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Quantitative susceptibility mapping

Maxime Lamontagne, Jean-Christophe Bérubé, Ma'en Obeidat, Michael H Cho, Brian D Hobbs, Phuwanat Sakornsakolpat, Kim de Jong, H Marike Boezen, David Nickle, Ke Hao, Wim Timens, Maarten van den Berge, Philippe Joubert, Michel Laviolette, Don D Sin, Peter D Paré, Yohan Bossé
Causal genes of chronic obstructive pulmonary disease (COPD) remain elusive. The current study aims at integrating genome-wide association studies (GWAS) and lung expression quantitative loci (eQTL) data to map COPD candidate causal genes and gain biological insights into the recently discovered COPD susceptibility loci. Two complementary genomic datasets on COPD were studied. First, the lung eQTL dataset which included whole-genome gene expression and genotyping data from 1,038 individuals. Second, the largest COPD GWAS to date from the International COPD Genetics Consortium (ICGC) with 13,710 cases and 38,062 controls...
March 14, 2018: Human Molecular Genetics
Mari Miyata, Shingo Kakeda, Kohsuke Kudo, Shigeru Iwata, Yoshiya Tanaka, Yi Wang, Yukunori Korogi
The purposes of this study are to assess the oxygen extraction fraction (OEF) changes on MRI-based quantitative susceptibility mapping (QSM) in systemic lupus erythematosus (SLE) patients and to determine whether QSM-OEF is associated with disease activity in SLE. We enrolled 42 SLE patients and 20 healthy subjects (HS) who had no pathologies on conventional brain MRI. Disease activity was assessed using SLE Disease Activity Index (SLEDAI). For the measurement of QSM-OEF, QSM data were analysed using the Perfusion Mismatch Analyzer software program...
January 1, 2018: Journal of Cerebral Blood Flow and Metabolism
Menuka Pallebage-Gamarallage, Sean Foxley, Ricarda A L Menke, Istvan N Huszar, Mark Jenkinson, Benjamin C Tendler, Chaoyue Wang, Saad Jbabdi, Martin R Turner, Karla L Miller, Olaf Ansorge
BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a clinically and histopathologically heterogeneous neurodegenerative disorder, in which therapy is hindered by the rapid progression of disease and lack of biomarkers. Magnetic resonance imaging (MRI) has demonstrated its potential for detecting the pathological signature and tracking disease progression in ALS. However, the microstructural and molecular pathological substrate is poorly understood and generally defined histologically...
March 13, 2018: BMC Neuroscience
Roxanne Labranche, Guillaume Gilbert, Milena Cerny, Kim-Nhien Vu, Denis Soulières, Damien Olivié, Jean-Sébastien Billiard, Takeshi Yokoo, An Tang
Iron overload is a systemic disorder and is either primary (genetic) or secondary (exogenous iron administration). Primary iron overload is most commonly associated with hereditary hemochromatosis and secondary iron overload with ineffective erythropoiesis (predominantly caused by β-thalassemia major and sickle cell disease) that requires long-term transfusion therapy, leading to transfusional hemosiderosis. Iron overload may lead to liver cirrhosis and hepatocellular carcinoma, in addition to cardiac and endocrine complications...
March 2018: Radiographics: a Review Publication of the Radiological Society of North America, Inc
Zixiang Wen, Ruijuan Tan, Shichen Zhang, Paul J Collins, Jiazheng Yuan, Wenyan Du, Cuihua Gu, Shujun Ou, Qijian Song, Yong-Qiang Charles An, John F Boyse, Martin I Chilvers, Dechun Wang
White mold of soybean, caused by Sclerotinia sclerotiorum (Lib.) de Bary, is a necrotrophic fungus capable of infecting a wide range of plants. To dissect the genetic architecture of resistance to white mold, a high-density customized single nucleotide polymorphism (SNP) array (52,041 SNPs) was used to genotype two soybean diversity panels. Combined with resistance variation data observed in the field and greenhouse environments, genome-wide association studies (GWAS) were conducted to identify quantitative trait loci (QTL) controlling resistance against white mold...
March 12, 2018: Plant Biotechnology Journal
A-G E Ausseil, J R Dymond, L Newstrom
Honey bees require nectar and pollen from flowers: nectar for energy and pollen for growth. The demand for nectar and pollen varies during the year, with more pollen needed in spring for colony population growth, and more nectar needed in summer to sustain the maximum colony size and collect surplus nectar stores for winter. Sufficient bee forage is therefore necessary to ensure a healthy bee colony. Land-use changes can reduce the availability of floral resources suitable for bees, thereby increasing the susceptibility of bees to other stressors such as disease and pesticides...
March 12, 2018: Ecological Applications: a Publication of the Ecological Society of America
Marisa A Patti, Vanessa Troiani
Atypical sulcogyral patterns in the orbitofrontal cortex (OFC) are associated with increased risk for schizophrenia, as well as with quantitative traits associated with schizophrenia, such as anhedonia. Here we conduct a cross-diagnostic comparison to assess whether atypical OFC sulcogyral patterns confer risk for multiple brain disorders. We examined structural images from 4 groups of adult participants (N = 189), including those diagnosed with schizophrenia (SZ; N = 49), bipolar disorder (BP; N = 46), attention deficit hyperactivity disorder (ADHD; N = 41), and controls (N = 53)...
2018: NeuroImage: Clinical
Zhixiang Yan, Ru Yan
Maximizing the recovery of meaningful biological information can facilitate proteomics guided early detection and precise treatment of diseases. However, the conventional protein and peptide level targeted quantification of untargeted data independent acquisition (DIA) such as sequential window acquisition of all theoretical spectra (SWATH) is not necessarily descriptive of all information. Untargeted all-ion quantification theoretically could retrieve more features in SWATH digital maps by circumventing the initial identification process but is intrinsically susceptible to errors because of the extremely complexity of proteome samples and the poor selectivity of a single ion...
March 9, 2018: Analytical Chemistry
Kofi Deh, Gerald D Ponath, Zaki Molvi, Gian-Carlo T Parel, Kelly M Gillen, Shun Zhang, Thanh D Nguyen, Pascal Spincemaille, Yinghua Ma, Ajay Gupta, Susan A Gauthier, David Pitt, Yi Wang
BACKGROUND: The pathological processes in the first weeks of multiple sclerosis (MS) lesion formation include myelin digestion that breaks chemical bonds in myelin lipid layers. This can increase lesion magnetic susceptibility, which is a potentially useful biomarker in MS patient management, but not yet investigated. PURPOSE: To understand and quantify the effects of myelin digestion on quantitative susceptibility mapping (QSM) of MS lesions. STUDY TYPE: Histological and QSM analyses on in vitro models of myelin breakdown and MS lesion formation in vivo...
March 8, 2018: Journal of Magnetic Resonance Imaging: JMRI
Junghun Cho, Youngwook Kee, Pascal Spincemaille, Thanh D Nguyen, Jingwei Zhang, Ajay Gupta, Shun Zhang, Yi Wang
PURPOSE: To map the cerebral metabolic rate of oxygen (CMRO2 ) by estimating the oxygen extraction fraction (OEF) from gradient echo imaging (GRE) using phase and magnitude of the GRE data. THEORY AND METHODS: 3D multi-echo gradient echo imaging and perfusion imaging with arterial spin labeling were performed in 11 healthy subjects. CMRO2 and OEF maps were reconstructed by joint quantitative susceptibility mapping (QSM) to process GRE phases and quantitative blood oxygen level-dependent (qBOLD) modeling to process GRE magnitudes...
March 7, 2018: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
Kelly M Gillen, Mayyan Mubarak, Thanh D Nguyen, David Pitt
Microglia are resident immune cells that fulfill protective and homeostatic functions in the central nervous system (CNS) but may also promote neurotoxicity in the aged brain and in chronic disease. In multiple sclerosis (MS), an autoimmune demyelinating disease of the CNS, microglia and macrophages contribute to the development of white matter lesions through myelin phagocytosis, and possibly to disease progression through diffuse activation throughout myelinated white matter. In this review, we discuss an additional compartment of myeloid cell activation in MS, i...
2018: Frontiers in Immunology
Fahimeh Darki, Torkel Klingberg
Most cortical areas send projections to the striatum. In some parts of the striatum, the connections converge from several cortical areas. It is unknown whether the convergence and non-convergence zones of the striatum differ functionally. Here, we used diffusion-weighted magnetic resonance imaging and probabilistic fiber tracking to parcellate the striatum based on its connections to dorsolateral prefrontal, parietal and orbitofrontal cortices in two different datasets (children aged 6-7 years and adults)...
February 28, 2018: NeuroImage
Hiroto Takahashi, Yoshiyuki Watanabe, Hisashi Tanaka, Masahito Mihara, Hideki Mochizuki, Tian Liu, Yi Wang, Noriyuki Tomiyama
OBJECTIVE: To quantify nigral changes with a focus on their spatial variation within the substantia nigra pars compacta (SNpc) for diagnosing early-stage Parkinson's disease (PD). METHODS: The study participants were 18 patients with early-stage PD (PD group) and 18 healthy controls (HC group) who underwent quantitative susceptibility mapping (QSM) and neuromelanin imaging. The QSM and neuromelanin values in each whole SNpc containing the entire nigrosome and dorsolateral SNpc containing nigrosome 1 were calculated...
March 2, 2018: British Journal of Radiology
J Kenneth Baillie, Andrew Bretherick, Christopher S Haley, Sara Clohisey, Alan Gray, Lucile P A Neyton, Jeffrey Barrett, Eli A Stahl, Albert Tenesa, Robin Andersson, J Ben Brown, Geoffrey J Faulkner, Marina Lizio, Ulf Schaefer, Carsten Daub, Masayoshi Itoh, Naoto Kondo, Timo Lassmann, Jun Kawai, Damian Mole, Vladimir B Bajic, Peter Heutink, Michael Rehli, Hideya Kawaji, Albin Sandelin, Harukazu Suzuki, Jack Satsangi, Christine A Wells, Nir Hacohen, Thomas C Freeman, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest, David A Hume
Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity. Accordingly, shared transcriptional activity (coexpression) may help prioritise loci associated with a given trait, and help to identify underlying biological processes. Using cap analysis of gene expression (CAGE) profiles of promoter- and enhancer-derived RNAs across 1824 human samples, we have analysed coexpression of RNAs originating from trait-associated regulatory regions using a novel quantitative method (network density analysis; NDA)...
March 1, 2018: PLoS Computational Biology
Timothy D O'Brien, Peilin Jia, Neil E Caporaso, Maria Teresa Landi, Zhongming Zhao
BACKGROUND: There are two main types of lung cancer: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). NSCLC has many subtypes, but the two most common are lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). These subtypes are mainly classified by physiological and pathological characteristics, although there is increasing evidence of genetic and molecular differences as well. Although some work has been done at the somatic level to explore the genetic and biological differences among subtypes, little work has been done that interrogates these differences at the germline level to characterize the unique and shared susceptibility genes for each subtype...
February 27, 2018: Genome Medicine
Sachin Kumar, Ron E Knox, Asheesh K Singh, Ron M DePauw, Heather L Campbell, Julio Isidro-Sanchez, Fran R Clarke, Curtis J Pozniak, Amidou N'Daye, Brad Meyer, Andrew Sharpe, Yuefeng Ruan, Richard D Cuthbert, Daryl Somers, George Fedak
Loose smut, caused by Ustilago tritici (Pers.) Rostr., is a systemic disease of tetraploid durum wheat (Triticum turgidum L.). Loose smut can be economically controlled by growing resistant varieties, making it important to find and deploy new sources of resistance. Blackbird, a variety of T. turgidum L. subsp. carthlicum (Nevski) A. Love & D. Love, carries a high level of resistance to loose smut. Blackbird was crossed with the loose smut susceptible durum cultivar Strongfield to produce a doubled haploid (DH) mapping population...
2018: PloS One
Sibel Saracoglu, Kazim Gumus, Selim Doganay, Gonca Koc, Ayse Kacar Bayram, Duran Arslan, Hakan Gumus
Background Wilson's disease (WD) is a copper metabolism disorder that causes hepatolenticular degeneration. It is important to diagnose WD before central nervous system involvement. Purpose To demonstrate the early susceptibility changes associated with the copper accumulation in the brain of neurologically asymptomatic pediatric patients with WD using quantitative susceptibility mapping (QSM). Material and Methods Twelve patients with neurologically asymptomatic WD (mean age = 13.7 ± 3.3 years) and 14 age-matched controls were prospectively examined using a 1...
January 1, 2018: Acta Radiologica
S Soman, Z Liu, G Kim, U Nemec, S J Holdsworth, K Main, B Lee, S Kolakowsky-Hayner, M Selim, A J Furst, P Massaband, J Yesavage, M M Adamson, P Spincemallie, M Moseley, Y Wang
BACKGROUND AND PURPOSE: Identifying cerebral microhemorrhage burden can aid in the diagnosis and management of traumatic brain injury, stroke, hypertension, and cerebral amyloid angiopathy. MR imaging susceptibility-based methods are more sensitive than CT for detecting cerebral microhemorrhage, but methods other than quantitative susceptibility mapping provide results that vary with field strength and TE, require additional phase maps to distinguish blood from calcification, and depict cerebral microhemorrhages as bloom artifacts...
February 22, 2018: AJNR. American Journal of Neuroradiology
Huimin Lin, Hongjiang Wei, Naying He, Caixia Fu, Shu Cheng, Jun Shen, Baisong Wang, Xu Yan, Chunlei Liu, Fuhua Yan
PURPOSES: To evaluate the feasibility of simultaneous quantification of liver iron concentration (LIC) and fat fraction (FF) using water-fat separation and quantitative susceptibility mapping (QSM). METHODS: Forty-five patients suspected of liver iron overload (LIO) were included. A volumetric interpolated breath-hold examination sequence for QSM and FF, a fat-saturated gradient echo sequence for R2 * , a spin echo sequence for LIC measurements and MRS analyses for FF (FF-MRS) were performed...
February 22, 2018: European Radiology
Huyen T T Phan, Kasia Rybak, Stefania Bertazzoni, Eiko Furuki, Eric Dinglasan, Lee T Hickey, Richard P Oliver, Kar-Chun Tan
The fungus Parastagonospora nodorum causes Septoria nodorum blotch (SNB) of wheat. A genetically diverse wheat panel was used to dissect the complexity of SNB and identify novel sources of resistance. The fungus Parastagonospora nodorum is the causal agent of Septoria nodorum blotch (SNB) of wheat. The pathosystem is mediated by multiple fungal necrotrophic effector-host sensitivity gene interactions that include SnToxA-Tsn1, SnTox1-Snn1, and SnTox3-Snn3. A P. nodorum strain lacking SnToxA, SnTox1, and SnTox3 (toxa13) retained wild-type-like ability to infect some modern wheat cultivars, suggesting evidence of other effector-mediated susceptibility gene interactions or the lack of host resistance genes...
February 22, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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