Moderate Intensity Exercise Training Improves Cardiorespiratory Fitness in Women

Among women, there is an increased prevalence of sedentary lifestyle and less participation in physical activity at levels recommended by the Surgeon General. As a result, women have been identified as a target group in public health initiatives to increase physical activity. The health-related benefits of habitual, moderate intensity physical activity are well documented in the epidemiological literature, but less is known about the effect of such physical activity on cardiorespiratory fitness. Our hypothesis was that moderate and vigorous exercise training regimens of similar estimated energy expenditure would result in similar changes in cardiorespiratory fitness. Eighteen sedentary premenopausal women with the following baseline characteristics [x ± SE]: maximal oxygen consumption (VO2max) = 29.5 ± 1.5ml ● kg-1 ● min-1; age=33 ± 1 years; height=162.6 ± 0.9 cm; mass = 62.7 ± 2.3 kg, were randomly assigned to either vigorous (HI, 80% VO2max, n=10) or moderate intensity (MOD, 40% VO2max, n=8) cycle ergometer training groups. Exercise training was conducted 3-4 (3.37 ± 0.05) days/week for 12 weeks in a supervised and progressive manner, with estimated exercise energy expenditure equated across both training groups. VO2max and time to exhaustion increased significantly in both groups (p\u3c0.05), with no difference between groups. Both groups had lower (p\u3c0.05) posttraining submaximal heart rates (HR), respiratory exchange ratios (RER), and ratings of perceived exertion (RPE) during graded exercise testing, with no significant differences between the groups in posttraining values. Women participating in moderate intensity exercise training as recommended in basic public health guidelines demonstrate an increase in cardiorespiratory fitness similar to that elicited by vigorous training

Arithmetical properties of Multiple Ramanujan sums

In the present paper, we introduce a multiple Ramanujan sum for arithmetic functions, which gives a multivariable extension of the generalized Ramanujan sum studied by D. R. Anderson and T. M. Apostol. We then find fundamental arithmetic properties of the multiple Ramanujan sum and study several types of Dirichlet series involving the multiple Ramanujan sum. As an application, we evaluate higher-dimensional determinants of higher-dimensional matrices, the entries of which are given by values of the multiple Ramanujan sum.Comment: 19 page

Recruitment, augmentation and apoptosis of rat osteoclasts in 1,25-(OH)2D3 response to short-term treatment with 1,25-dihydroxyvitamin D3in vivo

Background Although much is known about the regulation of osteoclast (OC) formation and activity, little is known about OC senescence. In particular, the fate of of OC seen after 1,25-(OH)2D3 administration in vivo is unclear. There is evidence that the normal fate of OC is to undergo apoptosis (programmed cell death). We have investigated the effect of short-term application of high dose 1,25-dihydroxyvitamin D3 (1,25-(OH)2D3) on OC apoptosis in an experimental rat model. Methods OC recruitment, augmentation and apoptosis was visualised and quantitated by staining histochemically for tartrate resistant acid phosphatase (TRAP), double staining for TRAP/ED1 or TRAP/DAPI, in situ DNA fragmentation end labelling and histomorphometric analysis. Results Short-term treatment with high-dose 1,25-(OH)2D3 increased the recruitment of OC precursors in the bone marrow resulting in a short-lived increase in OC numbers. This was rapidly followed by an increase in the number of apoptotic OC and their subsequent removal. The response of OC to 1,25-(OH)2D3 treatment was dose and site dependent; higher doses producing stronger, more rapid responses and the response in the tibiae being consistently stronger and more rapid than in the vertebrae. Conclusions This study demonstrates that (1) after recruitment, OC are removed from the resorption site by apoptosis (2) the combined use of TRAP and ED1 can be used to identify OC and their precursors in vivo (3) double staining for TRAP and DAPI or in situ DNA fragmentation end labelling can be used to identify apoptotic OC in vivo

Spin Waves and Quantum Criticality in the Frustrated XY Pyrochlore Antiferromagnet Er2Ti2O7

We report detailed measurements of the low temperature magnetic phase diagram of Er$_2$Ti$_2$O$_7$. Heat capacity and time-of-flight neutron scattering studies of single crystals, subject to magnetic fields applied along the crystallographic [110] direction, reveal unconventional low energy states. Er$^{3+}$ magnetic ions reside on a pyrochlore lattice in Er$_2$Ti$_2$O$_7$, where local XY anisotropy and antiferromagnetic interactions give rise to a unique frustrated system. In zero field, the ground state exhibits coexisting short and long range order, accompanied by soft collective spin excitations previously believed to be absent. The application of finite magnetic fields tunes the ground state continuously through a landscape of non-collinear phases, divided by a zero temperature phase transition at $\mu_0 H_c \sim$ 1.5 T. The characteristic energy scale for spin fluctuations is seen to vanish at the critical point, as expected for a second order quantum phase transition driven by quantum fluctuations.Comment: 5 pages, 4 figures, submitted for publicatio

Developing a decision support tool for assessing land use change and BMPs in ungauged watersheds based on decision rules provided by SWAT simulation

Decision making on water resources management at ungauged, especially large-scale watersheds relies on hydrological modeling. Physically based distributed hydrological models require complicated setup, calibration, and validation processes, which may delay their acceptance among decision makers. This study presents an approach to develop a simple decision support tool (DST) for decision makers and economists to evaluate multiyear impacts of land use change and best management practices (BMPs) on water quantity and quality for ungauged watersheds. The example DST developed in the present study was based on statistical equations derived from Soil and Water Assessment Tool (SWAT) simulations and applied to a small experimental watershed in northwest New Brunswick. The DST was subsequently tested against field measurements and SWAT simulations for a larger watershed. Results from DST could reproduce both field data and model simulations of annual stream discharge and sediment and nutrient loadings. The relative error of mean annual discharge and sediment, nitrate–nitrogen, and soluble-phosphorus loadings were −6, −52, 27, and −16&thinsp;%, respectively, for long-term simulation. Compared with SWAT, DST has fewer input requirements and can be applied to multiple watersheds without additional calibration. Also, scenario analyses with DST can be directly conducted for different combinations of land use and BMPs without complex model setup procedures. The approach in developing DST can be applied to other regions of the world because of its flexible structure.</p

A Unifying Model of Genome Evolution Under Parsimony

We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph $G$, a finite set of AVGs describe all parsimonious interpretations of $G$, and this set can be explored with a few sampling moves.Comment: 52 pages, 24 figure

Precise detection of rearrangement breakpoints in mammalian chromosomes

<p>Abstract</p> <p>Background</p> <p>Genomes undergo large structural changes that alter their organisation. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. We developed a method to precisely delimit rearrangement breakpoints on a genome by comparison with the genome of a related species. Contrary to current methods which search for synteny blocks and simply return what remains in the genome as breakpoints, we propose to go further and to investigate the breakpoints themselves in order to refine them.</p> <p>Results</p> <p>Given some reliable and non overlapping synteny blocks, the core of the method consists in refining the regions that are not contained in them. By aligning each breakpoint sequence against its specific orthologous sequences in the other species, we can look for weak similarities inside the breakpoint, thus extending the synteny blocks and narrowing the breakpoints. The identification of the narrowed breakpoints relies on a segmentation algorithm and is statistically assessed. Since this method requires as input synteny blocks with some properties which, though they appear natural, are not verified by current methods for detecting such blocks, we further give a formal definition and provide an algorithm to compute them.</p> <p>The whole method is applied to delimit breakpoints on the human genome when compared to the mouse and dog genomes. Among the 355 human-mouse and 240 human-dog breakpoints, 168 and 146 respectively span less than 50 Kb. We compared the resulting breakpoints with some publicly available ones and show that we achieve a better resolution. Furthermore, we suggest that breakpoints are rarely reduced to a point, and instead consist in often large regions that can be distinguished from the sequences around in terms of segmental duplications, similarity with related species, and transposable elements.</p> <p>Conclusion</p> <p>Our method leads to smaller breakpoints than already published ones and allows for a better description of their internal structure. In the majority of cases, our refined regions of breakpoint exhibit specific biological properties (no similarity, presence of segmental duplications and of transposable elements). We hope that this new result may provide some insight into the mechanism and evolutionary properties of chromosomal rearrangements.</p

Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C(chromosomeconformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r=0.9, P<2.2×1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016) and also have a significant positive correlation withsomeremote functional DNA elements like enhancers and promoters (Enhancer: hESC: r=0.997, P=2.3×10−4; IMR90: r=0.934, P=2×10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes

Bidirectional best hit r-window gene clusters

<p>Abstract</p> <p>Background</p> <p><it>Conserved gene clusters </it>are groups of genes that are located close to one another in the genomes of several species. They tend to code for proteins that have a functional interaction. The identification of conserved gene clusters is an important step towards understanding genome evolution and predicting gene function.</p> <p>Results</p> <p>In this paper, we propose a novel pairwise gene cluster model that combines the notion of bidirectional best hits with the <it>r</it>-window model introduced in 2003 by Durand and Sankoff. The bidirectional best hit (BBH) constraint removes the need to specify the minimum number of shared genes in the <it>r</it>-window model and improves the relevance of the results. We design a subquadratic time algorithm to compute the set of BBH <it>r</it>-window gene clusters efficiently.</p> <p>Conclusion</p> <p>We apply our cluster model to the comparative analysis of <it>E. coli </it>K-12 and <it>B. subtilis </it>and perform an extensive comparison between our new model and the gene teams model developed by Bergeron <it>et al</it>. As compared to the gene teams model, our new cluster model has a slightly lower recall but a higher precision at all levels of recall when the results were ranked using statistical tests. An analysis of the most significant BBH <it>r</it>-window gene cluster show that they correspond to known operons.</p

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression