Bragg spectroscopy of a strongly interacting Fermi gas

We present a comprehensive study of the Bose-Einstein condensate to Bardeen-Cooper-Schrieffer (BEC-BCS) crossover in fermionic $^6$Li using Bragg spectroscopy. A smooth transition from molecular to atomic spectra is observed with a clear signature of pairing at and above unitarity. These spectra probe the dynamic and static structure factors of the gas and provide a direct link to two-body correlations. We have characterised these correlations and measured their density dependence across the broad Feshbach resonance at 834 G.Comment: Replaced with published versio

Dynamical spin-flip susceptibility for a strongly interacting ultracold Fermi gas

The Stoner model predicts that a two-component Fermi gas at increasing repulsive interactions undergoes a ferromagnetic transition. Using the random-phase approximation we study the dynamical properties of the interacting Fermi gas. For an atomic Fermi gas under harmonic confinement we show that the transverse (spin-flip) dynamical susceptibility displays a clear signature of the ferromagnetic phase in a magnon peak emerging from the Stoner particle-hole continuum. The dynamical spin susceptibilities could be experimentally explored via spin-dependent Bragg spectroscopy.Comment: 4 pages, 3 figure

MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression

Background: Metagenomics is a genomics research discipline devoted to the study of microbial communities in environmental samples and human and animal organs and tissues. Sequenced metagenomic samples usually comprise reads from a large number of different bacterial communities and hence tend to result in large file sizes, typically ranging between 1–10 GB. This leads to challenges in analyzing, transferring and storing metagenomic data. In order to overcome these data processing issues, we introduce MetaCRAM, the first de novo, parallelized software suite specialized for FASTA and FASTQ format metagenomic read processing and lossless compression. Results: MetaCRAM integrates algorithms for taxonomy identification and assembly, and introduces parallel execution methods; furthermore, it enables genome reference selection and CRAM based compression. MetaCRAM also uses novel reference-based compression methods designed through extensive studies of integer compression techniques and through fitting of empirical distributions of metagenomic read-reference positions. MetaCRAM is a lossless method compatible with standard CRAM formats, and it allows for fast selection of relevant files in the compressed domain via maintenance of taxonomy information. The performance of MetaCRAM as a stand-alone compression platform was evaluated on various metagenomic samples from the NCBI Sequence Read Archive, suggesting 2- to 4-fold compression ratio improvements compared to gzip. On average, the compressed file sizes were 2-13 percent of the original raw metagenomic file sizes. Conclusions: We described the first architecture for reference-based, lossless compression of metagenomic data. The compression scheme proposed offers significantly improved compression ratios as compared to off-the-shelf methods such as zip programs. Furthermore, it enables running different components in parallel and it provides the user with taxonomic and assembly information generated during execution of the compression pipeline. Availability: The MetaCRAM software is freely available at http://web.engr.illinois.edu/~mkim158/metacram.html. The website also contains a README file and other relevant instructions for running the code. Note that to run the code one needs a minimum of 16 GB of RAM. In addition, virtual box is set up on a 4GB RAM machine for users to run a simple demonstration

An Exact Formula for the Average Run Length to False Alarm of the Generalized Shiryaev-Roberts Procedure for Change-Point Detection under Exponential Observations

We derive analytically an exact closed-form formula for the standard minimax Average Run Length (ARL) to false alarm delivered by the Generalized Shiryaev-Roberts (GSR) change-point detection procedure devised to detect a shift in the baseline mean of a sequence of independent exponentially distributed observations. Specifically, the formula is found through direct solution of the respective integral (renewal) equation, and is a general result in that the GSR procedure's headstart is not restricted to a bounded range, nor is there a "ceiling" value for the detection threshold. Apart from the theoretical significance (in change-point detection, exact closed-form performance formulae are typically either difficult or impossible to get, especially for the GSR procedure), the obtained formula is also useful to a practitioner: in cases of practical interest, the formula is a function linear in both the detection threshold and the headstart, and, therefore, the ARL to false alarm of the GSR procedure can be easily computed.Comment: 9 pages; Accepted for publication in Proceedings of the 12-th German-Polish Workshop on Stochastic Models, Statistics and Their Application

Regulation of DNA Repair Mechanism in Human Glioma Xenograft Cells both In Vitro and In Vivo in Nude Mice

Glioblastoma Multiforme (GBM) is the most lethal form of brain tumor. Efficient DNA repair and anti-apoptotic mechanisms are making glioma treatment difficult. Proteases such as MMP9, cathepsin B and urokinase plasminogen activator receptor (uPAR) are over expressed in gliomas and contribute to enhanced cancer cell proliferation. Non-homologous end joining (NHEJ) repair mechanism plays a major role in double strand break (DSB) repair in mammalian cells.Here we show that silencing MMP9 in combination with uPAR/cathepsin B effects NHEJ repair machinery. Expression of DNA PKcs and Ku70/80 at both mRNA and protein levels in MMP9-uPAR (pMU) and MMP9-cathepsin B (pMC) shRNA-treated glioma xenograft cells were reduced. FACS analysis showed an increase in apoptotic peak and proliferation assays revealed a significant reduction in the cell population in pMU- and pMC-treated cells compared to untreated cells. We hypothesized that reduced NHEJ repair led to DSBs accumulation in pMU- and pMC-treated cells, thereby initiating cell death. This hypothesis was confirmed by reduced Ku70/Ku80 protein binding to DSB, increased comet tail length and elevated γH2AX expression in treated cells compared to control. Immunoprecipitation analysis showed that EGFR-mediated lowered DNA PK activity in treated cells compared to controls. Treatment with pMU and pMC shRNA reduced the expression of DNA PKcs and ATM, and elevated γH2AX levels in xenograft implanted nude mice. Glioma cells exposed to hypoxia and irradiation showed DSB accumulation and apoptosis after pMU and pMC treatments compared to respective controls.Our results suggest that pMU and pMC shRNA reduce glioma proliferation by DSB accumulation and increase apoptosis under normoxia, hypoxia and in combination with irradiation. Considering the radio- and chemo-resistant cancers favored by hypoxia, our study provides important therapeutic potential of MMP9, uPAR and cathepsin B shRNA in the treatment of glioma from clinical stand point

Momentum-Resolved Bragg Spectroscopy in Optical Lattices

Strongly correlated many-body systems show various exciting phenomena in condensed matter physics such as high-temperature superconductivity and colossal magnetoresistance. Recently, strongly correlated phases could also be studied in ultracold quantum gases possessing analogies to solid-state physics, but moreover exhibiting new systems such as Fermi-Bose mixtures and magnetic quantum phases with high spin values. Particularly interesting systems here are quantum gases in optical lattices with fully tunable lattice and atomic interaction parameters. While in this context several concepts and ideas have already been studied theoretically and experimentally, there is still great demand for new detection techniques to explore these complex phases in detail. Here we report on measurements of a fully momentum-resolved excitation spectrum of a quantum gas in an optical lattice by means of Bragg spectroscopy. The bandstructure is measured with high resolution at several lattice depths. Interaction effects are identified and systematically studied varying density and excitation fraction.Comment: 13 pages, 5 figure

Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity.

Genome rearrangements, a hallmark of cancer, can result in gene fusions with oncogenic properties. Using DNA paired-end-tag (DNA-PET) whole-genome sequencing, we analyzed 15 gastric cancers (GCs) from Southeast Asians. Rearrangements were enriched in open chromatin and shaped by chromatin structure. We identified seven rearrangement hot spots and 136 gene fusions. In three out of 100 GC cases, we found recurrent fusions between CLDN18, a tight junction gene, and ARHGAP26, a gene encoding a RHOA inhibitor. Epithelial cell lines expressing CLDN18-ARHGAP26 displayed a dramatic loss of epithelial phenotype and long protrusions indicative of epithelial-mesenchymal transition (EMT). Fusion-positive cell lines showed impaired barrier properties, reduced cell-cell and cell-extracellular matrix adhesion, retarded wound healing, and inhibition of RHOA. Gain of invasion was seen in cancer cell lines expressing the fusion. Thus, CLDN18-ARHGAP26 mediates epithelial disintegration, possibly leading to stomach H(+) leakage, and the fusion might contribute to invasiveness once a cell is transformed. Cell Rep 2015 Jul 14; 12(2):272-285