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High Density mapping

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https://www.readbyqxmd.com/read/28331182/construction-of-a-high-density-genetic-map-and-quantitative-trait-locus-mapping-in-the-manila-clam-ruditapes-philippinarum
#1
Hongtao Nie, Xiwu Yan, Zhongming Huo, Liwen Jiang, Peng Chen, Hui Liu, Jianfeng Ding, Feng Yang
Genetic linkage maps are indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as mollusks. In this study, high-density linkage map was constructed for an ecologically and commercially important clam species, Ruditapes philippinarum. For the consensus linkage map, a total of 9658 markers spanning 1926...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28329756/functional-materials-discovery-using-energy-structure-function-maps
#2
Angeles Pulido, Linjiang Chen, Tomasz Kaczorowski, Daniel Holden, Marc A Little, Samantha Y Chong, Benjamin J Slater, David P McMahon, Baltasar Bonillo, Chloe J Stackhouse, Andrew Stephenson, Christopher M Kane, Rob Clowes, Tom Hasell, Andrew I Cooper, Graeme M Day
Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28328985/construction-and-evaluation-of-a-high-density-snp-array-for-the-pacific-oyster-crassostrea-gigas
#3
Haigang Qi, Kai Song, Chunyan Li, Wei Wang, Busu Li, Li Li, Guofan Zhang
Single nucleotide polymorphisms (SNPs) are widely used in genetics and genomics research. The Pacific oyster (Crassostrea gigas) is an economically and ecologically important marine bivalve, and it possesses one of the highest levels of genomic DNA variation among animal species. Pacific oyster SNPs have been extensively investigated; however, the mechanisms by which these SNPs may be used in a high-throughput, transferable, and economical manner remain to be elucidated. Here, we constructed an oyster 190K SNP array using Affymetrix Axiom genotyping technology...
2017: PloS One
https://www.readbyqxmd.com/read/28328350/risk-factors-for-and-spatial-distribution-of-lymphoproliferative-disease-virus-lpdv-in-wild-turkeys-meleagris-gallopavo-in-new-york-state-usa
#4
Katrina Alger, Elizabeth Bunting, Krysten Schuler, Christopher M Whipps
Lymphoproliferative disease virus (LPDV) is an oncogenic avian retrovirus that was previously thought to exclusively infect domestic turkeys but was recently shown to be widespread in Wild Turkeys ( Meleagris gallopavo ) throughout most of the eastern US. In commercial flocks, the virus spreads between birds housed in close quarters, but there is little information about potential risk factors for infection in wild birds. Initial studies focused on distribution of LPDV nationally, but investigation of state-level data is necessary to assess potential predictors of infection and detect patterns in disease prevalence and distribution...
March 22, 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/28328013/validation-of-surface-to-volume-ratio-measurements-derived-from-oscillating-gradient-spin-echo-on-a-clinical-scanner-using-anisotropic-fiber-phantoms
#5
Gregory Lemberskiy, Steven H Baete, Martijn A Cloos, Dmitry S Novikov, Els Fieremans
A diffusion measurement in the short-time surface-to-volume ratio (S/V) limit (Mitra et al., Phys Rev Lett. 1992;68:3555) can disentangle the free diffusion coefficient from geometric restrictions to diffusion. Biophysical parameters, such as the S/V of tissue membranes, can be used to estimate microscopic length scales non-invasively. However, due to gradient strength limitations on clinical MRI scanners, pulsed gradient spin echo (PGSE) measurements are impractical for probing the S/V limit. To achieve this limit on clinical systems, an oscillating gradient spin echo (OGSE) sequence was developed...
March 22, 2017: NMR in Biomedicine
https://www.readbyqxmd.com/read/28326127/detecting-peatland-drains-with-object-based-image-analysis-and-geoeye-1-imagery
#6
J Connolly, N M Holden
BACKGROUND: Peatlands play an important role in the global carbon cycle. They provide important ecosystem services including carbon sequestration and storage. Drainage disturbs peatland ecosystem services. Mapping drains is difficult and expensive and their spatial extent is, in many cases, unknown. An object based image analysis (OBIA) was performed on a very high resolution satellite image (Geoeye-1) to extract information about drain location and extent on a blanket peatland in Ireland...
December 2017: Carbon Balance and Management
https://www.readbyqxmd.com/read/28324950/a-preliminary-evaluation-of-myoelectrical-energy-distribution-of-the-front-neck-muscles-in-pharyngeal-phase-during-normal-swallowing
#7
Mingxing Zhu, Wanzhang Yang, Oluwarotimi Williams Samuel, Yun Xiang, Jianping Huang, Haiqing Zou, Guanglin Li
Pharyngeal phase is a central hub of swallowing in which food bolus pass through from the oral cavity to the esophageal. Proper understanding of the muscular activities in the pharyngeal phase is useful for assessing swallowing function and the occurrence of dysphagia in humans. In this study, high-density (HD) surface electromyography (sEMG) was used to study the muscular activities in the pharyngeal phase during swallowing tasks involving three healthy male subjects. The root mean square (RMS) of the HD sEMG data was computed by using a series of segmented windows as myoelectrical energy...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28323377/accuracy-of-pdff-estimation-by-magnitude-based-and-complex-based-mri-in-children-with-mr-spectroscopy-as-a-reference
#8
William M Haufe, Tanya Wolfson, Catherine A Hooker, Jonathan C Hooker, Yesenia Covarrubias, Alex N Schlein, Gavin Hamilton, Michael S Middleton, Jorge E Angeles, Diego Hernando, Scott B Reeder, Jeffrey B Schwimmer, Claude B Sirlin
PURPOSE: To assess and compare the accuracy of magnitude-based magnetic resonance imaging (MRI-M) and complex-based MRI (MRI-C) for estimating hepatic proton density fat fraction (PDFF) in children, using MR spectroscopy (MRS) as the reference standard. A secondary aim was to assess the agreement between MRI-M and MRI-C. MATERIALS AND METHODS: This was a HIPAA-compliant, retrospective analysis of data collected in children enrolled in prospective, Institutional Review Board (IRB)-approved studies between 2012 and 2014...
March 21, 2017: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/28317606/metabolic-phenotyping-of-diet-and-dietary-intake
#9
J Brignardello, E Holmes, I Garcia-Perez
Nutrition provides the building blocks for growth, repair, and maintenance of the body and is key to maintaining health. Exposure to fast foods, mass production of dietary components, and wider importation of goods have challenged the balance between diet and health in recent decades, and both scientists and clinicians struggle to characterize the relationship between this changing dietary landscape and human metabolism with its consequent impact on health. Metabolic phenotyping of foods, using high-density data-generating technologies to profile the biochemical composition of foods, meals, and human samples (pre- and postfood intake), can be used to map the complex interaction between the diet and human metabolism and also to assess food quality and safety...
2017: Advances in Food and Nutrition Research
https://www.readbyqxmd.com/read/28316346/invasion-trajectory-of-pacific-oysters-in-the-northern-wadden-sea
#10
Karsten Reise, Christian Buschbaum, Heike Büttger, Johannes Rick, K Mathias Wegner
Invasion trajectories of introduced alien species usually begin with a long establishment phase of low abundance, often followed by exponential expansion and subsequent adjustment phases. We review the first 26 years of feral Pacific oysters Crassostrea gigas around the island of Sylt in the Wadden Sea (North Sea, NE Atlantic), and reveal causal conditions for the invasion phases. Sea-based oyster farming with repeated introductions made establishment of feral oysters almost inevitable. Beds of mussels Mytilus edulis on mud flats offered firm substrate for attachment and ideal growth conditions around low tide level...
2017: Marine Biology
https://www.readbyqxmd.com/read/28314801/characterization-of-foci-and-breakthrough-sites-during-persistent-and-long-standing-persistent-atrial-fibrillation-in-patients-studies-using-high-density-510-512-electrodes-biatrial-epicardial-mapping
#11
Seungyup Lee, Jayakumar Sahadevan, Celeen M Khrestian, Alan Markowitz, Albert L Waldo
BACKGROUND: We previously demonstrated that persistent and long-standing persistent atrial fibrillation is maintained by activation emanating from foci and breakthrough sites of different cycle lengths (CLs). The purpose of this study was to characterize the behavior of focal and nonrandom breakthrough activation identified during high-density mapping of atrial fibrillation in these patients. METHODS AND RESULTS: During open heart surgery, we recorded activation from both atria simultaneously using 510 to 512 epicardial electrodes along with ECG lead II in 12 patients with persistent and long-standing persistent atrial fibrillation...
March 17, 2017: Journal of the American Heart Association
https://www.readbyqxmd.com/read/28306555/assessment-of-dosimetric-impact-of-system-specific-geometric-distortion-in-an-mri-only-based-radiotherapy-workflow-for-prostate
#12
C Gustafsson, F Nordström, E Persson, J Brynolfsson, L E Olsson
Dosimetric errors in a magnetic resonance imaging (MRI) only radiotherapy workflow may be caused by system specific geometric distortion from MRI. The aim of this study was to evaluate the impact on planned dose distribution and delineated structures for prostate patients, originating from this distortion. A method was developed, in which computer tomography (CT) images were distorted using the MRI distortion field. The displacement map for an optimized MRI treatment planning sequence was measured using a dedicated phantom in a 3 T MRI system...
March 17, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28301713/population-structure-and-genetic-basis-of-the-agronomic-traits-of-upland-cotton-in-china-revealed-by-a-genome-wide-association-study-using-high-density-snps
#13
Cong Huang, Xinhui Nie, Chao Shen, Chunyuan You, Wu Li, Wenxia Zhao, Xianlong Zhang, Zhongxu Lin
Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton producing and consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nation-wide population containing 503 G. hirsutum accessions was collected for a genome-wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high-density map based on this array were used for genotyping...
March 16, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28300291/are-rare-variants-really-independent
#14
Asuman Turkmen, Shili Lin
Recent advances in genotyping with high-density markers allow researchers access to genomic variants including rare ones. Linkage disequilibrium (LD) is widely used to provide insight into evolutionary history. It is also the basis for association mapping in humans and other species. Better understanding of the genomic LD structure may lead to better-informed statistical tests that can improve the power of association studies. Although rare variant associations with common diseases (RVCD) have been extensively studied recently, there is very limited understanding, and even controversial view of LD structures among rare variants and between rare and common variants...
March 16, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28297598/centimeter-scale-cvd-growth-of-highly-crystalline-single-layer-mos2-film-with-spatial-homogeneity-and-the-visualization-of-grain-boundaries
#15
Li Tao, Kun Chen, Zefeng Chen, Wenjun Chen, Xuchun Gui, Huanjun Chen, Xinming Li, Jian-Bin Xu
MoS2 monolayer attracts considerable attention due to its semiconducting nature with a direct bandgap which can be tuned by various approaches. Yet a controllable and low-cost method to produce large-scale, high-quality, and uniform MoS2 monolayer continuous film, which is of crucial importance for practical applications and optical measurements, remains a great challenge. Most previously reported MoS2 monolayer films had limited crystalline sizes, and the high density of grain boundaries inside the films greatly affected the electrical properties...
March 23, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28290316/food-losses-shelf-life-extension-and-environmental-impact-of-a-packaged-cheesecake-a-life-cycle-assessment
#16
Michele Mario Gutierrez, Marta Meleddu, Antonio Piga
Packaging is associated with a high environmental impact. This is also the case in the food industry despite packaging being necessary for maintaining food quality, safety assurance and preventing food waste. The aim of the present study was to identify improvements in food packaging solutions able to minimize environmental externalities while maximizing the economic sustainability. To this end, the life cycle assessment (LCA) methodology was applied to evaluate the environmental performance of new packaging solutions...
January 2017: Food Research International
https://www.readbyqxmd.com/read/28290194/inkjet-printed-photodetector-arrays-based-on-hybrid-perovskite-ch3nh3pbi3-microwires
#17
Yang Liu, Fushan Li, Chandrasekar Perumal Veeramalai, Wei Chen, Tailiang Guo, Chaoxing Wu, Tae Whan Kim
Hybrid perovskite CH3NH3PbI3 has attracted extensive research interests in optoelectronic devices in recent years. Herein, inkjet printing method has been employed to deposit a perovskite CH3NH3PbI3 layer. By choosing the proper solvent and controlling the crystal growth rate, hybrid perovskite CH3NH3PbI3 nanowires, microwires, network and islands were synthesized by means of inkjet printing. Electrode-gap-electrode lateral-structured photodetectors were fabricated with these different crystals, of which hybrid perovskite microwires-based photodetector would balance the uniformity and low defects to obtain switching ratio of 16000%, responsivity of 1...
March 14, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28283532/molecular-architecture-of-the-n-type-atpase-rotor-ring-from-burkholderia-pseudomallei
#18
Sarah Schulz, Martin Wilkes, Deryck J Mills, Werner Kühlbrandt, Thomas Meier
The genome of the highly infectious bacterium Burkholderia pseudomallei harbors an atp operon that encodes an N-type rotary ATPase, in addition to an operon for a regular F-type rotary ATPase. The molecular architecture of N-type ATPases is unknown and their biochemical properties and cellular functions are largely unexplored. We studied the B. pseudomallei N1No-type ATPase and investigated the structure and ion specificity of its membrane-embedded c-ring rotor by single-particle electron cryo-microscopy. Of several amphiphilic compounds tested for solubilizing the complex, the choice of the low-density, low-CMC detergent LDAO was optimal in terms of map quality and resolution...
March 10, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28282453/the-use-of-a-novel-signal-analysis-to-identify-the-origin-of-idiopathic-right-ventricular-outflow-tract-ventricular-tachycardia-during-sinus-rhythm-simultaneous-amplitude-frequency-electrogram-transformation-mapping
#19
Abigail Louise D Te, Satoshi Higa, Fa-Po Chung, Chin-Yu Lin, Men-Tzung Lo, Che-An Liu, Chen Lin, Yi-Chung Chang, Shih-Lin Chang, Li-Wei Lo, Yu-Feng Hu, Ta-Chuan Tuan, Tze-Fan Chao, Jonan Liao, Yao-Ting Chang, Chung-Hsing Lin, Yuan Hung, Shinya Yamada, Kuo-Li Pan, Yenn-Jiang Lin, Shih-Ann Chen
INTRODUCTION: The signal characteristics of intracardiac bipolar electrograms at the origin of idiopathic RVOT-VT during sinus rhythm remain unclear. OBJECTIVE: The study sought to develop a novel real-time/online technique, simultaneous amplitude frequency electrogram transformation (SAFE-T), to quantify and localize the diseased ventricular substrate in idiopathic RVOT-VT. METHODS: We retrospectively investigated the intracardiac bipolar recordings in 70 consecutive patients (26% male, mean age 42±12 years) who underwent successful radiofrequency catheter ablation of idiopathic RVOT-VT...
2017: PloS One
https://www.readbyqxmd.com/read/28281636/a-high-density-snp-genetic-map-consisting-of-a-complete-set-of-homologous-groups-in-autohexaploid-sweetpotato-ipomoea-batatas
#20
Kenta Shirasawa, Masaru Tanaka, Yasuhiro Takahata, Daifu Ma, Qinghe Cao, Qingchang Liu, Hong Zhai, Sang-Soo Kwak, Jae Cheol Jeong, Ung-Han Yoon, Hyeong-Un Lee, Hideki Hirakawa, Sachiko Isobe
Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I...
March 10, 2017: Scientific Reports
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