Regulatory T cells in melanoma revisited by a computational clustering of FOXP3+ T cell subpopulations

CD4+ T cells that express the transcription factor FOXP3 (FOXP3+ T cells) are commonly regarded as immunosuppressive regulatory T cells (Treg). FOXP3+ T cells are reported to be increased in tumour-bearing patients or animals, and considered to suppress anti-tumour immunity, but the evidence is often contradictory. In addition, accumulating evidence indicates that FOXP3 is induced by antigenic stimulation, and that some non-Treg FOXP3+ T cells, especially memory-phenotype FOXP3low cells, produce proinflammatory cytokines. Accordingly, the subclassification of FOXP3+ T cells is fundamental for revealing the significance of FOXP3+ T cells in tumour immunity, but the arbitrariness and complexity of manual gating have complicated the issue. Here we report a computational method to automatically identify and classify FOXP3+ T cells into subsets using clustering algorithms. By analysing flow cytometric data of melanoma patients, the proposed method showed that the FOXP3+ subpopulation that had relatively high FOXP3, CD45RO, and CD25 expressions was increased in melanoma patients, whereas manual gating did not produce significant results on the FOXP3+ subpopulations. Interestingly, the computationally-identified FOXP3+ subpopulation included not only classical FOXP3high Treg but also memory-phenotype FOXP3low cells by manual gating. Furthermore, the proposed method successfully analysed an independent dataset, showing that the same FOXP3+ subpopulation was increased in melanoma patients, validating the method. Collectively, the proposed method successfully captured an important feature of melanoma without relying on the existing criteria of FOXP3+ T cells, revealing a hidden association between the T cell profile and melanoma, and providing new insights into FOXP3+ T cells and Treg

Electronic excitation of carbonyl sulphide (COS) by high-resolution vacuum ultraviolet photoabsorption and electron-impact spectroscopy in the energy region from 4 to 11 eV

The electronic state spectroscopy of carbonyl sulphide, COS, has been investigated using high resolution vacuum ultraviolet photoabsorption spectroscopy and electron energy loss spectroscopy in the energy range of 4.0–10.8 eV. The spectrum reveals several new features not previously reported in the literature. Vibronic structure has been observed, notably in the low energy absorption dipole forbidden band assigned to the (4π←3π) (1Δ←1Σ+) transition, with a new weak transition assigned to (1Σ−←1Σ+) reported here for the first time. The absolute optical oscillator strengths are determined for ground state to 1Σ+ and 1Π transitions. Based on our recent measurements of differential cross sections for the optically allowed (1Σ+ and 1Π) transitions of COS by electron impact, the optical oscillator strength f0 value and integral cross sections (ICSs) are derived by applying a generalized oscillator strength analysis. Subsequently, ICSs predicted by the scaling are confirmed down to 60 eV in the intermediate energy region. The measured absolute photoabsorption cross sections have been used to calculate the photolysis lifetime of carbonyl sulphide in the upper stratosphere (20–50 km)

Z7Z_7 Orbifold Models in M-Theory

Among $T^7/\Gamma$ orbifold compactifications of $M$-theory, we examine models containing the particle physics Standard Model in four-dimensional spacetimes, which appear as fixed subspaces of the ten-dimensional spacetimes at each end of the interval, $I^1\simeq S^1/Z_2$, spanning the $11^\text{th}$ dimension. Using the $Z_7$ projection to break the $E_8$ gauge symmetry in each of the four-planes and a limiting relation to corresponding heterotic string compactifications, we discuss the restrictions on the possible resulting gauge field and matter spectra. In particular, some of the states are non-local: they connect two four-dimensional Worlds across the $11^\text{th}$ dimension. We illustrate our programmable calculations of the matter field spectrum, including the anomalous U(1) factor which satisfies a universal Green-Schwarz relation, discuss a Dynkin diagram technique to showcase a model with $SU(3)\times SU(2)\times U(1)^5$ gauge symmetry, and discuss generalizations to higher order orbifolds.Comment: 23 pages, 2 figures, 4 tables; LaTeX 3 time

Prospects for improving the sensitivity of KAGRA gravitational wave detector

KAGRA is a new gravitational wave detector which aims to begin joint observation with Advanced LIGO and Advanced Virgo from late 2019. Here, we present KAGRA's possible upgrade plans to improve the sensitivity in the decade ahead. Unlike other state-of-the-art detectors, KAGRA requires different investigations for the upgrade since it is the only detector which employs cryogenic cooling of the test mass mirrors. In this paper, investigations on the upgrade plans which can be realized by changing the input laser power, increasing the mirror mass, and injecting frequency dependent squeezed vacuum are presented. We show how each upgrade affects to the detector frequency bands and also discuss impacts on gravitational-wave science. We then propose an effective progression of upgrades based on technical feasibility and scientific scenarios

Elastic differential cross sections for C4F6 isomers in the 1.5-200 eV energy electron impact: Similarities with six fluorine containing molecules and evidence of F-atom like scattering

11 págs.; 4 figs.; 4 tabs.© 2014 AIP Publishing LLC. We report absolute elastic differential cross sections for electron interactions with the C4F6 isomers, hexafluoro-1,3-butadiene (1,3-C4F6), hexafluoro-2-butyne (2-C4F6), and hexafluorocyclobutene (c-C4F6). The incident electron energy range is 1.5-200 eV, and the scattered electron angular range for the differential measurements varies from 15° to 150°. In all cases the absolute scale of the differential cross section was set using the relative flow technique, with helium as the reference species. Atomic-like behaviour in these scattering systems is shown here for the first time, and is further investigated by comparing the elastic cross sections for the C4F6 isomers with other fluorinated molecules, such as SF6 and CnF6 (n = 2, 3, and 6). We note that for all the six-F containing molecules, the scattering process for electron energies above 30 eV is indistinguishable. Finally, we report results for calculations of elastic differential cross sections for electron scattering from each of these isomers, within an optical potential method and assuming a screened corrected independent atom representation. The level of agreement between these calculations and our measurements is found to be quite remarkable in all cases.F.B. and G.G. acknowledge the partial financial support from the Spanish Ministerio de Economia y Competitividad (Project No. FIS 2012-31230). This work forms part of the EU/ESF COST Action CM0805 programme “The Chemical Cosmos”.Peer Reviewe

Structure and mechanism of human DNA polymerase η

The variant form of the human syndrome xeroderma pigmentosum (XPV) is caused by a deficiency in DNA polymerase eta (Pol eta), a DNA polymerase that enables replication through ultraviolet-induced pyrimidine dimers. Here we report high-resolution crystal structures of human Pol eta at four consecutive steps during DNA synthesis through cis-syn cyclobutane thymine dimers. Pol eta acts like a 'molecular splint' to stabilize damaged DNA in a normal B-form conformation. An enlarged active site accommodates the thymine dimer with excellent stereochemistry for two-metal ion catalysis. Two residues conserved among Pol eta orthologues form specific hydrogen bonds with the lesion and the incoming nucleotide to assist translesion synthesis. On the basis of the structures, eight Pol eta missense mutations causing XPV can be rationalized as undermining the molecular splint or perturbing the active-site alignment. The structures also provide an insight into the role of Pol eta in replicating through D loop and DNA fragile sites

Genomic Aberrations and Cellular Heterogeneity in SV40-Immortalized Human Corneal Epithelial Cells

purpose. Simian virus (SV)40–immortalized human corneal epithelial (HCE-T) cells have been widely used as an in vitro model of human corneal epithelial cells. The nature of this cell line was assessed for genomic aberrations and cellular heterogeneity. methods. For the quantitative measurement of genomic aberrations, array-based comparative genomic hybridization (CGH) analysis was performed. For identification of cellular heterogeneity, cell morphology, growth kinetics, transepithelial electrical resistance, and transfection/transcriptional efficiency were analyzed. Real-time PCR and chromosomal fluorescent in situ hybridization (cFISH) against some gained or lost loci were performed, to assess genomic heterogeneity. Expressed sequence tags (ESTs) for this cell line were collected to assess differences in the gene expression profiles between HCE-T cells and normal corneal epithelial cells. Southern blot analysis and inverse PCR analyses were used to determine the genomic integration site of the SV40 large T antigen gene (LTAG). results. Array CGH analysis demonstrated that the genomic content of HCE-T cells is different from the normal healthy genome. The results from cellular functional assays, real-time PCR, and cFISH strongly indicated that HCE-T cells consist of a significant number of heterogeneous cell populations. The genomic integration site of the SV40 large T antigen was at p22.1 of chromosome 9. conclusions. The results indicate that HCE-T cells have an altered genomic content and that they are composed of heterogeneous cell populations. This should be considered when conducting experiments or interpreting the results of studies that use this cell line