Atomistic Simulations of Ge on Amorphous Silica Substrates

High-quality Ge substrates have numerous applications, including high-efficiency III-V multijunction solar cells and photodetectors. But the high cost of single-crystalline Ge makes the use of Ge-on-Si virtual substrates more practical for device fabrication. However, the lattice mismatch between Ge and Si leads to a highly strained Ge layer when grown directly on the Si lattice. The high mismatch strain unavoidably leads to defects, primarily dislocations, that degrade the Ge film quality. Several approaches for mitigating these defects have been proposed, including selective epitaxial growth (SEG), in which one employs an amorphous layer (most often SiO2) as a mask to reduce the epitaxial contact between the Ge and Si lattices to lower the mismatch strain. SEG has been demonstrated to successfully produce high-quality Ge films on Si, although defects are not fully eliminated. Further improvements will require quantitative understanding of the underlying atomic-scale mechanisms. In this work, we present a computational framework to atomistically model the components of the SEG system (Si/SiO2/Ge). The model is validated by comparing predictions to experimental observations and ab initio calculations of various properties related to crystalline Si and Ge and amorphous SiO2, as well as combinations of these materials. The framework is then applied to study in detail the deposition of Ge on amorphous SiO2. It is shown that the simulations are able to access experimentally meaningful deposition conditions and reproduce several quantities related to the island size distribution. We then extend our simulation framework for deposition to include coarse projective integration (CPI). CPI is a multiscale modeling technique well-suited for situations, like atomic deposition, in which a system exhibits fast, stochastic processes, superposed onto slowly-evolving dynamics. In particular, we demonstrate an approach for generating atomistic configurations from limited knowledge of an island size distribution, which represents one of the key challenges in applying CPI to atomistic deposition. The results generated here should be easily adaptable to other deposition systems

A Combined Perceptual, Physico-Chemical, and Imaging Approach to ‘Odour-Distances’ Suggests a Categorizing Function of the Drosophila Antennal Lobe

How do physico-chemical stimulus features, perception, and physiology relate? Given the multi-layered and parallel architecture of brains, the question specifically is where physiological activity patterns correspond to stimulus features and/or perception. Perceived distances between six odour pairs are defined behaviourally from four independent odour recognition tasks. We find that, in register with the physico-chemical distances of these odours, perceived distances for 3-octanol and n-amylacetate are consistently smallest in all four tasks, while the other five odour pairs are about equally distinct. Optical imaging in the antennal lobe, using a calcium sensor transgenically expressed in only first-order sensory or only second-order olfactory projection neurons, reveals that 3-octanol and n-amylacetate are distinctly represented in sensory neurons, but appear merged in projection neurons. These results may suggest that within-antennal lobe processing funnels sensory signals into behaviourally meaningful categories, in register with the physico-chemical relatedness of the odours

Group B Streptococcus GAPDH Is Released upon Cell Lysis, Associates with Bacterial Surface, and Induces Apoptosis in Murine Macrophages

Glyceraldehyde 3-phosphate dehydrogenases (GAPDH) are cytoplasmic glycolytic enzymes that, despite lacking identifiable secretion signals, have been detected at the surface of several prokaryotic and eukaryotic organisms where they exhibit non-glycolytic functions including adhesion to host components. Group B Streptococcus (GBS) is a human commensal bacterium that has the capacity to cause life-threatening meningitis and septicemia in newborns. Electron microscopy and fluorescence-activated cell sorter (FACS) analysis demonstrated the surface localization of GAPDH in GBS. By addressing the question of GAPDH export to the cell surface of GBS strain NEM316 and isogenic mutant derivatives of our collection, we found that impaired GAPDH presence in the surface and supernatant of GBS was associated with a lower level of bacterial lysis. We also found that following GBS lysis, GAPDH can associate to the surface of many living bacteria. Finally, we provide evidence for a novel function of the secreted GAPDH as an inducer of apoptosis of murine macrophages

Novel features of ARS selection in budding yeast Lachancea kluyveri

<p>Abstract</p> <p>Background</p> <p>The characterization of DNA replication origins in yeast has shed much light on the mechanisms of initiation of DNA replication. However, very little is known about the evolution of origins or the evolution of mechanisms through which origins are recognized by the initiation machinery. This lack of understanding is largely due to the vast evolutionary distances between model organisms in which origins have been examined.</p> <p>Results</p> <p>In this study we have isolated and characterized autonomously replicating sequences (ARSs) in <it>Lachancea kluyveri </it>- a pre-whole genome duplication (WGD) budding yeast. Through a combination of experimental work and rigorous computational analysis, we show that <it>L. kluyveri </it>ARSs require a sequence that is similar but much longer than the ARS Consensus Sequence well defined in <it>Saccharomyces cerevisiae</it>. Moreover, compared with <it>S. cerevisiae </it>and <it>K. lactis</it>, the replication licensing machinery in <it>L. kluyveri </it>seems more tolerant to variations in the ARS sequence composition. It is able to initiate replication from almost all <it>S. cerevisiae </it>ARSs tested and most <it>Kluyveromyces lactis </it>ARSs. In contrast, only about half of the <it>L. kluyveri </it>ARSs function in <it>S. cerevisiae </it>and less than 10% function in <it>K. lactis</it>.</p> <p>Conclusions</p> <p>Our findings demonstrate a replication initiation system with novel features and underscore the functional diversity within the budding yeasts. Furthermore, we have developed new approaches for analyzing biologically functional DNA sequences with ill-defined motifs.</p

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Genome-wide association meta-analysis identifies five novel loci for age-related hearing impairment

Previous research has shown that genes play a substantial role in determining a person's susceptibility to age-related hearing impairment. The existing studies on this subject have different results, which may be caused by difficulties in determining the phenotype or the limited number of participants involved. Here, we have gathered the largest sample to date (discovery n = 9,675; replication n = 10,963; validation n = 356,141), and examined phenotypes that represented low/mid and high frequency hearing loss on the pure tone audiogram. We identified 7 loci that were either replicated and/or validated, of which 5 loci are novel in hearing. Especially the ILDR1 gene is a high profile candidate, as it contains our top SNP, is a known hearing loss gene, has been linked to age-related hearing impairment before, and in addition is preferentially expressed within hair cells of the inner ear. By verifying all previously published SNPs, we can present a paper that combines all new and existing findings to date, giving a complete overview of the genetic architecture of age-related hearing impairment. This is of importance as age-related hearing impairment is highly prevalent in our ageing society and represents a large socio-economic burden

Modeling dust and soluble iron deposition to the South Atlantic Ocean

The global chemical transport model GEOS-Chem, implemented with a dust-iron dissolution scheme, was used to analyze the magnitude and spatial distribution of mineral dust and soluble-iron (sol-Fe) deposition to the South Atlantic Ocean (SAO). The comparison of model results with remotely sensed data shows that GEOS-Chem can capture dust source regions in Patagonia and characterize the temporal variability of dust outflow. For a year-long model simulation, 22 Tg of mineral dust and 4 Gg of sol-Fe were deposited to the surface waters of the entire SAO region, with roughly 30% of this dust and sol-Fe predicted to be deposited to possible high nitrate low chlorophyll oceanic regions. Model-predicted dissolved iron fraction of mineral dust over the SAO was small, on average only accounting for 0.57% of total iron. Simulations suggest that the primary reason for such a small fraction of sol-Fe is the low ambient concentrations of acidic trace gases available for mixing with dust plumes. Overall, the amount of acid added to the deliquesced aerosol solution was not enough to overcome the alkalinity buffer of Patagonian dust and initiate considerable acid dissolution of mineral-iron. Sensitivity studies show that the amount of sol-Fe deposited to the SAO was largely controlled by the initial amount of sol-Fe at the source region, with limited contribution from the spatial variability of Patagonian-desert topsoil mineralogy and natural sources of acidic trace gases. Simulations suggest that Patagonian dust should have a minor effect on biological productivity in the SAO.Fil: Johnson, Matthew S.. North Carolina Sate University; Estados UnidosFil: Meskhidze, Nicholas. North Carolina Sate University; Estados UnidosFil: Solmon, Fabien. French National Center for Scientific Research; FranciaFil: Gassó, Santiago. University of Maryland; Estados UnidosFil: Chuang, Patrick Y.. California State University; Estados UnidosFil: Gaiero, Diego Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Ciencias de la Tierra. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones en Ciencias de la Tierra; ArgentinaFil: Yantosca, Robert M.. Harvard University; Estados UnidosFil: Wu, Shiliang. Michigan Technological University; Estados UnidosFil: Wang, Yuxuan. Tsinghua University Beijing; ChinaFil: Carouge, Claire. Harvard University; Estados Unido