1.6:1 bandwidth two-layer antireflection structure for silicon matched to the 190–310 GHz atmospheric window

Although high-resistivity, low-loss silicon is an excellent material for terahertz transmission optics, its high refractive index necessitates an antireflection treatment. We fabricated a wide-bandwidth, two-layer antireflection treatment by cutting subwavelength structures into the silicon surface using multi-depth deep reactive-ion etching (DRIE). A wafer with this treatment on both sides has <−20  dB (<1%) reflectance over 187–317 GHz at a 15° angle of incidence in TE polarization. We also demonstrated that bonding wafers introduce no reflection features above the −20  dB level (also in TE at 15°), reproducing previous work. Together these developments immediately enable construction of wide-bandwidth silicon vacuum windows and represent two important steps toward gradient-index silicon optics with integral broadband antireflection treatment

1.6:1 bandwidth two-layer antireflection structure for silicon matched to the 190–310 GHz atmospheric window

Although high-resistivity, low-loss silicon is an excellent material for terahertz transmission optics, its high refractive index necessitates an antireflection treatment. We fabricated a wide-bandwidth, two-layer antireflection treatment by cutting subwavelength structures into the silicon surface using multi-depth deep reactive-ion etching (DRIE). A wafer with this treatment on both sides has <−20  dB (<1%) reflectance over 187–317 GHz at a 15° angle of incidence in TE polarization. We also demonstrated that bonding wafers introduce no reflection features above the −20  dB level (also in TE at 15°), reproducing previous work. Together these developments immediately enable construction of wide-bandwidth silicon vacuum windows and represent two important steps toward gradient-index silicon optics with integral broadband antireflection treatment

TIGER : The gene expression regulatory variation landscape of human pancreatic islets

Genome-wide association studies (GWASs) identified hundreds of signals associated with type 2 diabetes (T2D). To gain insight into their underlying molecular mechanisms, we have created the translational human pancreatic islet genotype tissue-expression resource (TIGER), aggregating >500 human islet genomic datasets from five cohorts in the Horizon 2020 consortium T2DSystems. We impute genotypes using four reference panels and meta-analyze cohorts to improve the coverage of expression quantitative trait loci (eQTL) and develop a method to combine allele-specific expression across samples (cASE). We identify >1 million islet eQTLs, 53 of which colocalize with T2D signals. Among them, a low-frequency allele that reduces T2D risk by half increases CCND2 expression. We identify eight cASE colocalizations, among which we found a T2D-associated SLC30A8 variant. We make all data available through the TIGER portal (http://tiger.bsc.es), which represents a comprehensive human islet genomic data resource to elucidate how genetic variation affects islet function and translates into therapeutic insight and precision medicine for T2D.Peer reviewe

DiRE: identifying distant regulatory elements of co-expressed genes

Regulation of gene expression in eukaryotic genomes is established through a complex cooperative activity of proximal promoters and distant regulatory elements (REs) such as enhancers, repressors and silencers. We have developed a web server named DiRE, based on the Enhancer Identification (EI) method, for predicting distant regulatory elements in higher eukaryotic genomes, namely for determining their chromosomal location and functional characteristics. The server uses gene co-expression data, comparative genomics and profiles of transcription factor binding sites (TFBSs) to determine TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is its ability to detect REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs and it also scores the association of individual transcription factors (TFs) with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. The DiRE web server is freely available at http://dire.dcode.org

Toolbox from the EC FP7 HOSANNA project for the reduction of road and rail traffic noise in the outdoor environment

yesThis paper offers a brief overview of innovative methods for road and rail traffic noise reduction between source and receiver. These include using new barrier designs, planting of trees, treatments of ground and road surfaces and greening of building façades and roofs using natural materials, like vegetation, soil and other substrates in combination with recycled materials and artificial elements. The abatements are assessed in terms of numerically predicted sound level reductions, perceptual effects and cost–benefit analysis. Useful reductions of noise from urban roads and tramways are predicted for 1-m-high urban noise barriers and these are increased by adding inter-lane barriers. A 3 m wide 0.3 m high lattice ground treatment, a carefully planted 15-m-wide tree belt and replacing 50 m of paved areas by grassland are predicted to give similar reductions. Tree belts are shown to be very cost-effective and combining tall barriers with a row of trees reduces the negative impact of wind. Green roofs may significantly reduce the noise at the quiet side of buildings

Unveiling Mycoplasma hyopneumoniae Promoters: Sequence Definition and Genomic Distribution

Several Mycoplasma species have had their genome completely sequenced, including four strains of the swine pathogen Mycoplasma hyopneumoniae. Nevertheless, little is known about the nucleotide sequences that control transcriptional initiation in these microorganisms. Therefore, with the objective of investigating the promoter sequences of M. hyopneumoniae, 23 transcriptional start sites (TSSs) of distinct genes were mapped. A pattern that resembles the σ70 promoter −10 element was found upstream of the TSSs. However, no −35 element was distinguished. Instead, an AT-rich periodic signal was identified. About half of the experimentally defined promoters contained the motif 5′-TRTGn-3′, which was identical to the −16 element usually found in Gram-positive bacteria. The defined promoters were utilized to build position-specific scoring matrices in order to scan putative promoters upstream of all coding sequences (CDSs) in the M. hyopneumoniae genome. Two hundred and one signals were found associated with 169 CDSs. Most of these sequences were located within 100 nucleotides of the start codons. This study has shown that the number of promoter-like sequences in the M. hyopneumoniae genome is more frequent than expected by chance, indicating that most of the sequences detected are probably biologically functional

IL-7 Promotes CD95-Induced Apoptosis in B Cells via the IFN-γ/STAT1 Pathway

Interleukin-7 (IL-7) concentrations are increased in the blood of CD4+ T cell depleted individuals, including HIV-1 infected patients. High IL-7 levels might stimulate T cell activation and, as we have shown earlier, IL-7 can prime resting T cell to CD95 induced apoptosis as well. HIV-1 infection leads to B cell abnormalities including increased apoptosis via the CD95 (Fas) death receptor pathway and loss of memory B cells. Peripheral B cells are not sensitive for IL-7, due to the lack of IL-7Ra expression on their surface; however, here we demonstrate that high IL-7 concentration can prime resting B cells to CD95-mediated apoptosis via an indirect mechanism. T cells cultured with IL-7 induced high CD95 expression on resting B cells together with an increased sensitivity to CD95 mediated apoptosis. As the mediator molecule responsible for B cell priming to CD95 mediated apoptosis we identified the cytokine IFN-γ that T cells secreted in high amounts in response to IL-7. These results suggest that the lymphopenia induced cytokine IL-7 can contribute to the increased B cell apoptosis observed in HIV-1 infected individuals