2D Raman band splitting in graphene: charge screening and lifting of the K-point Kohn anomaly

Pristine graphene encapsulated in hexagonal boron nitride has transport properties rivalling suspended graphene, while being protected from contamination and mechanical damage. For high quality devices, it is important to avoid and monitor accidental doping and charge fluctuations. The 2D Raman double peak in intrinsic graphene can be used to optically determine charge density, with decreasing peak split corresponding to increasing charge density. We find strong correlations between the 2D 1 and 2D 2 split vs 2D line widths, intensities, and peak positions. Charge density fluctuations can be measured with orders of magnitude higher precision than previously accomplished using the G-band shift with charge. The two 2D intrinsic peaks can be associated with the “inner” and “outer” Raman scattering processes, with the counterintuitive assignment of the phonon closer to the K point in the KM direction (outer process) as the higher energy peak. Even low charge screening lifts the phonon Kohn anomaly near the K point for graphene encapsulated in hBN, and shifts the dominant intensity from the lower to the higher energy peak.This work was supported by the United States National Science Foundation (DMR 1411008, DMR 1308659). J.C. thanks the Department of Defence (DoD), Air Force Office of Scientific Research for its support through the National Defence Science and Engineering Graduate (NDSEG) Fellowship, 32 CFR 168a. The authors would like to thank Cory Dean and Carlos Forsythe for the graphene encapsulated hBN sample. (DMR 1411008 - United States National Science Foundation; DMR 1308659 - United States National Science Foundation; 32 CFR 168a - Department of Defence (DoD), Air Force Office of Scientific Research through the National Defence Science and Engineering Graduate (NDSEG) Fellowship

Immune gene expression profiling of Proliferative Kidney Disease in rainbow trout Oncorhynchus mykiss reveals a dominance of anti-inflammatory, antibody and T helper cell-like activities

Peer reviewedPublisher PD

Characterization of BAFF and APRIL subfamily receptors in rainbow trout (Oncorhynchus mykiss). Potential role of the BAFF/APRIL axis in the pathogenesis of proliferative kidney disease

We would like to thank Lucia González for technical assistance and Rosario Castro for producing some of the cDNAs used in this study. This work was supported by the European Research Council (ERC Starting Grant 2011 280469) and by the European Commission under the 7th Framework Programme for Research and Technological Development (FP7) of the European Union (Grant Agreement 311993 TARGETFISH) and under the Horizon H2020 research and innovation programme (Grant H2020-634429 ParaFishControl). This work was also partially funded by project AGL2014-54456-JIN from the Spanish Ministry of Economy and Competitiveness (MINECO). JWH was supported by the Swiss National Science Foundation (grant reference CRSII3_147649-1).Peer reviewedPublisher PD

Epithelial cell specific Raptor is required for initiation of type 2 mucosal immunity in small intestine

AbstractIntestinal tuft cells are one of 4 secretory cell linages in the small intestine and the source of IL-25, a critical initiator of the type 2 immune response to parasite infection. When Raptor, a critical scaffold protein for mammalian target of rapamycin complex 1 (mTORC1), was acutely deleted in intestinal epithelium via Tamoxifen injection in Tritrichomonas muris (Tm) infected mice, tuft cells, IL-25 in epithelium and IL-13 in the mesenchyme were significantly reduced, but Tm burden was not affected. When Tm infected mice were treated with rapamycin, DCLK1 and IL-25 expression in enterocytes and IL-13 expression in mesenchyme were diminished. After massive small bowel resection, tuft cells and Tm were diminished due to the diet used postoperatively. The elimination of Tm and subsequent re-infection of mice with Tm led to type 2 immune response only in WT, but Tm colonization in both WT and Raptor deficient mice. When intestinal organoids were stimulated with IL-4, tuft cells and IL-25 were induced in both WT and Raptor deficient organoids. In summary, our study reveals that enterocyte specific Raptor is required for initiating a type 2 immune response which appears to function through the regulation of mTORC1 activity.</jats:p

Using calculus of variations to optimize paths of descent through ski race courses

Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Physics, 2005.Includes bibliographical references (p. 69-70).The goal of ski racing is to pass through a series of gates as quickly as possible. There are many paths from gate to gate, but there is only one path that is fastest. By knowing what the fastest path is, a racer could shave tenths of seconds off his or her time. That is a tremendous amount of time considering that races are won by hundredths of a second. This thesis attempts to calculate the fastest path through a ski race course using several simplifications such as neglecting friction. The method of attacking this problem is to modify the Brachistochrone problem. It is found that it is best if the skier places the apex of the turn at the gate, and that turning more after the gate is better than turning more above the gate. In the case of a rhythmical course, it is found that turning more below the gate is still true, but not as evident. Instead the optimal path appears more symmetric about the gate.by Jason W. Christopher.S.B

A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data

A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with highthroughput data including expression data, metabolomics, or DNA sequencing. The desired result is to increase predictive capability resulting in improved understanding of metabolism. The approach typically employed when only gene (or protein) intensities are available is the creation of tissue-specific models, which reduces the available reactions in an organism model, and does not provide an objective function for the estimation of fluxes, which is an important limitation in many modeling applications. We develop a method, flux assignment with LAD (least absolute deviation) convex objectives and normalization (FALCON), that employs metabolic network reconstructions along with expression data to estimate fluxes. In order to use such a method, accurate measures of enzyme complex abundance are needed, so we first present a new algorithm that addresses quantification of complex abundance. Our extensions to prior techniques include the capability to work with large models and significantly improved run-time performance even for smaller models, an improved analysis of enzyme complex formation logic, the ability to handle very large enzyme complex rules that may incorporate multiple isoforms, and depending on the model constraints, either maintained or significantly improved correlation with experimentally measured fluxes. FALCON has been implemented in MATLAB and ATS, and can be downloaded from: https://github.com/bbarker/FALCON. ATS is not required to compile the software, as intermediate C source code is available, and binaries are provided for Linux x86-64 systems. FALCON requires use of the COBRA Toolbox, also implemented in MATLAB.Comment: 30 pages, 12 figures, 4 table

Random Access in Nondelimited Variable-length Record Collections for Parallel Reading with Hadoop

The industry standard Packet CAPture (PCAP) format for storing network packet traces is normally only readable in serial due to its lack of delimiters, indexing, or blocking. This presents a challenge for parallel analysis of large networks, where packet traces can be many gigabytes in size. In this work we present RAPCAP, a novel method for random access into variable-length record collections like PCAP by identifying a record boundary within a small number of bytes of the access point. Unlike related heuristic methods that can limit scalability with a nonzero probability of error, the new method offers a correctness guarantee with a well formed file and does not rely on prior knowledge of the contents. We include a practical implementation of the algorithm with an extension to the Hadoop framework, and a performance comparison to serial ingestion. Finally, we present a number of similar storage types that could utilize a modified version of RAPCAP for random access

K2-231 b: A sub-Neptune exoplanet transiting a solar twin in Ruprecht 147

We identify a sub-Neptune exoplanet ($R_p = 2.5 \pm 0.2$ R$_\oplus$) transiting a solar twin in the Ruprecht 147 star cluster (3 Gyr, 300 pc, [Fe/H] = +0.1 dex). The ~81 day light curve for EPIC 219800881 (V = 12.71) from K2 Campaign 7 shows six transits with a period of 13.84 days, a depth of ~0.06%, and a duration of ~4 hours. Based on our analysis of high-resolution MIKE spectra, broadband optical and NIR photometry, the cluster parallax and interstellar reddening, and isochrone models from PARSEC, Dartmouth, and MIST, we estimate the following properties for the host star: $M_\star = 1.01 \pm 0.03$ M$_\odot$, $R_\star= 0.95 \pm 0.03$ R$_\odot$, and $T_{\rm eff} = 5695 \pm 50$ K. This star appears to be single, based on our modeling of the photometry, the low radial velocity variability measured over nearly ten years, and Keck/NIRC2 adaptive optics imaging and aperture-masking interferometry. Applying a probabilistic mass-radius relation, we estimate that the mass of this planet is $M_p = 7 +5 -3$ M$_\oplus$, which would cause a RV semi-amplitude of $K = 2 \pm 1$ m s$^{-1}$ that may be measurable with existing precise RV facilities. After statistically validating this planet with BLENDER, we now designate it K2-231 b, making it the second sub-stellar object to be discovered in Ruprecht 147 and the first planet; it joins the small but growing ranks of 23 other planets found in open clusters.Comment: 24 pages, 7 figures, light curve included as separate fil