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Structural variation

Xiaojun Deng
Incorporating the structure and connectivity of the river network to seasonal variations and different land use patterns can help improve the understanding the complex relationship between water quality and environmental factors. The present study first employed the grey relational analysis (GRA) to examine any existing correlations between the water quality and the structure and connectivity of river networks in the Southern Jiangsu Plain in Eastern China. All grey relational degree results were greater than the distinguishing coefficient (ρ = 0...
February 4, 2019: Science of the Total Environment
Claudia M Corbi-Botto, Hernán Morales-Durand, María E Zappa, Sebastián A Sadaba, Pilar Peral-García, Guillermo Giovambattista, Silvina Díaz
Copy number variation (CNV) has been proved to be widespread in human, animal and plant genomes. Together with single nucleotide polymorphisms (SNPs), CVNs play a key role in genetic diversity. In this study, genome-wide detection of CNVs was performed based on SNP data from 24 Criollo Argentino horses genotyped with the GGP Equine70k array. Overall, 165 CNVs meeting stringent quality control criteria were identified and then aggregated into 87 CNV regions (CNVRs), representing a horse genome coverage of 13...
February 11, 2019: Gene
Gyeongwon Kang, Muwen Yang, Michael Mattei, George C Schatz, Richard P Van Duyne
Electrochemical atomic force microscopy tip-enhanced Raman spectroscopy (EC-AFM-TERS) was used for the first time to spatially resolve local heterogeneity in redox behavior on an electrode surface in-situ and at the nanoscale. A structurally well-defined Au(111) nanoplate located on a polycrystalline ITO substrate was studied to examine nanoscale redox contrast across the two electrode materials. By monitoring the TERS intensity of adsorbed Nile Blue (NB) molecules on the electrode surface, TERS maps were acquired with different applied potentials...
February 14, 2019: Nano Letters
Joshua G Harrison, Matthew L Forister, Stephanie R Mcknight, Erin Nordin, Thomas L Parchman
PREMISE OF THE STUDY: Characteristics of rare taxa include small population sizes and limited geographical ranges. The genetic consequences of rarity are poorly understood for most taxa. A small geographical range could result in reduced opportunity for isolation by distance or environment, thereby limiting genetic structure and variation, but few studies explore genetic structure at small spatial scales with sufficient resolution to test this hypothesis. Moreover, few comparative genetic studies exist among infrataxa differing in rarity...
February 14, 2019: American Journal of Botany
Carlos R García-Alonso, Nerea Almeda, José A Salinas-Pérez, Mencía R Gutiérrez-Colosía, José J Uriarte-Uriarte, Luis Salvador-Carulla
Evidence-informed strategic planning is a top priority in Mental Health (MH) due to the burden associated with this group of disorders and its societal costs. However, MH systems are highly complex, and decision support tools should follow a systems thinking approach that incorporates expert knowledge. The aim of this paper is to introduce a new Decision Support System (DSS) to improve knowledge on the health ecosystem, resource allocation and management in regional MH planning. The Efficient Decision Support-Mental Health (EDeS-MH) is a DSS that integrates an operational model to assess the Relative Technical Efficiency (RTE) of small health areas, a Monte-Carlo simulation engine (that carries out the Monte-Carlo simulation technique), a fuzzy inference engine prototype and basic statistics as well as system stability and entropy indicators...
2019: PloS One
Keiji Tanimoto, Hitomi Matsuzaki, Eiichi Okamura, Aki Ushiki, Akiyoshi Fukamizu, James Douglas Engel
Long-range associations between enhancers and their target gene promoters have been shown to play critical roles in executing genome function. Recent variations of chromosome capture technology have revealed a comprehensive view of intra- and interchromosomal contacts between specific genomic sites. The locus control region of the β-globin genes (β-LCR) is a super-enhancer that is capable of activating all of the β-like globin genes within the locus in cis through physical interaction by forming DNA loops...
2019: PloS One
Maha Daghestani, Rituraj Purohit, Mazin Daghestani, Mamoon Daghistani, Arjumand Warsy
The Gln233Arg (A>G; rs1137101) polymorphism of the leptin receptor gene (LEPR) has been investigated extensively and is reported to be associated with different metabolic states. In this investigation, we aimed to study the frequency of Gln233Arg genotypes and alleles in a group of Saudi women stratified by their body mass index (BMI), to correlate the LEPR genotypes with variations in anthropometric, lipid and hormonal parameters and to investigate conformational and structural variations in the mutant LEPR using molecular dynamic (MD) investigations...
2019: PloS One
John Chambers, Madalina Garbi, Norman Briffa, Vishal Sharma, Rick Steeds
Echocardiography plays a vital role in the follow up of patients with replacement heart valves. However, there is considerable variation in international guidelines regarding the recommended time points after implantation at which routine echocardiography should be performed. The purpose of routine echocardiography is to detect early structural valve deterioration in biological valves to improve the timing of redo interventions. However the risk of valve deterioration depends on many valve-related factors (valve design, patient prosthesis mismatch) and patient-related factors (age, diabetes, systemic hypertension, renal dysfunction and smoking)...
February 1, 2019: Echo Research and Practice
Denis K Samuylov, Prateek Purwar, Gabor Szekely, Gregory Paul
Deblurring is a fundamental inverse problem in bioimaging. It requires modelling the point spread function (PSF), which captures the optical distortions entailed by the image formation process. The PSF limits the spatial resolution attainable for a given microscope. However, recent applications require a higher resolution, and have prompted the development of super-resolution techniques to achieve sub-pixel accuracy. This requirement restricts the class of suitable PSF models to analog ones. In addition, deblurring is computationally intensive, hence further requiring computationally efficient models...
February 11, 2019: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Jun Liu, Amir Shahroudy, Gang Wang, Ling-Yu Duan, Alex Kot Chichung
Action prediction is to recognize the class label of an ongoing activity when only a part of it is observed. In this paper, we focus on online action prediction in streaming 3D skeleton sequences. A dilated convolutional network is introduced to model the motion dynamics in temporal dimension via a sliding window over the temporal axis. Since there are significant temporal scale variations in the observed part of the ongoing action at different time steps, a novel window scale selection method is proposed to make our network focus on the performed part of the ongoing action and try to suppress the possible incoming interference from the previous actions at each step...
February 12, 2019: IEEE Transactions on Pattern Analysis and Machine Intelligence
Rajkamal Balu, Namita Choudhury, Jitendra P Mata, Liliana de Campo, Christine Rehm, Anita J Hill, Naba Kumar Dutta
The electrocatalyst layer (ECL) of proton-exchange membrane fuel cell (PEMFC) is commonly fabricated from colloidal catalyst ink containing carbon supported catalyst nanoparticles (NPs), ionomer stabilizer and dispersion medium (DM). The structure, stability and aggregate size distribution of fuel cell catalyst ink is critically dependent on the quality of the DM. However, understanding of the influence of the quality of the DM on the hierarchical structure of ECL is lacking. This work presents a systematic investigation of the effects of reducing alcohol content in isopropyl alcohol/water (IPA/H2O) binary mixtures as DM, on the structural evolution of green catalyst ink using contrast-variation small-angle and ultra-small-angle neutron scattering techniques...
February 14, 2019: ACS Applied Materials & Interfaces
Abdulrahman M Alfuraih, Ai Lyn Tan, Philip O'Connor, Paul Emery, Richard J Wakefield
BACKGROUND: Skeletal muscle undergoes structural changes with ageing which may alter its biomechanical properties. Shear wave elastography (SWE) may detect these changes by measuring muscle stiffness. AIMS: To investigate muscle stiffness in healthy young, middle-aged and elderly cohorts using SWE and correlate it with muscle strength and mass. METHODS: Shear wave velocity (SWV) was measured in the quadriceps, hamstrings and biceps brachii of 26 young (range 20-35 years), 21 middle-aged (40-55) and 30 elderly (77-94) volunteers...
February 14, 2019: Aging Clinical and Experimental Research
Miriam Luhnen, Barbara Prediger, Edmund A M Neugebauer, Tim Mathes
INTRODUCTION: The number of systematic reviews of health economic evaluations (SR-HEs) is increasing. We aimed at providing a detailed overview of the characteristics and applied methods in recently published SR-HEs. METHODS: We searched MEDLINE (03/2017) for SR-HEs published since 2015 using validated search filters. We included studies that performed a systematic review of full economic evaluations and searched at least one electronic database. We extracted data in a standardized, beforehand piloted form that was deduced from the items of the PRISMA and CHEERS checklists...
February 13, 2019: Research Synthesis Methods
Stella Campo, Luz Andreone, Verónica Ambao, Mariela Urrutia, Ricardo S Calandra, Susana B Rulli
The Follicle-Stimulating Hormone plays an important role in the regulation of gametogenesis. It is synthesized and secreted as a family of glycoforms with differing oligosaccharide structure, biological action, and half-life. The presence of these oligosaccharides is absolutely necessary for the full expression of hormone bioactivity at the level of the target cell. The endocrine milieu modulates the glycosylation of this hormone. During male sexual development a progressive increase in FSH sialylation and in the proportion of glycoforms bearing complex oligosaccharides are the main features in this physiological condition...
2019: Frontiers in Endocrinology
Edmund Barter, Thilo Gross
In the twenty-first century, ongoing rapid urbanization highlights the need to gain deeper insights into the social structure of cities. While work on this challenge can profit from abundant data sources, the complexity of this data itself proves to be a challenge. In this paper, we use diffusion maps, a manifold learning method, to discover hidden manifolds in the UK 2011 census dataset. The census key statistics and quick statistics report 1450 different statistical features for each census output area. Here, we focus primarily on the city of Bristol and the surrounding countryside, comprising 3490 of these output areas...
January 2019: Proceedings. Mathematical, Physical, and Engineering Sciences
Takeshi Mizuguchi, Takeshi Suzuki, Chihiro Abe, Ayako Umemura, Katsushi Tokunaga, Yosuke Kawai, Minoru Nakamura, Masao Nagasaki, Kengo Kinoshita, Yasunobu Okamura, Satoko Miyatake, Noriko Miyake, Naomichi Matsumoto
We report a family with progressive myoclonic epilepsy who underwent whole-exome sequencing but was negative for pathogenic variants. Similar clinical courses of a devastating neurodegenerative phenotype of two affected siblings were highly suggestive of a genetic etiology, which indicates that the survey of genetic variation by whole-exome sequencing was not comprehensive. To investigate the presence of a variant that remained unrecognized by standard genetic testing, PacBio long-read sequencing was performed...
February 13, 2019: Journal of Human Genetics
Chandra Sripada, Mike Angstadt, Saige Rutherford, Daniel Kessler, Yura Kim, Mike Yee, Elizaveta Levina
Resting state functional connectomes are massive and complex. It is an open question, however, whether connectomes differ across individuals in a correspondingly massive number of ways, or whether most differences take a small number of characteristic forms. We systematically investigated this question and found clear evidence of low-rank structure in which a modest number of connectomic components, around 50-150, account for a sizable portion of inter-individual connectomic variation. This number was convergently arrived at with multiple methods including estimation of intrinsic dimensionality and assessment of reconstruction of out-of-sample data...
February 13, 2019: Scientific Reports
Marzena Szwed, Tonje Sønstevold, Anders Øverbye, Nikolai Engedal, Beata Grallert, Ýrr Mørch, Einar Sulheim, Tore-Geir Iversen, Tore Skotland, Kirsten Sandvig, Maria L Torgersen
For optimal exploitation of nanoparticles (NPs) in biomedicine, and to predict nanotoxicity, detailed knowledge of the cellular responses to cell-bound or internalized NPs is imperative. The final outcome of NP-cell interaction is dictated by the type and magnitude of the NP insult and the cellular response. Here, this has been systematically studied by using poly(alkylcyanoacrylate) (PACA) particles differing only in their alkyl side chains; butyl (PBCA), ethylbutyl (PEBCA), or octyl (POCA), respectively. Surprisingly, these highly similar NPs induced different stress responses and modes of cell death in human cell lines...
February 14, 2019: Nanotoxicology
Mian Zhang, Man-Man Fu, Cheng-Wei Qiu, Fangbin Cao, Zhong-Hua Chen, Guoping Zhang, Feibo Wu
Tibetan wild barley has been identified to show large genetic variation and stress tolerance. A genome-wide association (GWA) analysis was performed to detect quantitative trait loci (QTLs) for drought tolerance using 777 Diversity Array Technology (DArT) markers and morphological and physiological traits of 166 Tibetan wild barley accessions in both hydroponic and pot experiments. Large genotypic variation for these traits was found; and population structure and kinship analysis identified three subpopulations among these barley genotypes...
February 12, 2019: International Journal of Molecular Sciences
Leif E Peterson
Natural and synthetic small molecules from the NCI Developmental Therapeutics Program (DTP) were employed in molecular dynamics-based docking with DNA repair proteins whose RNA-Seq based expression was associated with overall cancer survival (OS) after adjustment for the PCNA metagene. The compounds employed were required to elicit a sensitive response (vs. resistance) in more than half of the cell lines tested for each cancer. Methodological approaches included peptide sequence alignments and homology modeling for 3D protein structure determination, ligand preparation, docking, toxicity and ADME prediction...
February 12, 2019: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
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