Ge-on-Si single-photon avalanche diode detectors: design, modeling, fabrication, and characterization at wavelengths 1310 and 1550 nm

The design, modeling, fabrication, and characterization of single-photon avalanche diode detectors with an epitaxial Ge absorption region grown directly on Si are presented. At 100 K, a single-photon detection efficiency of 4% at 1310 nm wavelength was measured with a dark count rate of ~ 6 megacounts/s, resulting in the lowest reported noise-equivalent power for a Ge-on-Si single-photon avalanche diode detector (1×10-14 WHz-1/2). The first report of 1550 nm wavelength detection efficiency measurements with such a device is presented. A jitter of 300 ps was measured, and preliminary tests on after-pulsing showed only a small increase (a factor of 2) in the normalized dark count rate when the gating frequency was increased from 1 kHz to 1 MHz. These initial results suggest that optimized devices integrated on Si substrates could potentially provide performance comparable to or better than that of many commercially available discrete technologies

Predictive value of apoptosis, proliferation, HER-2, and topoisomerase IIalpha for anthracycline chemotherapy in locally advanced breast cancer

Purpose. Laboratory evidence indicates that tumor growth depends on the balance between cell proliferation and cell death, and many anticancer agents may exert their therapeutic effect by decreasing proliferation and increasing apoptosis. Additionally, clinical observations indicate that overexpression of HER-2 or topoisomerase II alpha ( topo II alpha) may be predictors of better response to anthracyclines in breast cancer. The objective of this study was to determine if proliferation ( Ki-67), apoptosis ( TUNEL), and expression of HER-2 and topo II alpha are affected by anthracycline treatment, and if these molecular markers predict anthracycline responsiveness. Experimental design. Thirty-three women with primary breast tumors >= 3 cm received either doxorubicin ( 75 mg/ m(2)) or epirubicin ( 120 mg/ m(2)) for 4 cycles before surgery. Clinical response was evaluated after 4 cycles of treatment. Changes in molecular markers were assessed from core needle biopsy taken before treatment (D0), at 24 - 48 h (Dl) and on day 7 (D7) while on treatment, and from the surgical specimen excised on day 84 (D84) after the fourth cycle of chemotherapy. Results. The overall clinical response rate was 51% (17 of 33 patients), with a 12% complete clinical response rate ( 4 of 33 patients). There were trends for tumors with higher apoptosis and topo IIa at baseline ( D0) to be more responsive to anthracyclines, p = 0.1 and p = 0.08, respectively. Median apoptosis increased from D0 to Dl ( p = 0.06) while median Ki-67 decreased ( p = 0.07). Overall, expression of HER-2 remained stable throughout the chemotherapy administration. By Day 84, topo II alpha had significantly decreased from baseline in responders, while it increased in non-responders, p = 0.03. Conclusions. In human primary breast cancer, anthracycline treatment causes an early increase in apoptosis and a decrease in proliferation. In this pilot study, higher apoptosis and topo II alpha a levels in primary tumors were associated with greater responsiveness to anthracyclines, and topo II alpha levels declined in responsive tumors

Extreme Ultra-Violet Spectroscopy of the Lower Solar Atmosphere During Solar Flares

The extreme ultraviolet portion of the solar spectrum contains a wealth of diagnostic tools for probing the lower solar atmosphere in response to an injection of energy, particularly during the impulsive phase of solar flares. These include temperature and density sensitive line ratios, Doppler shifted emission lines and nonthermal broadening, abundance measurements, differential emission measure profiles, and continuum temperatures and energetics, among others. In this paper I shall review some of the advances made in recent years using these techniques, focusing primarily on studies that have utilized data from Hinode/EIS and SDO/EVE, while also providing some historical background and a summary of future spectroscopic instrumentation.Comment: 34 pages, 8 figures. Submitted to Solar Physics as part of the Topical Issue on Solar and Stellar Flare

Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing

Most transcriptome-wide association studies (TWASs) so far focus on European ancestry and lack diversity. To overcome this limitation, we aggregated genome-wide association study (GWAS) summary statistics, whole-genome sequences and expression quantitative trait locus (eQTL) data from diverse ancestries. We developed a new approach, TESLA (multi-ancestry integrative study using an optimal linear combination of association statistics), to integrate an eQTL dataset with a multi-ancestry GWAS. By exploiting shared phenotypic effects between ancestries and accommodating potential effect heterogeneities, TESLA improves power over other TWAS methods. When applied to tobacco use phenotypes, TESLA identified 273 new genes, up to 55% more compared with alternative TWAS methods. These hits and subsequent fine mapping using TESLA point to target genes with biological relevance. In silico drug-repurposing analyses highlight several drugs with known efficacy, including dextromethorphan and galantamine, and new drugs such as muscle relaxants that may be repurposed for treating nicotine addiction

varDB: common ground for a shifting landscape

Antigenic variation is a phylogenetically widespread phenomenon thought to lead to survival benefits for the pathogen. Although governed by genetic mechanisms, antigenic variation is ultimately manifested in variant proteins. The varDB database is an attempt to gain an overview of common structures and functions of variant proteins related to enhanced survival. varDB provides a wealth of sequence data and several tools to facilitate their analysis, but current limitations preclude achievement of its full promise. A critique of this database and how it could serve the scientific community is provided here