Global Taxonomic Diversity of Anomodonts (Tetrapoda, Therapsida) and the Terrestrial Rock Record Across the Permian-Triassic Boundary

The end-Permian biotic crisis (∼252.5 Ma) represents the most severe extinction event in Earth's history. This paper investigates diversity patterns in Anomodontia, an extinct group of therapsid synapsids (‘mammal-like reptiles’), through time and in particular across this event. As herbivores and the dominant terrestrial tetrapods of their time, anomodonts play a central role in assessing the impact of the end-Permian extinction on terrestrial ecosystems. Taxonomic diversity analysis reveals that anomodonts experienced three distinct phases of diversification interrupted by the same number of extinctions, i.e. an end-Guadalupian, an end-Permian, and a mid-Triassic extinction. A positive correlation between the number of taxa and the number of formations per time interval shows that anomodont diversity is biased by the Permian-Triassic terrestrial rock record. Normalized diversity curves indicate that anomodont richness continuously declines from the Middle Permian to the Late Triassic, but also reveals all three extinction events. Taxonomic rates (origination and extinction) indicate that the end-Guadalupian and end-Permian extinctions were driven by increased rates of extinction as well as low origination rates. However, this pattern is not evident at the final decline of anomodont diversity during the Middle Triassic. Therefore, it remains unclear whether the Middle Triassic extinction represents a gradual or abrupt event that is unique to anomodonts or more common among terrestrial tetrapods. The end-Permian extinction represents the most distinct event in terms of decline in anomodont richness and turnover rates

Graphical Reasoning in Compact Closed Categories for Quantum Computation

Compact closed categories provide a foundational formalism for a variety of important domains, including quantum computation. These categories have a natural visualisation as a form of graphs. We present a formalism for equational reasoning about such graphs and develop this into a generic proof system with a fixed logical kernel for equational reasoning about compact closed categories. Automating this reasoning process is motivated by the slow and error prone nature of manual graph manipulation. A salient feature of our system is that it provides a formal and declarative account of derived results that can include `ellipses'-style notation. We illustrate the framework by instantiating it for a graphical language of quantum computation and show how this can be used to perform symbolic computation.Comment: 21 pages, 9 figures. This is the journal version of the paper published at AIS

Study design and participant characteristics of a randomized controlled trial of directly administered antiretroviral therapy in opioid treatment programs

<p>Abstract</p> <p>Background</p> <p>HIV-infected drug users are at higher risk of non-adherence and poor treatment outcomes than HIV-infected non-drug users. Prior work from our group and others suggests that directly administered antiretroviral therapy (DAART) delivered in opioid treatment programs (OTPs) may increase rates of viral suppression.</p> <p>Methods/Design</p> <p>We are conducting a randomized trial comparing DAART to self-administered therapy (SAT) in 5 OTPs in Baltimore, Maryland. Participants and investigators are aware of treatment assignments. The DAART intervention is 12 months. The primary outcome is HIV RNA < 50 copies/mL at 3, 6, and 12 months. To assess persistence of any study arm differences that emerge during the active intervention, we are conducting an 18-month visit (6 months after the intervention concludes). We are collecting electronic adherence data for 2 months in both study arms. Of 457 individuals screened, a total of 107 participants were enrolled, with 56 and 51 randomly assigned to DAART and SAT, respectively. Participants were predominantly African American, approximately half were women, and the median age was 47 years. Active use of cocaine and other drugs was common at baseline. HIV disease stage was advanced in most participants. The median CD4 count at enrollment was 207 cells/mm³, 66 (62%) had a history of an AIDS-defining opportunistic condition, and 21 (20%) were antiretroviral naïve.</p> <p>Conclusions</p> <p>This paper describes the rationale, methods, and baseline characteristics of subjects enrolled in a randomized clinical trial comparing DAART to SAT in opioid treatment programs.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov: <a href="http://www.clinicaltrials.gov/ct2/show/NCT00279110">NCT00279110</a></p

Ambient PM2.5 Exposure Up-regulates the Expression of Costimulatory Receptors on Circulating Monocytes in Diabetic Individuals

BACKGROUND: Exposure of humans to air pollutants such as ozone and particulate matter (PM) may result in airway and systemic inflammation and altered immune function. One putative mechanism may be through modification of cell-surface costimulatory molecules. OBJECTIVES: We examined whether changes in expression of costimulatory molecules on circulating cells are associated with ambient levels of fine PM [aerodynamic diameter ≤ 2.5 μm (PM2.5)] in a susceptible population of diabetic individuals. METHODS: Twenty subjects were studied for 4 consecutive days. Daily measurements of PM2.5 and meteorologic data were acquired on the rooftop of the exam site. Circulating cell-surface markers that mediate innate immune and inflammatory responses were assessed by flow cytometry on each day. Sensitivity analysis was conducted on glutathione S-transferase M1 (GSTM1) genotype, body mass index, and glycosylated hemoglobin A1c (HbA1c) levels to determine their role as effect modifiers. Data were analyzed using random effects models adjusting for season, weekday, and meteorology. RESULTS: We found significantly increased monocyte expression (mean fluorescent intensity) of CD80, CD40, CD86, HLA-DR, and CD23 per 10-μg/m3 increase in PM2.5 at 2- to 4-day lag times after exposure. These findings were significantly higher in obese individuals, in individuals with HbA1c > 7%, and in participants who were GSTM1 null. CONCLUSIONS: Exposure to PM2.5 can enhance antigen-presenting cell phenotypes on circulating cells, which may have consequences in the development of allergic or autoimmune diseases. These effects are amplified in diabetic individuals with characteristics that are associated with insulin resistance or with oxidative stress

Reduced Carotenoid and Retinoid Concentrations and Altered Lycopene Isomer Ratio in Plasma of Atopic Dermatitis Patients.

Carotenoids and retinoids are known to alter the allergic response with important physiological roles in the skin and the immune system. In the human organism various carotenoids are present, some of which are retinoid precursors. The bioactive derivatives of these retinoids are the retinoic acids, which can potently activate nuclear hormone receptors such as the retinoic acid receptor and the retinoid X receptor. In this study, we aimed to assess how plasma carotenoid and retinoid concentrations along with the ratio of their isomers are altered in atopic dermatitis (AD) patients (n = 20) compared to healthy volunteers (HV, n = 20). The study indicated that plasma levels of the carotenoids lutein (HV 198 ± 14 ng/mL, AD 158 ± 12 ng/mL, p = 0.02; all values in mean ± SEM), zeaxanthin (HV 349 ± 30 ng/mL, AD 236 ± 18 ng/mL, p ≤ 0.01), as well as the retinoids retinol (HV 216 ± 20 ng/mL, AD 167 ± 17 ng/mL, p = 0.04) and all-trans-retinoic acid (HV 1.1 ± 0.1 ng/mL, AD 0.7 ± 0.1 ng/mL, p = 0.04) were significantly lower in the AD-patients, while lycopene isomers, α-carotene, and β-carotene levels were comparable to that determined in the healthy volunteers. In addition, the ratios of 13-cis- vs. all-trans-lycopene (HV 0.31 ± 0.01, AD 0.45 ± 0.07, p = 0.03) as well as 13-cis- vs. all-trans-retinoic acid (HV 1.4 ± 0.2, AD 2.6 ± 0.6, p = 0.03) were increased in the plasma of AD-patients indicating an AD-specific 13-cis-isomerisation. A positive correlation with SCORAD was calculated with 13-cis- vs. all-trans-lycopene ratio (r = 0.40, p = 0.01), while a negative correlation was observed with zeaxanthin plasma levels (r = -0.42, p = 0.01). Based on our results, we conclude that in the plasma of AD-patients various carotenoids and retinoids are present at lower concentrations, while the ratio of selected lycopene isomers also differed in the AD-patient group. An increase in plasma isomers of both lycopene and retinoic acid may cause an altered activation of nuclear hormone receptor signaling pathways and thus may be partly responsible for the AD-phenotype

How manipulating task constraints in small-sided and conditioned games shapes emergence of individual and collective tactical behaviours in football: A systematic review

Background: Small-Sided and Conditioned Games are characterised by modifications of field dimensions, number of players, rules of the game, manipulations used to shape the key task constraints that performers need to satisfy in practice. Evidence has already demonstrated the importance of designing practice to enhance understanding of tactical behaviours in football, but there is a lack of information about how coaches can manipulate task constraints to support tactical learning. Objective: To investigate which task constraints have been most often manipulated in studies of SSCGs; and what impact each manipulation had on emerging tactical behaviours, technical–tactical actions, and positional relationships between players. Methods: PubMed, Web of Science, Scielo, and Academic Google databases were searched for relevant reports without time limits. The criteria adopted for inclusion were: a) studies performed with football players; b) studies that included SSCGs as an evaluation method; c) studies that investigated tactical behaviours in SSCGs; and d), articles in English and Portuguese. Results: The electronic database search included 24 articles in the review. Of these, five manipulated field dimensions, six manipulated number of players involved, five manipulated field dimensions and number of players, five used different scoring targets, two altered the number of players and scoring target, and one manipulated the number of players, field dimension, and scoring target. Conclusion: Among the task constraints analyzed in this systematic review, manipulation of number of players and playing field dimensions concomitantly occurred most frequentl

How manipulating task constraints in small-sided and conditioned games shapes emergence of individual and collective tactical behaviours in football: A systematic review

Background: Small-Sided and Conditioned Games are characterised by modifications of field dimensions, number of players, rules of the game, manipulations used to shape the key task constraints that performers need to satisfy in practice. Evidence has already demonstrated the importance of designing practice to enhance understanding of tactical behaviours in football, but there is a lack of information about how coaches can manipulate task constraints to support tactical learning. Objective: To investigate which task constraints have been most often manipulated in studies of SSCGs; and what impact each manipulation had on emerging tactical behaviours, technical–tactical actions, and positional relationships between players. Methods: PubMed, Web of Science, Scielo, and Academic Google databases were searched for relevant reports without time limits. The criteria adopted for inclusion were: a) studies performed with football players; b) studies that included SSCGs as an evaluation method; c) studies that investigated tactical behaviours in SSCGs; and d), articles in English and Portuguese. Results: The electronic database search included 24 articles in the review. Of these, five manipulated field dimensions, six manipulated number of players involved, five manipulated field dimensions and number of players, five used different scoring targets, two altered the number of players and scoring target, and one manipulated the number of players, field dimension, and scoring target. Conclusion: Among the task constraints analyzed in this systematic review, manipulation of number of players and playing field dimensions concomitantly occurred most frequentl

Unique and conserved MicroRNAs in wheat chromosome 5D revealed by next-generation sequencing

MicroRNAs are a class of short, non-coding, single-stranded RNAs that act as post-transcriptional regulators in gene expression. miRNA analysis of Triticum aestivum chromosome 5D was performed on 454 GS FLX Titanium sequences of flow sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. In silico and structural analyses revealed a total of 55 miRNAs; 48 and 42 miRNAs were found to be present on 5DL and 5DS respectively, of which 35 were common to both chromosome arms, while 13 miRNAs were specific to 5DL and 7 miRNAs were specific to 5DS. In total, 14 of the predicted miRNAs were identified in wheat for the first time. Representation (the copy number of each miRNA) was also found to be higher in 5DL (1,949) compared to 5DS (1,191). Targets were predicted for each miRNA, while expression analysis gave evidence of expression for 6 out of 55 miRNAs. Occurrences of the same miRNAs were also found in Brachypodium distachyon and Oryza sativa genome sequences to identify syntenic miRNA coding sequences. Based on this analysis, two other miRNAs: miR1133 and miR167 were detected in B. distachyon syntenic region of wheat 5DS. Five of the predicted miRNA coding regions (miR6220, miR5070, miR169, miR5085, miR2118) were experimentally verified to be located to the 5D chromosome and three of them : miR2118, miR169 and miR5085, were shown to be 5D specific. Furthermore miR2118 was shown to be expressed in Chinese Spring adult leaves. miRNA genes identified in this study will expand our understanding of gene regulation in bread wheat

Tiling array data analysis: a multiscale approach using wavelets

<p>Abstract</p> <p>Background</p> <p>Tiling array data is hard to interpret due to noise. The wavelet transformation is a widely used technique in signal processing for elucidating the true signal from noisy data. Consequently, we attempted to denoise representative tiling array datasets for ChIP-chip experiments using wavelets. In doing this, we used specific wavelet basis functions, <it>Coiflets</it>, since their triangular shape closely resembles the expected profiles of true ChIP-chip peaks.</p> <p>Results</p> <p>In our wavelet-transformed data, we observed that noise tends to be confined to small scales while the useful signal-of-interest spans multiple large scales. We were also able to show that wavelet coefficients due to non-specific cross-hybridization follow a log-normal distribution, and we used this fact in developing a thresholding procedure. In particular, wavelets allow one to set an unambiguous, absolute threshold, which has been hard to define in ChIP-chip experiments. One can set this threshold by requiring a similar confidence level at different length-scales of the transformed signal. We applied our algorithm to a number of representative ChIP-chip data sets, including those of Pol II and histone modifications, which have a diverse distribution of length-scales of biochemical activity, including some broad peaks.</p> <p>Conclusions</p> <p>Finally, we benchmarked our method in comparison to other approaches for scoring ChIP-chip data using spike-ins on the ENCODE Nimblegen tiling array. This comparison demonstrated excellent performance, with wavelets getting the best overall score.</p