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Allen human brain atlas

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https://www.readbyqxmd.com/read/29174593/brain-regions-showing-white-matter-loss-in%C3%A2-huntington-s-disease-are-enriched-for-synaptic-and-metabolic-genes
#1
Peter McColgan, Sarah Gregory, Kiran K Seunarine, Adeel Razi, Marina Papoutsi, Eileanoir Johnson, Alexandra Durr, Raymund A C Roos, Blair R Leavitt, Peter Holmans, Rachael I Scahill, Chris A Clark, Geraint Rees, Sarah J Tabrizi
BACKGROUND: The earliest white matter changes in Huntington's disease are seen before disease onset in the premanifest stage around the striatum, within the corpus callosum, and in posterior white matter tracts. While experimental evidence suggests that these changes may be related to abnormal gene transcription, we lack an understanding of the biological processes driving this regional vulnerability. METHODS: Here, we investigate the relationship between regional transcription in the healthy brain, using the Allen Institute for Brain Science transcriptome atlas, and regional white matter connectivity loss at three time points over 24 months in subjects with premanifest Huntington's disease relative to control participants...
October 26, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/29096577/human-brain-atlasing-past-present-and-future
#2
Wieslaw L Nowinski
We have recently witnessed an explosion of large-scale initiatives and projects addressing mapping, modeling, simulation and atlasing of the human brain, including the BRAIN Initiative, the Human Brain Project, the Human Connectome Project (HCP), the Big Brain, the Blue Brain Project, the Allen Brain Atlas, the Brainnetome, among others. Besides these large and international initiatives, there are numerous mid-size and small brain atlas-related projects. My contribution to these global efforts has been to create adult human brain atlases in health and disease, and to develop atlas-based applications...
December 2017: Neuroradiology Journal
https://www.readbyqxmd.com/read/29095968/characterization-of-the-glucagon-like-peptide-1-receptor-in-male-mouse-brain-using-a-novel-antibody-and-in-situ-hybridization
#3
Casper Bo Jensen, Charles Pyke, Morten Grønbech Rasch, Anders Bjorholm Dahl, Lotte Bjerre Knudsen, Anna Secher
Glucagon-like peptide-1 (GLP-1) is a physiological regulator of appetite and long-acting GLP-1 receptor agonists (GLP-1RA) lower food intake and bodyweight in both human and animal studies. The effects are mediated through brain GLP-1Rs, and several brain nuclei expressing the GLP-1R may be involved. To date, mapping the complete location of GLP-1R protein in the brain has been challenged by lack of good antibodies and the discrepancy between mRNA and protein especially relevant in neuronal axonal processes...
October 30, 2017: Endocrinology
https://www.readbyqxmd.com/read/29081736/human-ipsc-derived-cerebellar-neurons-from-a-patient-with-ataxia-telangiectasia-reveal-disrupted-gene-regulatory-networks
#4
Sam P Nayler, Joseph E Powell, Darya P Vanichkina, Othmar Korn, Christine A Wells, Refik Kanjhan, Jian Sun, Ryan J Taft, Martin F Lavin, Ernst J Wolvetang
Ataxia-telangiectasia (A-T) is a rare genetic disorder caused by loss of function of the ataxia-telangiectasia-mutated kinase and is characterized by a predisposition to cancer, pulmonary disease, immune deficiency and progressive degeneration of the cerebellum. As animal models do not faithfully recapitulate the neurological aspects, it remains unclear whether cerebellar degeneration is a neurodevelopmental or neurodegenerative phenotype. To address the necessity for a human model, we first assessed a previously published protocol for the ability to generate cerebellar neuronal cells, finding it gave rise to a population of precursors highly enriched for markers of the early hindbrain such as EN1 and GBX2, and later more mature cerebellar markers including PTF1α, MATH1, HOXB4, ZIC3, PAX6, and TUJ1...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28974727/timing-and-localization-of-human-dystrophin-isoform-expression-provide-insights-into-the-cognitive-phenotype-of-duchenne-muscular-dystrophy
#5
Nathalie Doorenweerd, Ahmed Mahfouz, Maaike van Putten, Rajaram Kaliyaperumal, Peter A C T' Hoen, Jos G M Hendriksen, Annemieke M Aartsma-Rus, Jan J G M Verschuuren, Erik H Niks, Marcel J T Reinders, Hermien E Kan, Boudewijn P F Lelieveldt
Duchenne muscular dystrophy (DMD) is a muscular dystrophy with high incidence of learning and behavioural problems and is associated with neurodevelopmental disorders. To gain more insights into the role of dystrophin in this cognitive phenotype, we performed a comprehensive analysis of the expression patterns of dystrophin isoforms across human brain development, using unique transcriptomic data from Allen Human Brain and BrainSpan atlases. Dystrophin isoforms show large changes in expression through life with pronounced differences between the foetal and adult human brain...
October 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28968835/cell-specific-gene-expression-profiles-and-cortical-thickness-in-the-human-brain
#6
Jean Shin, Leon French, Ting Xu, Gabriel Leonard, Michel Perron, G Bruce Pike, Louis Richer, Suzanne Veillette, Zdenka Pausova, Tomáš Paus
Neurobiological underpinnings of cortical thickness in the human brain are largely unknown. Here we use cell-type-specific gene markers to evaluate the contribution of 9 neural cell-types in explaining inter-regional variations in cortical thickness and age-related cortical thinning in the adolescent brain. Gene-expression data were derived from the Allen Human Brain Atlas (and validated using the BrainSpan Atlas). Values of cortical thickness/thinning were obtained with magnetic resonance imaging in a sample of 987 adolescents...
August 9, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28720872/associating-transcription-factors-and-conserved-rna-structures-with-gene-regulation-in-the-human-brain
#7
Nikolai Hecker, Stefan E Seemann, Asli Silahtaroglu, Walter L Ruzzo, Jan Gorodkin
Anatomical subdivisions of the human brain can be associated with different neuronal functions. This functional diversification is reflected by differences in gene expression. By analyzing post-mortem gene expression data from the Allen Brain Atlas, we investigated the impact of transcription factors (TF) and RNA secondary structures on the regulation of gene expression in the human brain. First, we modeled the expression of a gene as a linear combination of the expression of TFs. We devised an approach to select robust TF-gene interactions and to determine localized contributions to gene expression of TFs...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716961/structural-basis-of-large-scale-functional-connectivity-in-the-mouse
#8
Joanes Grandjean, Valerio Zerbi, Joshua Henk Balsters, Nicole Wenderoth, Markus Rudin
Translational neuroimaging requires approaches and techniques that can bridge between multiple different species and disease states. One candidate method that offers insights into the brain's functional connectivity (FC) is resting-state fMRI (rs-fMRI). In both humans and nonhuman primates, patterns of FC (often referred to as the functional connectome) have been related to the underlying structural connectivity (SC; also called the structural connectome). Given the recent rise in preclinical neuroimaging of mouse models, it is an important question whether the mouse functional connectome conforms to the underlying SC...
August 23, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28630769/comparing-the-expression-of-genes-related-to-serotonin-5-ht-in-c57bl-6j-mice-and-humans-based-on-data-available-at-the-allen-mouse-brain-atlas-and-allen-human-brain-atlas
#9
C A Acevedo-Triana, L A León, F P Cardenas
Brain atlases are tools based on comprehensive studies used to locate biological characteristics (structures, connections, proteins, and gene expression) in different regions of the brain. These atlases have been disseminated to the point where tools have been created to store, manage, and share the information they contain. This study used the data published by the Allen Mouse Brain Atlas (2004) for mice (C57BL/6J) and Allen Human Brain Atlas (2010) for humans (6 donors) to compare the expression of serotonin-related genes...
2017: Neurology Research International
https://www.readbyqxmd.com/read/28612935/early-adversity-and-brain-response-to-faces-in-young-adulthood
#10
Johannes Lieslehto, Vesa Kiviniemi, Pirjo Mäki, Jenni Koivukangas, Tanja Nordström, Jouko Miettunen, Jennifer H Barnett, Peter B Jones, Graham K Murray, Irma Moilanen, Tomáš Paus, Juha Veijola
Early stressors play a key role in shaping interindividual differences in vulnerability to various psychopathologies, which according to the diathesis-stress model might relate to the elevated glucocorticoid secretion and impaired responsiveness to stress. Furthermore, previous studies have shown that individuals exposed to early adversity have deficits in emotion processing from faces. This study aims to explore whether early adversities associate with brain response to faces and whether this association might associate with the regional variations in mRNA expression of the glucocorticoid receptor gene (NR3C1)...
September 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28558017/a-dual-strategy-expression-screen-for-candidate-connectivity-labels-in-the-developing-thalamus
#11
Olivia Bibollet-Bahena, Tatsuya Okafuji, Karsten Hokamp, Guy Tear, Kevin J Mitchell
The thalamus or "inner chamber" of the brain is divided into ~30 discrete nuclei, with highly specific patterns of afferent and efferent connectivity. To identify genes that may direct these patterns of connectivity, we used two strategies. First, we used a bioinformatics pipeline to survey the predicted proteomes of nematode, fruitfly, mouse and human for extracellular proteins containing any of a list of motifs found in known guidance or connectivity molecules. Second, we performed clustering analyses on the Allen Developing Mouse Brain Atlas data to identify genes encoding surface proteins expressed with temporal profiles similar to known guidance or connectivity molecules...
2017: PloS One
https://www.readbyqxmd.com/read/28515688/insulin-resistance-as-a-link-between-amyloid-beta-and-tau-pathologies-in-alzheimer-s-disease
#12
Roger J Mullins, Thomas C Diehl, Chee W Chia, Dimitrios Kapogiannis
Current hypotheses and theories regarding the pathogenesis of Alzheimer's disease (AD) heavily implicate brain insulin resistance (IR) as a key factor. Despite the many well-validated metrics for systemic IR, the absence of biomarkers for brain-specific IR represents a translational gap that has hindered its study in living humans. In our lab, we have been working to develop biomarkers that reflect the common mechanisms of brain IR and AD that may be used to follow their engagement by experimental treatments...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/28461466/oxytocin-under-opioid-antagonism-leads-to-supralinear-enhancement-of-social-attention
#13
Olga Dal Monte, Matthew Piva, Kevin M Anderson, Marios Tringides, Avram J Holmes, Steve W C Chang
To provide new preclinical evidence toward improving the efficacy of oxytocin (OT) in treating social dysfunction, we tested the benefit of administering OT under simultaneously induced opioid antagonism during dyadic gaze interactions in monkeys. OT coadministered with a μ-opioid receptor antagonist, naloxone, invoked a supralinear enhancement of prolonged and selective social attention, producing a stronger effect than the summed effects of each administered separately. These effects were consistently observed when averaging over entire sessions, as well as specifically following events of particular social importance, including mutual eye contact and mutual reward receipt...
May 16, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28420888/global-gene-expression-profiling-of-healthy-human-brain-and-its-application-in-studying-neurological-disorders
#14
Simarjeet K Negi, Chittibabu Guda
Brain function is governed by precise regulation of gene expression across its anatomically distinct structures; however, the expression patterns of genes across hundreds of brain structures are not clearly understood. Here, we describe a gene expression model, which is representative of the healthy human brain transcriptome by using data from the Allen Brain Atlas. Our in-depth gene expression profiling revealed that 84% of genes are expressed in at least one of the 190 brain structures studied. Hierarchical clustering based on gene expression profiles delineated brain regions into structurally tiered spatial groups and we observed striking enrichment for region-specific processes...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28334178/inter-regional-variations-in-gene-expression-and-age-related-cortical-thinning-in-the-adolescent-brain
#15
Angelita Pui-Yee Wong, Leon French, Gabriel Leonard, Michel Perron, G Bruce Pike, Louis Richer, Suzanne Veillette, Zdenka Pausova, Tomáš Paus
Age-related decreases in cortical thickness observed during adolescence may be related to fluctuations in sex and stress hormones. We examine this possibility by relating inter-regional variations in age-related cortical thinning (data from the Saguenay Youth Study) to inter-regional variations in expression levels of relevant genes (data from the Allen Human Brain Atlas); we focus on genes coding for glucocorticoid receptor (NR3C1), androgen receptor (AR), progesterone receptor (PGR), and estrogen receptors (ESR1 and ESR2)...
February 25, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28321948/gene-networks-show-associations-with-seed-region-connectivity
#16
Marie Forest, Yasser Iturria-Medina, Jennifer S Goldman, Claudia L Kleinman, Amanda Lovato, Kathleen Oros Klein, Alan Evans, Antonio Ciampi, Aurélie Labbe, Celia M T Greenwood
Primary patterns in adult brain connectivity are established during development by coordinated networks of transiently expressed genes; however, neural networks remain malleable throughout life. The present study hypothesizes that structural connectivity from key seed regions may induce effects on their connected targets, which are reflected in gene expression at those targeted regions. To test this hypothesis, analyses were performed on data from two brains from the Allen Human Brain Atlas, for which both gene expression and DW-MRI were available...
June 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28320311/a-receptor-based-analysis-of-local-ecosystems-in-the-human-brain
#17
Skirmantas Janušonis
BACKGROUND: As a complex system, the brain is a self-organizing entity that depends on local interactions among cells. Its regions (anatomically defined nuclei and areas) can be conceptualized as cellular ecosystems, but the similarity of their functional profiles is poorly understood. The study used the Allen Human Brain Atlas to classify 169 brain regions into hierarchically-organized environments based on their expression of 100 G protein-coupled neurotransmitter receptors, with no a priori reference to the regions' positions in the brain's anatomy or function...
March 20, 2017: BMC Neuroscience
https://www.readbyqxmd.com/read/28221363/premature-primary-tooth-eruption-in-cognitive-motor-delayed-adnp-mutated-children
#18
I Gozes, A Van Dijck, G Hacohen-Kleiman, I Grigg, G Karmon, E Giladi, M Eger, Y Gabet, M Pasmanik-Chor, E Cappuyns, O Elpeleg, R F Kooy, S Bedrosian-Sermone
A major flaw in autism spectrum disorder (ASD) management is late diagnosis. Activity-dependent neuroprotective protein (ADNP) is a most frequent de novo mutated ASD-related gene. Functionally, ADNP protects nerve cells against electrical blockade. In mice, complete Adnp deficiency results in dysregulation of over 400 genes and failure to form a brain. Adnp haploinsufficiency results in cognitive and social deficiencies coupled to sex- and age-dependent deficits in the key microtubule and ion channel pathways...
February 21, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28132031/brainscope-interactive-visual-exploration-of-the-spatial-and-temporal-human-brain-transcriptome
#19
Sjoerd M H Huisman, Baldur van Lew, Ahmed Mahfouz, Nicola Pezzotti, Thomas Höllt, Lieke Michielsen, Anna Vilanova, Marcel J T Reinders, Boudewijn P F Lelieveldt
Spatial and temporal brain transcriptomics has recently emerged as an invaluable data source for molecular neuroscience. The complexity of such data poses considerable challenges for analysis and visualization. We present BrainScope: a web portal for fast, interactive visual exploration of the Allen Atlases of the adult and developing human brain transcriptome. Through a novel methodology to explore high-dimensional data (dual t-SNE), BrainScope enables the linked, all-in-one visualization of genes and samples across the whole brain and genome, and across developmental stages...
June 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28105773/exosomal-biomarkers-of-brain-insulin-resistance-associated-with-regional-atrophy-in-alzheimer-s-disease
#20
Roger J Mullins, Maja Mustapic, Edward J Goetzl, Dimitrios Kapogiannis
Brain insulin resistance (IR), which depends on insulin-receptor-substrate-1 (IRS-1) phosphorylation, is characteristic of Alzheimer's disease (AD). Previously, we demonstrated higher pSer312-IRS-1 (ineffective insulin signaling) and lower p-panTyr-IRS-1 (effective insulin signaling) in neural origin-enriched plasma exosomes of AD patients vs. CONTROLS: Here, we hypothesized that these exosomal biomarkers associate with brain atrophy in AD. We studied 24 subjects with biomarker-supported probable AD (low CSF Aβ42 )...
April 2017: Human Brain Mapping
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