Residence Time Statistics for Normal and Fractional Diffusion in a Force Field

We investigate statistics of occupation times for an over-damped Brownian particle in an external force field. A backward Fokker-Planck equation introduced by Majumdar and Comtet describing the distribution of occupation times is solved. The solution gives a general relation between occupation time statistics and probability currents which are found from solutions of the corresponding problem of first passage time. This general relationship between occupation times and first passage times, is valid for normal Markovian diffusion and for non-Markovian sub-diffusion, the latter modeled using the fractional Fokker-Planck equation. For binding potential fields we find in the long time limit ergodic behavior for normal diffusion, while for the fractional framework weak ergodicity breaking is found, in agreement with previous results of Bel and Barkai on the continuous time random walk on a lattice. For non-binding potential rich physical behaviors are obtained, and classification of occupation time statistics is made possible according to whether or not the underlying random walk is recurrent and the averaged first return time to the origin is finite. Our work establishes a link between fractional calculus and ergodicity breaking.Comment: 12 page

Abundance of unknots in various models of polymer loops

A veritable zoo of different knots is seen in the ensemble of looped polymer chains, whether created computationally or observed in vitro. At short loop lengths, the spectrum of knots is dominated by the trivial knot (unknot). The fractional abundance of this topological state in the ensemble of all conformations of the loop of $N$ segments follows a decaying exponential form, $\sim \exp (-N/N_0)$, where $N_0$ marks the crossover from a mostly unknotted (ie topologically simple) to a mostly knotted (ie topologically complex) ensemble. In the present work we use computational simulation to look closer into the variation of $N_0$ for a variety of polymer models. Among models examined, $N_0$ is smallest (about 240) for the model with all segments of the same length, it is somewhat larger (305) for Gaussian distributed segments, and can be very large (up to many thousands) when the segment length distribution has a fat power law tail.Comment: 13 pages, 6 color figure

The effects of social determinants of health on acquired immune deficiency syndrome in a low-income population of Brazil: a retrospective cohort study of 28.3 million individuals.

BACKGROUND: Social determinants of health (SDH) include factors such as income, education, and race, that could significantly affect the human immunodeficiency virus and acquired immunodeficiency syndrome (HIV/AIDS). Studies on the effects of SDH on HIV/AIDS are limited, and do not yet provide a systematic understanding of how the various SDH act on important indicators of HIV/AIDS progression. We aimed to evaluate the effects of SDH on AIDS morbidity and mortality. METHODS: A retrospective cohort of 28.3 million individuals was evaluated over a 9-year period (from 2007 to 2015). Multivariable Poisson regression, with a hierarchical approach, was used to estimate the effects of SDH-at the individual and familial level-on AIDS incidence, mortality, and case-fatality rates. FINDINGS: A total of 28,318,532 individuals, representing the low-income Brazilian population, were assessed, who had a mean age of 36.18 (SD: 16.96) years, 52.69% (14,920,049) were female, 57.52% (15,360,569) were pardos, 34.13% (9,113,222) were white/Asian, 7.77% (2,075,977) were black, and 0.58% (154,146) were indigenous. Specific socioeconomic, household, and geographic factors were significantly associated with AIDS-related outcomes. Less wealth was strongly associated with a higher AIDS incidence (rate ratios-RR: 1.55; 95% confidence interval-CI: 1.43-1.68) and mortality (RR: 1.99; 95% CI: 1.70-2.34). Lower educational attainment was also greatly associated with higher AIDS incidence (RR: 1.46; 95% CI: 1.26-1.68), mortality (RR: 2.76; 95% CI: 1.99-3.82) and case-fatality rates (RR: 2.30; 95% CI: 1.31-4.01). Being black was associated with a higher AIDS incidence (RR: 1.53; 95% CI: 1.45-1.61), mortality (RR: 1.69; 95% CI: 1.57-1.83) and case-fatality rates (RR: 1.16; 95% CI: 1.03-1.32). Overall, also considering the other SDH, individuals experiencing greater levels of socioeconomic deprivation were, by far, more likely to acquire AIDS, and to die from it. INTERPRETATION: In the population studied, SDH related to poverty and social vulnerability are strongly associated with a higher burden of HIV/AIDS, most notably less wealth, illiteracy, and being black. In the absence of relevant social protection policies, the current worldwide increase in poverty and inequalities-due to the consequences of the COVID-19 pandemic, and the effects of war in the Ukraine-could reverse progress made in the fight against HIV/AIDS in low- and middle-income countries (LMIC). FUNDING: National Institute of Allergy and Infectious Diseases (NAIDS), National Institutes of Health (NIH), US Grant Number: 1R01AI152938

Cross-Species Analyses Identify the BNIP-2 and Cdc42GAP Homology (BCH) Domain as a Distinct Functional Subclass of the CRAL_TRIO/Sec14 Superfamily

The CRAL_TRIO protein domain, which is unique to the Sec14 protein superfamily, binds to a diverse set of small lipophilic ligands. Similar domains are found in a range of different proteins including neurofibromatosis type-1, a Ras GTPase-activating Protein (RasGAP) and Rho guanine nucleotide exchange factors (RhoGEFs). Proteins containing this structural protein domain exhibit a low sequence similarity and ligand specificity while maintaining an overall characteristic three-dimensional structure. We have previously demonstrated that the BNIP-2 and Cdc42GAP Homology (BCH) protein domain, which shares a low sequence homology with the CRAL_TRIO domain, can serve as a regulatory scaffold that binds to Rho, RhoGEFs and RhoGAPs to control various cell signalling processes. In this work, we investigate 175 BCH domain-containing proteins from a wide range of different organisms. A phylogenetic analysis with ∼100 CRAL_TRIO and similar domains from eight representative species indicates a clear distinction of BCH-containing proteins as a novel subclass within the CRAL_TRIO/Sec14 superfamily. BCH-containing proteins contain a hallmark sequence motif R(R/K)h(R/K)(R/K)NL(R/K)xhhhhHPs (‘h’ is large and hydrophobic residue and ‘s’ is small and weekly polar residue) and can be further subdivided into three unique subtypes associated with BNIP-2-N, macro- and RhoGAP-type protein domains. A previously unknown group of genes encoding ‘BCH-only’ domains is also identified in plants and arthropod species. Based on an analysis of their gene-structure and their protein domain context we hypothesize that BCH domain-containing genes evolved through gene duplication, intron insertions and domain swapping events. Furthermore, we explore the point of divergence between BCH and CRAL-TRIO proteins in relation to their ability to bind small GTPases, GAPs and GEFs and lipid ligands. Our study suggests a need for a more extensive analysis of previously uncharacterized BCH, ‘BCH-like’ and CRAL_TRIO-containing proteins and their significance in regulating signaling events involving small GTPases

Epitaxial Catalyst-Free Growth of InN Nanorods onc-Plane Sapphire

We report observation of catalyst-free hydride vapor phase epitaxy growth of InN nanorods. Characterization of the nanorods with transmission electron microscopy, and X-ray diffraction show that the nanorods are stoichiometric 2H–InN single crystals growing in the [0001] orientation. The InN rods are uniform, showing very little variation in both diameter and length. Surprisingly, the rods show clear epitaxial relations with thec-plane sapphire substrate, despite about 29% of lattice mismatch. Comparing catalyst-free with Ni-catalyzed growth, the only difference observed is in the density of nucleation sites, suggesting that Ni does not work like the typical vapor–liquid–solid catalyst, but rather functions as a nucleation promoter by catalyzing the decomposition of ammonia. No conclusive photoluminescence was observed from single nanorods, while integrating over a large area showed weak wide emissions centered at 0.78 and at 1.9 eV

Distinct phosphorylation requirements regulate cortactin activation by TirEPEC and its binding to N-WASP

<p>Abstract</p> <p>Background</p> <p>Cortactin activates the actin-related 2/3 (Arp2/3) complex promoting actin polymerization to remodel cell architecture in multiple processes (e.g. cell migration, membrane trafficking, invadopodia formation etc.). Moreover, it was called the Achilles' heel of the actin cytoskeleton because many pathogens hijack signals that converge on this oncogenic scaffolding protein. Cortactin is able to modulate N-WASP activation <it>in vitro </it>in a phosphorylation-dependent fashion. Thus Erk-phosphorylated cortactin is efficient in activating N-WASP through its SH3 domain, while Src-phosphorylated cortactin is not. This could represent a switch on/off mechanism controlling the coordinated action of both nucleator promoting factors (NPFs). Pedestal formation by enteropathogenic <it>Escherichia coli </it>(EPEC) requires N-WASP activation. N-WASP is recruited by the cell adapter Nck which binds a major tyrosine-phosphorylated site of a bacterial injected effector, Tir (translocated intimin receptor). Tir-Nck-N-WASP axis defines the current major pathway to actin polymerization on pedestals. In addition, it was recently reported that EPEC induces tyrosine phosphorylation of cortactin.</p> <p>Results</p> <p>Here we demonstrate that cortactin phosphorylation is absent on N-WASP deficient cells, but is recovered by re-expression of N-WASP. We used purified recombinant cortactin and Tir proteins to demonstrate a direct interaction of both that promoted Arp2/3 complex-mediated actin polymerization <it>in vitro</it>, independently of cortactin phosphorylation.</p> <p>Conclusion</p> <p>We propose that cortactin binds Tir through its N-terminal part in a tyrosine and serine phosphorylation independent manner while SH3 domain binding and activation of N-WASP is regulated by tyrosine and serine mediated phosphorylation of cortactin. Therefore cortactin could act on Tir-Nck-N-WASP pathway and control a possible cycling activity of N-WASP underlying pedestal formation.</p

Separation of Recombination and SOS Response in Escherichia coli RecA Suggests LexA Interaction Sites

RecA plays a key role in homologous recombination, the induction of the DNA damage response through LexA cleavage and the activity of error-prone polymerase in Escherichia coli. RecA interacts with multiple partners to achieve this pleiotropic role, but the structural location and sequence determinants involved in these multiple interactions remain mostly unknown. Here, in a first application to prokaryotes, Evolutionary Trace (ET) analysis identifies clusters of evolutionarily important surface amino acids involved in RecA functions. Some of these clusters match the known ATP binding, DNA binding, and RecA-RecA homo-dimerization sites, but others are novel. Mutation analysis at these sites disrupted either recombination or LexA cleavage. This highlights distinct functional sites specific for recombination and DNA damage response induction. Finally, our analysis reveals a composite site for LexA binding and cleavage, which is formed only on the active RecA filament. These new sites can provide new drug targets to modulate one or more RecA functions, with the potential to address the problem of evolution of antibiotic resistance at its root

The Sandia Fracture Challenge: blind round robin predictions of ductile tearing

Existing and emerging methods in computational mechanics are rarely validated against problems with an unknown outcome. For this reason, Sandia National Laboratories, in partnership with US National Science Foundation and Naval Surface Warfare Center Carderock Division, launched a computational challenge in mid-summer, 2012. Researchers and engineers were invited to predict crack initiation and propagation in a simple but novel geometry fabricated from a common off-the-shelf commercial engineering alloy. The goal of this international Sandia Fracture Challenge was to benchmark the capabilities for the prediction of deformation and damage evolution associated with ductile tearing in structural metals, including physics models, computational methods, and numerical implementations currently available in the computational fracture community. Thirteen teams participated, reporting blind predictions for the outcome of the Challenge. The simulations and experiments were performed independently and kept confidential. The methods for fracture prediction taken by the thirteen teams ranged from very simple engineering calculations to complicated multiscale simulations. The wide variation in modeling results showed a striking lack of consistency across research groups in addressing problems of ductile fracture. While some methods were more successful than others, it is clear that the problem of ductile fracture prediction continues to be challenging. Specific areas of deficiency have been identified through this effort. Also, the effort has underscored the need for additional blind prediction-based assessments