Nemo: a computational tool for analyzing nematode locomotion

The nematode Caenorhabditis elegans responds to an impressive range of chemical, mechanical and thermal stimuli and is extensively used to investigate the molecular mechanisms that mediate chemosensation, mechanotransduction and thermosensation. The main behavioral output of these responses is manifested as alterations in animal locomotion. Monitoring and examination of such alterations requires tools to capture and quantify features of nematode movement. In this paper, we introduce Nemo (nematode movement), a computationally efficient and robust two-dimensional object tracking algorithm for automated detection and analysis of C. elegans locomotion. This algorithm enables precise measurement and feature extraction of nematode movement components. In addition, we develop a Graphical User Interface designed to facilitate processing and interpretation of movement data. While, in this study, we focus on the simple sinusoidal locomotion of C. elegans, our approach can be readily adapted to handle complicated locomotory behaviour patterns by including additional movement characteristics and parameters subject to quantification. Our software tool offers the capacity to extract, analyze and measure nematode locomotion features by processing simple video files. By allowing precise and quantitative assessment of behavioral traits, this tool will assist the genetic dissection and elucidation of the molecular mechanisms underlying specific behavioral responses.Comment: 12 pages, 2 figures. accepted by BMC Neuroscience 2007, 8:8

Distribution-based bisimulation for labelled Markov processes

In this paper we propose a (sub)distribution-based bisimulation for labelled Markov processes and compare it with earlier definitions of state and event bisimulation, which both only compare states. In contrast to those state-based bisimulations, our distribution bisimulation is weaker, but corresponds more closely to linear properties. We construct a logic and a metric to describe our distribution bisimulation and discuss linearity, continuity and compositional properties.Comment: Accepted by FORMATS 201

Study on Microcystis aeruginosa growth in incubator experiments by combination of Logistic and Monod functions

A combination of Logistic and Monod functions was proposed in this paper to study Microcystis aeruginosa growth in incubator experiments. This enables the Microcystis aeruginosa growth dynamics to be better described in incubator experiments and its parameters to be calculated more accurately. This method was justified by the data from the experiment and applied to study the effect of prometryn on Microcystis aeruginosa growth. In the experiment, a different concentrations of prometryn (0, 50, 100 and 200 μg·L−1) were added to the culture medium; the algal cell density, concentrations of orthophosphate (PO43−-P) and ammonia nitrogen (NH4+-N) were measured. The results show that Microcystis aeruginosa growth with time can be well described using the Logistic function. The maximum algae densities of Microcystis aeruginosa corresponding to the four prometryn concentrations are 11.7 × 106, 8.1 × 106, 5.6 × 106and 3.0 × 106cells·mL−1, respectively. The derived formula for the specific growth rate, growth rate and inhibition rate using Logistic function agreed reasonably well with the measured data. It was found that variations of consumed nutrients concentrations (PO43−-P and NH4+-N) can also be well described by the Logistic function. A function that describes the relationship between algal densities and consumed nutrient (PO43−-P and NH4+-N) concentrations is also derived from the Logistic function. Combination of Monod and Logistic functions can better describe relationship between specific growth rates and nutrients concentrations compared to the use of Monod function alone. In general, the half saturation coefficient, Kcfor PO43−-P (4.74 × 10−4, 1.99 × 10−3, 5.54 × 10−3and 3.87 × 10−2mg·L−1) and Kcfor NH4+-N (1.80 × 10−3, 5.84 × 10−3, 5.23 × 10−3and 1.06 × 10−2mg·L−1) in Monod function increase with increasing prometryn concentrations, which indicates that the affinity of algae growth to PO43−-P and NH4+-N decrease with increasing prometryn concentrations. In addition, relationships between nutrients concentrations and time can be derived by combining of Monod and Logistic functions, which agree well with the measured data. It is concluded that the combined application of Monod and Logistic functions provides a promising and more robust method of studying algal growth in incubator experiments

Temperature determines the diversity and structure of N2O-reducing microbial assemblages

Micro-organisms harbouring the nosZ gene convert N O to N and play a critical role in reducing global N O emissions. As higher denitrifier diversity can result in higher denitrification rates, here we aimed to understand the diversity, composition and spatial structure of N O-reducing microbial assemblages in forest soils across a large latitudinal and temperature gradient. We sequenced nosZ gene amplicons of 126 soil samples from six forests with mean annual soil temperatures (MAST) ranging from 3.7 to 25.3°C and tested predictions of the metabolic theory of ecology (MTE) and metabolic-niche theory (MNT). As predicted, α-diversity of nosZ communities increased with increasing MAST, within-site β-diversity decreased and two (pH and soil moisture) of the three niche widths examined were larger with increasing MAST. We calculated β-nearest taxon distance and Raup–Crick metric to quantify the relative influence of the assembly processes determining nosZ assemblage structure. Environmental selection was the primary process driving assemblage structure in all six forests. Homogenizing dispersal was also important at one site, which could be explained by the site's much lower variability in soil chemistry. We used canonical correspondence analysis and multiple regression on matrices to examine relationships between nosZ communities and environmental factors, and found that temperature and spatial distance were significant predictors of nosZ assemblage structure. Overall our results support both theories (MTE and MNT) tested, showing that higher temperatures are correlated with higher local diversity, wider niche breadths and lower within-site turnover rates. A plain language summary is available for this article. 2 2 2

Primary extranodal soft-tissue B-cell lymphoma with abundant immunoglobulin inclusions mimicking adult rhabdomyoma: a case report

<p>Abstract</p> <p>Introduction</p> <p>Immunoglobulin inclusions are found in B-cell neoplasms as well as in crystal-storing histiocytosis associated with B-cell lymphoproliferative disorders. At times, the deposits may be so profound as to obscure the diagnosis and may even lead to misdiagnosis. We report one case of low-grade extranodal lymphoplasmacytic lymphoma with abundant immunoglobulin inclusions and emphasize the need for immunophenotyping and molecular assay to make the right decision in diagnosis. To the best of our knowledge, this is the first report of extranodal B-cell lymphoma with abundant intracellular immunoglobulin accumulation.</p> <p>Case presentation</p> <p>A 62-year-old Asian man from China presented with a 13-year history of a right shoulder mass with recent ongoing pain. A desmoplastic fibroma located in the posterior muscles of the neck was suggested by magnetic resonance imaging, and extended local excision was performed. A biopsy, however, revealed large, isolated rhabdoid cells in a diffuse pattern with mild atypia and eosinophilic cytoplasm. Clustered lymphoid cells were interspersed among these cells. The diagnosis was initially suggested to be adult rhabdomyoma. The final diagnosis of lymphoma was made after immunohistochemical, ultrastructural and molecular studies.</p> <p>Conclusion</p> <p>We emphasize this histopathologic and immunohistochemical finding because of the potential for confusion with other tumors or disorders, such as adult rhabdomyoma or crystal-storing histiocytosis.</p

A review of physical supply and EROI of fossil fuels in China

This paper reviews China’s future fossil fuel supply from the perspectives of physical output and net energy output. Comprehensive analyses of physical output of fossil fuels suggest that China’s total oil production will likely reach its peak, at about 230 Mt/year (or 9.6 EJ/year), in 2018; its total gas production will peak at around 350 Bcm/year (or 13.6 EJ/year) in 2040, while coal production will peak at about 4400 Mt/year (or 91.9 EJ/year) around 2020 or so. In terms of the forecast production of these fuels, there are significant differences among current studies. These differences can be mainly explained by different ultimately recoverable resources assumptions, the nature of the models used, and differences in the historical production data. Due to the future constraints on fossil fuels production, a large gap is projected to grow between domestic supply and demand, which will need to be met by increasing imports. Net energy analyses show that both coal and oil and gas production show a steady declining trend of EROI (energy return on investment) due to the depletion of shallow-buried coal resources and conventional oil and gas resources, which is generally consistent with the approaching peaks of physical production of fossil fuels. The peaks of fossil fuels production, coupled with the decline in EROI ratios, are likely to challenge the sustainable development of Chinese society unless new abundant energy resources with high EROI values can be found

DNA replication stress restricts ribosomal DNA copy number

Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100–200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how “normal” copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a “normal” rDNA copy number

The NLO QCD Corrections to BcB_c Meson Production in Z0Z^0 Decays

The decay width of $Z^0$ to $B_c$ meson is evaluated at the next-to-leading order(NLO) accuracy in strong interaction. Numerical calculation shows that the NLO correction to this process is remarkable. The quantum chromodynamics(QCD)renormalization scale dependence of the results is obviously depressed, and hence the uncertainties lying in the leading order calculation are reduced.Comment: 14 pages, 7 figures; references added; expressions and typos ammende

Effect of "no added salt diet" on blood pressure control and 24 hour urinary sodium excretion in mild to moderate hypertension

<p>Abstract</p> <p>Background</p> <p>The incidence of Hypertension as a major cardiovascular threat is increasing. The best known diet for hypertensives is 'no added salt diet'.</p> <p>In this study we evaluated the effect of 'no added salt diet' on a hypertensive population with high dietary sodium intake by measuring 24 hour urinary sodium excretion.</p> <p>Methods</p> <p>In this single center randomized study 80 patients (60 cases and 20 controls) not on any drug therapy for hypertension with mild to moderate hypertension were enrolled. 24 hour holter monitoring of BP and 24 hour urinary sodium excretion were measured before and after 6 weeks of 'no added salt diet'.</p> <p>Results</p> <p>There was no statistically significant difference between age, weight, sex, Hyperlipidemia, family history of hypertension, mean systolic and diastolic BP during the day and at night and mean urinary sodium excretion in 24 hour urine of case and control groups. Seventy eight percent of all patients had moderate to high salt intake.</p> <p>After 6 week of 'no added salt diet' systolic and diastolic BP significantly decreased during the day (mean decrease: 12.1/6.8 mmhg) and at night (mean decrease: 11.1/5.9 mmhg) which is statistically significant in comparison to control group (P 0.001 and 0.01).</p> <p>Urinary sodium excretion of 24 hour urine decreased by 37.1 meq/d ± 39,67 mg/dl in case group which is statistically significant in comparison to control group (p: 0.001).</p> <p>Only 36% of the patients, after no added salt diet, reached the pretreatment goal of 24 hour urinary sodium excretion of below 100 meq/dl (P:0.001).</p> <p>Conclusion</p> <p>Despite modest effect on dietary sodium restriction, no added salt diet significantly decreased systolic and diastolic BP and so it should be advised to every hypertensive patient.</p> <p>Trial Registration</p> <p>Clinicaltrial.govnumber NCT00491881</p