Optimized polar-azimuthal orientations for polarized light illumination of different Superconducting Nanowire Single-Photon Detector designs

The optimal orientations are determined for polarized substrate side illumination of three superconducting nanowire single-photon detector (SNSPD) designs: (1) periodic niobium-nitride (NbN) stripes standing in air with dimensions according to conventional SNSPDs, (2) same NbN patterns below ~quarter-wavelength hydrogensilsesquioxane-filled nano-cavity, (3) analogous NbN patterns in HSQ nano-cavity closed by a thin gold reflector. Numerical computation results have shown that the optical response and near-field distribution vary significantly with polar-angle, fi, and these variations are analogous across all azimuthal-angles, gamma, but are fundamentally different in various device designs. Larger absorptance is available due to p-polarized illumination of NbN patterns in P-structure configuration, while s-polarized illumination results in higher absorptance in S-structure arrangement. As a result of p-polarized illumination a global maximum appears on absorptance of bare NbN pattern at polar angle corresponding to NbN-related ATIR; integration with HSQ nano-cavity results in a global absorptance maximum at polar angle corresponding to TIR at sapphire-air interface; while the highest absorptance is observable at perpendicular incidence on P-structures aligned below gold reflector covered HSQ nano-cavity. S-polarized light illumination results in a global absorptance maximum at TIR on bare NbN patterns; the highest absorptance is available below HSQ nano-cavity at polar angle corresponding to ATIR phenomenon; while the benefit of gold reflector is large and polar angle independent absorptance.Comment: 24 pages, 7 figure

Culture in Reduced Levels of Oxygen Promotes Clonogenic Sympathoadrenal Differentiation by Isolated Neural Crest Stem Cells

Isolated neural crest stem cells (NCSCs) differentiate to autonomic neurons in response to bone morphogenetic protein 2 (BMP2) in clonal cultures, but these neurons do not express sympathoadrenal (SA) lineage markers. Whether this reflects a developmental restriction in NCSCs or simply inappropriate culture conditions was not clear. We tested the growth and differentiation potential of NCSCs at ∼5% O_2, which more closely approximates physiological oxygen levels. Eighty-three percent of p75^+P_0 ^− cells isolated from embryonic day 14.5 sciatic nerve behaved as stem cells under these conditions, suggesting that this is a nearly pure population. Furthermore, addition of BMP2 plus forskolin in decreased oxygen cultures elicited differentiation of thousands of cells expressing tyrosine hydroxylase, dopamine-β-hydroxylase, and the SA lineage marker SA-1 in nearly all colonies. Such cells also synthesized and released dopamine and norepinephrine. These data demonstrate that isolated mammalian NCSCs uniformly possess SA lineage capacity and further suggest that oxygen levels can influence cell fate. Parallel results indicating that reduced oxygen levels can also promote the survival, proliferation, and catecholaminergic differentiation of CNS stem cells (Studer et al., 2000) suggests that neural stem cells may exhibit a conserved response to reduced oxygen levels

Calibration of dosemeters used in mammography with different X ray qualities: Euromet Project No. 526

The effect of different X ray radiation qualities on the calibration of mammographic dosemeters was investigated within the framework of a EUROMET (European Collaboration in Measurement Standards) project. The calibration coefficients for two ionization chambers and two semiconductor detectors were established in 13 dosimetry calibration laboratories for radiation qualities used in mammography. They were compared with coefficients for other radiation qualities, including those defined in ISO 4037-1, with first half value layers in the mammographic range. The results indicate that the choice of the radiation quality is not crucial for instruments with a small energy dependence of the response. However, the radiation quality has to be chosen carefully if instruments with a marked dependence of their response to the radiation energy are calibrate

Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum

Halobacterium salinarum is a bioenergetically flexible, halophilic microorganism that can generate energy by respiration, photosynthesis, and the fermentation of arginine. In a previous study, using a genome-scale metabolic model, we have shown that the archaeon unexpectedly degrades essential amino acids under aerobic conditions, a behavior that can lead to the termination of growth earlier than necessary. Here, we further integratively investigate energy generation, nutrient utilization, and biomass production using an extended methodology that accounts for dynamically changing transport patterns, including those that arise from interactions among the supplied metabolites. Moreover, we widen the scope of our analysis to include phototrophic conditions to explore the interplay between different bioenergetic modes. Surprisingly, we found that cells also degrade essential amino acids even during phototropy, when energy should already be abundant. We also found that under both conditions considerable amounts of nutrients that were taken up were neither incorporated into the biomass nor used as respiratory substrates, implying the considerable production and accumulation of several metabolites in the medium. Some of these are likely the products of forms of overflow metabolism. In addition, our results also show that arginine fermentation, contrary to what is typically assumed, occurs simultaneously with respiration and photosynthesis and can contribute energy in levels that are comparable to the primary bioenergetic modes, if not more. These findings portray a picture that the organism takes an approach toward growth that favors the here and now, even at the cost of longer-term concerns. We believe that the seemingly "greedy" behavior exhibited actually consists of adaptations by the organism to its natural environments, where nutrients are not only irregularly available but may altogether be absent for extended periods that may span several years. Such a setting probably predisposed the cells to grow as much as possible when the conditions become favorable

Centralized Modularity of N-Linked Glycosylation Pathways in Mammalian Cells

Glycosylation is a highly complex process to produce a diverse repertoire of cellular glycans that are attached to proteins and lipids. Glycans are involved in fundamental biological processes, including protein folding and clearance, cell proliferation and apoptosis, development, immune responses, and pathogenesis. One of the major types of glycans, N-linked glycans, is formed by sequential attachments of monosaccharides to proteins by a limited number of enzymes. Many of these enzymes can accept multiple N-linked glycans as substrates, thereby generating a large number of glycan intermediates and their intermingled pathways. Motivated by the quantitative methods developed in complex network research, we investigated the large-scale organization of such N-linked glycosylation pathways in mammalian cells. The N-linked glycosylation pathways are extremely modular, and are composed of cohesive topological modules that directly branch from a common upstream pathway of glycan synthesis. This unique structural property allows the glycan production between modules to be controlled by the upstream region. Although the enzymes act on multiple glycan substrates, indicating cross-talk between modules, the impact of the cross-talk on the module-specific enhancement of glycan synthesis may be confined within a moderate range by transcription-level control. The findings of the present study provide experimentally-testable predictions for glycosylation processes, and may be applicable to therapeutic glycoprotein engineering

Criminal Justice Reform as HIV and TB Prevention in African Prisons

Katherine Todrys and Joseph Amon argue for criminal justice system reforms in sub-Saharan Africa to reduce HIV and TB transmission in prisons and to guarantee detainees' human rights and health

Deterministic and stochastic descriptions of gene expression dynamics

A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or implicitly etc. Here we consider simple systems of unregulated (constitutive) gene expression and compare different mathematical descriptions systematically to obtain insight into the errors that are introduced by various common approximations such as describing cell growth and division by an effective protein degradation term. In particular, we show that the population average of protein content of a cell exhibits a subtle dependence on the dynamics of growth and division, the specific model for volume growth and the age structure of the population. Nevertheless, the error made by models with implicit cell growth and division is quite small. Furthermore, we compare various models that are partially stochastic to investigate the impact of different sources of (intrinsic) noise. This comparison indicates that different sources of noise (protein synthesis, partitioning in cell division) contribute comparable amounts of noise if protein synthesis is not or only weakly bursty. If protein synthesis is very bursty, the burstiness is the dominant noise source, independent of other details of the model. Finally, we discuss two sources of extrinsic noise: cell-to-cell variations in protein content due to cells being at different stages in the division cycles, which we show to be small (for the protein concentration and, surprisingly, also for the protein copy number per cell) and fluctuations in the growth rate, which can have a significant impact.Comment: 23 pages, 5 figures; Journal of Statistical physics (2012