Quantum Walks driven by many coins

Quantum random walks have been much studied recently, largely due to their highly nonclassical behavior. In this paper, we study one possible route to classical behavior for the discrete quantum random walk on the line: the use of multiple quantum ``coins'' in order to diminish the effects of interference between paths. We find solutions to this system in terms of the single coin random walk, and compare the asymptotic limit of these solutions to numerical simulations. We find exact analytical expressions for the time-dependence of the first two moments, and show that in the long time limit the ``quantum mechanical'' behavior of the one-coin walk persists. We further show that this is generic for a very broad class of possible walks, and that this behavior disappears only in the limit of a new coin for every step of the walk.Comment: 36 pages RevTeX 4.0 + 5 figures (encapsulated Postscript). Submitted to Physical Review

NASA Light Emitting Diode Medical Applications from Deep Space to Deep Sea

This work is supported and managed through the NASA Marshall Space Flight Center-SBIR Program. LED-technology developed for NASA plant growth experiments in space shows promise for delivering light deep into tissues of the body to promote wound healing and human tissue growth. We present the results of LED-treatment of cells grown in culture and the effects of LEDs on patients’ chronic and acute wounds. LED-technology is also biologically optimal for photodynamic therapy of cancer and we discuss our successes using LEDs in conjunction with light-activated chemotherapeutic drugs

Impact Factor: outdated artefact or stepping-stone to journal certification?

A review of Garfield's journal impact factor and its specific implementation as the Thomson Reuters Impact Factor reveals several weaknesses in this commonly-used indicator of journal standing. Key limitations include the mismatch between citing and cited documents, the deceptive display of three decimals that belies the real precision, and the absence of confidence intervals. These are minor issues that are easily amended and should be corrected, but more substantive improvements are needed. There are indications that the scientific community seeks and needs better certification of journal procedures to improve the quality of published science. Comprehensive certification of editorial and review procedures could help ensure adequate procedures to detect duplicate and fraudulent submissions.Comment: 25 pages, 12 figures, 6 table

Cystatin C is glucocorticoid responsive, directs recruitment of Trem2+ macrophages, and predicts failure of cancer immunotherapy

Cystatin C (CyC), a secreted cysteine protease inhibitor, has unclear biological functions. Many patients exhibit elevated plasma CyC levels, particularly during glucocorticoid (GC) treatment. This study links GCs with CyC’s systemic regulation by utilizing genome-wide association and structural equation modeling to determine CyC production genetics in the UK Biobank. Both CyC production and a polygenic score (PGS) capturing predisposition to CyC production were associated with increased all-cause and cancer-specific mortality. We found that the GC receptor directly targets CyC, leading to GC-responsive CyC secretion in macrophages and cancer cells. CyC-knockout tumors displayed significantly reduced growth and diminished recruitment of TREM2+ macrophages, which have been connected to cancer immunotherapy failure. Furthermore, the CyC-production PGS predicted checkpoint immunotherapy failure in 685 patients with metastatic cancer from combined clinical trial cohorts. In conclusion, CyC may act as a GC effector pathway via TREM2+ macrophage recruitment and may be a potential target for combination cancer immunotherapy.publishedVersio

Sources of variation in simulated ecosystem carbon storage capacity from the 5th Climate Model Intercomparison Project (CMIP5)

Ecosystem carbon (C) storage strongly regulates climate-C cycle feedback and is largely determined by both C residence time and C input from net primary productivity (NPP). However, spatial patterns of ecosystem C storage and its variation have not been well quantified in earth system models (ESMs), which is essential to predict future climate change and guide model development. We intended to evaluate spatial patterns of ecosystem C storage capacity simulated by ESMs as part of the 5th Climate Model Intercomparison Project (CMIP5) and explore the sources of multi-model variation from mean residence time (MRT) and/or C inputs. Five ESMs were evaluated, including C inputs (NPP and [gross primary productivity] GPP), outputs (autotrophic/heterotrophic respiration) and pools (vegetation, litter and soil C). ESMs reasonably simulated the NPP and NPP/GPP ratio compared with Moderate Resolution Imaging Spectroradiometer (MODIS) estimates except NorESM. However, all of the models significantly underestimated ecosystem MRT, resulting in underestimation of ecosystem C storage capacity. CCSM predicted the lowest ecosystem C storage capacity (~10 kg C m−2) with the lowest MRT values (14 yr), while MIROC-ESM estimated the highest ecosystem C storage capacity (~36 kg C m−2) with the longest MRT (44 yr). Ecosystem C storage capacity varied considerably among models, with larger variation at high latitudes and in Australia, mainly resulting from the differences in the MRTs across models. Our results indicate that additional research is needed to improve post-photosynthesis C-cycle modelling, especially at high latitudes, so that ecosystem C residence time and storage capacity can be appropriately simulated

Dynamic Emotional and Neural Responses to Music Depend on Performance Expression and Listener Experience

Apart from its natural relevance to cognition, music provides a window into the intimate relationships between production, perception, experience, and emotion. Here, emotional responses and neural activity were observed as they evolved together with stimulus parameters over several minutes. Participants listened to a skilled music performance that included the natural fluctuations in timing and sound intensity that musicians use to evoke emotional responses. A mechanical performance of the same piece served as a control. Before and after fMRI scanning, participants reported real-time emotional responses on a 2-dimensional rating scale (arousal and valence) as they listened to each performance. During fMRI scanning, participants listened without reporting emotional responses. Limbic and paralimbic brain areas responded to the expressive dynamics of human music performance, and both emotion and reward related activations during music listening were dependent upon musical training. Moreover, dynamic changes in timing predicted ratings of emotional arousal, as well as real-time changes in neural activity. BOLD signal changes correlated with expressive timing fluctuations in cortical and subcortical motor areas consistent with pulse perception, and in a network consistent with the human mirror neuron system. These findings show that expressive music performance evokes emotion and reward related neural activations, and that music's affective impact on the brains of listeners is altered by musical training. Our observations are consistent with the idea that music performance evokes an emotional response through a form of empathy that is based, at least in part, on the perception of movement and on violations of pulse-based temporal expectancies

Exploring the Switchgrass Transcriptome Using Second-Generation Sequencing Technology

Background: Switchgrass (Panicum virgatum L.) is a C4 perennial grass and widely popular as an important bioenergy crop. To accelerate the pace of developing high yielding switchgrass cultivars adapted to diverse environmental niches, the generation of genomic resources for this plant is necessary. The large genome size and polyploid nature of switchgrass makes whole genome sequencing a daunting task even with current technologies. Exploring the transcriptional landscape using next generation sequencing technologies provides a viable alternative to whole genome sequencing in switchgrass. Principal Findings: Switchgrass cDNA libraries from germinating seedlings, emerging tillers, flowers, and dormant seeds were sequenced using Roche 454 GS-FLX Titanium technology, generating 980,000 reads with an average read length of 367 bp. De novo assembly generated 243,600 contigs with an average length of 535 bp. Using the foxtail millet genome as a reference greatly improved the assembly and annotation of switchgrass ESTs. Comparative analysis of the 454-derived switchgrass EST reads with other sequenced monocots including Brachypodium, sorghum, rice and maize indicated a 70– 80 % overlap. RPKM analysis demonstrated unique transcriptional signatures of the four tissues analyzed in this study. More than 24,000 ESTs were identified in the dormant seed library. In silico analysis indicated that there are more than 2000 EST-SSRs in this collection. Expression of several orphan ESTs was confirmed by RT-PCR. Significance: We estimate that about 90 % of the switchgrass gene space has been covered in this analysis. This study nearl

Presynaptically Localized Cyclic GMP-Dependent Protein Kinase 1 Is a Key Determinant of Spinal Synaptic Potentiation and Pain Hypersensitivity

Electrophysiological and behavioral experiments in mice reveal that a cGMP-dependent kinase amplifies neurotransmitter release from peripheral pain sensors, potentiates spinal synapses, and leads to exaggerated pain

Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving

<p>Abstract</p> <p>Background</p> <p>Several susceptibility genetic variants for autoimmune diseases have been identified. A subset of these polymorphisms displays an opposite risk profile in different autoimmune conditions. This observation open interesting questions on the evolutionary forces shaping the frequency of these alleles in human populations.</p> <p>We aimed at testing the hypothesis whereby balancing selection has shaped the frequency of opposite risk alleles.</p> <p>Results</p> <p>Since balancing selection signatures are expected to extend over short genomic portions, we focused our analyses on 11 regions carrying putative functional polymorphisms that may represent the disease variants (and the selection targets). No exceptional nucleotide diversity was observed for <it>ZSCAN23</it>, <it>HLA-DMB</it>, <it>VARS2</it>, <it>PTPN22</it>, <it>BAT3</it>, <it>C6orf47</it>, and <it>IL10</it>; summary statistics were consistent with evolutionary neutrality for these gene regions. Conversely, <it>CDSN/PSORS1C1</it>, <it>TRIM10/TRIM40</it>, <it>BTNL2</it>, and <it>TAP2 </it>showed extremely high nucleotide diversity and most tests rejected neutrality, suggesting the action of balancing selection. For <it>TAP2 </it>and <it>BTNL2 </it>these signatures are not secondary to linkage disequilibrium with HLA class II genes. Nonetheless, with the exception of variants in <it>TRIM40 </it>and <it>CDSN</it>, our data suggest that opposite risk SNPs are not selection targets but rather have accumulated as neutral variants.</p> <p>Conclusion</p> <p>Data herein indicate that balancing selection is common within the extended MHC region and involves several non-HLA loci. Yet, the evolutionary history of most SNPs with an opposite effect for autoimmune diseases is consistent with evolutionary neutrality. We suggest that variants with an opposite effect on autoimmune diseases should not be considered a distinct class of disease alleles from the evolutionary perspective and, in a few cases, the opposite effect on distinct diseases may derive from complex haplotype structures in regions with high genetic diversity.</p

The Transcriptional Repressor TupA in Aspergillus niger Is Involved in Controlling Gene Expression Related to Cell Wall Biosynthesis, Development, and Nitrogen Source Availability.

The Tup1-Cyc8 (Ssn6) complex is a well characterized and conserved general transcriptional repressor complex in eukaryotic cells. Here, we report the identification of the Tup1 (TupA) homolog in the filamentous fungus Aspergillus niger in a genetic screen for mutants with a constitutive expression of the agsA gene. The agsA gene encodes a putative alpha-glucan synthase, which is induced in response to cell wall stress in A. niger. Apart from the constitutive expression of agsA, the selected mutant was also found to produce an unknown pigment at high temperatures. Complementation analysis with a genomic library showed that the tupA gene could complement the phenotypes of the mutant. Screening of a collection of 240 mutants with constitutive expression of agsA identified sixteen additional pigment-secreting mutants, which were all mutated in the tupA gene. The phenotypes of the tupA mutants were very similar to the phenotypes of a tupA deletion strain. Further analysis of the tupA-17 mutant and the DeltatupA mutant revealed that TupA is also required for normal growth and morphogenesis. The production of the pigment at 37 degrees C is nitrogen source-dependent and repressed by ammonium. Genome-wide expression analysis of the tupA mutant during exponential growth revealed derepression of a large group of diverse genes, including genes related to development and cell wall biosynthesis, and also protease-encoding genes that are normally repressed by ammonium. Comparison of the transcriptome of up-regulated genes in the tupA mutant showed limited overlap with the transcriptome of caspofungin-induced cell wall stress-related genes, suggesting that TupA is not a general suppressor of cell wall stress-induced genes. We propose that TupA is an important repressor of genes related to development and nitrogen metabolism