Lattice QCD at the physical point: Simulation and analysis details

We give details of our precise determination of the light quark masses m_{ud}=(m_u+m_d)/2 and m_s in 2+1 flavor QCD, with simulated pion masses down to 120 MeV, at five lattice spacings, and in large volumes. The details concern the action and algorithm employed, the HMC force with HEX smeared clover fermions, the choice of the scale setting procedure and of the input masses. After an overview of the simulation parameters, extensive checks of algorithmic stability, autocorrelation and (practical) ergodicity are reported. To corroborate the good scaling properties of our action, explicit tests of the scaling of hadron masses in N_f=3 QCD are carried out. Details of how we control finite volume effects through dedicated finite volume scaling runs are reported. To check consistency with SU(2) Chiral Perturbation Theory the behavior of M_\pi^2/m_{ud} and F_\pi as a function of m_{ud} is investigated. Details of how we use the RI/MOM procedure with a separate continuum limit of the running of the scalar density R_S(\mu,\mu') are given. This procedure is shown to reproduce the known value of r_0m_s in quenched QCD. Input from dispersion theory is used to split our value of m_{ud} into separate values of m_u and m_d. Finally, our procedure to quantify both systematic and statistical uncertainties is discussed.Comment: 45 page

Expression of Distal-less, dachshund, and optomotor blind in Neanthes arenaceodentata (Annelida, Nereididae) does not support homology of appendage-forming mechanisms across the Bilateria

The similarity in the genetic regulation of arthropod and vertebrate appendage formation has been interpreted as the product of a plesiomorphic gene network that was primitively involved in bilaterian appendage development and co-opted to build appendages (in modern phyla) that are not historically related as structures. Data from lophotrochozoans are needed to clarify the pervasiveness of plesiomorphic appendage forming mechanisms. We assayed the expression of three arthropod and vertebrate limb gene orthologs, Distal-less (Dll), dachshund (dac), and optomotor blind (omb), in direct-developing juveniles of the polychaete Neanthes arenaceodentata. Parapodial Dll expression marks premorphogenetic notopodia and neuropodia, becoming restricted to the bases of notopodial cirri and to ventral portions of neuropodia. In outgrowing cephalic appendages, Dll activity is primarily restricted to proximal domains. Dll expression is also prominent in the brain. dac expression occurs in the brain, nerve cord ganglia, a pair of pharyngeal ganglia, presumed interneurons linking a pair of segmental nerves, and in newly differentiating mesoderm. Domains of omb expression include the brain, nerve cord ganglia, one pair of anterior cirri, presumed precursors of dorsal musculature, and the same pharyngeal ganglia and presumed interneurons that express dac. Contrary to their roles in outgrowing arthropod and vertebrate appendages, Dll, dac, and omb lack comparable expression in Neanthes appendages, implying independent evolution of annelid appendage development. We infer that parapodia and arthropodia are not structurally or mechanistically homologous (but their primordia might be), that Dll’s ancestral bilaterian function was in sensory and central nervous system differentiation, and that locomotory appendages possibly evolved from sensory outgrowths

Detection of infectious disease outbreaks in twenty-two fragile states, 2000-2010: a systematic review.

Fragile states are home to a sixth of the world's population, and their populations are particularly vulnerable to infectious disease outbreaks. Timely surveillance and control are essential to minimise the impact of these outbreaks, but little evidence is published about the effectiveness of existing surveillance systems. We did a systematic review of the circumstances (mode) of detection of outbreaks occurring in 22 fragile states in the decade 2000-2010 (i.e. all states consistently meeting fragility criteria during the timeframe of the review), as well as time lags from onset to detection of these outbreaks, and from detection to further events in their timeline. The aim of this review was to enhance the evidence base for implementing infectious disease surveillance in these complex, resource-constrained settings, and to assess the relative importance of different routes whereby outbreak detection occurs.We identified 61 reports concerning 38 outbreaks. Twenty of these were detected by existing surveillance systems, but 10 detections occurred following formal notifications by participating health facilities rather than data analysis. A further 15 outbreaks were detected by informal notifications, including rumours.There were long delays from onset to detection (median 29 days) and from detection to further events (investigation, confirmation, declaration, control). Existing surveillance systems yielded the shortest detection delays when linked to reduced barriers to health care and frequent analysis and reporting of incidence data.Epidemic surveillance and control appear to be insufficiently timely in fragile states, and need to be strengthened. Greater reliance on formal and informal notifications is warranted. Outbreak reports should be more standardised and enable monitoring of surveillance systems' effectiveness

Nutritional and Metabolic Requirements for the Infection of HeLa Cells by Salmonella enterica Serovar Typhimurium

Salmonella is the causative agent of a spectrum of human and animal diseases ranging from gastroenteritis to typhoid fever. It is a food - and water - borne pathogen and infects via ingestion followed by invasion of intestinal epithelial cells and phagocytic cells. In this study we employed a mutational approach to define the nutrients and metabolic pathways required by Salmonella enterica serovar Typhimurium during infection of a human epithelial cell line (HeLa). We deleted the key glycolytic genes, pfkA and pfkB to show that S. Typhimurium utilizes glycolysis for replication within HeLa cells; however, glycolysis was not absolutely essential for intracellular replication. Using S. Typhimurium strains deleted for genes encoding components of the phosphotransferase system and glucose transport, we show that glucose is a major substrate required for the intracellular replication of S. Typhimurium in HeLa cells. We also deleted genes encoding enzymes involved in the utilization of gluconeogenic substrates and the glyoxylate shunt and show that neither of these pathways were required for intracellular replication of S. Typhimurium within HeLa cells

Extensive telomere erosion is consistent with localised clonal expansions in Barrett’s metaplasia

Barrett’s oesophagus is a premalignant metaplastic condition that predisposes patients to the development of oesophageal adenocarcinoma. However, only a minor fraction of Barrett’s oesophagus patients progress to adenocarcinoma and it is thus essential to determine bio-molecular markers that can predict the progression of this condition. Telomere dysfunction is considered to drive clonal evolution in several tumour types and telomere length analysis provides clinically relevant prognostic and predictive information. The aim of this work was to use high-resolution telomere analysis to examine telomere dynamics in Barrett’s oesophagus. Telomere length analysis of XpYp, 17p, 11q and 9p, chromosome arms that contain key cancer related genes that are known to be subjected to copy number changes in Barrett’s metaplasia, revealed similar profiles at each chromosome end, indicating that no one specific telomere is likely to suffer preferential telomere erosion. Analysis of patient matched tissues (233 samples from 32 patients) sampled from normal squamous oesophagus, Z-line, and 2 cm intervals within Barrett’s metaplasia, plus oesophago-gastric junction, gastric body and antrum, revealed extensive telomere erosion in Barrett’s metaplasia to within the length ranges at which telomere fusion is detected in other tumour types. Telomere erosion was not uniform, with distinct zones displaying more extensive erosion and more homogenous telomere length profiles. These data are consistent with an extensive proliferative history of cells within Barrett’s metaplasia and are indicative of localised clonal growth. The extent of telomere erosion highlights the potential of telomere dysfunction to drive genome instability and clonal evolution in Barrett’s metaplasia

A laboratory study of anisotropic geomaterials incorporating recent micromechanical understanding

This paper presents an experimental investigation revisiting the anisotropic stress–strain–strength behaviour of geomaterials in drained monotonic shear using hollow cylinder apparatus. The test programme has been designed to cover the effect of material anisotropy, preshearing, material density and intermediate principal stress on the behaviour of Leighton Buzzard sand. Experiments have also been performed on glass beads to understand the effect of particle shape. This paper explains phenomenological observations based on recently acquired understanding in micromechanics, with attention focused on strength anisotropy and deformation non-coaxiality, i.e. non-coincidence between the principal stress direction and the principal strain rate direction. The test results demonstrate that the effects of initial anisotropy produced during sample preparation are significant. The stress–strain–strength behaviour of the specimen shows strong dependence on the principal stress direction. Preloading history, material density and particle shape are also found to be influential. In particular, it was found that non-coaxiality is more significant in presheared specimens. The observations on the strength anisotropy and deformation non-coaxiality were explained based on the stress–force–fabric relationship. It was observed that intermediate principal stress parameter b(b = (σ2 − σ3)/(σ1 − σ3)) has a significant effect on the non-coaxiality of sand. The lower the b-value, the higher the degree of non-coaxiality is induced. Visual inspection of shear band formed at the end of HCA testing has also been presented. The inclinations of the shear bands at different loading directions can be predicted well by taking account of the relative direction of the mobilized planes to the bedding plane

The Transcriptional Repressor TupA in Aspergillus niger Is Involved in Controlling Gene Expression Related to Cell Wall Biosynthesis, Development, and Nitrogen Source Availability.

The Tup1-Cyc8 (Ssn6) complex is a well characterized and conserved general transcriptional repressor complex in eukaryotic cells. Here, we report the identification of the Tup1 (TupA) homolog in the filamentous fungus Aspergillus niger in a genetic screen for mutants with a constitutive expression of the agsA gene. The agsA gene encodes a putative alpha-glucan synthase, which is induced in response to cell wall stress in A. niger. Apart from the constitutive expression of agsA, the selected mutant was also found to produce an unknown pigment at high temperatures. Complementation analysis with a genomic library showed that the tupA gene could complement the phenotypes of the mutant. Screening of a collection of 240 mutants with constitutive expression of agsA identified sixteen additional pigment-secreting mutants, which were all mutated in the tupA gene. The phenotypes of the tupA mutants were very similar to the phenotypes of a tupA deletion strain. Further analysis of the tupA-17 mutant and the DeltatupA mutant revealed that TupA is also required for normal growth and morphogenesis. The production of the pigment at 37 degrees C is nitrogen source-dependent and repressed by ammonium. Genome-wide expression analysis of the tupA mutant during exponential growth revealed derepression of a large group of diverse genes, including genes related to development and cell wall biosynthesis, and also protease-encoding genes that are normally repressed by ammonium. Comparison of the transcriptome of up-regulated genes in the tupA mutant showed limited overlap with the transcriptome of caspofungin-induced cell wall stress-related genes, suggesting that TupA is not a general suppressor of cell wall stress-induced genes. We propose that TupA is an important repressor of genes related to development and nitrogen metabolism

Results of isolated posterolateral corner reconstruction

BACKGROUND: Isolated posterolateral corner (PLC) tears are relatively rare events. Various surgical techniques to treat posterolateral knee instability have been described; because surgical results are linked to cruciate reconstructions it has been difficult to date to define whether one surgical procedure has better prognosis than another. The goal of this study is to determine the clinical outcome of PLC reconstruction following fibular-based technique. MATERIALS AND METHODS: We retrospectively evaluated a case series of patients who received isolated PLC reconstruction between March 2005 and January 2007. Ten patients were surgically treated for isolated injuries and were available for follow-up; average patient age was 27.4 years (range 16-47 years). All patients were treated following the fibular-based technique: double femoral tunnel was performed in six patients, while in the remaining four patients, the reconstruction of the PLC was performed with a single femoral tunnel. Six patients had semitendinosus allograft and four had semitendinosus autograft. All patients had the same evaluation and the same rehabilitation protocol. RESULTS: Mean follow-up was 27.5 months (range 18-40 months). Mean range of motion (ROM) was 143.5 degrees for flexion (range 135-150 degrees) and 0.5 degrees for extension (range 0-3 degrees). Three patients showed 1+ on varus stress test, while on Dial test another three patients showed 10 degrees reduction of external rotation compared with contralateral knee. The average Lysholm score was 94 points (range 83-100), and the mean International Knee Documentation Committee (IKDC) subjective result was 88.48 (range 74-96.5). Based on Lysholm score, the results were excellent in eight knees and good in two knees. On IKDC evaluation, two patients were grade A and eight were grade B. No significant difference in clinical results was observed between single and double femoral tunnel. CONCLUSION: Fibular-based technique showed good results in terms of clinical outcome, restoring varus and rotation stability of knees in treatment of chronic isolated PLC injury

Synbiotic approach restores intestinal homeostasis and prolongs survival in leukaemia mice with cachexia

Cancer cachexia is a multifactorial syndrome that includes muscle wasting and inflammation. As gut microbes influence host immunity and metabolism, we investigated the role of the gut microbiota in the therapeutic management of cancer and associated cachexia. A community-wide analysis of the caecal microbiome in two mouse models of cancer cachexia (acute leukaemia or subcutaneous transplantation of colon cancer cells) identified common microbial signatures, including decreased Lactobacillus spp. and increased Enterobacteriaceae and Parabacteroides goldsteinii/ASF 519. Building on this information, we administered a synbiotic containing inulin-type fructans and live Lactobacillus reuteri 100-23 to leukaemic mice. This treatment restored the Lactobacillus population and reduced the Enterobacteriaceae levels. It also reduced hepatic cancer cell proliferation, muscle wasting and morbidity, and prolonged survival. Administration of the synbiotic was associated with restoration of the expression of antimicrobial proteins controlling intestinal barrier function and gut immunity markers, but did not impact the portal metabolomics imprinting of energy demand. In summary, this study provided evidence that the development of cancer outside the gut can impact intestinal homeostasis and the gut microbial ecosystem and that a synbiotic intervention, by targeting some alterations of the gut microbiota, confers benefits to the host, prolonging survival and reducing cancer proliferation and cachexia

"Flogging dead horses": evaluating when have clinical trials achieved sufficiency and stability? A case study in cardiac rehabilitation

<p>Abstract</p> <p>Background</p> <p>Most systematic reviews conclude that another clinical trial is needed. Measures of sufficiency and stability may indicate whether this is true.</p> <p>Objectives: To show how evidence accumulated on centre-based versus home-based cardiac rehabilitation, including estimates of sufficiency and stability</p> <p>Methods</p> <p>Systematic reviews of clinical trials of home versus centre-based cardiac rehabilitation were used to develop a cumulative meta-analysis over time. We calculated the standardised mean difference (SMD) in effect, confidence intervals and indicators of sufficiency and stability. Sufficiency refers to whether the meta-analytic database adequately demonstrates that an intervention works - is statistically superior to another. It does this by assessing the number of studies with null results that would be required to make the meta-analytic effect non-statistically significant. Stability refers to whether the direction and size of the effect is stable as new studies are added to the meta-analysis.</p> <p>Results</p> <p>The standardised mean effect difference reduced over fourteen comparisons from a non-significant difference favouring home-based cardiac rehabilitation to a very small difference favouring hospital (SMD -0.10, 95% CI -0.32 to 0.13). This difference did not reach the sufficiency threshold (failsafe ratio 0.039 < 1) but did achieve the criteria for stability (cumulative slope 0.003 < 0.005).</p> <p>Conclusions</p> <p>The evidence points to a relatively small effect difference which was stable but not sufficient in terms of the suggested thresholds. Sufficiency should arguably be based on substantive significance and decided by patients. Research on patient preferences should be the priority. Sufficiency and stability measures are useful tools that need to be tested in further case studies.</p