A well-separated pairs decomposition algorithm for k-d trees implemented on multi-core architectures

Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI.Variations of k-d trees represent a fundamental data structure used in Computational Geometry with numerous applications in science. For example particle track tting in the software of the LHC experiments, and in simulations of N-body systems in the study of dynamics of interacting galaxies, particle beam physics, and molecular dynamics in biochemistry. The many-body tree methods devised by Barnes and Hutt in the 1980s and the Fast Multipole Method introduced in 1987 by Greengard and Rokhlin use variants of k-d trees to reduce the computation time upper bounds to O(n log n) and even O(n) from O(n2). We present an algorithm that uses the principle of well-separated pairs decomposition to always produce compressed trees in O(n log n) work. We present and evaluate parallel implementations for the algorithm that can take advantage of multi-core architectures.The Science and Technology Facilities Council, UK

Static Friction between Elastic Solids due to Random Asperities

Several workers have established that the Larkin domains for two three dimensional nonmetallic elastic solids in contact with each other at a disordered interface are enormously large. This implies that there should be negligible static friction per unit area in the macroscopic solid limit. The present work argues that the fluctuations in the heights of the random asperities at the interface that occur in the Greenwood-Williamson model can account for static friction.Comment: Contains some improvements in the treatment of the subjec

Control of intestinal stem cell function and proliferation by mitochondrial pyruvate metabolism.

Most differentiated cells convert glucose to pyruvate in the cytosol through glycolysis, followed by pyruvate oxidation in the mitochondria. These processes are linked by the mitochondrial pyruvate carrier (MPC), which is required for efficient mitochondrial pyruvate uptake. In contrast, proliferative cells, including many cancer and stem cells, perform glycolysis robustly but limit fractional mitochondrial pyruvate oxidation. We sought to understand the role this transition from glycolysis to pyruvate oxidation plays in stem cell maintenance and differentiation. Loss of the MPC in Lgr5-EGFP-positive stem cells, or treatment of intestinal organoids with an MPC inhibitor, increases proliferation and expands the stem cell compartment. Similarly, genetic deletion of the MPC in Drosophila intestinal stem cells also increases proliferation, whereas MPC overexpression suppresses stem cell proliferation. These data demonstrate that limiting mitochondrial pyruvate metabolism is necessary and sufficient to maintain the proliferation of intestinal stem cells

The antimicrobial polymer PHMB enters cells and selectively condenses bacterial chromosomes

To combat infection and antimicrobial resistance, it is helpful to elucidate drug mechanism(s) of action. Here we examined how the widely used antimicrobial polyhexamethylene biguanide (PHMB) kills bacteria selectively over host cells. Contrary to the accepted model of microbial membrane disruption by PHMB, we observed cell entry into a range of bacterial species, and treated bacteria displayed cell division arrest and chromosome condensation, suggesting DNA binding as an alternative antimicrobial mechanism. A DNA-level mechanism was confirmed by observations that PHMB formed nanoparticles when mixed with isolated bacterial chromosomal DNA and its effects on growth were suppressed by pairwise combination with the DNA binding ligand Hoechst 33258. PHMB also entered mammalian cells, but was trapped within endosomes and excluded from nuclei. Therefore, PHMB displays differential access to bacterial and mammalian cellular DNA and selectively binds and condenses bacterial chromosomes. Because acquired resistance to PHMB has not been reported, selective chromosome condensation provides an unanticipated paradigm for antimicrobial action that may not succumb to resistance

Extrinsic factors regulate partial agonist efficacy of strychnine-sensitive glycine receptors

BACKGROUND: Strychnine-sensitive glycine receptors in many adult forebrain regions consist of alpha(2 )+ beta heteromeric channels. This subunit composition is distinct from the alpha(1 )+ beta channels found throughout the adult spinal cord. Unfortunately, the pharmacology of forebrain alpha(2)beta receptors are poorly defined compared to 'neonatal' alpha(2 )homomeric channels or 'spinal' alpha(1)beta heteromers. In addition, the pharmacologic properties of native alpha(2)beta glycine receptors have been generally distinct from receptors produced by heterologous expression. To identify subtype-specific pharmacologic tools for the forebrain alpha(2)beta receptors, it is important to identify a heterologous expression system that closely resembles these native glycine-gated chloride channels. RESULTS: While exploring pharmacological properties of alpha(2)beta glycine receptors compared to alpha(2)-homomers, we found that distinct heterologous expression systems appeared to differentially influence partial agonist pharmacology. The β-amino acid taurine possessed 30–50% efficacy for alpha(2)-containing receptor isoforms when expressed in HEK 293 cells. However, taurine efficacy was dramatically reduced in L-cell fibroblasts. Similar results were obtained for β-alanine. The efficacy of these partial agonists was also strongly reduced by the beta subunit. There were no significant differences in apparent strychnine affinity values calculated from concentration-response data between expression systems or subunit combinations. Nor did relative levels of expression correlate with partial agonist efficacy when compared within or between several different expression systems. Finally, disruption of the tubulin cytoskeleton reduced the efficacy of partial agonists in a subunit-dependent, but system-independent, fashion. CONCLUSIONS: Our results suggest that different heterologous expression systems can dramatically influence the agonist pharmacology of strychnine-sensitive glycine receptors. In the systems examine here, these effects are independent of both absolute expression level and any system-related alterations in the agonist binding site. We conclude that complex interactions between receptor composition and extrinsic factors may play a significant role in determining strychnine-sensitive glycine receptor partial agonist pharmacology

Skin microbiota differs between Black and White patients with cutaneous T-cell lymphoma

Cutaneous T-cell lymphoma (CTCL) disproportionately affects Black patients, who experience higher rates of sepsis and mortality. This study examines differences in the lesional and non-lesional skin microbiomes of Black and White CTCL patients using 16S rRNA and tuf gene sequencing. Results reveal distinct microbial compositions, with increased Staphylococcus aureus abundance in Black patients. Our team contributed by developing RStudio-based code to visualize and analyze microbiome sequencing data, facilitating clearer interpretation of microbial differences. These findings suggest microbial factors may contribute to racial disparities in CTCL outcomes, highlighting the need for targeted therapeutic interventions and further microbiome research

Simultaneous free-volume modeling of the self-diffusion coefficient and dynamic viscosity at high pressure

International audienceA free-volume model of the dynamic viscosity and the self-diffusion coefficients was discussed. The temperature-pressure variations of the dynamic viscosity and the self-diffusion coefficients of small molecules were predicted. The compounds, carbon tetrachloride, cyclohexane, benzene, chlorotrifluoromethane, tetramethylsilane and methylcyclohexane were used for the investigation. The relation between microstructure, free volume and different complex thermophysical properties were emphasized by the model

Ventilatory muscle strength, diaphragm thickness and pulmonary function in world-class powerlifters.

Resistance training activates the ventilatory muscles providing a stimulus similar to ventilatory muscle training. We examined the effects of elite powerlifting training upon ventilatory muscle strength, pulmonary function and diaphragm thickness in world-class powerlifters (POWER) and a control group (CON) with no history of endurance or resistance training, matched for age, height and body mass

An examination of the association between seeing smoking in films and tobacco use in young adults in the west of Scotland: cross-sectional study

The objective is to examine the association between the amount of smoking seen in films and current smoking in young adults living in the west of Scotland in the UK. Cross-sectional analyses (using multivariable logistic regression) of data collected at age 19 (2002–04) from a longitudinal cohort originally surveyed at age 11 (1994–95) were conducted. The main outcome measure is smoking at age 19. No association was found between the number of occurrences of smoking estimated to have been seen in films (film smoking exposure) and current (or ever) smoking in young adults. This lack of association was unaffected by adjustment for predictors of smoking, including education, risk-taking orientation and smoking among peers. There was no association between film smoking exposure and smoking behaviour for any covariate-defined subgroup. Associations have been found between film smoking exposure and smoking initiation in younger adolescents in the United States. In this study, conducted in Scotland, no similar association was seen, suggesting that there may be age or cultural limitations on the effects of film smoking exposure on smoking. The lack of association could be due to methodological issues or greater sophistication of older adolescents and young adults in interpreting media images or the greater ubiquity of real-life smoking instances in Scotland. If the latter, film smoking exposure could become a more important risk factor for smoking uptake and maintenants in older adolescents following the recent ban on smoking in public places in Scotland