Accurate determination of the chiral indices of individual carbon nanotubes by combining electron diffraction and Resonant Raman spectroscopy

The experimental approach combining high resolution transmission electron microscopy (HRTEM), electron diffraction (ED) and resonant Raman spectroscopy (RRS) on the same free-standing individual carbon nanotubes (CNT) is the most efficient method to determine unambiguously the intrinsic features of the Raman-active phonons. In this paper, we review the main results obtained by the approach regarding the intrinsic features of the phonons of single-walled (SWNT) and double-walled carbon nanotubes (DWNT). First, we detail the different methods to identify the structure of SWNTs and DWNTs from the analysis of their electron diffraction patterns (EDP). In the following, we remind the principal features of the Raman response of SWNTs, unambiguously index-identified by ED. A special attention is devoted to the effect of the inter-layer interaction on the frequencies of the Raman-active phonons in index-identified DWNTs. The information obtained on index-identified SWNT and DWNT allows us to propose Raman criteria, which help identifying CNT when the ED fails to propose a single assignment. The efficiency of the Raman criteria as the complement to the ED information for the index-assignment of a few SWNTs and DWNTs is shown. The same approach to index-assign a triple-walled carbon nanotube (TWNT), by combining ED and RRS information, is reported

Interlayer Dependence of G-Modes in Semiconducting Double-Walled Carbon Nanotubes

A double-walled carbon nanotube (DWNT), a coaxial composite of two single walled carbon nanotubes (SWNT), provides a unique model to study interactions between thetwo constituent SWNTs. Combining high resolution transmission electron microscopy (HRTEM), electron diffraction (ED), and resonant Raman scattering (RRS) experiments on the same individual suspended DWNT is the ultimate way to relate unambiguously its atomicstructure, defined by the chiral indices of the coaxial outer/inner SWNTs, and its Raman-active vibration modes. This approach is used to investigate the intertube distance dependence of theG-modes of individual index-identified DWNTs composed of two semiconducting SWNTs.We state the main features of the dependence of the G-mode frequencies on the distance between the inner and outer layers: (i) When the interlayer distance is larger than the nominal van der Waals distance (close to 0.34 nm), a downshift of the inner-layer G-modes with respectto the G-modes in the equivalent SWNTs is measured. (ii) The amplitude of the downshiftdepends on the interlayer distance, or in other words, on the negative pressure felt by the innerlayer in DWNT. (iii) No shift is observed for an intertube distance close to 0.34 nm

FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

Background Likelihood (ML)-based phylogenetic inference has become a popular method for estimating the evolutionary relationships among species based on genomic sequence data. This method is used in applications such as RAxML, GARLI, MrBayes, PAML, and PAUP. The Phylogenetic Likelihood Function (PLF) is an important kernel computation for this method. The PLF consists of a loop with no conditional behavior or dependencies between iterations. As such it contains a high potential for exploiting parallelism using micro-architectural techniques. In this paper, we describe a technique for mapping the PLF and supporting logic onto a Field Programmable Gate Array (FPGA)-based co-processor. By leveraging the FPGA\u27s on-chip DSP modules and the high-bandwidth local memory attached to the FPGA, the resultant co-processor can accelerate ML-based methods and outperform state-of-the-art multi-core processors. Results We use the MrBayes 3 tool as a framework for designing our co-processor. For large datasets, we estimate that our accelerated MrBayes, if run on a current-generation FPGA, achieves a 10× speedup relative to software running on a state-of-the-art server-class microprocessor. The FPGA-based implementation achieves its performance by deeply pipelining the likelihood computations, performing multiple floating-point operations in parallel, and through a natural log approximation that is chosen specifically to leverage a deeply pipelined custom architecture. Conclusions Heterogeneous computing, which combines general-purpose processors with special-purpose co-processors such as FPGAs and GPUs, is a promising approach for high-performance phylogeny inference as shown by the growing body of literature in this field. FPGAs in particular are well-suited for this task because of their low power consumption as compared to many-core processors and Graphics Processor Units (GPUs)

Full-length human placental sFlt-1-e15a isoform induces distinct maternal phenotypes of preeclampsia in mice

<div><p>Objective</p><p>Most anti-angiogenic preeclampsia models in rodents utilized the overexpression of a truncated soluble fms-like tyrosine kinase-1 (sFlt-1) not expressed in any species. Other limitations of mouse preeclampsia models included stressful blood pressure measurements and the lack of postpartum monitoring. We aimed to 1) develop a mouse model of preeclampsia by administering the most abundant human placental sFlt-1 isoform (hsFlt-1-e15a) in preeclampsia; 2) determine blood pressures in non-stressed conditions; and 3) develop a survival surgery that enables the collection of fetuses and placentas and postpartum (PP) monitoring.</p><p>Methods</p><p>Pregnancy status of CD-1 mice was evaluated with high-frequency ultrasound on gestational days (GD) 6 and 7. Telemetry catheters were implanted in the carotid artery on GD7, and their positions were verified by ultrasound on GD13. Mice were injected through tail-vein with adenoviruses expressing hsFlt-1-e15a (n = 11) or green fluorescent protein (GFP; n = 9) on GD8/GD11. Placentas and pups were delivered by cesarean section on GD18 allowing PP monitoring. Urine samples were collected with cystocentesis on GD6/GD7, GD13, GD18, and PPD8, and albumin/creatinine ratios were determined. GFP and hsFlt-1-e15a expression profiles were determined by qRT-PCR. Aortic ring assays were performed to assess the effect of hsFlt-1-e15a on endothelia.</p><p>Results</p><p>Ultrasound predicted pregnancy on GD7 in 97% of cases. Cesarean section survival rate was 100%. Mean arterial blood pressure was higher in hsFlt-1-e15a-treated than in GFP-treated mice (∆MAP = 13.2 mmHg, p = 0.00107; GD18). Focal glomerular changes were found in hsFlt-1-e15a -treated mice, which had higher urine albumin/creatinine ratios than controls (109.3±51.7μg/mg vs. 19.3±5.6μg/mg, p = 4.4x10^-2; GD18). Aortic ring assays showed a 46% lesser microvessel outgrowth in hsFlt-1-e15a-treated than in GFP-treated mice (p = 1.2x10^-2). Placental and fetal weights did not differ between the groups. One mouse with liver disease developed early-onset preeclampsia-like symptoms with intrauterine growth restriction (IUGR).</p><p>Conclusions</p><p>A mouse model of late-onset preeclampsia was developed with the overexpression of hsFlt-1-e15a, verifying the <i>in vivo</i> pathologic effects of this primate-specific, predominant placental sFlt-1 isoform. HsFlt-1-e15a induced early-onset preeclampsia-like symptoms associated with IUGR in a mouse with a liver disease. Our findings support that hsFlt-1-e15a is central to the terminal pathway of preeclampsia, and it can induce the full spectrum of symptoms in this obstetrical syndrome.</p></div

Superconducting Photoinjector

One of the frontiers in FEL science is that of high power. In order to reach power in the megawatt range, one requires a current of the order of one ampere with a reasonably good emittance. The superconducting laser-photocathode RF gun with a high quantum efficiency photocathode is the most natural candidate to provide this performance. The development of a 1/2 cell superconducting photoinjector designed to operate at up to a current of 0.5 amperes and beam energy of 2 MeV and its photocathode system are the subjects covered in this paper. The main issues are the photocathode and its insertion mechanism, the power coupling and High Order Mode damping. This technology is being developed at BNL for DOE nuclear physics applications such as electron cooling at high energy and electron ion colliders.

Gluons and the quark sea at high energies:distributions, polarization, tomography

This report is based on a ten-week program on "Gluons and the quark sea at high-energies", which took place at the Institute for Nuclear Theory in Seattle in Fall 2010. The principal aim of the program was to develop and sharpen the science case for an Electron-Ion Collider (EIC), a facility that will be able to collide electrons and positrons with polarized protons and with light to heavy nuclei at high energies, offering unprecedented possibilities for in-depth studies of quantum chromodynamics. This report is organized around four major themes: i) the spin and flavor structure of the proton, ii) three-dimensional structure of nucleons and nuclei in momentum and configuration space, iii) QCD matter in nuclei, and iv) Electroweak physics and the search for physics beyond the Standard Model. Beginning with an executive summary, the report contains tables of key measurements, chapter overviews for each of the major scientific themes, and detailed individual contributions on various aspects of the scientific opportunities presented by an EIC

High-throughput profiling of caenorhabditis elegans starvation-responsive microRNAs

MicroRNAs (miRNAs) are non-coding RNAs of ~22 nucleotides in length that regulate gene expression by interfering with the stability and translation of mRNAs. Their expression is regulated during development, under a wide variety of stress conditions and in several pathological processes. In nature, animals often face feast or famine conditions. We observed that subjecting early L4 larvae from Caenorhabditis elegans to a 12-hr starvation period produced worms that are thinner and shorter than well-fed animals, with a decreased lipid accumulation, diminished progeny, reduced gonad size, and an increased lifespan. Our objective was to identify which of the 302 known miRNAs of C. elegans changed their expression under starvation conditions as compared to well-fed worms by means of deep sequencing in early L4 larvae. Our results indicate that 13 miRNAs (miR-34-3p, the family of miR-35-3p to miR-41-3p, miR-39-5p, miR-41-5p, miR-240-5p, miR-246-3p and miR-4813-5p) were upregulated, while 2 miRNAs (let-7-3p and miR-85-5p) were downregulated in 12-hr starved vs. well-fed early L4 larvae. Some of the predicted targets of the miRNAs that changed their expression in starvation conditions are involved in metabolic or developmental process. In particular, miRNAs of the miR-35 family were upregulated 6-20 fold upon starvation. Additionally, we showed that the expression of gld-1, important in oogenesis, a validated target of miR-35-3p, was downregulated when the expression of miR-35-3p was upregulated. The expression of another reported target, the cell cycle regulator lin-23, was unchanged during starvation. This study represents a starting point for a more comprehensive understanding of the role of miRNAs during starvation in C. elegans