Role of hydrogen in volatile behaviour of defects in SiO2-based electronic devices

Charge capture and emission by point defects in gate oxides of metal–oxide–semiconductor field-effect transistors (MOSFETs) strongly affect reliability and performance of electronic devices. Recent advances in experimental techniques used for probing defect properties have led to new insights into their characteristics. In particular, these experimental data show a repeated dis- and reappearance (the so-called volatility) of the defect-related signals. We use multiscale modelling to explain the charge capture and emission as well as defect volatility in amorphous SiO2 gate dielectrics. We first briefly discuss the recent experimental results and use a multiphonon charge capture model to describe the charge-trapping behaviour of defects in silicon-based MOSFETs. We then link this model to ab initio calculations that investigate the three most promising defect candidates. Statistical distributions of defect characteristics obtained from ab initio calculations in amorphous SiO2 are compared with the experimentally measured statistical properties of charge traps. This allows us to suggest an atomistic mechanism to explain the experimentally observed volatile behaviour of defects. We conclude that the hydroxyl-E′ centre is a promising candidate to explain all the observed features, including defect volatility

Mass production of Bacillus subtilis and Trichoderma viride for the control of Phyllosticta citricarpa (Teleomorph: Guignardia citricarpa).

The work was aimed at studying the production of cells and metabolites of Bacilius subtilis (ACB-69) and of Trichoderma viride conidia (ACB-14) on different substrates, since they can potentially control Phyllosticta citricarpa. Our results showed that the medium consisting of cotton meal added of hydrolized protein provided the highest yield of B. subtiiis cells (2.44 x IO9 cells/mL), after the culture had been incubated for three days. This liquid substrate also provided conditions for the bacterium to produce thermostable metabolites, in sufficient amounts to inhibit the plant pathogen's micelial growth. The production of B. subtilis under the solid fermentation system performed better on the brewers rice substrate; the number of bactéria; cells decreased as the substrate concentration increased. In general, the liquid medium yielded a higher amount of B. subtilis than the solid medium. With regard to the large scale production of T. viride, it was verified that the substrates tested had a low spore production; the best substrate among those tested (com cob + hydrolized protein) only yielded 2.17 x IO6 conidia/mL. O objetivo foi estudar a produção de células e de metabólitos de Bacillus subtilis (ACB-69) e de conídios de Trichoderma viride (ACB-14) em diferentes substratos, pois apresentam potencial para o controle de Phyllosticta citricarpa. O meio constituído de farelo de algodão acrescido de proteína hidrolisada foi o que proporcionou maior produção de células de B. subtilis (2,4 x 109 células/mL), após três dias de incubação da cultura. Esse substrato líquido também propiciou condições para que a bactéria produzisse metabólitos termoestáveis e, em quantidades suficientes para inibir o crescimento micelial do fitopatógeno. A produção de B. subtilis pelo sistema de fermentação sólida foi melhor no substrato quirera de arroz sendo que o número de células da bactéria diminuiu à medida que aumentou a concentração do substrato. De um modo geral, o meio líquido foi superior ao sólido para a produção de B. subtilis. Com relação à produção de T. viride, verificou-se que os substratos testados apresentaram baixa produção de esporos, sendo que o melhor substrato testado (sabugo de milho + proteína hidrolisada) produziu apenas 2,2 x 106 conídios/mL

Validation and assessment of variant calling pipelines for next-generation sequencing

Background: The processing and analysis of the large scale data generated by next-generation sequencing (NGS) experiments is challenging and is a burgeoning area of new methods development. Several new bioinformatics tools have been developed for calling sequence variants from NGS data. Here, we validate the variant calling of these tools and compare their relative accuracy to determine which data processing pipeline is optimal. Results: We developed a unified pipeline for processing NGS data that encompasses four modules: mapping, filtering, realignment and recalibration, and variant calling. We processed 130 subjects from an ongoing whole exome sequencing study through this pipeline. To evaluate the accuracy of each module, we conducted a series of comparisons between the single nucleotide variant (SNV) calls from the NGS data and either gold-standard Sanger sequencing on a total of 700 variants or array genotyping data on a total of 9,935 single-nucleotide polymorphisms. A head to head comparison showed that Genome Analysis Toolkit (GATK) provided more accurate calls than SAMtools (positive predictive value of 92.55% vs. 80.35%, respectively). Realignment of mapped reads and recalibration of base quality scores before SNV calling proved to be crucial to accurate variant calling. GATK HaplotypeCaller algorithm for variant calling outperformed the UnifiedGenotype algorithm. We also showed a relationship between mapping quality, read depth and allele balance, and SNV call accuracy. However, if best practices are used in data processing, then additional filtering based on these metrics provides little gains and accuracies of >99% are achievable. Conclusions: Our findings will help to determine the best approach for processing NGS data to confidently call variants for downstream analyses. To enable others to implement and replicate our results, all of our codes are freely available at http://metamoodics.org/wes

CASSIS: The Cornell Atlas of Spitzer/Infrared Spectrograph Sources. II. High-resolution observations

The Infrared Spectrograph (IRS) on board the Spitzer Space Telescope observed about 15,000 objects during the cryogenic mission lifetime. Observations provided low-resolution (R~60-127) spectra over ~5-38um and high-resolution (R~600) spectra over ~10-37um. The Cornell Atlas of Spitzer/IRS Sources (CASSIS) was created to provide publishable quality spectra to the community. Low-resolution spectra have been available in CASSIS since 2011, and we present here the addition of the high-resolution spectra. The high-resolution observations represent approximately one third of all staring observations performed with the IRS instrument. While low-resolution observations are adapted to faint objects and/or broad spectral features (e.g., dust continuum, molecular bands), high-resolution observations allow more accurate measurements of narrow features (e.g., ionic emission lines) as well as a better sampling of the spectral profile of various features. Given the narrow aperture of the two high-resolution modules, cosmic ray hits and spurious features usually plague the spectra. Our pipeline is designed to minimize these effects through various improvements. A super sampled point-spread function was created in order to enable the optimal extraction in addition to the full aperture extraction. The pipeline selects the best extraction method based on the spatial extent of the object. For unresolved sources, the optimal extraction provides a significant improvement in signal-to-noise ratio over a full aperture extraction. We have developed several techniques for optimal extraction, including a differential method that eliminates low-level rogue pixels (even when no dedicated background observation was performed). The updated CASSIS repository now includes all the spectra ever taken by the IRS, with the exception of mapping observations

Advanced Modeling of Charge Trapping: RTN, 1/f noise, SILC, and BTI (Invited Paper)

Abstract-In the course of years, several models have been put forward to explain noise phenomena, bias temperature instability (BTI), and gate leakage currents amongst other reliability issues. Mostly, these models have been developed independently and without considering that they may be caused by the same physical phenomenon. However, new experimental techniques have emerged, which are capable of studying these reliability issue on a microscopic level. One of them is the time-dependent defect spectroscopy (TDDS). Its intensive use has led to several interesting findings, including the fact that the recoverable component of BTI is due to reaction-limited processes. As a consequence, a quite detailed picture of the processes governing BTI has emerged. Interestingly, this picture has also been found to match the observations made for other reliability issues, such as random telegraph noise, 1/f noise, as well as gate leakage currents. Furthermore, the findings based on TDDS have lead to the development of capture/emission time (CET) maps, which can be used to understand the dynamic response of the defects given their widely distributed parameters

Advanced Modeling of Charge Trapping: RTN, 1/f noise, SILC, and BTI (Invited Paper)

Abstract-In the course of years, several models have been put forward to explain noise phenomena, bias temperature instability (BTI), and gate leakage currents amongst other reliability issues. Mostly, these models have been developed independently and without considering that they may be caused by the same physical phenomenon. However, new experimental techniques have emerged, which are capable of studying these reliability issue on a microscopic level. One of them is the time-dependent defect spectroscopy (TDDS). Its intensive use has led to several interesting findings, including the fact that the recoverable component of BTI is due to reaction-limited processes. As a consequence, a quite detailed picture of the processes governing BTI has emerged. Interestingly, this picture has also been found to match the observations made for other reliability issues, such as random telegraph noise, 1/f noise, as well as gate leakage currents. Furthermore, the findings based on TDDS have lead to the development of capture/emission time (CET) maps, which can be used to understand the dynamic response of the defects given their widely distributed parameters

Intrapartum and neonatal mortality among low-risk women in midwife-led versus obstetrician-led care in the Amsterdam region of the Netherlands : A propensity score matched study

BWM is supported by a NHMRC Practitioner Fellowship (GNT1082548).Peer reviewedPublisher PD

A Hybrid Likelihood Model for Sequence-Based Disease Association Studies

In the past few years, case-control studies of common diseases have shifted their focus from single genes to whole exomes. New sequencing technologies now routinely detect hundreds of thousands of sequence variants in a single study, many of which are rare or even novel. The limitation of classical single-marker association analysis for rare variants has been a challenge in such studies. A new generation of statistical methods for case-control association studies has been developed to meet this challenge. A common approach to association analysis of rare variants is the burden-style collapsing methods to combine rare variant data within individuals across or within genes. Here, we propose a new hybrid likelihood model that combines a burden test with a test of the position distribution of variants. In extensive simulations and on empirical data from the Dallas Heart Study, the new model demonstrates consistently good power, in particular when applied to a gene set (e.g., multiple candidate genes with shared biological function or pathway), when rare variants cluster in key functional regions of a gene, and when protective variants are present. When applied to data from an ongoing sequencing study of bipolar disorder (191 cases, 107 controls), the model identifies seven gene sets with nominal p-values<0.05, of which one MAPK signaling pathway (KEGG) reaches trend-level significance after correcting for multiple testing. © 2013 Chen et al

Evidence for solar wind modulation of lightning

The response of lightning rates over Europe to arrival of high speed solar wind streams at Earth is investigated using a superposed epoch analysis. Fast solar wind stream arrival is determined from modulation of the solar wind V y component, measured by the Advanced Composition Explorer spacecraft. Lightning rate changes around these event times are determined from the very low frequency arrival time difference (ATD) system of the UK Met Office. Arrival of high speed streams at Earth is found to be preceded by a decrease in total solar irradiance and an increase in sunspot number and Mg II emissions. These are consistent with the high speed stream's source being co-located with an active region appearing on the Eastern solar limb and rotating at the 27 d period of the Sun. Arrival of the high speed stream at Earth also coincides with a small (~1%) but rapid decrease in galactic cosmic ray flux, a moderate (~6%) increase in lower energy solar energetic protons (SEPs), and a substantial, statistically significant increase in lightning rates. These changes persist for around 40 d in all three quantities. The lightning rate increase is corroborated by an increase in the total number of thunder days observed by UK Met stations, again persisting for around 40 d after the arrival of a high speed solar wind stream. This result appears to contradict earlier studies that found an anti-correlation between sunspot number and thunder days over solar cycle timescales. The increase in lightning rates and thunder days that we observe coincides with an increased flux of SEPs which, while not being detected at ground level, nevertheless penetrate the atmosphere to tropospheric altitudes. This effect could be further amplified by an increase in mean lightning stroke intensity that brings more strokes above the detection threshold of the ATD system. In order to remove any potential seasonal bias the analysis was repeated for daily solar wind triggers occurring during the summer months (June to August). Though this reduced the number of solar wind triggers to 32, the response in both lightning and thunder day data remained statistically significant. This modulation of lightning by regular and predictable solar wind events may be beneficial to medium range forecasting of hazardous weather