Hadron Masses From Novel Fat-Link Fermion Actions

The hadron mass spectrum is calculated in lattice QCD using a novel fat-link clover fermion action in which only the irrelevant operators in the fermion action are constructed using smeared links. The simulations are performed on a 16^3 x 32 lattice with a lattice spacing of a=0.125 fm. We compare actions with n=4 and 12 smearing sweeps with a smearing fraction of 0.7. The n=4 Fat-Link Irrelevant Clover (FLIC) action provides scaling which is superior to mean-field improvement, and offers advantages over nonperturbative 0(a) improvement, including a reduced exceptional configuration problem.Comment: 12 pages, 4 figures, new simulation with mean-field improved clover, further discussion of actio

Mixed correlation functions in the 2-matrix model, and the Bethe ansatz

Using loop equation technics, we compute all mixed traces correlation functions of the 2-matrix model to large N leading order. The solution turns out to be a sort of Bethe Ansatz, i.e. all correlation functions can be decomposed on products of 2-point functions. We also find that, when the correlation functions are written collectively as a matrix, the loop equations are equivalent to commutation relations.Comment: 38 pages, LaTex, 24 figures. misprints corrected, references added, a technical part moved to appendi

Theoretical investigations of a highly mismatched interface: the case of SiC/Si(001)

Using first principles, classical potentials, and elasticity theory, we investigated the structure of a semiconductor/semiconductor interface with a high lattice mismatch, SiC/Si(001). Among several tested possible configurations, a heterostructure with (i) a misfit dislocation network pinned at the interface and (ii) reconstructed dislocation cores with a carbon substoichiometry is found to be the most stable one. The importance of the slab approximation in first-principles calculations is discussed and estimated by combining classical potential techniques and elasticity theory. For the most stable configuration, an estimate of the interface energy is given. Finally, the electronic structure is investigated and discussed in relation with the dislocation array structure. Interface states, localized in the heterostructure gap and located on dislocation cores, are identified

A 4-gene expression score associated with high levels of Wilms Tumor-1 (WT1) expression is an adverse prognostic factor in acute myeloid leukaemia

Wilms Tumor-1 (WT1) expression level is implicated in the prognosis of acute myeloid leukaemia (AML). We hypothesized that a gene expression profile associated with WT1 expression levels might be a good surrogate marker. We identified high WT1 gene sets by comparing the gene expression profiles in the highest and lowest quartiles of WT1 expression in two large AML studies. Two high WT1 gene sets were found to be highly correlated in terms of the altered genes and expression profiles. We identified a 17-probe set signature of the high WT1 set as the optimal prognostic predictor in the first AML set, and showed that it was able to predict prognosis in the second AML series after adjustment for Europe

Methods for interpreting lists of affected genes obstained in a DNA microarray experiment

Background - The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria. Results - Several conceptually different analytical approaches, using both commercial and public available software, were applied by the participating groups. The following tools were used: Ingenuity Pathway Analysis, MAPPFinder, LIMMA, GOstats, GOEAST, GOTM, Globaltest, TopGO, ArrayUnlock, Pathway Studio, GIST and AnnotationDbi. The main focus of the approaches was to utilise the relation between probes/genes and their gene ontology and pathways to interpret the affected probes/genes. The lack of a well-annotated chicken genome did though limit the possibilities to fully explore the tools. The main results from these analyses showed that the biological interpretation is highly dependent on the statistical method used but that some common biological conclusions could be reached. Conclusion - It is highly recommended to test different analytical methods on the same data set and compare the results to obtain a reliable biological interpretation of the affected genes in a DNA microarray experimen

Alkyne Functionalization of a Photoactivated Ruthenium Polypyridyl Complex for Click-Enabled Serum Albumin Interaction Studies

Studying metal-protein interactions is key for understanding the fate of metallodrugs in biological systems. When a metal complex is not emissive and too weakly bound for mass spectrometry analysis, however, it may become challenging to study such interactions. In this work a synthetic procedure was developed for the alkyne functionalization of a photolabile ruthenium polypyridyl complex, [Ru(tpy)(bpy)(Hmte)](PF6)2, where tpy = 2,2′:6′,2′′-terpyridine, bpy = 2,2′-bipyridine, and Hmte = 2-(methylthio)ethanol. In the functionalized complex [Ru(HCC-tpy)(bpy)(Hmte)](PF6)2, where HCC-tpy = 4′-ethynyl-2,2′:6′,2′′-terpyridine, the alkyne group can be used for bioorthogonal ligation to an azide-labeled fluorophore using copper-catalyzed “click” chemistry. We developed a gel-based click chemistry method to study the interaction between this ruthenium complex and bovine serum albumin (BSA). Our results demonstrate that visualization of the interaction between the metal complex and the protein is possible, even when this interaction is too weak to be studied by conventional means such as UV–vis spectroscopy or ESI mass spectrometry. In addition, the weak metal complex-protein interaction is controlled by visible light irradiation, i.e., the complex and the protein do not interact in the dark, but they do interact via weak van der Waals interactions after light activation of the complex, which triggers photosubstitution of the Hmte ligand.Metals in Catalysis, Biomimetics & Inorganic MaterialsBio-organic Synthesi

Colloquium: Mechanical formalisms for tissue dynamics

The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes being expressed. This information suggests that ourunderstanding of the respective contributions of gene expression and mechanics, and of their crucialentanglement, will soon leap forward. Biomechanics increasingly benefits from models, which assistthe design and interpretation of experiments, point out the main ingredients and assumptions, andultimately lead to predictions. The newly accessible local information thus calls for a reflectionon how to select suitable classes of mechanical models. We review both mechanical ingredientssuggested by the current knowledge of tissue behaviour, and modelling methods that can helpgenerate a rheological diagram or a constitutive equation. We distinguish cell scale ("intra-cell")and tissue scale ("inter-cell") contributions. We recall the mathematical framework developpedfor continuum materials and explain how to transform a constitutive equation into a set of partialdifferential equations amenable to numerical resolution. We show that when plastic behaviour isrelevant, the dissipation function formalism appears appropriate to generate constitutive equations;its variational nature facilitates numerical implementation, and we discuss adaptations needed in thecase of large deformations. The present article gathers theoretical methods that can readily enhancethe significance of the data to be extracted from recent or future high throughput biomechanicalexperiments.Comment: 33 pages, 20 figures. This version (26 Sept. 2015) contains a few corrections to the published version, all in Appendix D.2 devoted to large deformation

Large adaptive optics survey for substellar objects around Young, Nearby, Low-mass Stars with Robo-AO

We present results from the Large Adaptive optics Survey for Substellar Objects, where the goal is to directly image new substellar companions (<70 MJup) at wide orbital separations (≳50 au) around young (≲300 Myr), nearby (<100 pc), low-mass (≈0.1–0.8 M☉) stars. We report on 427 young stars imaged in the visible (i′) and near-infrared (J or H) simultaneously with Robo-AO on the Kitt Peak 2.1 m telescope and later the Maunakea University of Hawaii 2.2 m telescope. To undertake the observations, we commissioned a new infrared camera for Robo-AO that uses a low-noise high-speed SAPHIRA avalanche photodiode detector. We detected 121 companion candidates around 111 stars, of which 62 companions are physically associated based on Gaia DR2 parallaxes and proper motions, another 45 require follow-up observations to confirm physical association, and 14 are background objects. The companion separations range from 2 to 1101 au and reach contrast ratios of 7.7 mag in the near-infrared compared to the primary. The majority of confirmed and pending candidates are stellar companions, with ∼5 being potentially substellar and requiring follow-up observations for confirmation. We also detected a 43 ± 9 MJup and an 81 ± 5 MJup companion that were previously reported. We found 34 of our targets have acceleration measurements detected using Hipparcos–Gaia proper motions. Of those, 58-+1412% of the 12 stars with imaged companion candidates have significant accelerations (c2 > 11.8), while only 23-+611% of the remaining 22 stars with no detected companion have significant accelerations. The significance of the acceleration decreases with increasing companion separation. These young accelerating low-mass stars with companions will eventually yield dynamical masses with future orbit monitoring

Biological approaches to artificial photosynthesis: general discussion

Metals in Catalysis, Biomimetics & Inorganic Material

Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus

A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk