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high-density mapping

Jessica Lee, Richard Rosen
Diabetic retinopathy is a progressive microvascular disease that leads to increased vessel permeability, retinal ischemia, and retinal neovascularization. Optical coherence tomography angiography (OCTA) is a novel angiography technique that has the capability to advance our understanding of diabetic eye disease by providing high-resolution images of retinal and choroidal microvasculature blood flow and structure. Using OCTA, the vascular changes of diabetic retinopathy including microaneurysms, retinal non-perfusion, intraretinal microvascular abnormalities, and neovascularization can be clearly visualized...
December 2016: Current Diabetes Reports
Tetsuya Narushima, Hiromi Okamoto
In this work, we developed a circular dichroism (CD) imaging microscope with a device to suppress the commingling of linear birefringence (LB) and linear dichroism (LD) signals. CD signals are, in principle, free from the commingling influence of LD and LB if the sample is illuminated with pure circularly polarized light, with no linear polarization contribution. Based on this idea, we here propose a novel circular polarization modulation method to suppress the contribution of linear polarization, which enables high-sensitivity CD detection (10(-4) level in optical density unit or mdeg level in ellipticity) for microscopic imaging at a nearly diffraction limited spatial resolution (sub-μm level)...
October 20, 2016: Scientific Reports
Hanne Gro Olsen, Tim Martin Knutsen, Anna M Lewandowska-Sabat, Harald Grove, Torfinn Nome, Morten Svendsen, Mariann Arnyasi, Marte Sodeland, Kristil K Sundsaasen, Sandra Rinne Dahl, Bjørg Heringstad, Hanne H Hansen, Ingrid Olsaker, Matthew Peter Kent, Sigbjørn Lien
BACKGROUND: Clinical mastitis is an inflammation of the mammary gland and causes significant costs to dairy production. It is unfavourably genetically correlated to milk production, and, thus, knowledge of the mechanisms that underlie these traits would be valuable to improve both of them simultaneously through breeding. A quantitative trait locus (QTL) that affects both clinical mastitis and milk production has recently been fine-mapped to around 89 Mb on bovine chromosome 6 (BTA6), but identification of the gene that underlies this QTL was not possible due to the strong linkage disequilibrium between single nucleotide polymorphisms (SNPs) within this region...
October 19, 2016: Genetics, Selection, Evolution: GSE
Bianca Ferreira Olivieri, Maria Eugênia Zerlotti Mercadante, Joslaine Noely Dos Santos Gonçalves Cyrillo, Renata Helena Branco, Sarah Figueiredo Martins Bonilha, Lucia Galvão de Albuquerque, Rafael Medeiros de Oliveira Silva, Fernando Baldi
The objective of this study was to identify genomic regions and metabolic pathways associated with dry matter intake, average daily gain, feed efficiency and residual feed intake in an experimental Nellore cattle population. The high-density SNP chip (Illumina High-Density Bovine BeadChip, 777k) was used to genotype the animals. The SNP markers effects and their variances were estimated using the single-step genome wide association method. The (co)variance components were estimated by Bayesian inference. The chromosome segments that are responsible for more than 1...
2016: PloS One
Grzegorz Bauman, Francesco Santini, Orso Pusterla, Oliver Bieri
PURPOSE: To present a technique for simultaneous mapping of T1 , T2 , and relative spin density (M0 ) in human lung using inversion recovery ultra-fast steady-state free precession (IR-ufSSFP) imaging. METHODS: Pulmonary relaxometry with IR-ufSSFP is based on an interleaved time series acquisition of 2D images acquired at 1.5T. The technique was tested in a phantom and in four healthy volunteers using breath-hold and electrocardiogram triggering. Typically, 30 transient state images were acquired in a single breath-hold within < 10 s...
October 19, 2016: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
Michael Poteser, Gerd Leitinger, Elisabeth Pritz, Dieter Platzer, Irene Frischauf, Christoph Romanin, Klaus Groschner
Nanometer-spaced appositions between endoplasmic reticulum and plasma membrane (ER-PM junctions) stabilized by membrane-joining protein complexes are critically involved in cellular Ca(2+)-handling and lipid trafficking. ER-PM junctional architecture and plasticity associated with inter-membrane communication are as yet barely understood. Here, we introduce a method to precisely characterize ER-PM junction morphology and dynamics with high temporal resolution and minimal disturbance of junctional intermembrane communication...
October 19, 2016: Scientific Reports
Aditi Gupta, Garima Juyal, Ajit Sood, Vandana Midha, Keiko Yamazaki, Arnau Vich Vila, Motohiro Esaki, Toshiyuki Matsui, Atsushi Takahashi, Michiaki Kubo, Rinse K Weersma, B K Thelma
The first ever genome-wide association study (GWAS) of ulcerative colitis in genetically distinct north Indian population identified two novel genes namely CFB and SLC44A4. Considering their biological relevance, we investigated allelic/genetic heterogeneity in these genes among ulcerative colitis cohorts of north Indian, Japanese and Dutch origin using high-density ImmunoChip case-control genotype data. Comparative linkage disequilibrium profiling and test of association were performed. Of the 28 CFB SNPs, similar strength of association was observed for rs4151657 (novel ulcerative colitis GWAS SNP) in north Indians (P=1...
October 19, 2016: European Journal of Human Genetics: EJHG
Matthew E Fagan, Ruth S DeFries, Steven E Sesnie, J Pablo Arroyo-Mora, Robin L Chazdon
Re-establishing connectivity between protected areas isolated by habitat clearing is a key conservation goal in the humid tropics. In northeastern Costa Rica, payments for environmental services (PES) and a government ban on deforestation have subsidized forest protection and reforestation in the San Juan-La Selva Biological Corridor (SJLSBC), resulting in a decline in mature forest loss and the expansion of tree plantations. We use field studies and graph models to assess how conservation efforts have altered functional connectivity over the last 25 years for four species of insectivorous understory birds...
July 2016: Ecological Applications: a Publication of the Ecological Society of America
Guilherme V T Ribeiro, Alberto L Teixido, Newton P U Barbosa, Fernando A O Silveira
Sampling biases permeate ecological research and result in knowledge gaps that have vital consequences for conservation planning. The consequences of knowledge gaps on species identity and distribution (the Wallacean and Linnean shortfalls, respectively) have become apparent recently, but we know little about the extent that research biases and knowledge gaps on traits that influence species' niches (the Hutchinsonian shortfall) affect conservation policy. To examine whether knowledge of species' traits based on seed ecology is geographically, phylogenetically, and ecologically biased, we retrieved research data on seed germination, seed dormancy, seed dispersal, seed banks, seed predation, and seed removal from a database of 847 papers, 1648 species, and 5322 cases...
October 2016: Ecological Applications: a Publication of the Ecological Society of America
Nadja Danner, Anna Maria Molitor, Susanne Schiele, Stephan Härtel, Ingolf Steffan-Dewenter
Honey bees (Apis mellifera L.) show a large variation in foraging distances and use a broad range of plant species as pollen resources, even in regions with intensive agriculture. However, it is unknown how increasing areas of mass-flowering crops like oilseed rape (Brassica napus; OSR) or a decrease of seminatural habitats (SNH) change the temporal and spatial availability of pollen resources for honey bee colonies, and thus foraging distances and frequency in different habitat types. We studied pollen foraging of honey bee colonies in 16 agricultural landscapes with independent gradients of OSR and SNH area within 2 km and used waggle dances and digital geographic maps with major land cover types to reveal the distance and visited habitat type on a landscape level...
September 2016: Ecological Applications: a Publication of the Ecological Society of America
Shengfu Zhong, Lixia Ma, Syeda Akash Fatima, Jiezhi Yang, Wanquan Chen, Taiguo Liu, Yuting Hu, Qing Li, Jingwei Guo, Min Zhang, Li Lei, Xin Li, Shengwen Tang, Peigao Luo
The wheat powdery mildew resistance gene Pm40, which is located on chromosomal arm 7BS, is effective against nearly all prevalent races of Blumeria graminis f. sp tritici (Bgt) in China and is carried by the common wheat germplasm PI 672538. A set of the F1, F2 and F2:3 populations from the cross of the resistant PI 672538 with the susceptible line L1034 were used to conduct genetic analysis of powdery mildew resistance and construct a high-density linkage map of the Pm40 gene. We constructed a high-density linkage genetic map with a total length of 6...
2016: PloS One
Thomas Sannicolo, David Muñoz-Rojas, Ngoc Duy Nguyen, Stéphane Moreau, Caroline Celle, Jean-Pierre Simonato, Yves Bréchet, Daniel Bellet
Advancement in the science and technology of random metallic nanowire (MNW) networks is crucial for their appropriate integration in many applications, including transparent electrodes for optoelectronics and transparent film heaters. We have recently highlighted the discontinuous activation of efficient percolating pathways (EPPs) for networks having densities slightly above the percolation threshold. Such networks exhibit abrupt drops of electrical resistance when thermal or electrical annealing is performed, giving rise to a "geometrically quantized percolation"...
October 18, 2016: Nano Letters
Zheng Liu, Cristina Gutierrez-Vargas, Jia Wei, Robert A Grassucci, Noel Espina, Susan Madison-Antenucci, Liang Tong, Joachim Frank
With the advance of new instruments and algorithms, and the accumulation of experience over decades, single-particle cryo-EM has become a pivotal part of structural biology. Recently, we determined the structure of a eukaryotic ribosome at 2.5 Å for the large subunit. The ribosome was derived from Trypanosoma cruzi, the protozoan pathogen of Chagas disease. The high-resolution density map allowed us to discern a large number of unprecedented details including rRNA modifications, water molecules, and ions such as Mg(2+) and Zn(2+) ...
October 17, 2016: Protein Science: a Publication of the Protein Society
Joseph E Logan, Katherine A Fowler, Nimeshkumar P Patel, Kristin M Holland
INTRODUCTION: Suicide among military personnel and young Veterans remains a health concern. This study examined stateside distribution of suicides by U.S. county to help focus prevention efforts. METHODS: Using 2005-2012 National Violent Death Reporting System data from 16 states (963 counties, or county-equivalent entities), this study mapped the county-level distribution of suicides among current military and Veteran decedents aged 18-35 years. This study also compared incident circumstances of death between decedents in high-density counties (i...
November 2016: American Journal of Preventive Medicine
Jinhyeok Choi, Hyeonjin Kim
To improve the efficacy of undersampled MRI, a method of designing adaptive sampling functions is proposed that is simple to implement on an MR scanner and yet effectively improves the performance of the sampling functions. An approximation of the energy distribution of an image (E-map) is estimated from highly undersampled k-space data acquired in a prescan and efficiently recycled in the main scan. An adaptive probability density function (PDF) is generated by combining the E-map with a modeled PDF. A set of candidate sampling functions are then prepared from the adaptive PDF, among which the one with maximum energy is selected as the final sampling function...
October 10, 2016: Journal of Magnetic Resonance
Carmen Capel, Fernando J Yuste-Lisbona, Gloria López-Casado, Trinidad Angosto, Jesús Cuartero, Rafael Lozano, Juan Capel
QTL and codominant genetic markers for fruit cracking have been identified in a tomato genetic map derived from a RIL population, providing molecular tools for marker-assisted breeding of this trait. In tomato, as well as in other fleshy fruits, one of the main disorders that widely limit quality and production is fruit cracking or splitting of the epidermis that is observed on the fruit skin and flesh at any stage of fruit growth and maturation. To elucidate the genetic basis of fruit cracking, a quantitative trait loci (QTL) analysis was conducted in a recombinant inbred line (RIL) population derived from a cross between tomato (Solanum lycopersicum) and the wild-relative species S...
October 14, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Atanu Patra, Monodeep Chakraborty, Anushree Roy
Herein, we report the graded electronic band gap along the axis of individual heterostructured WZ-ZB InAs/InSb0.12As0.88 nanowires. Resonance Raman imaging has been exploited to map the axial variation in the second excitation gap energy (E1) at the high symmetry point (L point) of the Brillouin zone. We relate the origin of the observed evolution of the gap energy to the fine tuning of the alloy composition from the tip towards the interface of the nanowire. The electronic band structures of InAs, InSb and InSbxAs1-x alloy systems at x = 0...
October 14, 2016: Nanoscale
Eduardo Ortega, Arturo Ponce, Ulises Santiago, Diego Alducin, Alfredo Benitez-Lara, Germán Plascencia-Villa, Miguel José-Yacamán
The present work explores electron diffraction methods for studying the structure of metallic clusters stabilized with thiol groups, which are susceptible to structural damage caused by electron beam irradiation. There is a compromise between the electron dose used and the size of the clusters since they have small interaction volume with electrons and as a consequence weak reflections in the diffraction patterns. The common approach of recording individual clusters using nanobeam diffraction has the problem of an increased current density...
2017: Adv Struct Chem Imaging
Marinela Dukić, Daniel Berner, Marius Roesti, Christoph R Haag, Dieter Ebert
BACKGROUND: Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology...
October 13, 2016: BMC Genetics
Liliana R Cisneros Castillo, Andrei-Dumitru Oancea, Christian Stüllein, Anne Régnier-Vigouroux
Multicellular tumor spheroids (MCTSs) embedded in a matrix are re-emerging as a powerful alternative to monolayer-based cultures. The primary information gained from a three-dimensional model is the invasiveness of treatment-exposed MCTSs through the acquisition of light microscopy images. The amount and complexity of the acquired data and the bias arisen by their manual analysis are disadvantages calling for an automated, high-throughput analysis. We present a universal algorithm we developed with the scope of being robust enough to handle images of various qualities and various invasion profiles...
October 12, 2016: Scientific Reports
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