Coulomb oscillations of the Fano-Kondo effect and zero bias anomalies in the double dot meso-transistor

We investigate theoretically the transport properties of the side-coupled double quantum dots in connection with the experimental study of Sasaki {\it et al.} Phys.Rev.Lett.{\bf 103}, 266806 (2009). The novelty of the set-up consists in connecting the Kondo dot directly to the leads, while the side dot provides an interference path which affects the Kondo correlations. We analyze the oscillations of the source-drain current due to the periodical Coulomb blockade of the many-level side-dot at the variation of the gate potential applied on it. The Fano profile of these oscillations may be controlled by the temperature, gate potential and interdot coupling. The non-equilibrium conductance of the double dot system exhibits zero bias anomaly which, besides the usual enhancement, may show also a suppression (a dip-like aspect) which occurs around the Fano {\it zero}. In the same region, the weak temperature dependence of the conductance indicates the suppression of the Kondo effect. Scaling properties of the non-equilibrium conductance in the Fano-Kondo regime are discussed. Since the SIAM Kondo temperature is no longer the proper scaling parameter, we look for an alternative specific to the double-dot. The extended Anderson model, Keldysh formalism and equation of motion technique are used.Comment: 19 pages, 8 figure

Infra-red divergences in plane wave backgrounds

We show that the emission of soft photons via nonlinear Compton scattering in a pulsed plane wave (laser field) is in general infra-red divergent. We give examples of both soft and soft-collinear divergences, and we pay particular attention to the case of crossed fields in both classical and quantum theories.Comment: 15 pages, 7 figure

Geographically weighted linear combination test for gene-set analysis of a continuous spatial phenotype as applied to intratumor heterogeneity.

Background: The impact of gene-sets on a spatial phenotype is not necessarily uniform across different locations of cancer tissue. This study introduces a computational platform, GWLCT, for combining gene set analysis with spatial data modeling to provide a new statistical test for location-specific association of phenotypes and molecular pathways in spatial single-cell RNA-seq data collected from an input tumor sample. Methods: The main advantage of GWLCT consists of an analysis beyond global significance, allowing the association between the gene-set and the phenotype to vary across the tumor space. At each location, the most significant linear combination is found using a geographically weighted shrunken covariance matrix and kernel function. Whether a fixed or adaptive bandwidth is determined based on a cross-validation cross procedure. Our proposed method is compared to the global version of linear combination test (LCT), bulk and random-forest based gene-set enrichment analyses using data created by the Visium Spatial Gene Expression technique on an invasive breast cancer tissue sample, as well as 144 different simulation scenarios. Results: In an illustrative example, the new geographically weighted linear combination test, GWLCT, identifies the cancer hallmark gene-sets that are significantly associated at each location with the five spatially continuous phenotypic contexts in the tumors defined by different well-known markers of cancer-associated fibroblasts. Scan statistics revealed clustering in the number of significant gene-sets. A spatial heatmap of combined significance over all selected gene-sets is also produced. Extensive simulation studies demonstrate that our proposed approach outperforms other methods in the considered scenarios, especially when the spatial association increases. Conclusion: Our proposed approach considers the spatial covariance of gene expression to detect the most significant gene-sets affecting a continuous phenotype. It reveals spatially detailed information in tissue space and can thus play a key role in understanding the contextual heterogeneity of cancer cells

Globaltest and GOEAST: two different approaches for Gene Ontology analysis

Background Gene set analysis is a commonly used method for analysing microarray data by considering groups of functionally related genes instead of individual genes. Here we present the use of two gene set analysis approaches: Globaltest and GOEAST. Globaltest is a method for testing whether sets of genes are significantly associated with a variable of interest. GOEAST is a freely accessible web-based tool to test GO term enrichment within given gene sets. The two approaches were applied in the analysis of gene lists obtained from three different contrasts in a microarray experiment conducted to study the host reactions in broilers following Eimeria infection. Results The Globaltest identified significantly associated gene sets in one of the three contrasts made in the microarray experiment whereas the functional analysis of the differentially expressed genes using GOEAST revealed enriched GO terms in all three contrasts. Conclusion Globaltest and GOEAST gave different results, probably due to the different algorithms and the different criteria used for evaluating the significance of GO terms

The relation between stimulated salivary flow and the temporal consumption experience of a liquid oral nutritional supplement

Use of oral nutritional supplements (ONS) in undernourished patients has proven clinical benefits, but this can be hampered by low adherence due to poor experience of palatability. Many patients, particularly older patients, experience hyposalivation which can cause taste changes and reduce the enjoyment of foods. The aim of this study was to investigate differences in the temporal consumption experience (comprising sensory perception, in-mouth aroma release and subjective appetite) of a clinically relevant portion of ONS, for groups differing in saliva flow rates (SFR). The SFR (mL/min) of thirty healthy individuals was measured on three occasions. This data was used to categorise individuals into three groups using quartile analysis: low flow (LF) (0.3–0.6 mL/min, n = 5), medium flow (MF) (0.7–1.2 mL/min, n = 16) and high flow (HF) (1.3–1.8 mL/min, n = 9). Over the consumption of eight 15 mL sips of ONS, individuals rated their sensory perception and subjective appetite perception using line scales. Additionally, in-mouth aroma release was measured for each sip, using atmospheric pressure chemical ionisation (APCI). Compared with the MF and HF group, the LF group reported a significantly greater increase of mouth-drying over increased sips (p = 0.02). The LF group also experienced significantly higher aftertaste perception (p < 0.001), and more intense in-mouth aroma release (p = 0.015), compared with the HF group. These findings occurred concurrently with relatively lower hunger sensations in the LF and MF group. Many patients who are prescribed ONS likely experience reduced salivary flow rates. The unique sensory experiences of these individuals should be considered in order to optimise palatability and nutritional intake

Supporting Roma Voices

The Supporting Roma Voice project has aimed to address emerging knowledge gaps in the way in which the inclusion of migrant Roma in the UK is being addressed. Specifically, research by Brown, Scullion and Martin (2013) identified a demand from public authorities for social inclusion work directed towards migrant Roma communities to be developed and delivered by members of migrant Roma communities themselves. However, what was also lacking was an adequate evidence base about the settlement of migrant Roma in the UK and the varied experiences associated with this transition. This report explores the views and experiences of a large number of Roma people who have migrated to the UK in recent years. The research was designed in partnership with a team of researchers from the Roma communities and undertaken wholly by these researchers. The research study aimed to explore the following issues: - The settlement and integration experiences of Roma migrants living in areas across the UK. - The specific areas of community relations, housing, education, employment and social welfare and their role in settlement in the UK. - The provision of knowledge that would enable local authorities and other services to enhance the settlement experience of Roma migrants now and in the future. A total of 159 people participated in 19 focus groups, which took place in the following locations: Glasgow, Leicester, London, Oldham, Salford and Sheffield. It should be noted that owing to the heterogeneity of the Roma population this report does not attempt to make definitive statements about the situation and views of all Roma migrants in the UK. This report was co-authored by members of the academic team in partnership with community researchers. The fieldwork was undertaken in early 2016 prior to the UK’s referendum on staying in the European Union

Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets

<p>Abstract</p> <p>Background</p> <p>Analysis of microarray experiments often involves testing for the overrepresentation of pre-defined sets of genes among lists of genes deemed individually significant. Most popular gene set testing methods assume the independence of genes within each set, an assumption that is seriously violated, as extensive correlation between genes is a well-documented phenomenon.</p> <p>Results</p> <p>We conducted a meta-analysis of over 200 datasets from the Gene Expression Omnibus in order to demonstrate the practical impact of strong gene correlation patterns that are highly consistent across experiments. We show that a common independence assumption-based gene set testing procedure produces very high false positive rates when applied to data sets for which treatment groups have been randomized, and that gene sets with high internal correlation are more likely to be declared significant. A reanalysis of the same datasets using an array resampling approach properly controls false positive rates, leading to more parsimonious and high-confidence gene set findings, which should facilitate pathway-based interpretation of the microarray data.</p> <p>Conclusions</p> <p>These findings call into question many of the gene set testing results in the literature and argue strongly for the adoption of resampling based gene set testing criteria in the peer reviewed biomedical literature.</p

Prototype ATLAS IBL Modules using the FE-I4A Front-End Readout Chip

The ATLAS Collaboration will upgrade its semiconductor pixel tracking detector with a new Insertable B-layer (IBL) between the existing pixel detector and the vacuum pipe of the Large Hadron Collider. The extreme operating conditions at this location have necessitated the development of new radiation hard pixel sensor technologies and a new front-end readout chip, called the FE-I4. Planar pixel sensors and 3D pixel sensors have been investigated to equip this new pixel layer, and prototype modules using the FE-I4A have been fabricated and characterized using 120 GeV pions at the CERN SPS and 4 GeV positrons at DESY, before and after module irradiation. Beam test results are presented, including charge collection efficiency, tracking efficiency and charge sharing.Comment: 45 pages, 30 figures, submitted to JINS