A dislocation dynamics study of the strength of stacking fault tetrahedra. Part II: interactions with mixed and edge dislocations

In this paper we present the sequel to Part I and present a comprehensive dislocation dynamics study of the strength of stacking fault tetrahedra to mixed and edge dislocation glides in fcc Cu

A "kilonova" associated with short-duration gamma-ray burst 130603B

Short-duration gamma-ray bursts (SGRBs) are intense flashes of cosmic gamma-rays, lasting less than ~2 s, whose origin is one of the great unsolved questions of astrophysics today. While the favoured hypothesis for their production, a relativistic jet created by the merger of two compact stellar objects (specifically, two neutron stars, NS-NS, or a neutron star and a black hole, NS-BH), is supported by indirect evidence such as their host galaxy properties, unambiguous confirmation of the model is still lacking. Mergers of this kind are also expected to create significant quantities of neutron-rich radioactive species, whose decay should result in a faint transient in the days following the burst, a so-called "kilonova". Indeed, it is speculated that this mechanism may be the predominant source of stable r-process elements in the Universe. Recent calculations suggest much of the kilonova energy should appear in the near-infrared (nIR) due to the high optical opacity created by these heavy r-process elements. Here we report strong evidence for such an event accompanying SGRB 130603B. If this simplest interpretation of the data is correct, it provides (i) support for the compact object merger hypothesis of SGRBs, (ii) confirmation that such mergers are likely sites of significant r-process production and (iii) quite possibly an alternative, un-beamed electromagnetic signature of the most promising sources for direct detection of gravitational waves.Comment: preprint of paper appearing in Nature (3 Aug 2013

Quantifying Inactive Lithium in Lithium Metal Batteries

Inactive lithium (Li) formation is the immediate cause of capacity loss and catastrophic failure of Li metal batteries. However, the chemical component and the atomic level structure of inactive Li have rarely been studied due to the lack of effective diagnosis tools to accurately differentiate and quantify Li+ in solid electrolyte interphase (SEI) components and the electrically isolated unreacted metallic Li0, which together comprise the inactive Li. Here, by introducing a new analytical method, Titration Gas Chromatography (TGC), we can accurately quantify the contribution from metallic Li0 to the total amount of inactive Li. We uncover that the Li0, rather than the electrochemically formed SEI, dominates the inactive Li and capacity loss. Using cryogenic electron microscopies to further study the microstructure and nanostructure of inactive Li, we find that the Li0 is surrounded by insulating SEI, losing the electronic conductive pathway to the bulk electrode. Coupling the measurements of the Li0 global content to observations of its local atomic structure, we reveal the formation mechanism of inactive Li in different types of electrolytes, and identify the true underlying cause of low Coulombic efficiency in Li metal deposition and stripping. We ultimately propose strategies to enable the highly efficient Li deposition and stripping to enable Li metal anode for next generation high energy batteries

Flexible graph matching and graph edit distance using answer set programming

The graph isomorphism, subgraph isomorphism, and graph edit distance problems are combinatorial problems with many applications. Heuristic exact and approximate algorithms for each of these problems have been developed for different kinds of graphs: directed, undirected, labeled, etc. However, additional work is often needed to adapt such algorithms to different classes of graphs, for example to accommodate both labels and property annotations on nodes and edges. In this paper, we propose an approach based on answer set programming. We show how each of these problems can be defined for a general class of property graphs with directed edges, and labels and key-value properties annotating both nodes and edges. We evaluate this approach on a variety of synthetic and realistic graphs, demonstrating that it is feasible as a rapid prototyping approach.Comment: To appear, PADL 202

Mechanical activation of vinculin binding to talin locks talin in an unfolded conformation

The force-dependent interaction between talin and vinculin plays a crucial role in the initiation and growth of focal adhesions. Here we use magnetic tweezers to characterise the mechano-sensitive compact N-terminal region of the talin rod, and show that the three helical bundles R1-R3 in this region unfold in three distinct steps consistent with the domains unfolding independently. Mechanical stretching of talin R1-R3 enhances its binding to vinculin and vinculin binding inhibits talin refolding after force is released. Mutations that stabilize R3 identify it as the initial mechano-sensing domain in talin, unfolding at ~5 pN, suggesting that 5 pN is the force threshold for vinculin binding and adhesion progression

Conformal Quivers and Melting Molecules

Quiver quantum mechanics describes the low energy dynamics of a system of wrapped D-branes. It captures several aspects of single and multicentered BPS black hole geometries in four-dimensional $\mathcal{N} = 2$ supergravity such as the presence of bound states and an exponential growth of microstates. The Coulomb branch of an Abelian three node quiver is obtained by integrating out the massive strings connecting the D-particles. It allows for a scaling regime corresponding to a deep AdS$_2$ throat on the gravity side. In this scaling regime, the Coulomb branch is shown to be an $SL(2,\mathbb{R})$ invariant multi-particle superconformal quantum mechanics. Finally, we integrate out the strings at finite temperature---rather than in their ground state---and show how the Coulomb branch `melts' into the Higgs branch at high enough temperatures. For scaling solutions the melting occurs for arbitrarily small temperatures, whereas bound states can be metastable and thus long lived. Throughout the paper, we discuss how far the analogy between the quiver model and the gravity picture, particularly within the AdS$_2$ throat, can be taken.Comment: 49 pages, 16 figure

Validating child vaccination status in a demographic surveillance system using data from a clinical cohort study: evidence from rural South Africa

<p><b>Background:</b> Childhood vaccination coverage can be estimated from a range of sources. This study aims to validate vaccination data from a longitudinal population-based demographic surveillance system (DSS) against data from a clinical cohort study.</p> <p><b>Methods:</b> The sample includes 821 children in the Vertical Transmission cohort Study (VTS), who were born between December 2001 and April 2005, and were matched to the Africa Centre DSS, in northern KwaZulu-Natal. Vaccination information in the surveillance was collected retrospectively, using standardized questionnaires during bi-annual household visits, when the child was 12 to 23 months of age. DSS vaccination information was based on extraction from a vaccination card or, if the card was not available, on maternal recall. In the VTS, vaccination data was collected at scheduled maternal and child clinic visits when a study nurse administered child vaccinations. We estimated the sensitivity of the surveillance in detecting vaccinations conducted as part of the VTS during these clinic visits.</p> <p><b>Results:</b> Vaccination data in matched children in the DSS was based on the vaccination card in about two-thirds of the cases and on maternal recall in about one-third. The sensitivity of the vaccination variables in the surveillance was high for all vaccines based on either information from a South African Road-to-Health (RTH) card (0.94-0.97) or maternal recall (0.94-0.98). Addition of maternal recall to the RTH card information had little effect on the sensitivity of the surveillance variable (0.95-0.97). The estimates of sensitivity did not vary significantly, when we stratified the analyses by maternal antenatal HIV status. Addition of maternal recall of vaccination status of the child to the RTH card information significantly increased the proportion of children known to be vaccinated across all vaccines in the DSS.</p> <p><b>Conclusion:</b> Maternal recall performs well in identifying vaccinated children aged 12-23 months (both in HIV-infected and HIV-uninfected mothers), with sensitivity similar to information extracted from vaccination cards. Information based on both maternal recall and vaccination cards should be used if the aim is to use surveillance data to identify children who received a vaccination.</p&gt

Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-depleted Murine Embryonic Stem Cells

Embryonic stem cells (ESC) have the potential to self-renew indefinitely and to differentiate into any of the three germ layers. The molecular mechanisms for self-renewal, maintenance of pluripotency and lineage specification are poorly understood, but recent results point to a key role for epigenetic mechanisms. In this study, we focus on quantifying the impact of histone 3 acetylation (H3K9,14ac) on gene expression in murine embryonic stem cells. We analyze genome-wide histone acetylation patterns and gene expression profiles measured over the first five days of cell differentiation triggered by silencing Nanog, a key transcription factor in ESC regulation. We explore the temporal and spatial dynamics of histone acetylation data and its correlation with gene expression using supervised and unsupervised statistical models. On a genome-wide scale, changes in acetylation are significantly correlated to changes in mRNA expression and, surprisingly, this coherence increases over time. We quantify the predictive power of histone acetylation for gene expression changes in a balanced cross-validation procedure. In an in-depth study we focus on genes central to the regulatory network of Mouse ESC, including those identified in a recent genome-wide RNAi screen and in the PluriNet, a computationally derived stem cell signature. We find that compared to the rest of the genome, ESC-specific genes show significantly more acetylation signal and a much stronger decrease in acetylation over time, which is often not reflected in an concordant expression change. These results shed light on the complexity of the relationship between histone acetylation and gene expression and are a step forward to dissect the multilayer regulatory mechanisms that determine stem cell fate.Comment: accepted at PLoS Computational Biolog

Lateral Gene Expression in Drosophila Early Embryos Is Supported by Grainyhead-Mediated Activation and Tiers of Dorsally-Localized Repression

The general consensus in the field is that limiting amounts of the transcription factor Dorsal establish dorsal boundaries of genes expressed along the dorsal-ventral (DV) axis of early Drosophila embryos, while repressors establish ventral boundaries. Yet recent studies have provided evidence that repressors act to specify the dorsal boundary of intermediate neuroblasts defective (ind), a gene expressed in a stripe along the DV axis in lateral regions of the embryo. Here we show that a short 12 base pair sequence (“the A-box”) present twice within the ind CRM is both necessary and sufficient to support transcriptional repression in dorsal regions of embryos. To identify binding factors, we conducted affinity chromatography using the A-box element and found a number of DNA-binding proteins and chromatin-associated factors using mass spectroscopy. Only Grainyhead (Grh), a CP2 transcription factor with a unique DNA-binding domain, was found to bind the A-box sequence. Our results suggest that Grh acts as an activator to support expression of ind, which was surprising as we identified this factor using an element that mediates dorsally-localized repression. Grh and Dorsal both contribute to ind transcriptional activation. However, another recent study found that the repressor Capicua (Cic) also binds to the A-box sequence. While Cic was not identified through our A-box affinity chromatography, utilization of the same site, the A-box, by both factors Grh (activator) and Cic (repressor) may also support a “switch-like” response that helps to sharpen the ind dorsal boundary. Furthermore, our results also demonstrate that TGF-β signaling acts to refine ind CRM expression in an A-box independent manner in dorsal-most regions, suggesting that tiers of repression act in dorsal regions of the embryo