Tomography of photon-number resolving continuous-output detectors

We report a comprehensive approach to analysing continuous-output photon detectors. We employ principal component analysis to maximise the information extracted, followed by a novel noise-tolerant parameterised approach to the tomography of PNRDs. We further propose a measure for rigorously quantifying a detector's photon-number-resolving capability. Our approach applies to all detectors with continuous-output signals. We illustrate our methods by applying them to experimental data obtained from a transition-edge sensor (TES) detector.Comment: 5 pages, 3 figures, also includes supplementary informatio

Ground and Excited States of Bis‐4‐Methoxybenzyl‐Substituted Diketopyrrolopyrroles: Spectroscopic and Electrochemical Studies

A series of symmetrically bis‐4‐methoxybenzyl (4MB) N‐substituted 1,4‐diketopyrrolo[3,4‐c]pyrrole (DPP) derivatives have been synthesized. The 4MB unit makes the DPP core soluble, and shows subtle modification of up to 0.2 eV in ground and excited states of the core when compared with related alkyl derivatives. Absorption and emission spectroscopy, as well as electrochemical and computational methods have been employed to prove the importance of the peripheral aryl units on the donor/ acceptor properties of the molecules. The 4MB products are highly fluorescent (quantum yields approaching 100 % in solution), with a unique distribution of frontier states shown by spectroelectrochemistry. The solid‐state fluorescence correlates with the X‐ray crystal structures of the compounds, a Stokes shift of approximately 80 nm is seen for two of the compounds. The frontier energy levels show that this subtle substitutional change could be of future use in molecular energy level tailoring in these, and related, materials for organic (opto)electronics

How much does emotional valence of action outcomes affect temporal binding?

Temporal binding refers to the compression of the perceived time interval between voluntary actions and their sensory consequences. Research suggests that the emotional content of an action outcome can modulate the effects of temporal binding. We attempted to conceptually replicate these findings using a time interval estimation task and different emotionally-valenced action outcomes (Experiments 1 and 2) than used in previous research. Contrary to previous findings, we found no evidence that temporal binding was affected by the emotional valence of action outcomes. After validating our stimuli for equivalence of perceived emotional valence and arousal (Experiment 3), in Experiment 4 we directly replicated Yoshie and Haggard’s (2013) original experiment using sound vocalizations as action outcomes and failed to detect a significant effect of emotion on temporal binding. These studies suggest that the emotional valence of action outcomes exerts little influence on temporal binding. The potential implications of these findings are discussed

The Balloon-borne Large Aperture Submillimeter Telescope (BLAST) 2006: Calibration and Flight Performance

The Balloon-borne Large Aperture Submillimeter Telescope (BLAST) operated successfully during a 250-hour flight over Antarctica in December 2006 (BLAST06). As part of the calibration and pointing procedures, the red hypergiant star VY CMa was observed and used as the primary calibrator. Details of the overall BLAST06 calibration procedure are discussed. The 1-sigma absolute calibration is accurate to 10, 12, and 13% at the 250, 350, and 500 micron bands, respectively. The errors are highly correlated between bands resulting in much lower error for the derived shape of the 250-500 micron continuum. The overall pointing error is <5" rms for the 36, 42, and 60" beams. The performance of the optics and pointing systems is discussed.Comment: Accepted for publication in the Astrophysical Journal. Maps available at http://blastexperiment.info

Impact of Human FcγR Gene Polymorphisms on IgG-Triggered Cytokine Release: Critical Importance of Cell Assay Format

Monoclonal antibody (mAb) immunotherapy has transformed the treatment of allergy, autoimmunity, and cancer. The interaction of mAb with Fc gamma receptors (FcγR) is often critical for efficacy. The genes encoding the low-affinity FcγR have single nucleotide polymorphisms (SNPs) and copy number variation that can impact IgG Fc:FcγR interactions. Leukocyte-based in vitro assays remain one of the industry standards for determining mAb efficacy and predicting adverse responses in patients. Here we addressed the impact of FcγR genetics on immune cell responses in these assays and investigated the importance of assay format. FcγR genotyping of 271 healthy donors was performed using a Multiplex Ligation-Dependent Probe Amplification assay. Freeze-thawed/pre-cultured peripheral blood mononuclear cells (PBMCs) and whole blood samples from donors were stimulated with reagents spanning different mAb functional classes to evaluate the association of FcγR genotypes with T-cell proliferation and cytokine release. Using freeze-thawed/pre-cultured PBMCs, agonistic T-cell-targeting mAb induced T-cell proliferation and the highest levels of cytokine release, with lower but measurable responses from mAb which directly require FcγR-mediated cellular effects for function. Effects were consistent for individual donors over time, however, no significant associations with FcγR genotypes were observed using this assay format. In contrast, significantly elevated IFN-γ release was associated with the FCGR2A-131H/H genotype compared to FCGR2A-131R/R in whole blood stimulated with Campath (p ≤ 0.01) and IgG1 Fc hexamer (p ≤ 0.05). Donors homozygous for both the high affinity FCGR2A-131H and FCGR3A-158V alleles mounted stronger IFN-γ responses to Campath (p ≤ 0.05) and IgG1 Fc Hexamer (p ≤ 0.05) compared to donors homozygous for the low affinity alleles. Analysis revealed significant reductions in the proportion of CD14hi monocytes, CD56dim NK cells (p ≤ 0.05) and FcγRIIIa expression (p ≤ 0.05), in donor-matched freeze-thawed PBMC compared to whole blood samples, likely explaining the difference in association between FcγR genotype and mAb-mediated cytokine release in the different assay formats. These findings highlight the significant impact of FCGR2A and FCGR3A SNPs on mAb function and the importance of using fresh whole blood assays when evaluating their association with mAb-mediated cytokine release in vitro. This knowledge can better inform on the utility of in vitro assays for the prediction of mAb therapy outcome in patients

Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom

<p>Abstract</p> <p>Background</p> <p>As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modification has been a major task for bioenergy feedstock improvement. The study of the evolution and function of lignin biosynthesis genes thus has two-fold implications. First, the lignin biosynthesis pathway provides an excellent model to study the coordinative evolution of a biochemical pathway in plants. Second, understanding the function and evolution of lignin biosynthesis genes will guide us to develop better strategies for bioenergy feedstock improvement.</p> <p>Results</p> <p>We analyzed lignin biosynthesis genes from fourteen plant species and one symbiotic fungal species. Comprehensive comparative genome analysis was carried out to study the distribution, relatedness, and family expansion of the lignin biosynthesis genes across the plant kingdom. In addition, we also analyzed the comparative synteny map between rice and sorghum to study the evolution of lignin biosynthesis genes within the <it>Poaceae </it>family and the chromosome evolution between the two species. Comprehensive lignin biosynthesis gene expression analysis was performed in rice, poplar and <it>Arabidopsis</it>. The representative data from rice indicates that different fates of gene duplications exist for lignin biosynthesis genes. In addition, we also carried out the biomass composition analysis of nine <it>Arabidopsis </it>mutants with both MBMS analysis and traditional wet chemistry methods. The results were analyzed together with the genomics analysis.</p> <p>Conclusion</p> <p>The research revealed that, among the species analyzed, the complete lignin biosynthesis pathway first appeared in moss; the pathway is absent in green algae. The expansion of lignin biosynthesis gene families correlates with substrate diversity. In addition, we found that the expansion of the gene families mostly occurred after the divergence of monocots and dicots, with the exception of the C4H gene family. Gene expression analysis revealed different fates of gene duplications, largely confirming plants are tolerant to gene dosage effects. The rapid expansion of lignin biosynthesis genes indicated that the translation of transgenic lignin modification strategies from model species to bioenergy feedstock might only be successful between the closely relevant species within the same family.</p

Integrated quantum photonic sensor based on Hong-Ou-Mandel interference

Photonic-crystal-based integrated optical systems have been used for a broad range of sensing applications with great success. This has been motivated by several advantages such as high sensitivity, miniaturization, remote sensing, selectivity and stability. Many photonic crystal sensors have been proposed with various fabrication designs that result in improved optical properties. In parallel, integrated optical systems are being pursued as a platform for photonic quantum information processing using linear optics and Fock states. Here we propose a novel integrated Fock state optical sensor architecture that can be used for force, refractive index and possibly local temperature detection. In this scheme, two coupled cavities behave as an “effective beam splitter”. The sensor works based on fourth order interference (the Hong-Ou-Mandel effect) and requires a sequence of single photon pulses and consequently has low pulse power. Changes in the parameter to be measured induce variations in the effective beam splitter reflectivity and result in changes to the visibility of interference. We demonstrate this generic scheme in coupled L3 photonic crystal cavities as an example and find that this system, which only relies on photon coincidence detection and does not need any spectral resolution, can estimate forces as small as 10^−7 Newtons and can measure one part per million change in refractive index using a very low input power of 10−10W. Thus linear optical quantum photonic architectures can achieve comparable sensor performance to semiclassical devices

Global Systems-Level Analysis of Hfq and SmpB Deletion Mutants in Salmonella: Implications for Virulence and Global Protein Translation

Using sample-matched transcriptomics and proteomics measurements it is now possible to begin to understand the impact of post-transcriptional regulatory programs in Enterobacteria. In bacteria post-transcriptional regulation is mediated by relatively few identified RNA-binding protein factors including CsrA, Hfq and SmpB. A mutation in any one of these three genes, csrA, hfq, and smpB, in Salmonella is attenuated for mouse virulence and unable to survive in macrophages. CsrA has a clearly defined specificity based on binding to a specific mRNA sequence to inhibit translation. However, the proteins regulated by Hfq and SmpB are not as clearly defined. Previous work identified proteins regulated by hfq using purification of the RNA-protein complex with direct sequencing of the bound RNAs and found binding to a surprisingly large number of transcripts. In this report we have used global proteomics to directly identify proteins regulated by Hfq or SmpB by comparing protein abundance in the parent and isogenic hfq or smpB mutant. From these same samples we also prepared RNA for microarray analysis to determine if alteration of protein expression was mediated post-transcriptionally. Samples were analyzed from bacteria grown under four different conditions; two laboratory conditions and two that are thought to mimic the intracellular environment. We show that mutants of hfq and smpB directly or indirectly modulate at least 20% and 4% of all possible Salmonella proteins, respectively, with limited correlation between transcription and protein expression. These proteins represent a broad spectrum of Salmonella proteins required for many biological processes including host cell invasion, motility, central metabolism, LPS biosynthesis, two-component regulatory systems, and fatty acid metabolism. Our results represent one of the first global analyses of post-transcriptional regulons in any organism and suggest that regulation at the translational level is widespread and plays an important role in virulence regulation and environmental adaptation for Salmonella