345 research outputs found

    Characterization of the errors of the FMM in particle simulations

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    The Fast Multipole Method (FMM) offers an acceleration for pairwise interaction calculation, known as NN-body problems, from O(N2)\mathcal{O}(N^2) to O(N)\mathcal{O}(N) with NN particles. This has brought dramatic increase in the capability of particle simulations in many application areas, such as electrostatics, particle formulations of fluid mechanics, and others. Although the literature on the subject provides theoretical error bounds for the FMM approximation, there are not many reports of the measured errors in a suite of computational experiments. We have performed such an experimental investigation, and summarized the results of about 1000 calculations using the FMM algorithm, to characterize the accuracy of the method in relation with the different parameters available to the user. In addition to the more standard diagnostic of the maximum error, we supply illustrations of the spatial distribution of the errors, which offers visual evidence of all the contributing factors to the overall approximation accuracy: multipole expansion, local expansion, hierarchical spatial decomposition (interaction lists, local domain, far domain). This presentation is a contribution to any researcher wishing to incorporate the FMM acceleration to their application code, as it aids in understanding where accuracy is gained or compromised.Comment: 34 pages, 38 image

    Temperature dependent resistivity of spin-split subbands in GaAs 2D hole system

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    We calculate the temperature dependent resistivity in spin-split subbands induced by the inversion asymmetry of the confining potential in GaAs 2D hole systems. By considering both temperature dependent multisubband screening of impurity disorder and hole-hole scattering we find that the strength of the metallic behavior depends on the symmetry of the confining potential (i.e., spin-splitting) over a large range of hole density. At low density above the metal-insulator transition we find that effective disorder reduces the enhancement of the metallic behavior induced by spin-splitting. Our theory is in good qualitative agreement with existing experiments

    The Co-occurrence of child and intimate partner maltreatment in the family: characteristics of the violent perpetrators

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    This study considers the characteristics associated with mothers and fathers who maltreat their child and each other in comparison to parents who only maltreat their child. One hundred and sixty-two parents who had allegations of child maltreatment made against them were considered. The sample consisted of 43 fathers (Paternal Family—PF) and 23 mothers (Maternal Family—MF) who perpetrated both partner and child maltreatment, together with 23 fathers (Paternal Child—PC) and 26 mothers (Maternal Child—MC) who perpetrated child maltreatment only. In addition, 2 fathers (Paternal Victim—PV) and 23 mothers (Maternal Victim—MV) were victims of intimate partner maltreatment and perpetrators of child maltreatment and 7 fathers (Paternal Non-abusive Carer—PNC) and 15 mothers (Maternal Non-abusive Carer—MNC) did not maltreat the child but lived with an individual who did. Within their family unit, 40.7% of parents perpetrated both intimate partner and child maltreatment. However, fathers were significantly more likely to maltreat both their partner and child than mothers and mothers were significantly more likely to be victims of intimate partner violence than fathers. PF fathers conducted the highest amount of physical and/or sexual child maltreatment while MC and MV mothers perpetrated the highest amount of child neglect. Few significant differences between mothers were found. PF fathers had significantly more factors associated with development of a criminogenic lifestyle than PC fathers. Marked sex differences were demonstrated with PF fathers demonstrating significantly more antisocial characteristics, less mental health problems and fewer feelings of isolation than MF mothers. MC mothers had significantly more childhood abuse, mental health problems, parenting risk factors and were significantly more likely to be biologically related to the child than PC fathers. This study suggests that violent families should be assessed and treated in a holistic manner, considering the effects of partner violence upon all family members, rather than exclusively intervening with the violent man

    Molecular and cellular mechanisms underlying the evolution of form and function in the amniote jaw.

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    The amniote jaw complex is a remarkable amalgamation of derivatives from distinct embryonic cell lineages. During development, the cells in these lineages experience concerted movements, migrations, and signaling interactions that take them from their initial origins to their final destinations and imbue their derivatives with aspects of form including their axial orientation, anatomical identity, size, and shape. Perturbations along the way can produce defects and disease, but also generate the variation necessary for jaw evolution and adaptation. We focus on molecular and cellular mechanisms that regulate form in the amniote jaw complex, and that enable structural and functional integration. Special emphasis is placed on the role of cranial neural crest mesenchyme (NCM) during the species-specific patterning of bone, cartilage, tendon, muscle, and other jaw tissues. We also address the effects of biomechanical forces during jaw development and discuss ways in which certain molecular and cellular responses add adaptive and evolutionary plasticity to jaw morphology. Overall, we highlight how variation in molecular and cellular programs can promote the phenomenal diversity and functional morphology achieved during amniote jaw evolution or lead to the range of jaw defects and disease that affect the human condition

    Heterologous Expression of Alteromonas macleodii and Thiocapsa roseopersicina [NiFe] Hydrogenases in Synechococcus elongatus

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    Oxygen-tolerant [NiFe] hydrogenases may be used in future photobiological hydrogen production systems once the enzymes can be heterologously expressed in host organisms of interest. To achieve heterologous expression of [NiFe] hydrogenases in cyanobacteria, the two hydrogenase structural genes from Alteromonas macleodii Deep ecotype (AltDE), hynS and hynL, along with the surrounding genes in the gene operon of HynSL were cloned in a vector with an IPTG-inducible promoter and introduced into Synechococcus elongatus PCC7942. The hydrogenase protein was expressed at the correct size upon induction with IPTG. The heterologously-expressed HynSL hydrogenase was active when tested by in vitro H2 evolution assay, indicating the correct assembly of the catalytic center in the cyanobacterial host. Using a similar expression system, the hydrogenase structural genes from Thiocapsa roseopersicina (hynSL) and the entire set of known accessory genes were transferred to S. elongatus. A protein of the correct size was expressed but had no activity. However, when the 11 accessory genes from AltDE were co-expressed with hynSL, the T. roseopersicina hydrogenase was found to be active by in vitro assay. This is the first report of active, heterologously-expressed [NiFe] hydrogenases in cyanobacteria

    The genetic architecture of membranous nephropathy and its potential to improve non-invasive diagnosis

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    Membranous Nephropathy (MN) is a rare autoimmune cause of kidney failure. Here we report a genome-wide association study (GWAS) for primary MN in 3,782 cases and 9,038 controls of East Asian and European ancestries. We discover two previously unreported loci, NFKB1 (rs230540, OR = 1.25, P = 3.4 × 10−12) and IRF4 (rs9405192, OR = 1.29, P = 1.4 × 10−14), fine-map the PLA2R1 locus (rs17831251, OR = 2.25, P = 4.7 × 10−103) and report ancestry-specific effects of three classical HLA alleles: DRB1*1501 in East Asians (OR = 3.81, P = 2.0 × 10−49), DQA1*0501 in Europeans (OR = 2.88, P = 5.7 × 10−93), and DRB1*0301 in both ethnicities (OR = 3.50, P = 9.2 × 10−23 and OR = 3.39, P = 5.2 × 10−82, respectively). GWAS loci explain 32% of disease risk in East Asians and 25% in Europeans, and correctly re-classify 20–37% of the cases in validation cohorts that are antibody-negative by the serum anti-PLA2R ELISA diagnostic test. Our findings highlight an unusual genetic architecture of MN, with four loci and their interactions accounting for nearly one-third of the disease risk

    Differences in topological progression profile among neurodegenerative diseases from imaging data

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    The spatial distribution of atrophy in neurodegenerative diseases suggests that brain connectivity mediates disease propagation. Different descriptors of the connectivity graph potentially relate to different underlying mechanisms of propagation. Previous approaches for evaluating the influence of connectivity on neurodegeneration consider each descriptor in isolation and match predictions against late-stage atrophy patterns. We introduce the notion of a topological profile - a characteristic combination of topological descriptors that best describes the propagation of pathology in a particular disease. By drawing on recent advances in disease progression modeling, we estimate topological profiles from the full course of pathology accumulation, at both cohort and individual levels. Experimental results comparing topological profiles for Alzheimer's disease, multiple sclerosis and normal ageing show that topological profiles explain the observed data better than single descriptors. Within each condition, most individual profiles cluster around the cohort-level profile, and individuals whose profiles align more closely with other cohort-level profiles show features of that cohort. The cohort-level profiles suggest new insights into the biological mechanisms underlying pathology propagation in each disease

    Listeriolysin O Is Strongly Immunogenic Independently of Its Cytotoxic Activity

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    The presentation of microbial protein antigens by Major Histocompatibility Complex (MHC) molecules is essential for the development of acquired immunity to infections. However, most biochemical studies of antigen processing and presentation deal with a few relatively inert non-microbial model antigens. The bacterial pore-forming toxin listeriolysin O (LLO) is paradoxical in that it is cytotoxic at nanomolar concentrations as well as being the source of dominant CD4 and CD8 T cell epitopes following infection with Listeria monocytogenes. Here, we examined the relationship of LLO toxicity to its antigenicity and immunogenicity. LLO offered to antigen presenting cells (APC) as a soluble protein, was presented to CD4 T cells at picomolar to femtomolar concentrations- doses 3000–7000-fold lower than free peptide. This presentation required a dose of LLO below the cytotoxic level. Mutations of two key tryptophan residues reduced LLO toxicity by 10–100-fold but had no effect on its presentation to CD4 T cells. Thus there was a clear dissociation between the cytotoxic properties of LLO and its very high antigenicity. Presentation of LLO to CD8 T cells was not as robust as that seen in CD4 T cells, but still occurred in the nanomolar range. APC rapidly bound and internalized LLO, then disrupted endosomal compartments within 4 hours of treatment, allowing endosomal contents to access the cytosol. LLO was also immunogenic after in vivo administration into mice. Our results demonstrate the strength of LLO as an immunogen to both CD4 and CD8 T cells
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