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https://www.readbyqxmd.com/read/28192130/ielvis-an-open-source-matlab-toolbox-for-localizing-and-visualizing-human-intracranial-electrode-data
#1
David M Groppe, Stephan Bickel, Andrew R Dykstra, Xiuyuan Wang, Pierre Mégevand, Manuel R Mercier, Fred A Lado, Ashesh D Mehta, Christopher J Honey
BACKGROUND: Intracranial electrical recordings (iEEG) and brain stimulation (iEBS) are invaluable human neuroscience methodologies. However, the value of such data is often unrealized as many laboratories lack tools for localizing electrodes relative to anatomy. To remedy this, we have developed a MATLAB toolbox for intracranial electrode localization and visualization, iELVis. NEW METHOD: iELVis uses existing tools (BioImage Suite, FSL, and FreeSurfer) for preimplant magnetic resonance imaging (MRI) segmentation, neuroimaging coregistration, and manual identification of electrodes in postimplant neuroimaging...
February 9, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28188873/an-improved-fsl-first-pipeline-for-subcortical-gray-matter-segmentation-to-study-abnormal-brain-anatomy-using-quantitative-susceptibility-mapping-qsm
#2
Xiang Feng, Andreas Deistung, Michael G Dwyer, Jesper Hagemeier, Paul Polak, Jessica Lebenberg, Frédérique Frouin, Robert Zivadinov, Jürgen R Reichenbach, Ferdinand Schweser
Accurate and robust segmentation of subcortical gray matter (SGM) nuclei is required in many neuroimaging applications. FMRIB's Integrated Registration and Segmentation Tool (FIRST) is one of the most popular software tools for automated subcortical segmentation based on T1-weighted (T1w) images. In this work, we demonstrate that FIRST tends to produce inaccurate SGM segmentation results in the case of abnormal brain anatomy, such as present in atrophied brains, due to a poor spatial match of the subcortical structures with the training data in the MNI space as well as due to insufficient contrast of SGM structures on T1w images...
February 7, 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/28182655/regional-analysis-of-volumes-and-reproducibilities-of-automatic-and-manual-hippocampal-segmentations
#3
Fabian Bartel, Hugo Vrenken, Fetsje Bijma, Frederik Barkhof, Marcel van Herk, Jan C de Munck
PURPOSE: Precise and reproducible hippocampus outlining is important to quantify hippocampal atrophy caused by neurodegenerative diseases and to spare the hippocampus in whole brain radiation therapy when performing prophylactic cranial irradiation or treating brain metastases. This study aimed to quantify systematic differences between methods by comparing regional volume and outline reproducibility of manual, FSL-FIRST and FreeSurfer hippocampus segmentations. MATERIALS AND METHODS: This study used a dataset from ADNI (Alzheimer's Disease Neuroimaging Initiative), including 20 healthy controls, 40 patients with mild cognitive impairment (MCI), and 20 patients with Alzheimer's disease (AD)...
2017: PloS One
https://www.readbyqxmd.com/read/28171781/increased-white-matter-radial-diffusivity-is-associated-with-prefrontal-cortical-folding-deficits-in-schizophrenia
#4
C Christoph Schultz, Gerd Wagner, Claudia Schachtzabel, Jürgen R Reichenbach, Ralf G M Schlösser, Heinrich Sauer, Kathrin Koch
The neuronal underpinnings of cortical folding alterations in schizophrenia remain unclear. Theories on the physiological development of cortical folds stress the importance of white matter fibers for this process and disturbances of fiber tracts might be relevant for cortical folding alterations in schizophrenia. Nine-teen patients with schizophrenia and 19 healthy subjects underwent T1-weighted MRI and DTI. Cortical folding was computed using a surface based approach. DTI was analyzed using FSL and SPM 5...
February 4, 2017: Psychiatry Research
https://www.readbyqxmd.com/read/28166799/toll-like-receptor-3-activation-selectively-reverses-hiv-latency-in-microglial-cells
#5
David Alvarez-Carbonell, Yoelvis Garcia-Mesa, Stephanie Milne, Biswajit Das, Curtis Dobrowolski, Roxana Rojas, Jonathan Karn
BACKGROUND: Multiple toll-like receptors (TLRs) are expressed in cells of the monocytic lineage, including microglia, which constitute the major reservoir for human immunodeficiency virus (HIV) infection in the brain. We hypothesized that TLR receptor mediated responses to inflammatory conditions by microglial cells in the central nervous system (CNS) are able to induce latent HIV proviruses, and contribute to the etiology of HIV-associated neurocognitive disorders. RESULTS: Newly developed human microglial cell lines (hµglia), obtained by immortalizing human primary microglia with simian virus-40 (SV40) large T antigen and the human telomerase reverse transcriptase, were used to generate latently infected cells using a single-round HIV virus carrying a green fluorescence protein reporter (hµglia/HIV, clones HC01 and HC69)...
February 6, 2017: Retrovirology
https://www.readbyqxmd.com/read/28124794/evaluation-of-kodecytes-using-function-spacer-lipid-constructs-as-a-survey-material-for-external-proficiency-testing-for-abo-subgrouping
#6
Young Ae Lim, Seon Joo Kang
BACKGROUND: It is not easy to find natural red blood cells (RBCs) with weak A (Aw ) or weak B phenotype (Bw ) for use as quality controls in ABO subgroup testing (subgrouping). The aim of this study was to prepare RBC kodecytes with synthetic blood group A and/or B function-spacer-lipid (FSL) constructs and to evaluate the possibility of using such kodecytes as a survey material for an external proficiency test (PT) to improve the quality of subgroup analysis. METHODS: Three types of survey samples, including O phenotype RBCs and A kodecytes with Aw (0...
January 26, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28104084/access-to-vagal-projections-via-cutaneous-electrical-stimulation-of-the-neck-fmri-evidence-in-healthy-humans
#7
Eleni Frangos, Barry R Komisaruk
BACKGROUND: Stimulation of the vagus nerve via implanted electrodes is currently used to treat refractory epilepsy and depression. Recently, a non-invasive approach to vagal stimulation has demonstrated similar beneficial effects, but it remains unclear whether these effects are mediated via activation of afferent vagal fibers. OBJECTIVE: The present study was designed to ascertain whether afferent vagal projections can be accessed non-invasively by transcutaneous electrical stimulation of the antero-lateral surface of the neck, which overlies the course of the vagus nerve...
January 2017: Brain Stimulation
https://www.readbyqxmd.com/read/28100092/sample-size-requirements-for-one-year-treatment-effects-using-deep-gray-matter-volume-from-3t-mri-in-progressive-forms-of-multiple-sclerosis
#8
Gloria Kim, Renxin Chu, Fawad Yousuf, Shahamat Tauhid, Lynn Stazzone, Maria K Houtchens, James M Stankiewicz, Christopher Severson, Dorlan Kimbrough, Francisco Quintana, Tanuja Chitnis, Howard L Weiner, Brian C Healy, Rohit Bakshi
OBJECTIVE: The subcortical deep gray matter (DGM) develops selective, progressive, and clinically-relevant atrophy in progressive forms of multiple sclerosis (PMS). This patient population is the target of active neurotherapeutic development, requiring the availability of outcome measures. We tested a fully automated MRI analysis pipeline to assess DGM atrophy in PMS. DESIGN/METHODS: Consistent 3D T1-weighted high-resolution 3T brain MRI was obtained over one year in 19 consecutive patients with PMS [15 secondary progressive, 4 primary progressive, 53% women, age (mean±SD) 50...
January 19, 2017: International Journal of Neuroscience
https://www.readbyqxmd.com/read/28087979/rapid-antidepressant-effect-of-ketamine-correlates-with-astroglial-plasticity-in-the-hippocampus
#9
Maryam Ardalan, Ali H Rafati, Jens R Nyengaard, Gregers Wegener
BACKGROUND AND PURPOSE: Astroglia contribute to the pathophysiology of major depression and antidepressant drugs act by modulating synaptic plasticity; therefore, the present study investigated whether the fast antidepressant action of ketamine is reflected in a rapid alteration of the astrocytes' morphology in a genetic animal model of depression. EXPERIMENTAL APPROACH: S-Ketamine (15 mg·kg(-1) ) or saline was administered as a single injection to Flinders Line (FSL/ FRL) rats...
January 14, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28086899/evaluations-of-diffusion-tensor-image-registration-based-on-fiber-tractography
#10
Yi Wang, Yu Shen, Dongyang Liu, Guoqin Li, Zhe Guo, Yangyu Fan, Yilong Niu
BACKGROUND: Diffusion Tensor Magnetic Resonance Imaging (DT-MRI, also known as DTI) measures the diffusion properties of water molecules in tissues and to date is one of the main techniques that can effectively study the microstructures of the brain in vivo. Presently, evaluation of DTI registration techniques is still in an initial stage of development. METHODS AND RESULTS: In this paper, six well-known open source DTI registration algorithms: Elastic, Rigid, Affine, DTI-TK, FSL and SyN were applied on 11 subjects from an open-access dataset, among which one was randomly chosen as the template...
January 10, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28069966/inherited-human-irak-1-deficiency-selectively-impairs-tlr-signaling-in-fibroblasts
#11
Erika Della Mina, Alessandro Borghesi, Hao Zhou, Salim Bougarn, Sabri Boughorbel, Laura Israel, Ilaria Meloni, Maya Chrabieh, Yun Ling, Yuval Itan, Alessandra Renieri, Iolanda Mazzucchelli, Sabrina Basso, Piero Pavone, Raffaele Falsaperla, Roberto Ciccone, Rosa Maria Cerbo, Mauro Stronati, Capucine Picard, Orsetta Zuffardi, Laurent Abel, Damien Chaussabel, Nico Marr, Xiaoxia Li, Jean-Laurent Casanova, Anne Puel
Most members of the Toll-like receptor (TLR) and interleukin-1 receptor (IL-1R) families transduce signals via a canonical pathway involving the MyD88 adapter and the interleukin-1 receptor-associated kinase (IRAK) complex. This complex contains four molecules, including at least two (IRAK-1 and IRAK-4) active kinases. In mice and humans, deficiencies of IRAK-4 or MyD88 abolish most TLR (except for TLR3 and some TLR4) and IL-1R signaling in both leukocytes and fibroblasts. TLR and IL-1R responses are weak but not abolished in mice lacking IRAK-1, whereas the role of IRAK-1 in humans remains unclear...
January 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28052997/human-three-dimensional-endometrial-epithelial-cell-model-to-study-host-interactions-with-vaginal-bacteria-and-neisseria-gonorrhoeae
#12
Paweł Łaniewski, Adriana Gomez, Geoffrey Hire, Magdalene So, Melissa M Herbst-Kralovetz
Colonization of the endometrium by pathogenic bacteria, ascending from the lower female reproductive tract (FRT), is associated with many gynecologic and obstetric health complications. To study these host-microbe interactions in vitro, we developed a human three-dimensional (3-D) endometrial epithelial cell (EEC) model using the HEC-1A cell line and rotating wall vessel (RWV) bioreactor technology. Our model, composed of 3-D EEC aggregates, recapitulates several functional/structural characteristics of human endometrial epithelial tissue including cell differentiation, junctional complexes/desmosomes, microvilli, membrane-associated mucins and Toll-like receptors (TLRs)...
January 4, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28047531/su-g-iep1-15-towards-accurate-cerebral-blood-flow-quantification-with-distortion-corrected-pseudo-continuous-arterial-spin-labeling
#13
M Hoff, S Rane-Levandovsky, J Andre
PURPOSE: Traditional arterial spin labeling (ASL) acquisitions with echo planar imaging (EPI) readouts suffer from image distortion due to susceptibility effects, compromising ASL's ability to accurately quantify cerebral blood flow (CBF) and assess disease-specific patterns associated with CBF abnormalities. Phase labeling for additional coordinate encoding (PLACE) can remove image distortion; our goal is to apply PLACE to improve the quantitative accuracy of ASL CBF in humans. METHODS: Four subjects were imaged on a 3T Philips Ingenia scanner using a 16-channel receive coil with a 21/21/10cm (frequency/phase/slice direction) field-of-view...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046971/th-cd-206-01-expectation-maximization-algorithm-based-tissue-mixture-quantification-for-perfusion-mri
#14
H Han, Z Liang, L Li, L Xing
PURPOSE: To investigate the feasibility of estimating the tissue mixture perfusions and quantifying cerebral blood flow change in arterial spin labeled (ASL) perfusion MR images. METHODS: The proposed perfusion MR image analysis framework consists of 5 steps: (1) Inhomogeneity correction was performed on the T1- and T2-weighted images, which are available for each studied perfusion MR dataset. (2) We used the publicly available FSL toolbox to strip off the non-brain structures from the T1- and T2-weighted MR images...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28034997/influence-of-t1-weighted-signal-intensity-on-fsl-voxel-based-morphometry-and-freesurfer-cortical-thickness
#15
S Chung, X Wang, Y W Lui
The effect of T1 signal on FSL voxel-based morphometry modulated GM density and FreeSurfer cortical thickness is explored. The techniques rely on different analyses, but both are commonly used to detect spatial changes in GM. Standard pipelines show FSL voxel-based morphometry is sensitive to T1 signal alterations within a physiologic range, and results can appear discordant between FSL voxel-based morphometry and FreeSurfer cortical thickness. Care should be taken in extrapolating results to the effect on brain volume...
December 29, 2016: AJNR. American Journal of Neuroradiology
https://www.readbyqxmd.com/read/28030782/a-comprehensive-review-of-group-level-model-performance-in-the-presence-of-heteroscedasticity-can-a-single-model-control-type-i-errors-in-the-presence-of-outliers
#16
Jeanette A Mumford
Even after thorough preprocessing and a careful time series analysis of functional magnetic resonance imaging (fMRI) data, artifact and other issues can lead to violations of the assumption that the variance is constant across subjects in the group level model. This is especially concerning when modeling a continuous covariate at the group level, as the slope is easily biased by outliers. Various models have been proposed to deal with outliers including models that use the first level variance or that use the group level residual magnitude to differentially weight subjects...
February 15, 2017: NeuroImage
https://www.readbyqxmd.com/read/28017479/diffusion-characteristics-of-the-fornix-in-patients-with-alzheimer-s-disease
#17
Shou Xian Tang, Qing Liang Feng, Gui Hong Wang, Shaofeng Duan, Bao Ci Shan, Jian Ping Dai
White matter degradation is a major part of the pathogenesis of Alzheimer's disease (AD). The fornix is the predominant outflow tract from the hippocampus, and alterations to its microstructure in patients with AD are still being explored. Diffusion tensor imaging (DTI) is an in vivo neuroimaging technique that can provide unique information about alterations in tissue microstructure, which can indicate underlying neurobiological process at the microstructural level. In this prospective study, DTI was used to assess and analyze the microstructural features of the fornix in subjects with AD (n = 17), mild cognitive impairment (MCI; n = 12) and healthy controls (n = 17)...
October 1, 2016: Psychiatry Research
https://www.readbyqxmd.com/read/27990364/blood-pressure-change-during-phacoemulsification-and-femtosecond-laser-assisted-cataract-surgery
#18
Hung-Yuan Lin, Ching-Jen Tung, Guo-Xing Xu, Chun-Chi Wang, Hsin-Yang Chen, Ya-Jung Chuang, Wen-Fu Li, Pi-Jung Lin
AIM: To evaluate blood pressure (BP) changes during phacoemulsification (PC) and femtosecond laser (FSL)-assisted cataract surgery. METHODS: A retrospective chart review was performed for all patients who received traditional phacoemulsification surgery (PC group) and FSL-assisted cataract surgery (FS group) from July 2013 to December 2014. Totally 206 eyes from 133 patients receiving the two types of procedures were included. Patient characteristics (age, gender, and hypertension history), pre- and post-operative BPs were collected...
2016: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/27956745/altered-brain-processing-of-decision-making-in-healthy-first-degree-biological-relatives-of-suicide-completers
#19
Y Ding, F Pereira, A Hoehne, M-M Beaulieu, M Lepage, G Turecki, F Jollant
Suicidal behavior is heritable, with the transmission of risk being related to the transmission of vulnerability traits. Previous studies suggest that risky decision-making may be an endophenotype of suicide. Here, we aimed at investigating brain processing of decision-making in relatives of suicide completers in order to shed light on heritable mechanisms of suicidal vulnerability. Seventeen healthy first-degree biological relatives of suicide completers with no personal history of suicidal behavior, 16 relatives of depressed patients without any personal or family history of suicidal behavior, and 19 healthy controls were recruited...
December 13, 2016: Molecular Psychiatry
https://www.readbyqxmd.com/read/27925164/brain-volume-change-in-first-episode-psychosis-an-effect-of-antipsychotic-medication-independent-of-bmi-change
#20
K N Jørgensen, R Nesvåg, S Nerland, L Mørch-Johnsen, L T Westlye, E H Lange, U K Haukvik, C B Hartberg, I Melle, O A Andreassen, I Agartz
OBJECTIVE: The effect of antipsychotic medication on brain structure remains unclear. Given the prevalence of weight gain as a side-effect, body mass index (BMI) change could be a confounder. METHOD: Patients with first-episode psychosis (n = 78) and healthy controls (n = 119) underwent two 1.5T MRI scans with a 1-year follow-up interval. siena (fsl 5.0) was used to measure whole-brain volume change. Weight and height were measured at both time points. Antipsychotic medication use at baseline and follow-up was converted into chlorpromazine equivalent dose and averaged...
February 2017: Acta Psychiatrica Scandinavica
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