Two-photon interference with continuous-wave multi-mode coherent light

We report two-photon interference with continuous-wave multi-mode coherent light. We show that the two-photon interference, in terms of the detection time difference, reveals two-photon beating fringes with the visibility $V = 0.5$. While scanning the optical delay of the interferometer, Hong-Ou-Mandel dips or peaks are measured depending on the chosen detection time difference. The HOM dips/peaks are repeated when the optical delay and the first-order coherence revival period of the multi-mode coherent light are the same.Comment: 9 pages, 5 figure

Comparison of Power Dependence of Microwave Surface Resistance of Unpatterned and Patterned YBCO Thin Film

The effect of the patterning process on the nonlinearity of the microwave surface resistance $R_S$ of YBCO thin films is investigated. With the use of a sapphire dielectric resonator and a stripline resonator, the microwave $R_S$ of YBCO thin films was measured before and after the patterning process, as a function of temperature and the rf peak magnetic field in the film. The microwave loss was also modeled, assuming a $J_{rf}^2$ dependence of $Z_S(J_{rf})$ on current density $J_{rf}$. Experimental and modeled results show that the patterning has no observable effect on the microwave residual $R_S$ or on the power dependence of $R_S$.Comment: Submitted to IEEE Trans. MT

CpG Island Methylation in Colorectal Cancer: Past, Present and Future

The concept of a CpG island methylator phenotype, or CIMP, quickly became the focus of several colorectal cancer studies describing its clinical and pathological features after its introduction in 1999 by Toyota and colleagues. Further characterization of CIMP in tumors lead to widespread acceptance of the concept, as expressed by Shen and Issa in their 2005 editorial, “CIMP, at last.” Since that time, extensive research efforts have brought great insights into the epidemiology and prognosis of CIMP+ tumors and other epigenetic mechanisms underlying tumorigenesis. With the advances in technology and subsequent cataloging of the human methylome in cancer and normal tissue, new directions in research to understand CIMP and its role in complex biological systems yield hope for future epigenetically based diagnostics and treatments

Exploring multilocus associations of inflammation genes and colorectal cancer risk using hapConstructor

<p>Abstract</p> <p>Background</p> <p>In candidate-gene association studies of single nucleotide polymorphisms (SNPs), multilocus analyses are frequently of high dimensionality when considering haplotypes or haplotype pairs (diplotypes) and differing modes of expression. Often, while candidate genes are selected based on their biological involvement in a given pathway, little is known about the functionality of SNPs to guide association studies. Investigators face the challenge of exploring multiple SNP models to elucidate which variants, independently or in combination, might be associated with a disease of interest. A data mining module, hapConstructor (freely-available in Genie software) performs systematic construction and association testing of multilocus genotype data in a Monte Carlo framework. Our objective was to assess its utility to guide statistical analyses of haplotypes within a candidate region (or combined genotypes across candidate genes) beyond that offered by a standard logistic regression approach.</p> <p>Methods</p> <p>We applied the hapConstructor method to a multilocus investigation of candidate genes involved in pro-inflammatory cytokine IL6 production, <it>IKBKB</it>, <it>IL6</it>, and <it>NFKB1 </it>(16 SNPs total) hypothesized to operate together to alter colorectal cancer risk. Data come from two U.S. multicenter studies, one of colon cancer (1,556 cases and 1,956 matched controls) and one of rectal cancer (754 cases and 959 matched controls).</p> <p>Results</p> <p>HapConstrcutor enabled us to identify important associations that were further analyzed in logistic regression models to simultaneously adjust for confounders. The most significant finding (nominal <it>P </it>= 0.0004; false discovery rate <it>q </it>= 0.037) was a combined genotype association across <it>IKBKB </it>SNP rs5029748 (1 or 2 variant alleles), <it>IL6 </it>rs1800797 (1 or 2 variant alleles), and <it>NFKB1 </it>rs4648110 (2 variant alleles) which conferred an ~80% decreased risk of colon cancer.</p> <p>Conclusions</p> <p>Strengths of hapConstructor were: systematic identification of multiple loci within and across genes important in CRC risk; false discovery rate assessment; and efficient guidance of subsequent logistic regression analyses.</p

ArborX: A Performance Portable Geometric Search Library

Searching for geometric objects that are close in space is a fundamental component of many applications. The performance of search algorithms comes to the forefront as the size of a problem increases both in terms of total object count as well as in the total number of search queries performed. Scientific applications requiring modern leadership-class supercomputers also pose an additional requirement of performance portability, i.e. being able to efficiently utilize a variety of hardware architectures. In this paper, we introduce a new open-source C++ search library, ArborX, which we have designed for modern supercomputing architectures. We examine scalable search algorithms with a focus on performance, including a highly efficient parallel bounding volume hierarchy implementation, and propose a flexible interface making it easy to integrate with existing applications. We demonstrate the performance portability of ArborX on multi-core CPUs and GPUs, and compare it to the state-of-the-art libraries such as Boost.Geometry.Index and nanoflann

Development of the Model Marine Diatom Phaeodactylum tricornutum for Synthetic Biology Applications

Harnessing organisms for protein and chemical production is useful to the scientific community and has applications in the fuel, food, and pharmaceutical industries. Biological systems commonly used for industrial chemical production include yeast and bacteria due to their fast growth rates and potential for high product yields. However, biologically active proteins, such as for human therapeutics, usually require production in mammalian and insect systems that are prohibitively expensive to grow at scale. Recently, photoautotrophic microalgae have emerged as promising platforms, as some species can be grown quickly and inexpensively at large scales and have the potential to produce biologically active proteins that mimic those produced in mammalian systems. Thus, they combine advantages from several traditional biological systems, but require further genetic and biotechnological development for their full potential to be unlocked. Ideal biological production systems generally possess a variety of genetic tools to enable foreign gene expression, and genome editing systems to create desired genetic modifications. Here I present a robust gene editing system, novel genetic tools, and valuable strains for the microalga Phaeodactylum tricornutum. First, I identify novel endogenous regulatory elements that can drive expression of foreign genes in P. tricornutum, and design a plasmid-based Cas9 gene editing system for this species. Next, I demonstrate the utility of these tools with the generation of auxotrophic P. tricornutum strains through the genetic knockout of key enzymes in the uracil and histidine biosynthesis pathways. I complement the phenotype of the auxotrophs by introducing intact versions of these genes on replicating plasmids and demonstrate that these genes function as selective markers for transformation of their respective auxotrophic strain. Finally, I highlight the potential of these tools by creating a P. tricornutum expression system for the production of SARS-CoV-2 antigens. This will potentially address the need for a cheap, scalable source of serologically-active antigens for population-wide serological testing to combat the SARS-CoV-2 pandemic, and this system can be rapidly adapted to tackle future pandemics. I hope that these novel tools and strains will broaden the potential applications of P. tricornutum for industrial production of high-value products, and further the study of diatom biology

Genetic Variation in Selenoprotein Genes, Lifestyle, and Risk of Colon and Rectal Cancer

BACKGROUND: Associations between selenium and cancer have directed attention to role of selenoproteins in the carcinogenic process. METHODS: We used data from two population-based case-control studies of colon (n = 1555 cases, 1956 controls) and rectal (n = 754 cases, 959 controls) cancer. We evaluated the association between genetic variation in TXNRD1, TXNRD2, TXNRD3, C11orf31 (SelH), SelW, SelN1, SelS, SepX, and SeP15 with colorectal cancer risk. RESULTS: After adjustment for multiple comparisons, several associations were observed. Two SNPs in TXNRD3 were associated with rectal cancer (rs11718498 dominant OR 1.42 95% CI 1.16,1.74 pACT 0.0036 and rs9637365 recessive 0.70 95% CI 0.55,0.90 pACT 0.0208). Four SNPs in SepN1 were associated with rectal cancer (rs11247735 recessive OR 1.30 95% CI 1.04,1.63 pACT 0.0410; rs2072749 GGvsAA OR 0.53 95% CI 0.36,0.80 pACT 0.0159; rs4659382 recessive OR 0.58 95% CI 0.39,0.86 pACT 0.0247; rs718391 dominant OR 0.76 95% CI 0.62,0.94 pACT 0.0300). Interaction between these genes and exposures that could influence these genes showed numerous significant associations after adjustment for multiple comparisons. Two SNPs in TXNRD1 and four SNPs in TXNRD2 interacted with aspirin/NSAID to influence colon cancer; one SNP in TXNRD1, two SNPs in TXNRD2, and one SNP in TXNRD3 interacted with aspirin/NSAIDs to influence rectal cancer. Five SNPs in TXNRD2 and one in SelS, SeP15, and SelW1 interacted with estrogen to modify colon cancer risk; one SNP in SelW1 interacted with estrogen to alter rectal cancer risk. Several SNPs in this candidate pathway influenced survival after diagnosis with colon cancer (SeP15 and SepX1 increased HRR) and rectal cancer (SepX1 increased HRR). CONCLUSIONS: Findings support an association between selenoprotein genes and colon and rectal cancer development and survival after diagnosis. Given the interactions observed, it is likely that the impact of cancer susceptibility from genotype is modified by lifestyle

Drag coefficients of microscopic spheres in free-molecule flow

Drag coefficients of microscopic spheres in free molecule flo