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Find video protocols related to scientific articles indexed in Pubmed.
Semantic Memory Impairment for Biological and Man-Made Objects in Individuals With Amnestic Mild Cognitive Impairment or Late-Life Depression.
J Geriatr Psychiatry Neurol
PUBLISHED: 10-26-2014
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Amnestic mild cognitive impairment (aMCI) and late-life depression (LLD) both increase the risk of developing Alzheimer disease (AD). Very little is known about the similarities and differences between these syndromes. The present study addresses this issue by examining the nature of semantic memory impairment (more precisely, object-based knowledge) in patients at risk of developing AD.
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Identification of the Pharmacophore of the CC Chemokine-binding Proteins Evasin-1 and -4 Using Phage Display.
J. Biol. Chem.
PUBLISHED: 09-29-2014
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To elucidate the ligand-binding surface of the CC chemokine-binding proteins Evasin-1 and Evasin-4, produced by the tick Rhipicephalus sanguineus, we sought to identify the key determinants responsible for their different chemokine selectivities by expressing Evasin mutants using phage display. We first designed alanine mutants based on the Evasin-1·CCL3 complex structure and an in silico model of Evasin-4 bound to CCL3. The mutants were displayed on M13 phage particles, and binding to chemokine was assessed by ELISA. Selected variants were then produced as purified proteins and characterized by surface plasmon resonance analysis and inhibition of chemotaxis. The method was validated by confirming the importance of Phe-14 and Trp-89 to the inhibitory properties of Evasin-1 and led to the identification of a third crucial residue, Asn-88. Two amino acids, Glu-16 and Tyr-19, were identified as key residues for binding and inhibition of Evasin-4. In a parallel approach, we identified one clone (Y28Q/N60D) that showed a clear reduction in binding to CCL3, CCL5, and CCL8. It therefore appears that Evasin-1 and -4 use different pharmacophores to bind CC chemokines, with the principal binding occurring through the C terminus of Evasin-1, but through the N-terminal region of Evasin-4. However, both proteins appear to target chemokine N termini, presumably because these domains are key to receptor signaling. The results also suggest that phage display may offer a useful approach for rapid investigation of the pharmacophores of small inhibitory binding proteins.
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Selective antibody intervention of Toll-like receptor 4 activation through Fc ? receptor tethering.
J. Biol. Chem.
PUBLISHED: 04-15-2014
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Inflammation is mediated mainly by leukocytes that express both Toll-like receptor 4 (TLR4) and Fc ? receptors (Fc?R). Dysregulated activation of leukocytes via exogenous and endogenous ligands of TLR4 results in a large number of inflammatory disorders that underlie a variety of human diseases. Thus, differentially blocking inflammatory cells while sparing structural cells, which are Fc?R-negative, represents an elegant strategy when targeting the underlying causes of human diseases. Here, we report a novel tethering mechanism of the Fv and Fc portions of anti-TLR4 blocking antibodies that achieves increased potency on inflammatory cells. In the presence of ligand (e.g. lipopolysaccharide (LPS)), TLR4 traffics into glycolipoprotein microdomains, forming concentrated protein platforms that include Fc?Rs. This clustering produces a microenvironment allowing anti-TLR4 antibodies to co-engage TLR4 and Fc?Rs, increasing their avidity and thus substantially increasing their inhibitory potency. Tethering of antibodies to both TLR4 and Fc?Rs proves valuable in ameliorating inflammation in vivo. This novel mechanism of action therefore has the potential to enable selective intervention of relevant cell types in TLR4-driven diseases.
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FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project.
Am. J. Hum. Genet.
PUBLISHED: 03-21-2014
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Inherited monogenic disease has an enormous impact on the well-being of children and their families. Over half of the children living with one of these conditions are without a molecular diagnosis because of the rarity of the disease, the marked clinical heterogeneity, and the reality that there are thousands of rare diseases for which causative mutations have yet to be identified. It is in this context that in 2010 a Canadian consortium was formed to rapidly identify mutations causing a wide spectrum of pediatric-onset rare diseases by using whole-exome sequencing. The FORGE (Finding of Rare Disease Genes) Canada Consortium brought together clinicians and scientists from 21 genetics centers and three science and technology innovation centers from across Canada. From nation-wide requests for proposals, 264 disorders were selected for study from the 371 submitted; disease-causing variants (including in 67 genes not previously associated with human disease; 41 of these have been genetically or functionally validated, and 26 are currently under study) were identified for 146 disorders over a 2-year period. Here, we present our experience with four strategies employed for gene discovery and discuss FORGE's impact in a number of realms, from clinical diagnostics to the broadening of the phenotypic spectrum of many diseases to the biological insight gained into both disease states and normal human development. Lastly, on the basis of this experience, we discuss the way forward for rare-disease genetic discovery both in Canada and internationally.
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Cloning, reformatting, and small-scale expression of monoclonal antibody isolated from mouse, rat, or hamster hybridoma.
Methods Mol. Biol.
PUBLISHED: 02-12-2014
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The hybridoma technology, first described in 1975 by Milstein and Köhler, is still to date one of the most commonly used approaches to produce monoclonal antibodies. However, despite many advantages, this approach suffers from limitations like limited antibody productivity. Here, we describe a method for efficient cloning of antibody VH and VL produced by mouse, rat, or hamster hybridoma before reformatting in full-length IgG and small-scale expression in mammalian cell line.
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GlycoDelete engineering of mammalian cells simplifies N-glycosylation of recombinant proteins.
Nat. Biotechnol.
PUBLISHED: 01-17-2014
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Heterogeneity in the N-glycans on therapeutic proteins causes difficulties for protein purification and process reproducibility and can lead to variable therapeutic efficacy. This heterogeneity arises from the multistep process of mammalian complex-type N-glycan synthesis. Here we report a glycoengineering strategy--which we call GlycoDelete--that shortens the Golgi N-glycosylation pathway in mammalian cells. This shortening results in the expression of proteins with small, sialylated trisaccharide N-glycans and reduced complexity compared to native mammalian cell glycoproteins. GlycoDelete engineering does not interfere with the functioning of N-glycans in protein folding, and the physiology of cells modified by GlycoDelete is similar to that of wild-type cells. A therapeutic human IgG expressed in GlycoDelete cells had properties, such as reduced initial clearance, that might be beneficial when the therapeutic goal is antigen neutralization. This strategy for reducing N-glycan heterogeneity on mammalian proteins could lead to more consistent performance of therapeutic proteins and modulation of biopharmaceutical functions.
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Anti-CD79 antibody induces B cell anergy that protects against autoimmunity.
J. Immunol.
PUBLISHED: 01-17-2014
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B cells play a major role in the pathogenesis of many autoimmune disorders, including rheumatoid arthritis, systemic lupus erythematosus, multiple sclerosis, and type I diabetes mellitus, as indicated by the efficacy of B cell-targeted therapies in these diseases. Therapeutic effects of the most commonly used B cell-targeted therapy, anti-CD20 mAb, are contingent upon long-term depletion of peripheral B cells. In this article, we describe an alternative approach involving the targeting of CD79, the transducer subunit of the B cell AgR. Unlike anti-CD20 mAbs, the protective effects of CD79-targeted mAbs do not require cell depletion; rather, they act by inducing an anergic-like state. Thus, we describe a novel B cell-targeted approach predicated on the induction of B cell anergy.
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Genetic determinants of heel bone properties: genome-wide association meta-analysis and replication in the GEFOS/GENOMOS consortium.
Alireza Moayyeri, Yi-Hsiang Hsu, David Karasik, Karol Estrada, Su-Mei Xiao, Carrie Nielson, Priya Srikanth, Sylvie Giroux, Scott G Wilson, Hou-Feng Zheng, Albert V Smith, Stephen R Pye, Paul J Leo, Alexander Teumer, Joo-Yeon Hwang, Claes Ohlsson, Fiona McGuigan, Ryan L Minster, Caroline Hayward, José M Olmos, Leo-Pekka Lyytikäinen, Joshua R Lewis, Karin M A Swart, Laura Masi, Chris Oldmeadow, Elizabeth G Holliday, Sulin Cheng, Natasja M van Schoor, Nicholas C Harvey, Marcin Kruk, Fabiola Del Greco M, Wilmar Igl, Olivia Trummer, Efi Grigoriou, Robert Luben, Ching-Ti Liu, Yanhua Zhou, Ling Oei, Carolina Medina-Gomez, Joseph Zmuda, Greg Tranah, Suzanne J Brown, Frances M Williams, Nicole Soranzo, Johanna Jakobsdottir, Kristin Siggeirsdottir, Kate L Holliday, Anke Hannemann, Min Jin Go, Melissa Garcia, Ozren Polašek, Marika Laaksonen, Kun Zhu, Anke W Enneman, Mark McEvoy, Roseanne Peel, Pak Chung Sham, Maciej Jaworski, Asa Johansson, Andrew A Hicks, Pawel Pludowski, Rodney Scott, Rosalie A M Dhonukshe-Rutten, Nathalie van der Velde, Mika Kähönen, Jorma S Viikari, Harri Sievänen, Olli T Raitakari, Jesús González-Macías, José L Hernández, Dan Mellström, Osten Ljunggren, Yoon Shin Cho, Uwe Völker, Matthias Nauck, Georg Homuth, Henry Völzke, Robin Haring, Matthew A Brown, Eugene McCloskey, Geoffrey C Nicholson, Richard Eastell, John A Eisman, Graeme Jones, Ian R Reid, Elaine M Dennison, John Wark, Steven Boonen, Dirk Vanderschueren, Frederick C W Wu, Thor Aspelund, J Brent Richards, Doug Bauer, Albert Hofman, Kay-Tee Khaw, George Dedoussis, Barbara Obermayer-Pietsch, Ulf Gyllensten, Peter P Pramstaller, Roman S Lorenc, Cyrus Cooper, Annie Wai Chee Kung, Paul Lips, Markku Alen, John Attia, Maria Luisa Brandi, Lisette C P G M de Groot, Terho Lehtimäki, José A Riancho, Harry Campbell, Yongmei Liu, Tamara B Harris, Kristina Akesson, Magnus Karlsson, Jong-Young Lee, Henri Wallaschofski, Emma L Duncan, Terence W O'Neill, Vilmundur Gudnason, Timothy D Spector, François Rousseau, Eric Orwoll, Steven R Cummings, Nick J Wareham, Fernando Rivadeneira, André G Uitterlinden, Richard L Prince, Douglas P Kiel, Jonathan Reeve, Stephen K Kaptoge.
Hum. Mol. Genet.
PUBLISHED: 01-14-2014
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Quantitative ultrasound of the heel captures heel bone properties that independently predict fracture risk and, with bone mineral density (BMD) assessed by X-ray (DXA), may be convenient alternatives for evaluating osteoporosis and fracture risk. We performed a meta-analysis of genome-wide association (GWA) studies to assess the genetic determinants of heel broadband ultrasound attenuation (BUA; n = 14 260), velocity of sound (VOS; n = 15 514) and BMD (n = 4566) in 13 discovery cohorts. Independent replication involved seven cohorts with GWA data (in silico n = 11 452) and new genotyping in 15 cohorts (de novo n = 24 902). In combined random effects, meta-analysis of the discovery and replication cohorts, nine single nucleotide polymorphisms (SNPs) had genome-wide significant (P < 5 × 10(-8)) associations with heel bone properties. Alongside SNPs within or near previously identified osteoporosis susceptibility genes including ESR1 (6q25.1: rs4869739, rs3020331, rs2982552), SPTBN1 (2p16.2: rs11898505), RSPO3 (6q22.33: rs7741021), WNT16 (7q31.31: rs2908007), DKK1 (10q21.1: rs7902708) and GPATCH1 (19q13.11: rs10416265), we identified a new locus on chromosome 11q14.2 (rs597319 close to TMEM135, a gene recently linked to osteoblastogenesis and longevity) significantly associated with both BUA and VOS (P < 8.23 × 10(-14)). In meta-analyses involving 25 cohorts with up to 14 985 fracture cases, six of 10 SNPs associated with heel bone properties at P < 5 × 10(-6) also had the expected direction of association with any fracture (P < 0.05), including three SNPs with P < 0.005: 6q22.33 (rs7741021), 7q31.31 (rs2908007) and 10q21.1 (rs7902708). In conclusion, this GWA study reveals the effect of several genes common to central DXA-derived BMD and heel ultrasound/DXA measures and points to a new genetic locus with potential implications for better understanding of osteoporosis pathophysiology.
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Identification of trisomy 18, trisomy 13, and Down syndrome from maternal plasma.
Appl Clin Genet
PUBLISHED: 01-01-2014
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Current prenatal diagnosis for fetal aneuploidies (including trisomy 21 [T21]) generally relies on an initial biochemical serum-based noninvasive prenatal testing (NIPT) after which women who are deemed to be at high risk are offered an invasive confirmatory test (amniocentesis or chorionic villi sampling for a fetal karyotype), which is associated with a risk of fetal miscarriage. Recently, genomics-based NIPT (gNIPT) was proposed for the analysis of fetal genomic DNA circulating in maternal blood. The diffusion of this technology in routine prenatal care could be a major breakthrough in prenatal diagnosis, since initial research studies suggest that this novel approach could be very effective and could reduce substantially the number of invasive procedures. However, the limitations of gNIPT may be underappreciated. In this review, we examine currently published literature on gNIPT to highlight advantages and limitations. At this time, the performance of gNIPT is relatively well-documented only in high-risk pregnancies for T21 and trisomy 18. This additional screening test may be an option for women classified as high-risk of aneuploidy who wish to avoid invasive diagnostic tests, but it is crucial that providers carefully counsel patients about the test's advantages and limitations. The gNIPT is currently not recommended as a first-tier prenatal screening test for T21. Since gNIPT is not considered as a diagnostic test, a positive gNIPT result should always be confirmed by an invasive test, such as amniocentesis or chorionic villus sampling. Validation studies are needed to optimally introduce this technology into the existing routine workflow of prenatal care.
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Reflections on the cost of "low-cost" whole genome sequencing: framing the health policy debate.
PLoS Biol.
PUBLISHED: 11-01-2013
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The cost of whole genome sequencing is dropping rapidly. There has been a great deal of enthusiasm about the potential for this technological advance to transform clinical care. Given the interest and significant investment in genomics, this seems an ideal time to consider what the evidence tells us about potential benefits and harms, particularly in the context of health care policy. The scale and pace of adoption of this powerful new technology should be driven by clinical need, clinical evidence, and a commitment to put patients at the centre of health care policy.
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On high-resolution image estimation using low-resolution brain MRI.
Conf Proc IEEE Eng Med Biol Soc
PUBLISHED: 10-11-2013
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In the context of medical imaging, super-resolution (SR) is currently a promising post-processing technique to increase the image resolution. However, although many SR methods have been proposed in the literature, the gain of this type of approach in a real situation has not been precisely quantified. In this work, we evaluate image acquisition protocols and SR algorithms using in-vivo brain MR data as gold standard. The results show that using orthogonal image acquisition protocols lead to better reconstructed images than overlapping parallel low-resolution image stacks. Moreover, if the preprocessing steps (such as image denoising and intensity correction) are carefully performed, there is no significant differences between the evaluated SR algorithms.
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A unified approach to diffusion direction sensitive slice registration and 3D DTI reconstruction from moving fetal brain anatomy.
IEEE Trans Med Imaging
PUBLISHED: 09-30-2013
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This paper presents an approach to 3D Diffusion Tensor Image (DTI) reconstruction from multi-slice Diffusion Weighted (DW) MRI acquisitions of the moving fetal brain. Motion scatters the slice measurements in the spatial and spherical diffusion domain with respect to the underlying anatomy. Previous image registration techniques have been described to estimate the between slice fetal head motion, allowing the reconstruction of 3D a diffusion estimate on a regular grid using interpolation. We propose Approach to Unified Diffusion Sensitive Slice Alignment and Reconstruction (AUDiSSAR) that explicitly formulates a process for diffusion direction sensitive DW-slice-to-DTI-volume alignment. This also incorporates image resolution modeling to iteratively deconvolve the effects of the imaging point spread function using the multiple views provided by thick slices acquired in different anatomical planes. The algorithm is implemented using a multi-resolution iterative scheme and multiple real and synthetic data are used to evaluate the performance of the technique. An accuracy experiment using synthetically created motion data of an adult head and a experiment using synthetic motion added to sedated fetal monkey dataset show a significant improvement in motion-trajectory estimation compared to a state-of-the-art approaches. The performance of the method is then evaluated on challenging but clinically typical in-utero fetal scans of four different human cases, showing improved rendition of cortical anatomy and extraction of white matter tracts. While the experimental work focuses on DTI reconstruction (secondorder tensor model), the proposed reconstruction framework can employ any 5D diffusion volume model that can be represented by the spatial parameterizations of an Orientation Distribution Function (ODF).
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Meta-analysis of genome-wide studies identifies WNT16 and ESR1 SNPs associated with bone mineral density in premenopausal women.
J. Bone Miner. Res.
PUBLISHED: 08-30-2013
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Previous genome-wide association studies (GWAS) have identified common variants in genes associated with variation in bone mineral density (BMD), although most have been carried out in combined samples of older women and men. Meta-analyses of these results have identified numerous single-nucleotide polymorphisms (SNPs) of modest effect at genome-wide significance levels in genes involved in both bone formation and resorption, as well as other pathways. We performed a meta-analysis restricted to premenopausal white women from four cohorts (n?=?4061 women, aged 20 to 45 years) to identify genes influencing peak bone mass at the lumbar spine and femoral neck. After imputation, age- and weight-adjusted bone-mineral density (BMD) values were tested for association with each SNP. Association of an SNP in the WNT16 gene (rs3801387; p?=?1.7?×?10(-9) ) and multiple SNPs in the ESR1/C6orf97 region (rs4870044; p?=?1.3?×?10(-8) ) achieved genome-wide significance levels for lumbar spine BMD. These SNPs, along with others demonstrating suggestive evidence of association, were then tested for association in seven replication cohorts that included premenopausal women of European, Hispanic-American, and African-American descent (combined n?=?5597 for femoral neck; n?=?4744 for lumbar spine). When the data from the discovery and replication cohorts were analyzed jointly, the evidence was more significant (WNT16 joint p?=?1.3?×?10(-11) ; ESR1/C6orf97 joint p?=?1.4?×?10(-10) ). Multiple independent association signals were observed with spine BMD at the ESR1 region after conditioning on the primary signal. Analyses of femoral neck BMD also supported association with SNPs in WNT16 and ESR1/C6orf97 (p?
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An economic evaluation: Simulation of the cost-effectiveness and cost-utility of universal prevention strategies against osteoporosis-related fractures.
J. Bone Miner. Res.
PUBLISHED: 06-28-2013
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A patient-level Markov decision model was used to simulate a virtual cohort of 500,000 women 40 years old and over, in relation to osteoporosis-related hip, clinical vertebral, and wrist bone fractures events. Sixteen different screening options of three main scenario groups were compared: (1) the status quo (no specific national prevention program); (2) a universal primary prevention program; and (3) a universal screening and treatment program based on the 10-year absolute risk of fracture. The outcomes measured were total directs costs from the perspective of the public health care system, number of fractures, and quality-adjusted life-years (QALYs). Results show that an option consisting of a program promoting physical activity and treatment if a fracture occurs is the most cost-effective (CE) (cost/fracture averted) alternative and also the only cost saving one, especially for women 40 to 64 years old. In women who are 65 years and over, bone mineral density (BMD)-based screening and treatment based on the 10-year absolute fracture risk calculated using a Canadian Association of Radiologists and Osteoporosis Canada (CAROC) tool is the best next alternative. In terms of cost-utility (CU), results were similar. For women less than 65 years old, a program promoting physical activity emerged as cost-saving but BMD-based screening with pharmacological treatment also emerged as an interesting alternative. In conclusion, a program promoting physical activity is the most CE and CU option for women 40 to 64 years old. BMD screening and pharmacological treatment might be considered a reasonable alternative for women 65 years old and over because at a healthcare capacity of $50,000 Canadian dollars ($CAD) for each additional fracture averted or for one QALY gained its probabilities of cost-effectiveness compared to the program promoting physical activity are 63% and 75%, respectively, which could be considered socially acceptable. Consideration of the indirect costs could change these findings.
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On the estimation and correction of bias in local atrophy estimations using example atrophy simulations.
Comput Med Imaging Graph
PUBLISHED: 06-01-2013
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Brain atrophy is considered an important marker of disease progression in many chronic neuro-degenerative diseases such as multiple sclerosis (MS). A great deal of attention is being paid toward developing tools that manipulate magnetic resonance (MR) images for obtaining an accurate estimate of atrophy. Nevertheless, artifacts in MR images, inaccuracies of intermediate steps and inadequacies of the mathematical model representing the physical brain volume change, make it rather difficult to obtain a precise and unbiased estimate. This work revolves around the nature and magnitude of bias in atrophy estimations as well as a potential way of correcting them. First, we demonstrate that for different atrophy estimation methods, bias estimates exhibit varying relations to the expected atrophy and these bias estimates are of the order of the expected atrophies for standard algorithms, stressing the need for bias correction procedures. Next, a framework for estimating uncertainty in longitudinal brain atrophy by means of constructing confidence intervals is developed. Errors arising from MRI artifacts and bias in estimations are learned from example atrophy simulations and anatomies. Results are discussed for three popular non-rigid registration approaches with the help of simulated localized brain atrophy in real MR images.
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Quantifying and modelling tissue maturation in the living human fetal brain.
Int. J. Dev. Neurosci.
PUBLISHED: 05-08-2013
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Recent advances in medical imaging are beginning to allow us to quantify brain tissue maturation in the growing human brain prior to normal term age, and are beginning to shed new light on early human brain growth. These advances compliment the work already done in cellular level imaging in animal and post mortem studies of brain development. The opportunities for collaborative research that bridges the gap between macroscopic and microscopic windows on the developing brain are significant. The aim of this paper is to provide a review of the current research into MR imaging of the living fetal brain with the aim of motivating improved interfaces between the two fields. The review begins with a description of faster MRI techniques that are capable of freezing motion of the fetal head during the acquisition of a slice, and how these have been combined with advanced post-processing algorithms to build 3D images from motion scattered slices. Such rich data has motivated the development of techniques to automatically label developing tissue zones within MRI data allowing their quantification in 3D and 4D within the normally growing fetal brain. These methods have provided the basis for later work that has created the first maps of tissue growth rate and cortical folding in normally developing brains in-utero. These measurements provide valuable findings that compliment those derived from post-mortem anatomy, and additionally allow for the possibility of larger population studies of the influence of maternal environmental and genes on early brain development.
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Deep sequencing of phage display libraries to support antibody discovery.
Methods
PUBLISHED: 02-18-2013
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The use of next generation sequencing (NGS) for the analysis of antibody sequences both in phage display libraries and during in vitro selection processes has become increasingly popular in the last few years. Here, our methods developed for DNA preparation, sequencing and data analysis are presented. A key parameter has also been to develop new software designed for high throughput antibody sequence analysis that is used in combination with publicly available tools. As an example of our methods, we provide data from the extensive analysis of five scFv libraries generated using different heavy chain CDR3 diversification strategies. The results not only confirm that the library designs were correct but also reveal differences in quality not easily identified by standard DNA sequencing approaches. The very large number of reads permits extensive sequence coverage after the selection process. Furthermore, as samples can be multiplexed, costs decrease and more information is gained per NGS run. Using examples of results obtained post phage display selections against two antigens, frequency and clustering analysis identified novel antibody fragments that were then shown to be specific for the target antigen. In summary, the methods described here demonstrate how NGS analysis enhances quality control of complex antibody libraries as well as facilitates the antibody discovery process.
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Dabigatran versus warfarin under standard or pharmacogenetic-guided management for the prevention of stroke and systemic thromboembolism in patients with atrial fibrillation: a cost/utility analysis using an analytic decision model.
Thromb J
PUBLISHED: 01-18-2013
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Atrial fibrillation (AF) is the most common form of heart arrhythmia and a leading cause of stroke and systemic embolism. Chronic anticoagulation is recommended for preventing those complications. Our study aimed to compare the cost/utility (CU) of three main anticoagulation options: 1) standard warfarin dosing (SD-W) 2) warfarin dosage under the guidance of CYP2C9 and VKORC1 genotyping (GT-W) and 3) dabigatran 150 mg twice a day.
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Dual specificity of anti-CXCL10-CXCL9 antibodies is governed by structural mimicry.
J. Biol. Chem.
PUBLISHED: 10-31-2011
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Dual-specific antibodies are characterized by an antigen-combining site mediating specific interactions with two different antigens. We have generated five dual-specific single chain variable fragments (scFv) that neutralize the activity of the two chemokines, CXCL9 and CXCL10, to bind to their receptor CXCR3. To better understand how these dual-specific scFvs bind these two chemokines that only share a 37% sequence identity, we mapped their epitopes on human CXCL9 and CXCL10 and identified serine 13 (Ser(13)) as a critical residue. It is conserved between the two chemokines but not in the third ligand for CXCR3, CXCL11. Furthermore, Ser(13) is exposed in the tetrameric structure of CXCL10, which is consistent with our finding that the scFvs are able to bind to CXCL9 and CXCL10 immobilized on glycosaminoglycans. Overall, the data indicate that these dual-specific scFvs bind to a conserved surface involved in CXCR3 receptor interaction for CXCL10 and CXCL9. Thus, structural mimicry between the two targets is likely to be responsible for the observed dual specificity of these antibody fragments.
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Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction.
Proteins
PUBLISHED: 10-21-2011
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One goal of the CASP community wide experiment on the critical assessment of techniques for protein structure prediction is to identify the current state of the art in protein structure prediction and modeling. A fundamental principle of CASP is blind prediction on a set of relevant protein targets, that is, the participating computational methods are tested on a common set of experimental target proteins, for which the experimental structures are not known at the time of modeling. Therefore, the CASP experiment would not have been possible without broad support of the experimental protein structural biology community. In this article, several experimental groups discuss the structures of the proteins which they provided as prediction targets for CASP9, highlighting structural and functional peculiarities of these structures: the long tail fiber protein gp37 from bacteriophage T4, the cyclic GMP-dependent protein kinase I? dimerization/docking domain, the ectodomain of the JTB (jumping translocation breakpoint) transmembrane receptor, Autotaxin in complex with an inhibitor, the DNA-binding J-binding protein 1 domain essential for biosynthesis and maintenance of DNA base-J (?-D-glucosyl-hydroxymethyluracil) in Trypanosoma and Leishmania, an so far uncharacterized 73 residue domain from Ruminococcus gnavus with a fold typical for PDZ-like domains, a domain from the phycobilisome core-membrane linker phycobiliprotein ApcE from Synechocystis, the heat shock protein 90 activators PFC0360w and PFC0270w from Plasmodium falciparum, and 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae.
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Atlas-free surface reconstruction of the cortical grey-white interface in infants.
PLoS ONE
PUBLISHED: 10-11-2011
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The segmentation of the cortical interface between grey and white matter in magnetic resonance images (MRI) is highly challenging during the first post-natal year. First, the heterogeneous brain maturation creates important intensity fluctuations across regions. Second, the cortical ribbon is highly folded creating complex shapes. Finally, the low tissue contrast and partial volume effects hamper cortex edge detection in parts of the brain.
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Clinical validity of karyotyping for the diagnosis of chromosomal imbalance following array comparative genomic hybridisation.
J. Med. Genet.
PUBLISHED: 10-01-2011
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Array comparative genomic hybridisation (aCGH) represents a major advance in the ability to detect chromosomal imbalances (CI). A recent meta-analysis recommended aCGH for replacing karyotyping for patients with unexplained disabilities. However, favouring aCGH over karyotyping must be based on solid evidence due to the major implications of selecting a preferential diagnostic tool.
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The fragile x mental retardation syndrome 20 years after the FMR1 gene discovery: an expanding universe of knowledge.
Clin Biochem Rev
PUBLISHED: 09-14-2011
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The fragile X mental retardation (FXMR) syndrome is one of the most frequent causes of mental retardation. Affected individuals display a wide range of additional characteristic features including behavioural and physical phenotypes, and the extent to which individuals are affected is highly variable. For these reasons, elucidation of the pathophysiology of this disease has been an important challenge to the scientific community. 1991 marks the year of the discovery of both the FMR1 gene mutations involved in this disease, and of their dynamic nature. Although a mouse model for the disease has been available for 16 years and extensive research has been performed on the FMR1 protein (FMRP), we still understand little about how the disease develops, and no treatment has yet been shown to be effective. In this review, we summarise current knowledge on FXMR with an emphasis on the technical challenges of molecular diagnostics, on its prevalence and dynamics among populations, and on the potential of screening for FMR1 mutations.
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The structure of the extracellular domain of the jumping translocation breakpoint protein reveals a variation of the midkine fold.
J. Mol. Biol.
PUBLISHED: 08-30-2011
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Jumping Translocation Breakpoint (JTB) is an orphan receptor that is conserved from nematodes to humans and whose gene expression in humans is strikingly upregulated in diverse types of cancers. Translocations occur frequently at the hJTB genomic locus, leading to multiple copies of a truncated JTB gene, which potentially encodes a soluble secreted ectodomain. In addition, JTB and its orthologs likely represent a unique and ancient protein family since homologs could not be identified by direct sequence comparison. In the present study, we have determined the NMR solution structure of the N-terminal ectodomain of human JTB, showing that its fold architecture is a new variant of a three-?-strand antiparallel ?-meander. The JTB structure has a distant relationship to the midkine/pleiotrophin fold, particularly in the conservation of distinctive disulfide bridge patterns. The structure of this newly characterized small cysteine-rich domain suggests potential involvement of JTB in interactions with proteins or extracellular matrix and may help to uncover the elusive biological functions of this protein.
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Inositol polyphosphate 4-phosphatase B as a regulator of bone mass in mice and humans.
Cell Metab.
PUBLISHED: 07-21-2011
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Osteoporosis is a multifactorial genetic disease characterized by reduction of bone mass due to dysregulation of osteoclast differentiation or maturation. Herein, we identified a regulator of osteoclastogenesis, the murine homolog of inositol polyphosphate 4-phosphatase type II? (Inpp4b?). Expression of Inpp4b? is detected from early osteoclast differentiation to activation stage. Targeted expression of native Inpp4b? ex vivo repressed whereas phosphatase-inactive Inpp4b? stimulated osteoclast differentiation. Inpp4b? acts on intracellular calcium level that modulates NFATc1 nuclear translocation and activation. In vivo mice deficient in Inpp4b displayed increased osteoclast differentiation rate and potential resulting in decreased bone mass and osteoporosis. Importantly, INPP4B in human was identified as a susceptibility locus for osteoporosis. This study defined Inpp4b as a major modulator of the osteoclast differentiation and as a gene linked to variability of bone mineral density in mice and humans.
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The relation between depressive symptoms and semantic memory in amnestic mild cognitive impairment and in late-life depression.
J Int Neuropsychol Soc
PUBLISHED: 07-05-2011
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Semantic deficits have been documented in the prodromal phase of Alzheimers disease, but it is unclear whether these deficits are associated with non-cognitive manifestations. For instance, recent evidence indicates that cognitive deficits in elders with amnestic mild cognitive impairment (aMCI) are modulated by concomitant depressive symptoms. The purposes of this study were to (i) investigate if semantic memory impairment in aMCI is modulated according to the presence (aMCI-D group) or absence (aMCI group) of depressive symptoms, and (ii) compare semantic memory performance of aMCI and aMCI-D groups to that of patients with late-life depression (LLD). Seventeen aMCI, 16 aMCI-D, 15 LLD, and 26 healthy control participants were administered a semantic questionnaire assessing famous person knowledge. Results showed that performance of aMCI-D patients was impaired compared to the control and LLD groups. However, in the aMCI group performance was comparable to that of all other groups. Overall, these findings suggest that semantic deficits in aMCI are somewhat associated with the presence of concomitant depressive symptoms. However, depression alone cannot account solely for the semantic deficits since LLD patients showed no semantic memory impairment in this study. Future studies should aim at clarifying the association between depression and semantic deficits in older adults meeting aMCI criteria. (JINS, 2011, 17, 865-874).
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[Combining biochemical and ultrasonographic markers in predicting preeclampsia: a systematic review].
Ann. Biol. Clin. (Paris)
PUBLISHED: 06-11-2011
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Using a series of keywords, we reviewed electronic databases (Medline, Embase, all records to May 2009) reporting the performance of biological and ultrasonographic markers to predict preeclampsia, both single markers and combinations of markers. We analyzed the data according to gestational age and risk levels of the studied populations. We evaluated the methodological quality of included publications using QUADAS (quality assessment of diagnostic accuracy studies). We identified 37 relevant studies that assessed 71 different combinations of biochemical and ultrasonographic markers. Most studies were performed during the second trimester on small-scale high-risk populations with few cases of preeclampsia. Combinations of markers generally led to an increase in sensitivity and/or specificity compared with single markers. In low-risk populations, combinations including placental protein 13 (PP13), pregnancy-associated plasma protein A (PAPP-A), a disintegrin and metalloprotease-12 (ADAM12), activin A, or inhibin Ameasured in first or early second trimester and uterine artery Doppler in second trimester appear promising (sensitivity 60%-80%, specificity > 80%). In high-risk populations, the combination of PP13 and pulsatility index in first trimester showed 90% sensitivity and 90% specificity in a single study limited to severe preeclampsia. Combinations of biochemical and ultrasonographic markers improved the performance of early prediction of preeclampsia. From a perspective of integrative medicine, large population-based studies evaluating algorithms combining multiple markers are needed, if screening approaches are to be eventually implemented.
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Early folding patterns and asymmetries of the normal human brain detected from in utero MRI.
Cereb. Cortex
PUBLISHED: 05-12-2011
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Early cortical folding and the emergence of structural brain asymmetries have been previously analyzed by neuropathology as well as qualitative analysis of magnetic resonance imaging (MRI) of fetuses and preterm neonates. In this study, we present a dedicated image analysis framework and its application for the detection of folding patterns during the critical period for the formation of many primary sulci (20-28 gestational weeks). Using structural information from in utero MRI, we perform morphometric analysis of cortical plate surface development and modeling of early folding in the normal fetal brain. First, we identify regions of the fetal brain surface that undergo significant folding changes during this developmental period and provide precise temporal staging of these changes for each region of interest. Then, we highlight the emergence of interhemispheric structural asymmetries that may be related to future functional specialization of cortical areas. Our findings complement previous descriptions of early sulcogenesis based on neuropathology and qualitative evaluation of 2D in utero MRI by accurate spatial and temporal mapping of the emergence of individual sulci as well as structural brain asymmetries. The study provides the missing starting point for their developmental trajectories and extends our understanding of normal cortical folding.
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Bias field inconsistency correction of motion-scattered multislice MRI for improved 3D image reconstruction.
IEEE Trans Med Imaging
PUBLISHED: 04-19-2011
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A common solution to clinical MR imaging in the presence of large anatomical motion is to use fast multislice 2D studies to reduce slice acquisition time and provide clinically usable slice data. Recently, techniques have been developed which retrospectively correct large scale 3D motion between individual slices allowing the formation of a geometrically correct 3D volume from the multiple slice stacks. One challenge, however, in the final reconstruction process is the possibility of varying intensity bias in the slice data, typically due to the motion of the anatomy relative to imaging coils. As a result, slices which cover the same region of anatomy at different times may exhibit different sensitivity. This bias field inconsistency can induce artifacts in the final 3D reconstruction that can impact both clinical interpretation of key tissue boundaries and the automated analysis of the data. Here we describe a framework to estimate and correct the bias field inconsistency in each slice collectively across all motion corrupted image slices. Experiments using synthetic and clinical data show that the proposed method reduces intensity variability in tissues and improves the distinction between key tissue types.
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Late-onset-psychosis: cognition.
Int Psychogeriatr
PUBLISHED: 03-22-2011
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The objectives of the study were to characterize and compare the cognitive profile and natural evolution of patients presenting late-onset psychotic symptoms (LOPS: onset ? 50 years old) to those of elderly patients (? 50 years old) with life-long/early-onset schizophrenia (EOS: onset <40 years old).
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Local tissue growth patterns underlying normal fetal human brain gyrification quantified in utero.
J. Neurosci.
PUBLISHED: 03-19-2011
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Existing knowledge of growth patterns in the living fetal human brain is based upon in utero imaging studies by magnetic resonance imaging (MRI) and ultrasound, which describe overall growth and provide mainly qualitative findings. However, formation of the complex folded cortical structure of the adult brain requires, in part, differential rates of regional tissue growth. To better understand these local tissue growth patterns, we applied recent advances in fetal MRI motion correction and computational image analysis techniques to 40 normal fetal human brains covering a period of primary sulcal formation (20-28 gestational weeks). Growth patterns were mapped by quantifying tissue locations that were expanding more or less quickly than the overall cerebral growth rate, which reveal increasing structural complexity. We detected increased local relative growth rates in the formation of the precentral and postcentral gyri, right superior temporal gyrus, and opercula, which differentiated between the constant growth rate in underlying cerebral mantle and the accelerating rate in the cortical plate undergoing folding. Analysis focused on the cortical plate revealed greater volume increases in parietal and occipital regions compared to the frontal lobe. Cortical plate growth patterns constrained to narrower age ranges showed that gyrification, reflected by greater growth rates, was more pronounced after 24 gestational weeks. Local hemispheric volume asymmetry was located in the posterior peri-Sylvian area associated with structural lateralization in the mature brain. These maps of fetal brain growth patterns construct a spatially specific baseline of developmental biomarkers with which to correlate abnormal development in the human.
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Reconstruction of scattered data in fetal diffusion MRI.
Med Image Anal
PUBLISHED: 02-14-2011
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In this paper we present a method for reconstructing diffusion-weighted MRI data on regular grids from scattered data. The proposed method has the advantage that no specific diffusion model needs to be assumed. Previous work assume the tensor model, but this is not suitable under certain conditions like intravoxel orientational heterogeneity (IVOH). Data reconstruction is particularly important when studying the fetal brain in utero, since registration methods applied for movement and distortion correction produce scattered data in spatial and diffusion domains. We propose the use of a groupwise registration method, and a dual spatio-angular interpolation by using radial basis functions (RBF). Leave-one-out experiments performed on adult data showed a high accuracy of the method. The application to fetal data showed an improvement in the quality of the sequences according to objective criteria based on fractional anisotropy (FA) maps, and differences in the tractography results.
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Prenatal screening for Down syndrome: a survey of willingness in women and family physicians to engage in shared decision-making.
Prenat. Diagn.
PUBLISHED: 01-26-2011
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To assess the willingness of women and their family physicians (FPs) to engage in shared decision-making (SDM) as regards prenatal Down-syndrome screening and the factors that might influence their willingness to do so.
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Developing and user-testing Decision boxes to facilitate shared decision making in primary care--a study protocol.
BMC Med Inform Decis Mak
PUBLISHED: 01-17-2011
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Applying evidence is one of the most challenging steps of evidence-based clinical practice. Healthcare professionals have difficulty interpreting evidence and translating it to patients. Decision boxes are summaries of the most important benefits and harms of diagnostic, therapeutic, and preventive health interventions provided to healthcare professionals before they meet the patient. Our hypothesis is that Decision boxes will prepare clinicians to help patients make informed value-based decisions. By acting as primers, the boxes will enhance the application of evidence-based practices and increase shared decision making during the clinical encounter. The objectives of this study are to provide a framework for developing Decision boxes and testing their value to users.
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Non-iterative relative bias correction for 3D reconstruction of in utero fetal brain MR imaging.
Conf Proc IEEE Eng Med Biol Soc
PUBLISHED: 11-25-2010
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The slice intersection motion correction (SIMC) method is a powerful tool to compensate for motion that occurs during in utero acquisition of the multislice magnetic resonance (MR) images of the human fetal brain. The SIMC method makes use of the slice intersection intensity profiles of orthogonally planned slice pairs to simultaneously correct for the relative motion occurring between all the acquired slices. This approach is based on the assumption that the bias field is consistent between slices. However, for some clinical studies where there is a strong bias field combined with significant fetal motion relative to the coils, this assumption is broken and the resulting motion estimate and the reconstruction to a 3D volume can both contain errors. In this work, we propose a method to correct for the relative differences in bias field between all slice pairs. For this, we define the energy function as the mean square difference of the intersection profiles, that is then minimized with respect to the bias field parameters of the slices. A non iterative method which considers the relative bias between each slice simultaneously is used to efficiently remove inconsistencies. The method, when tested on synthetic simulations and actual clinical imaging studies where bias was an issue, brought a significant improvement to the final reconstructed image.
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IL-27 structural analysis demonstrates similarities with ciliary neurotrophic factor (CNTF) and leads to the identification of antagonistic variants.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 10-25-2010
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IL-27, consisting of the subunits IL-27p28 and Epstein-Barr virus-induced gene 3 (EBI3), is a heterodimeric cytokine belonging to the IL-6/IL-12 family of cytokines. IL-27p28 is a four-helical cytokine requiring association with the soluble receptor EBI3 to be efficiently secreted and functionally active. Computational and biological analyses of the IL-27 binding site 1 to its receptor revealed important structural proximities with the ciliary neurotrophic factor group of cytokines and highlighted the contribution of p28 Trp(97), as well as of EBI3 Phe(97), Asp(210), and Glu(159), as key residues in the interactions between both cytokine subunits. WSX-1 (IL-27R) and gp130 compose the IL-27 receptor-signaling complex, recruiting the STAT-1 and STAT-3 pathways. A study of IL-27 binding site 3 showed that Trp(197) was crucial for the cytokines interaction with gp130, but that the mutated cytokine still recognized IL-27R on the cell surface. IL-27 exerts both pro- and anti-inflammatory functions, promoting proliferation and differentiation of Th1 and inhibiting Th17 differentiation. Our results led us to develop mutated forms of human and mouse IL-27 with antagonistic activities. Using an in vivo mouse model of concanavalin A-induced Th1-cell-mediated hepatitis, we showed that the murine IL-27 antagonist W195A decreased liver inflammation by downregulating the synthesis of CXCR3 ligands and several acute phase proteins. Together, these data suggest that IL-27 antagonism could be of interest in down-modulating acute IL-27-driven Th1-cell-mediated immune response.
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Nucleic acid reference materials (NARMs): definitions and issues.
Clin. Chem. Lab. Med.
PUBLISHED: 10-25-2010
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Molecular diagnostics is one of the most rapidly growing areas of laboratory medicine. This rapid growth of clinical molecular tests has outpaced the availability and development of reference methods and reference materials. Such methods and materials are important for the development, validation, and interpretation of diagnostic methods and tests. Yet, there is a lack of harmonization between the numerous international organizations currently either certifying or defining reference materials. The objective of this position paper is to review and clarify the definition, attributes and applications for the use of reference materials in the context of molecular diagnostics.
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Rapid testing versus karyotyping in Downs syndrome screening: cost-effectiveness and detection of clinically significant chromosome abnormalities.
Eur. J. Hum. Genet.
PUBLISHED: 09-15-2010
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In all, 80% of antenatal karyotypes are generated by Downs syndrome screening programmes (DSSP). After a positive screening, women are offered prenatal foetus karyotyping, the gold standard. Reliable molecular methods for rapid aneuploidy diagnosis (RAD: fluorescence in situ hybridization (FISH) and quantitative fluorescence PCR (QF-PCR)) can detect common aneuploidies, and are faster and less expensive than karyotyping.In the UK, RAD is recommended as a standalone approach in DSSP, whereas the US guidelines recommend that RAD be followed up by karyotyping. A cost-effectiveness (CE) analysis of RAD in various DSSP is lacking. There is a debate over the significance of chromosome abnormalities (CA) detected with karyotyping but not using RAD. Our objectives were to compare the CE of RAD versus karyotyping, to evaluate the clinically significant missed CA and to determine the impact of detecting the missed CA. We performed computer simulations to compare six screening options followed by FISH, PCR or karyotyping using a population of 110948 pregnancies. Among the safer screening strategies, the most cost-effective strategy was contingent screening with QF-PCR (CE ratio of $24084 per Downs syndrome (DS) detected). Using karyotyping, the CE ratio increased to $27898. QF-PCR missed only six clinically significant CA of which only one was expected to confer a high risk of an abnormal outcome. The incremental CE ratio (ICER) to find the CA missed by RAD was $66608 per CA. These costs are much higher than those involved for detecting DS cases. As the DSSP are mainly designed for DS detection, it may be relevant to question the additional costs of karyotyping.
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Development and description of GETT: a genetic testing evidence tracking tool.
Clin. Chem. Lab. Med.
PUBLISHED: 07-27-2010
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The completion of the Human Genome Project has increased the pace of discovery of genetic markers for disease. Despite tremendous efforts in fundamental research, clinical applications still lag behind expectations, partly due to the lack of effective tools to systematically search for and summarize published data relative to the clinical assessment of new diagnostic molecular tests.
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High-density polymorphisms analysis of 23 candidate genes for association with bone mineral density.
Bone
PUBLISHED: 04-19-2010
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Osteoporosis is a bone disease characterized by low bone mineral density (BMD), a highly heritable and polygenic trait. Women are more prone than men to develop osteoporosis due to a lower peak bone mass and accelerated bone loss at menopause. Peak bone mass has been convincingly shown to be due to genetic factors with heritability up to 80%. Menopausal bone loss has been shown to have around 38% to 49% heritability depending on the site studied. To have more statistical power to detect small genetic effects we focused on premenopausal women. We studied 23 candidate genes, some involved in calcium and vitamin-D regulation and others because estrogens strongly induced their gene expression in mice where it was correlated with humerus trabecular bone density. High-density polymorphisms were selected to cover the entire gene variability and 231 polymorphisms were genotyped in a first sample of 709 premenopausal women. Positive associations were retested in a second, independent, sample of 673 premenopausal women. Ten polymorphisms remained associated with BMD in the combined samples and one was further associated in a large sample of postmenopausal women (1401 women). This associated polymorphism was located in the gene CSF3R (granulocyte colony stimulating factor receptor) that had never been associated with BMD before. The results reported in this study suggest a role for CSF3R in the determination of bone density in women.
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Cost-effectiveness and accuracy of prenatal Down syndrome screening strategies: should the combined test continue to be widely used?
Am. J. Obstet. Gynecol.
PUBLISHED: 03-23-2010
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We analyzed the cost-effectiveness (CE) and performances of commonly used prenatal Down syndrome (DS) screening strategies.
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A non-local approach for image super-resolution using intermodality priors.
Med Image Anal
PUBLISHED: 02-11-2010
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Image enhancement is of great importance in medical imaging where image resolution remains a crucial point in many image analysis algorithms. In this paper, we investigate brain hallucination (Rousseau, 2008), or generating a high-resolution brain image from an input low-resolution image, with the help of another high-resolution brain image. We propose an approach for image super-resolution by using anatomical intermodality priors from a reference image. Contrary to interpolation techniques, in order to be able to recover fine details in images, the reconstruction process is based on a physical model of image acquisition. Another contribution to this inverse problem is a new regularization approach that uses an example-based framework integrating non-local similarity constraints to handle in a better way repetitive structures and texture. The effectiveness of our approach is demonstrated by experiments on realistic Brainweb Magnetic Resonance images and on clinical images from ADNI, generating automatically high-quality brain images from low-resolution input.
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A spatiotemporal atlas of MR intensity, tissue probability and shape of the fetal brain with application to segmentation.
Neuroimage
PUBLISHED: 02-06-2010
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Modeling and analysis of MR images of the developing human brain is a challenge due to rapid changes in brain morphology and morphometry. We present an approach to the construction of a spatiotemporal atlas of the fetal brain with temporal models of MR intensity, tissue probability and shape changes. This spatiotemporal model is created from a set of reconstructed MR images of fetal subjects with different gestational ages. Groupwise registration of manual segmentations and voxelwise nonlinear modeling allow us to capture the appearance, disappearance and spatial variation of brain structures over time. Applying this model to atlas-based segmentation, we generate age-specific MR templates and tissue probability maps and use them to initialize automatic tissue delineation in new MR images. The choice of model parameters and the final performance are evaluated using clinical MR scans of young fetuses with gestational ages ranging from 20.57 to 24.71 weeks. Experimental results indicate that quadratic temporal models can correctly capture growth-related changes in the fetal brain anatomy and provide improvement in accuracy of atlas-based tissue segmentation.
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Atlas-based segmentation of developing tissues in the human brain with quantitative validation in young fetuses.
Hum Brain Mapp
PUBLISHED: 01-29-2010
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Imaging of the human fetus using magnetic resonance (MR) is an essential tool for quantitative studies of normal as well as abnormal brain development in utero. However, because of fundamental differences in tissue types, tissue properties and tissue distribution between the fetal and adult brain, automated tissue segmentation techniques developed for adult brain anatomy are unsuitable for this data. In this paper, we describe methodology for automatic atlas-based segmentation of individual tissue types in motion-corrected 3D volumes reconstructed from clinical MR scans of the fetal brain. To generate anatomically correct automatic segmentations, we create a set of accurate manual delineations and build an in utero 3D statistical atlas of tissue distribution incorporating developing gray and white matter as well as transient tissue types such as the germinal matrix. The probabilistic atlas is associated with an unbiased average shape and intensity template for registration of new subject images to the space of the atlas. Quantitative whole brain 3D validation of tissue labeling performed on a set of 14 fetal MR scans (20.57-22.86 weeks gestational age) demonstrates that this atlas-based EM segmentation approach achieves consistently high DSC performance for the main tissue types in the fetal brain. This work indicates that reliable measures of brain development can be automatically derived from clinical MR imaging and opens up possibility of further 3D volumetric and morphometric studies with multiple fetal subjects.
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Combining biochemical and ultrasonographic markers in predicting preeclampsia: a systematic review.
Clin. Chem.
PUBLISHED: 01-02-2010
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Early identification of pregnant women at risk for preeclampsia is a priority to implement preventive measures. Some biochemical and ultrasonographic parameters have shown promising predictive performance, but so far there is no clinically validated screening procedure.
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Molecular dissection of human interleukin-31-mediated signal transduction through site-directed mutagenesis.
J. Biol. Chem.
PUBLISHED: 11-17-2009
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Interleukin (IL)-31 is a recently described cytokine, preferentially produced by T helper 2 lymphocytes and associated with skin diseases, such as atopic dermatitis. IL-31 is a member of the four alpha-helix bundle cytokine family and is related to the IL-6 subgroup. Its heterodimeric membrane receptor is composed of the gp130-like receptor (GPL) subunit associated to the oncostatin M receptor subunit. We identified critical amino acids implicated in the ligand receptor interaction by computational analysis combined with site-directed mutagenesis. Six IL-31 residues selected for their putative involvement in cytokine receptor contact sites were alanine-substituted, and the corresponding proteins were expressed in mammalian and bacterial systems. Biochemical, membrane binding, cell signaling, and cell proliferation analyses showed that mutation E44A, E106A, or H110A abolished IL-31 binding to GPL and the subsequent signaling events. A second ligand receptor-binding site involved Lys(134), with alanine substitution leading to a protein that still binds GPL, but is unable to recruit the second receptor subunit and the subsequent signaling pathways. The results indicate that IL-31 recognizes its receptor complex through two different binding sites, and we propose a three-dimensional model for IL-31.
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Considerations for the development of a reference method for sequencing of haploid DNA--an opinion paper on behalf of the IFCC Committee on Molecular Diagnostics, International Federation of Clinical Chemistry and Laboratory Medicine.
Clin. Chem. Lab. Med.
PUBLISHED: 10-13-2009
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Following the completion of sequencing of the human genome, there has been a very rapid increase in the development of new molecular diagnostic tests. However, the numerous genetic tests and genetic testing technologies offered do not always satisfy essential quality criteria required to ensure confidence in the results that are produced. This is of particular importance for genetic tests since many patients may be tested for a particular genetic defect only once in their lifetime. Thus, there is a pressing need for comprehensive guidelines for the validation of molecular diagnostic tests and procedures, including DNA sequencing, the latter being a fundamental aspect of the development and validation of most genetic tests. To that end, the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) Committee for Molecular Diagnostics has prepared the following paper that describes a possible approach to the development of a reference method for sequencing of haploid DNA. We discuss various aspects which should be considered before, during and after applying the sequencing procedure, in order to achieve results with a known level of confidence, including robustness and assessments of quality.
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Intersection based motion correction of multislice MRI for 3-D in utero fetal brain image formation.
IEEE Trans Med Imaging
PUBLISHED: 09-09-2009
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In recent years, postprocessing of fast multislice magnetic resonance imaging (MRI) to correct fetal motion has provided the first true 3-D MR images of the developing human brain in utero. Early approaches have used reconstruction based algorithms, employing a two-step iterative process, where slices from the acquired data are realigned to an approximate 3-D reconstruction of the fetal brain, which is then refined further using the improved slice alignment. This two step slice-to-volume process, although powerful, is computationally expensive in needing a 3-D reconstruction, and is limited in its ability to recover subvoxel alignment. Here, we describe an alternative approach which we term slice intersection motion correction (SIMC), that seeks to directly co-align multiple slice stacks by considering the matching structure along all intersecting slice pairs in all orthogonally planned slices that are acquired in clinical imaging studies. A collective update scheme for all slices is then derived, to simultaneously drive slices into a consistent match along their lines of intersection. We then describe a 3-D reconstruction algorithm that, using the final motion corrected slice locations, suppresses through-plane partial volume effects to provide a single high isotropic resolution 3-D image. The method is tested on simulated data with known motions and is applied to retrospectively reconstruct 3-D images from a range of clinically acquired imaging studies. The quantitative evaluation of the registration accuracy for the simulated data sets demonstrated a significant improvement over previous approaches. An initial application of the technique to studying clinical pathology is included, where the proposed method recovered up to 15 mm of translation and 30 degrees of rotation for individual slices, and produced full 3-D reconstructions containing clinically useful additional information not visible in the original 2-D slices.
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Comparison of different strategies in prenatal screening for Downs syndrome: cost effectiveness analysis of computer simulation.
BMJ
PUBLISHED: 02-17-2009
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To assess and compare the cost effectiveness of three different strategies for prenatal screening for Downs syndrome (integrated test, sequential screening, and contingent screenings) and to determine the most useful cut-off values for risk.
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Joint filtering estimation of Stokes vector images based on a nonlocal means approach.
J Opt Soc Am A Opt Image Sci Vis
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Conventional estimation techniques of Stokes images from observed radiance images through different polarization filters suffer from noise contamination that hampers correct interpretation or even leads to unphysical estimated signatures. This paper presents an efficient restoration technique based on nonlocal means, permitting accurate estimation of smoothly variable polarization signatures in the Stokes image while preserving sharp transitions. The method is assessed on simulated data as well as on real images.
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BTK: an open-source toolkit for fetal brain MR image processing.
Comput Methods Programs Biomed
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Studies about brain maturation aim at providing a better understanding of brain development and links between brain changes and cognitive development. Such studies are of great interest for diagnosis help and clinical course of development and treatment of illnesses. However, the processing of fetal brain MR images remains complicated which limits the translation from the research to the clinical domain. In this article, we describe an open-source image processing toolkit dedicated to these images. In this toolkit various tools are included such as: denoising, image reconstruction, super-resolution and tractography. The BTK resource program (distributed under CeCILL-B license) is developed in C++ and relies on common medical imaging libraries such as Insight Toolkit (ITK), Visualization Toolkit (VTK) and Open Multi-Processing (OpenMP).
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"I want to know whats in Pandoras Box": comparing stakeholder perspectives on incidental findings in clinical whole genomic sequencing.
Am. J. Med. Genet. A
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Whole genomic sequencing (WGS) promises significant personalized health benefits, and its increasingly low cost makes wide clinical use inevitable. However, a core challenge is "incidental findings" (IF). Using focus groups, we explored attitudes about the disclosure of IF in clinical settings from three perspectives: Genetics health-care professionals, the general public, and parents whose children have experienced genetic testing. Analysis was based on a framework approach. All three groups considered practical and ethical considerations. There was consensus that IF presented challenges for disclosure and a pre-test patient-clinician discussion was vital for clarification and agreement. The professionals favored targeted analysis to limit data handling and focus pre-test discussions on medical relevance. Their perspective highlighted ethical concepts of justice and beneficence. The lay groups standpoint emphasized autonomy and patients rights to choose what findings they receive, and that patients accept the consequences of any potential anxiety and uncertainty. The lay groups also felt that it was their responsibility to check genomic developments over time with their original test results and saw patient responsibility as an important part of patient choice.
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Decision boxes for clinicians to support evidence-based practice and shared decision making: the user experience.
Implement Sci
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This project engages patients and physicians in the development of Decision Boxes, short clinical topic summaries covering medical questions that have no single best answer. Decision Boxes aim to prepare the clinician to communicate the risks and benefits of the available options to the patient so they can make an informed decision together.
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Candidate biochemical markers for screening of pre-eclampsia in early pregnancy.
Clin. Chem. Lab. Med.
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Pre-eclampsia (PE) and other hypertensive disorders of pregnancy (HDP) are a leading cause of adverse outcomes. Their pathophysiology remains elusive, hampering the development of efficient prevention. The onset of HDP and PE and the severity of their clinical manifestations are heterogeneous. The advent of preventive measures, such as low-dose aspirin that targets high-risk women, emphasizes the need of better prediction. Until recently, only environmental information and maternal risk factors were considered, with equivocal predictive value. No validated screening procedures were available to identify at-risk women despite the emergence of Doppler ultrasonography parameters for the uterine artery (e.g., pulsatility index and bilateral notching) and pathophysiological biochemical markers (e.g., angiogenesis, inflammation, and endothelial dysfunction). Owing to its heterogeneity and lack of specific, sensitive markers among those studied so far (>200), PE is unlikely to be detected early by a single predictive parameter. Systematic reviews have concluded that no single test fulfilling World Health Organization criteria for biomarker selection can diagnose/predict a disease. However, by combining antenatal risk factors, clinical parameters, as well as biophysical and biochemical markers into multivariate algorithms, the risk of PE can be estimated with performance levels that could reach clinical utility. Performance characteristics of selected algorithms will be presented and discussed with respect to transferability to different geographic and healthcare environments.
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Assessment of gene-by-sex interaction effect on bone mineral density.
Ching-Ti Liu, Karol Estrada, Laura M Yerges-Armstrong, Najaf Amin, Evangelos Evangelou, Guo Li, Ryan L Minster, Melanie A Carless, Candace M Kammerer, Ling Oei, Yanhua Zhou, Nerea Alonso, Zoe Dailiana, Joel Eriksson, Natalia Garcia-Giralt, Sylvie Giroux, Lise Bjerre Husted, Rita I Khusainova, Theodora Koromila, Annie Waichee Kung, Joshua R Lewis, Laura Masi, Simona Mencej-Bedrač, Xavier Noguès, Millan S Patel, Janez Prezelj, J Brent Richards, Pak Chung Sham, Timothy Spector, Liesbeth Vandenput, Su-Mei Xiao, Hou-Feng Zheng, Kun Zhu, Susana Balcells, Maria Luisa Brandi, Morten Frost, David Goltzman, Jesús González-Macías, Magnus Karlsson, Elza K Khusnutdinova, Panagoula Kollia, Bente Lomholt Langdahl, Osten Ljunggren, Mattias Lorentzon, Janja Marc, Dan Mellström, Claes Ohlsson, José M Olmos, Stuart H Ralston, José A Riancho, François Rousseau, Roser Urreizti, Wim Van Hul, María T Zarrabeitia, Martha Castano-Betancourt, Serkalem Demissie, Elin Grundberg, Lizbeth Herrera, Tony Kwan, Carolina Medina-Gomez, Tomi Pastinen, Gunnar Sigurdsson, Gudmar Thorleifsson, Joyce Bj Vanmeurs, John Blangero, Albert Hofman, Yongmei Liu, Braxton D Mitchell, Jeffrey R O'Connell, Ben A Oostra, Jerome I Rotter, Kari Stefansson, Elizabeth A Streeten, Unnur Styrkarsdottir, Unnur Thorsteinsdottir, Frances A Tylavsky, André Uitterlinden, Jane A Cauley, Tamara B Harris, John Pa Ioannidis, Bruce M Psaty, John A Robbins, M Carola Zillikens, Cornelia M Vanduijn, Richard L Prince, David Karasik, Fernando Rivadeneira, Douglas P Kiel, L Adrienne Cupples, Yi-Hsiang Hsu.
J. Bone Miner. Res.
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Sexual dimorphism in various bone phenotypes, including bone mineral density (BMD), is widely observed; however, the extent to which genes explain these sex differences is unclear. To identify variants with different effects by sex, we examined gene-by-sex autosomal interactions genome-wide, and performed expression quantitative trait loci (eQTL) analysis and bioinformatics network analysis. We conducted an autosomal genome-wide meta-analysis of gene-by-sex interaction on lumbar spine (LS) and femoral neck (FN) BMD in 25,353 individuals from 8 cohorts. In a second stage, we followed up the 12 top single-nucleotide polymorphisms (SNPs; p?
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Self-determination: a buffer against suicide ideation.
Suicide Life Threat Behav
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Self-determination was examined as a protective factor against the detrimental impact of negative life events on suicide ideation in adolescents. It is postulated that for highly self-determined adolescents, negative life events have a weaker impact on both hopelessness and suicide ideation than for non-self-determined adolescents. In turn, hopelessness is hypothesized to generate less suicide ideation for highly self-determined individuals. Results from multigroup analyses confirm that both the direct and indirect links between negative life events and suicide ideation were significantly weaker among participants high in self-determination. The protective role of self-determination against negative life events is discussed.
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White matter atrophy and cognitive dysfunctions in neuromyelitis optica.
PLoS ONE
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Neuromyelitis optica (NMO) is an inflammatory disease of central nervous system characterized by optic neuritis and longitudinally extensive acute transverse myelitis. NMO patients have cognitive dysfunctions but other clinical symptoms of brain origin are rare. In the present study, we aimed to investigate cognitive functions and brain volume in NMO. The study population consisted of 28 patients with NMO and 28 healthy control subjects matched for age, sex and educational level. We applied a French translation of the Brief Repeatable Battery (BRB-N) to the NMO patients. Using SIENAx for global brain volume (Grey Matter, GM; White Matter, WM; and whole brain) and VBM for focal brain volume (GM and WM), NMO patients and controls were compared. Voxel-level correlations between diminished brain concentration and cognitive performance for each tests were performed. Focal and global brain volume of NMO patients with and without cognitive impairment were also compared. Fifteen NMO patients (54%) had cognitive impairment with memory, executive function, attention and speed of information processing deficits. Global and focal brain atrophy of WM but not Grey Matter (GM) was found in the NMO patients group. The focal WM atrophy included the optic chiasm, pons, cerebellum, the corpus callosum and parts of the frontal, temporal and parietal lobes, including superior longitudinal fascicle. Visual memory, verbal memory, speed of information processing, short-term memory and executive functions were correlated to focal WM volumes. The comparison of patients with, to patients without cognitive impairment showed a clear decrease of global and focal WM, including brainstem, corticospinal tracts, corpus callosum but also superior and inferior longitudinal fascicles. Cognitive impairment in NMO patients is correlated to the decreased of global and focal WM volume of the brain. Further studies are needed to better understand the precise origin of cognitive impairment in NMO patients, particularly in the WM.
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Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
Karol Estrada, Unnur Styrkarsdottir, Evangelos Evangelou, Yi-Hsiang Hsu, Emma L Duncan, Evangelia E Ntzani, Ling Oei, Omar M E Albagha, Najaf Amin, John P Kemp, Daniel L Koller, Guo Li, Ching-Ti Liu, Ryan L Minster, Alireza Moayyeri, Liesbeth Vandenput, Dana Willner, Su-Mei Xiao, Laura M Yerges-Armstrong, Hou-Feng Zheng, Nerea Alonso, Joel Eriksson, Candace M Kammerer, Stephen K Kaptoge, Paul J Leo, Gudmar Thorleifsson, Scott G Wilson, James F Wilson, Ville Aalto, Markku Alen, Aaron K Aragaki, Thor Aspelund, Jacqueline R Center, Zoe Dailiana, David J Duggan, Melissa Garcia, Natalia Garcia-Giralt, Sylvie Giroux, Göran Hallmans, Lynne J Hocking, Lise Bjerre Husted, Karen A Jameson, Rita Khusainova, Ghi Su Kim, Charles Kooperberg, Theodora Koromila, Marcin Kruk, Marika Laaksonen, Andrea Z LaCroix, Seung Hun Lee, Ping C Leung, Joshua R Lewis, Laura Masi, Simona Mencej-Bedrač, Tuan V Nguyen, Xavier Noguès, Millan S Patel, Janez Prezelj, Lynda M Rose, Serena Scollen, Kristin Siggeirsdottir, Albert V Smith, Olle Svensson, Stella Trompet, Olivia Trummer, Natasja M van Schoor, Jean Woo, Kun Zhu, Susana Balcells, Maria Luisa Brandi, Brendan M Buckley, Sulin Cheng, Claus Christiansen, Cyrus Cooper, George Dedoussis, Ian Ford, Morten Frost, David Goltzman, Jesús González-Macías, Mika Kähönen, Magnus Karlsson, Elza Khusnutdinova, Jung-Min Koh, Panagoula Kollia, Bente Lomholt Langdahl, William D Leslie, Paul Lips, Osten Ljunggren, Roman S Lorenc, Janja Marc, Dan Mellström, Barbara Obermayer-Pietsch, José M Olmos, Ulrika Pettersson-Kymmer, David M Reid, José A Riancho, Paul M Ridker, François Rousseau, P Eline Slagboom, Nelson L S Tang, Roser Urreizti, Wim Van Hul, Jorma Viikari, María T Zarrabeitia, Yurii S Aulchenko, Martha Castano-Betancourt, Elin Grundberg, Lizbeth Herrera, Thorvaldur Ingvarsson, Hrefna Johannsdottir, Tony Kwan, Rui Li, Robert Luben, Carolina Medina-Gomez, Stefan Th Palsson, Sjur Reppe, Jerome I Rotter, Gunnar Sigurdsson, Joyce B J van Meurs, Dominique Verlaan, Frances M K Williams, Andrew R Wood, Yanhua Zhou, Kaare M Gautvik, Tomi Pastinen, Soumya Raychaudhuri, Jane A Cauley, Daniel I Chasman, Graeme R Clark, Steven R Cummings, Patrick Danoy, Elaine M Dennison, Richard Eastell, John A Eisman, Vilmundur Gudnason, Albert Hofman, Rebecca D Jackson, Graeme Jones, J Wouter Jukema, Kay-Tee Khaw, Terho Lehtimäki, Yongmei Liu, Mattias Lorentzon, Eugene McCloskey, Braxton D Mitchell, Kannabiran Nandakumar, Geoffrey C Nicholson, Ben A Oostra, Munro Peacock, Huibert A P Pols, Richard L Prince, Olli Raitakari, Ian R Reid, John Robbins, Philip N Sambrook, Pak Chung Sham, Alan R Shuldiner, Frances A Tylavsky, Cornelia M van Duijn, Nick J Wareham, L Adrienne Cupples, Michael J Econs, David M Evans, Tamara B Harris, Annie Wai Chee Kung, Bruce M Psaty, Jonathan Reeve, Timothy D Spector, Elizabeth A Streeten, M Carola Zillikens, Unnur Thorsteinsdottir, Claes Ohlsson, David Karasik, J Brent Richards, Matthew A Brown, Kari Stefansson, André G Uitterlinden, Stuart H Ralston, John P A Ioannidis, Douglas P Kiel, Fernando Rivadeneira.
Nat. Genet.
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Bone mineral density (BMD) is the most widely used predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and east Asian ancestry. We tested the top BMD-associated markers for replication in 50,933 independent subjects and for association with risk of low-trauma fracture in 31,016 individuals with a history of fracture (cases) and 102,444 controls. We identified 56 loci (32 new) associated with BMD at genome-wide significance (P < 5 × 10(-8)). Several of these factors cluster within the RANK-RANKL-OPG, mesenchymal stem cell differentiation, endochondral ossification and Wnt signaling pathways. However, we also discovered loci that were localized to genes not known to have a role in bone biology. Fourteen BMD-associated loci were also associated with fracture risk (P < 5 × 10(-4), Bonferroni corrected), of which six reached P < 5 × 10(-8), including at 18p11.21 (FAM210A), 7q21.3 (SLC25A13), 11q13.2 (LRP5), 4q22.1 (MEPE), 2p16.2 (SPTBN1) and 10q21.1 (DKK1). These findings shed light on the genetic architecture and pathophysiological mechanisms underlying BMD variation and fracture susceptibility.
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Mapping directionality specific volume changes using tensor based morphometry: an application to the study of gyrogenesis and lateralization of the human fetal brain.
Neuroimage
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Tensor based morphometry (TBM) is a powerful approach to analyze local structural changes in brain anatomy. However, conventional scalar TBM methods do not completely capture all direction specific volume changes required to model complex changes such as those during brain growth. In this paper, we describe novel TBM descriptors for studying direction-specific changes in a subject population which can be used in conjunction with scalar TBM to analyze local patterns in directionality of volume change during brain development. We also extend the methodology to provide a new approach to mapping directional asymmetry in deformation tensors associated with the emergence of structural asymmetry in the developing brain. We illustrate the use of these methods by studying developmental patterns in the human fetal brain, in vivo. Results show that fetal brain development exhibits a distinct spatial pattern of anisotropic growth. The most significant changes in the directionality of growth occur in the cortical plate at major sulci. Our analysis also detected directional growth asymmetry in the peri-Sylvian region and the medial frontal lobe of the fetal brain.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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