 American Cancer Society.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/58591/1/23420_ftp.pd

Canadian 24-hour movement guidelines for adults aged 18-64 years and adults aged 65 years or older: an integration of physical activity, sedentary behaviour, and sleep

The Canadian Society for Exercise Physiology assembled a Consensus Panel representing national organizations, content experts, methodologists, stakeholders, and end-users and followed an established guideline development procedure to create the Canadian 24-Hour Movement Guidelines for Adults aged 18-64 years and Adults aged 65 years or older: An Integration of Physical Activity, Sedentary Behaviour, and Sleep. These guidelines underscore the importance of movement behaviours across the whole 24-h day. The development process followed the strategy outlined in the Appraisal of Guidelines for Research and Evaluation (AGREE) II instrument. A large body of evidence was used to inform the guidelines including 2 de novo systematic reviews and 4 overviews of reviews examining the relationships among movement behaviours (physical activity, sedentary behaviour, sleep, and all behaviours together) and several health outcomes. Draft guideline recommendations were discussed at a 4-day in-person Consensus Panel meeting. Feedback from stakeholders was obtained by survey (n = 877) and the draft guidelines were revised accordingly. The final guidelines provide evidence-based recommendations for a healthy day (24-h), comprising a combination of sleep, sedentary behaviours, and light-intensity and moderate-to-vigorous-intensity physical activity. Dissemination and implementation efforts with corresponding evaluation plans are in place to help ensure that guideline awareness and use are optimized. Novelty First ever 24-Hour Movement Guidelines for Adults aged 18-64 years and Adults aged 65 years or older with consideration of a balanced approach to physical activity, sedentary behaviour, and sleep Finalizes the suite of 24-Hour Movement Guidelines for Canadians across the lifespa

Measuring Five Dimensions of Religiosity Across Adolescence

This paper theorizes and tests a latent variable model of adolescent religiosity in which five dimensions of religiosity are interrelated: religious beliefs, religious exclusivity, external religiosity, private practice, and religious salience. Research often theorizes overlapping and independent influences of single items or dimensions of religiosity on outcomes such as adolescent sexual behavior, but rarely operationalizes the dimensions in a measurement model accounting for their associations with each other and across time. We use longitudinal structural equation modeling (SEM) with latent variables to analyze data from two waves of the National Study of Youth and Religion. We test our hypothesized measurement model as compared to four alternate measurement models and find that our proposed model maintains superior fit. We then discuss the associations between the five dimensions of religiosity we measure and how these change over time. Our findings suggest how future research might better operationalize multiple dimensions of religiosity in studies of the influence of religion in adolescence

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease

<div><p>Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity. Accordingly, shared transcriptional activity (coexpression) may help prioritise loci associated with a given trait, and help to identify underlying biological processes. Using cap analysis of gene expression (CAGE) profiles of promoter- and enhancer-derived RNAs across 1824 human samples, we have analysed coexpression of RNAs originating from trait-associated regulatory regions using a novel quantitative method (network density analysis; NDA). For most traits studied, phenotype-associated variants in regulatory regions were linked to tightly-coexpressed networks that are likely to share important functional characteristics. Coexpression provides a new signal, independent of phenotype association, to enable fine mapping of causative variants. The NDA coexpression approach identifies new genetic variants associated with specific traits, including an association between the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. NDA strongly implicates particular cell types and tissues in disease pathogenesis. For example, distinct groupings of disease-associated regulatory regions implicate two distinct biological processes in the pathogenesis of ulcerative colitis; a further two separate processes are implicated in Crohn’s disease. Thus, our functional analysis of genetic predisposition to disease defines new distinct disease endotypes. We predict that patients with a preponderance of susceptibility variants in each group are likely to respond differently to pharmacological therapy. Together, these findings enable a deeper biological understanding of the causal basis of complex traits.</p></div

Economic Analysis of Knowledge: The History of Thought and the Central Themes

Following the development of knowledge economies, there has been a rapid expansion of economic analysis of knowledge, both in the context of technological knowledge in particular and the decision theory in general. This paper surveys this literature by identifying the main themes and contributions and outlines the future prospects of the discipline. The wide scope of knowledge related questions in terms of applicability and alternative approaches has led to the fragmentation of research. Nevertheless, one can identify a continuing tradition which analyses various aspects of the generation, dissemination and use of knowledge in the economy

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease

The FANTOM5 consortium utilised cap analysis of gene expression (CAGE) to provide an unprecedented insight into transcriptional regulation in human cells and tissues. In the current study, we have used CAGE-based transcriptional profiling on an extended dense time course of the response of human monocyte-derived macrophages grown in macrophage colony-stimulating factor (CSF1) to bacterial lipopolysaccharide (LPS). We propose that this system provides a model for the differentiation and adaptation of monocytes entering the intestinal lamina propria. The response to LPS is shown to be a cascade of successive waves of transient gene expression extending over at least 48 hours, with hundreds of positive and negative regulatory loops. Promoter analysis using motif activity response analysis (MARA) identified some of the transcription factors likely to be responsible for the temporal profile of transcriptional activation. Each LPS-inducible locus was associated with multiple inducible enhancers, and in each case, transient eRNA transcription at multiple sites detected by CAGE preceded the appearance of promoter-associated transcripts. LPS-inducible long non-coding RNAs were commonly associated with clusters of inducible enhancers. We used these data to re-examine the hundreds of loci associated with susceptibility to inflammatory bowel disease (IBD) in genome-wide association studies. Loci associated with IBD were strongly and specifically (relative to rheumatoid arthritis and unrelated traits) enriched for promoters that were regulated in monocyte differentiation or activation. Amongst previously-identified IBD susceptibility loci, the vast majority contained at least one promoter that was regulated in CSF1-dependent monocyte-macrophage transitions and/or in response to LPS. On this basis, we concluded that IBD loci are strongly-enriched for monocyte-specific genes, and identified at least 134 additional candidate genes associated with IBD susceptibility from reanalysis of published GWA studies. We propose that dysregulation of monocyte adaptation to the environment of the gastrointestinal mucosa is the key process leading to inflammatory bowel disease

Somatic retrotransposition alters the genetic landscape of the human brain

Retrotransposons are mobile genetic elements that use a germline 'copy-and-paste' mechanism to spread throughout metazoan genomes. At least 50 per cent of the human genome is derived from retrotransposons, with three active families (L1, Alu and SVA) associated with insertional mutagenesis and disease. Epigenetic and post-transcriptional suppression block retrotransposition in somatic cells, excluding early embryo development and some malignancies. Recent reports of L1 expression and copy number variation in the human brain suggest that L1 mobilization may also occur during later development. However, the corresponding integration sites have not been mapped. Here we apply a high-throughput method to identify numerous L1, Alu and SVA germline mutations, as well as 7,743 putative somatic L1 insertions, in the hippocampus and caudate nucleus of three individuals. Surprisingly, we also found 13,692 somatic Alu insertions and 1,350 SVA insertions. Our results demonstrate that retrotransposons mobilize to protein-coding genes differentially expressed and active in the brain. Thus, somatic genome mosaicism driven by retrotransposition may reshape the genetic circuitry that underpins normal and abnormal neurobiological processes

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. © 2021, The Author(s)