Single cell analysis shows decreasing FoxP3 and TGFβ1 coexpressing CD4+CD25+ regulatory T cells during autoimmune diabetes

Natural CD4+CD25+ regulatory T (CD4+CD25+ T reg) cells play a key role in the immunoregulation of autoimmunity. However, little is known about the interactions between CD4+CD25+ T reg cells and autoreactive T cells. This is due, in part, to the difficulty of using cell surface markers to identify CD4+CD25+ T reg cells accurately. Using a novel real-time PCR assay, mRNA copy number of FoxP3, TGFβ1, and interleukin (IL)-10 was measured in single cells to characterize and quantify CD4+CD25+ T reg cells in the nonobese diabetic (NOD) mouse, a murine model for type 1 diabetes (T1D). The suppressor function of CD4+CD25+CD62Lhi T cells, mediated by TGFβ, declined in an age-dependent manner. This loss of function coincided with a temporal decrease in the percentage of FoxP3 and TGFβ1 coexpressing T cells within pancreatic lymph node and islet infiltrating CD4+CD25+CD62Lhi T cells, and was detected in female NOD mice but not in NOD male mice, or NOR or C57BL/6 female mice. These results demonstrate that the majority of FoxP3-positive CD4+CD25+ T reg cells in NOD mice express TGFβ1 but not IL-10, and that a defect in the maintenance and/or expansion of this pool of immunoregulatory effectors is associated with the progression of T1D

Translation and Community in the work of Elizabeth Cary

Explores the role of female community within Elizabeth Cary\u27s translations and her play, The Tragedy of Mariam

Optimum detection for extracting maximum information from symmetric qubit sets

We demonstrate a class of optimum detection strategies for extracting the maximum information from sets of equiprobable real symmetric qubit states of a single photon. These optimum strategies have been predicted by Sasaki et al. [Phys. Rev. A{\bf 59}, 3325 (1999)]. The peculiar aspect is that the detections with at least three outputs suffice for optimum extraction of information regardless of the number of signal elements. The cases of ternary (or trine), quinary, and septenary polarization signals are studied where a standard von Neumann detection (a projection onto a binary orthogonal basis) fails to access the maximum information. Our experiments demonstrate that it is possible with present technologies to attain about 96% of the theoretical limit.Comment: 10 pages, 11 figures, to be submitted to Phys. Rev. A Converted to REVTeX4 format, and a few other minor modifications according to the comments from PRA referre

Application of Low Coverage Genotyping by Sequencing in Selectively Bred Arctic Charr (Salvelinus alpinus)

Arctic charr (Salvelinus alpinus) is a species of high economic value for the aquaculture industry, and of high ecological value due to its Holarctic distribution in both marine and freshwater environments. Novel genome sequencing approaches enable the study of population and quantitative genetic parameters even on species with limited or no prior genomic resources. Low coverage genotyping by sequencing (GBS) was applied in a selected strain of Arctic charr in Sweden originating from a landlocked freshwater population. For the needs of the current study, animals from year classes 2013 (171 animals, parental population) and 2017 (759 animals; 13 full sib families) were used as a template for identifying genome wide single nucleotide polymorphisms (SNPs). GBS libraries were constructed using the PstI and MspI restriction enzymes. Approximately 14.5K SNPs passed quality control and were used for estimating a genomic relationship matrix. Thereafter a wide range of analyses were conducted in order to gain insights regarding genetic diversity and investigate the efficiency of the genomic information for parentage assignment and breeding value estimation. Heterozygosity estimates for both year classes suggested a slight excess of heterozygotes. Furthermore, F-ST estimates among the families of year class 2017 ranged between 0.009 - 0.066. Principal components analysis (PCA) and discriminant analysis of principal components (DAPC) were applied aiming to identify the existence of genetic clusters among the studied population. Results obtained were in accordance with pedigree records allowing the identification of individual families. Additionally, DNA parentage verification was performed, with results in accordance with the pedigree records with the exception of a putative dam where full sib genotypes suggested a potential recording error. Breeding value estimation for juvenile growth through the usage of the estimated genomic relationship matrix clearly outperformed the pedigree equivalent in terms of prediction accuracy (0.51 opposed to 0.31). Overall, low coverage GBS has proven to be a cost-effective genotyping platform that is expected to boost the selection efficiency of the Arctic charr breeding program

Spin-Charge Separation, Anomalous Scaling and the Coherence of Hopping in exactly solved Two Chain Models

The coherence of transport between two one-dimensional interacting Fermi liquids, coupled by single particle hopping and interchain interaction, is examined in the context of two exactly soluble models. It is found that the coherence of the inter-chain hopping depends on the interplay between inter-chain hopping and inter-chain interaction terms, and not simply on the ground state spectral properties of an isolated chain. Specifically, the splitting of levels in associated with interchain hopping in a $g_4$ soluble model is found to be enhanced by the introduction of interchain interaction. It is also shown that, for an exactly solvable model with both $g_2$ and $g_4$ interactions, coherent interchain hopping coexists with anomalous scaling and non-Fermi liquid behavior in the chain direction.Comment: Two postscript figure

Analysis of detector performance in a gigahertz clock rate quantum key distribution system

We present a detailed analysis of a gigahertz clock rate environmentally robust phase-encoded quantum key distribution (QKD) system utilizing several different single-photon detectors, including the first implementation of an experimental resonant cavity thin-junction silicon single-photon avalanche diode. The system operates at a wavelength of 850 nm using standard telecommunications optical fibre. A general-purpose theoretical model for the performance of QKD systems is presented with reference to these experimental results before predictions are made about realistic detector developments in this system. We discuss, with reference to the theoretical model, how detector operating parameters can be further optimized to maximize key exchange rates

Ba3Ga3N5 - A Novel Host Lattice for Eu2+ - Doped Luminescent Materials with Unexpected Nitridogallate Substructure

The alkaline earth nitridogallate Ba3Ga3N5 was synthesized from the elements in a sodium flux at 760°C utilizing weld shut tantalum ampules. The crystal structure was solved and refined on the basis of single-crystal X-ray diffraction data. Ba3Ga3N5 (space group C2/c (No. 15), a = 16.801(3), b = 8.3301(2), c = 11.623(2) Å, β = 109.92 (3)°, Z = 8) contains a hitherto unknown structural motif in nitridogallates, namely, infinite strands made up of GaN4 tetrahedra, each sharing two edges and at least one corner with neighboring GaN4 units. There are three Ba2+ sites with coordination numbers six or eight, respectively, and one Ba2+ position exhibiting a low coordination number 4 corresponding to a distorted tetrahedron. Eu2+ - doped samples show red luminescence when excited by UV irradiation at room temperature. Luminescence investigations revealed a maximum emission intensity at 638 nm (FWHM =2123 cm−1). Ba3Ga3N5 is the first nitridogallate for which parity allowed broadband emission due to Eu2+ - doping has been found. The electronic structure of both Ba3Ga3N5 as well as isoelectronic but not isostructural Sr3Ga3N5 was investigated by DFT methods. The calculations revealed a band gap of 1.53 eV for Sr3Ga3N5 and 1.46 eV for Ba3Ga3N5

Universal coding for classical-quantum channel

We construct a universal code for stationary and memoryless classical-quantum channel as a quantum version of the universal coding by Csisz\'{a}r and K\"{o}rner. Our code is constructed by the combination of irreducible representation, the decoder introduced through quantum information spectrum, and the packing lemma

An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data

Regulatory networks play a central role in cellular behavior and decision making. Learning these regulatory networks is a major task in biology, and devising computational methods and mathematical models for this task is a major endeavor in bioinformatics. Boolean networks have been used extensively for modeling regulatory networks. In this model, the state of each gene can be either ‘on’ or ‘off’ and that next-state of a gene is updated, synchronously or asynchronously, according to a Boolean rule that is applied to the current-state of the entire system. Inferring a Boolean network from a set of experimental data entails two main steps: first, the experimental time-series data are discretized into Boolean trajectories, and then, a Boolean network is learned from these Boolean trajectories. In this paper, we consider three methods for data discretization, including a new one we propose, and three methods for learning Boolean networks, and study the performance of all possible nine combinations on four regulatory systems of varying dynamics complexities. We find that employing the right combination of methods for data discretization and network learning results in Boolean networks that capture the dynamics well and provide predictive power. Our findings are in contrast to a recent survey that placed Boolean networks on the low end of the ‘‘faithfulness to biological reality’’ and ‘‘ability to model dynamics’’ spectra. Further, contrary to the common argument in favor of Boolean networks, we find that a relatively large number of time points in the timeseries data is required to learn good Boolean networks for certain data sets. Last but not least, while methods have been proposed for inferring Boolean networks, as discussed above, missing still are publicly available implementations thereof. Here, we make our implementation of the methods available publicly in open source at http://bioinfo.cs.rice.edu/