DOCSLIB.ORG

Downloaded from the HCP Website

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Downloaded from the HCP Website What do anatomical properties of the brain reveal about the ontology of human cognitive abilities? Daniel Kristanto1, Xinyang Liu2,3, Werner Sommer4, Andrea Hildebrandt2,5*#, Changsong Zhou1,6*# 1: Department of Physics, Centre for Nonlinear Studies and Beijing-Hong Kong-Singapore Joint Centre for Nonlinear and Complex Systems (Hong Kong), Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Kowloon Tong, Hong Kong 2: Department of Psychology, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg, Germany 3: Shanghai Key Laboratory of Brain Functional Genomics (Ministry of Education), School of Psychology and Cognitive Science, East China Normal University, 200062 Shanghai, China 4: Department of Psychology, Humboldt University at Berlin, Berlin, Germany, Department of Psychology, Zhejiang Normal University, Jin Hua, China 5: Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Germany 6: Department of Physics, Zhejiang University, 310000 Hangzhou, China *Corresponding authors. E-mail addresses: [email protected] (A. Hildebrandt), [email protected] (C. Zhou). # Senior authors Abstract Over the past decades, the neuropsychological science community has endeavored to determine the number and nature of distinguishable human cognitive abilities. Based on covariance structure analyses of inter-individual performance differences in multiple cognitive tasks, the ability structure has been substantiated with sufficient consensus. However, there remains a crucial open question that must be answered to develop unified theoretical views and translations toward neuropsychological applications: Is the cognitive ability structure ascertained at the behavioral level similarly reflected in the anatomical and functional properties of the brain? In the current study, we explored the cognitive ability structure derived from positive and negative networks 1 reflected by the brain’s anatomical properties (thickness, myelination, curvature, and sulcus depth) that were found to be associated with performance in 15 cognitive tasks. The derived neurometric ontological structure was contrasted with the entities of psychometric ontology. Overall, we observed that the brain-derived ontological structures are partly consistent with each other, but also show interesting differences that complement the psychometric ontology. Moreover, we discovered that brain areas associated with the inferred abilities are segregated, with little or no overlap between the abilities. Nevertheless, they are also integrated as they are densely connected by white matter projections with an average connection density higher than the brain connectome. The consistency and differences between psychometric and neurometric ontologies are crucial for theory building, diagnostics, and neuropsychological therapy, which highlights the need for their simultaneous and complementary consideration. Keywords: Cognitive ontology, individual differences, neuroanatomical properties of the brain, brain networks, segregation and integration Introduction Broadly accepted cognitive ontologies are crucial for unified neuro-psychological theories, cognitive diagnostics and mental health therapy. Over the past decades, research on human cognition and intelligence, aimed at describing, measuring, and classifying abilities and unveiling their ontological structure, has mainly been based on inter-individual covariations of performance across multiple tasks. Since the synthesis model known as Cattell–Horn–Carroll (CHC) theory of cognitive abilities was compiled and disseminated (1), there has been a widespread consensus on the psychometric ontology of intelligence, notwithstanding some caveats (2). According to the CHC model, stratum I comprises individual differences in a large number of cognitive tasks that require maximal performance in terms of speed or/and accuracy. Stratum II incorporates broad latent (not directly observable but task-derived) abilities, e.g., fluid reasoning (Gf), comprehension knowledge (Gc, also called crystallized intelligence), short-term memory (Gsm), long-term storage and retrieval (Glr), and cognitive processing speed (Gs). These broad, domain-specific abilities are all positively associated with each other. The CHC model accounts for this positive manifold by assuming a general factor of intelligence (g) at stratum III. A somewhat separate literature on ontological entities of human intelligence concerns executive functions (EF). Most suggestions 2 about the ontological entities of EF derived from psychometric tasks encompass working memory, shifting, and inhibition (e.g., (3)). Cognitive neuroscience is a much younger discipline than the psychometrics of intelligence and investigates among others the anatomical properties and neural mechanisms underlying the ontological entities of human cognition. Early studies focused on stratum I, aiming at understanding the neuroanatomical basis and neurofunctional mechanisms underpinning the mastery of specific cognitive tasks. Following this research direction, several studies adopted connectome-based predictive modeling (4, 5), a method to map brain properties and performance scores on specific cognitive tasks (6–9). As a further step toward generalization, latent cognitive abilities in stratum II of the CHC model were mapped to brain structure and activity (10–17). Such studies are highly valuable for generating neuroanatomical and neurofunctional explanations of the psychometric ontological entities of cognition beyond specific tasks. However, the quest for brain-derived ontological entities of cognition has recently gained prominence, such that the psychometric entities are not be taken as granted but rather explored in a bottom-up fashion, i.e., from the brain to psychological constructs (18). The cognitive neuroscience community has thus far not sufficiently appreciated the psychometric desiderata—expressed already by Cronbach and Meehl (1955)—of not conflating psychological constructs with their operational measures (19). That is, a task is only a task and ontological entities of cognition must be determined by analysis beyond single tasks. Consequently, modern cognitive neuroscience approaches to derive ontological entities of cognition must use multiple tasks to explore distinct indicators of anatomical and functional properties of the brain to support the existence of stratum II ontological entities of cognition (the top-down approach), and also to mine the brain to derive ontological entities that do not take psychometric entities for granted (the bottom-up approach, see (20)). The availability of large-scale, multivariate cognitive neuroscience databases enables such an alternative bottom-up approach, which involves the exploration of potential ontological entities of human cognition on the basis of brain properties (21). For example, Bolt and colleagues investigated which cognitive entities are revealed by brain activation patterns observed when performing a series of cognitive tasks (22). However, they did not systematically discuss the consistency and disparity between their brain-derived ontology and those established in 3 psychometrics. We argue that such direct comparisons are necessary to better substantiate the ontology of human cognition, which should accommodate both the covariance structures of task performance and the brain networks producing these abilities (20, 23). The present study contributes to the establishment of a formal ontology for psychology, cognitive neuroscience, and their applied disciplines by adopting a bottom-up approach (see (20)). We explored the cognitive ontology derived from the brain’s anatomical properties, including thickness, myelination, curvature, and sulcus depth, which are associated with performance in 15 psychometric tasks. Moreover, we went beyond existing approaches by comparing the derived cognitive ontologies with the psychometric ontology revealed by the same tasks. Specifically, we investigated the extent to which brain-derived ontologies as reflected by shared brain areas across the 15 cognitive tasks (stratum I) are consistent with or distinct to the established psychometric ontologies at stratum II of the CHC model. Next, as suggested in the literature (20), we expected that the ability-related brain areas would be segregated, to support differentiation between the inferred cognitive ontologies. Furthermore, we investigated how the ability-related brain areas are coupled via the underlying network connectivity to form the positive manifold underlying the general intelligence that is captured at stratum III of the CHC model. Results Our overall methodological framework is illustrated in Fig. 1. We first identified task- related brain areas based on linear associations between brain properties (thickness, myelination, curvature, and sulcus depth) and task performances collected by the Washington University and University of Minnesota Consortium’s (WU-Minn) Human Connectome Project (HCP; see Materials, Table 1, and SI Appendix Table S1 for the task descriptions and further details). Next, we quantified the overlap between task-related brain areas with these different anatomical properties, by using an Intersect Over Union (IOU) index to create IOU matrices. These matrices were then subjected to exploratory factor analysis (EFA) to obtain a brain-derived cognitive ontology. This ontology was descriptively compared with the psychometric ontology derived from covariances across the same
Load more

Recommended publications
  • Imaging Genetic Strategies for Predicting the Quality of Sleep Using Depression-Specific Biomarkers
    Imaging genetic strategies for predicting the quality of sleep using depression-specific biomarkers Mansu Kim 1, Xiaohui Yao 1, Bo-yong Park 2, Jingwen Yan 3, and Li Shen1,* 1Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, USA 2McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Canada 3Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University, USA * Correspondence to [email protected] Overview Joint-connectivity-based sparse CCA Background: Sleep is an essential phenomenon for SNP connectivity Imaging genetics model: The joint-connectivity-based sparse canonical ··· X* samples × maintaining good health and wellbeing [1]. correlation analysis (JCB-SCCA) was applied on preprocessed features n Some studies reported that genetic and p SNPs (Figure 1). JCB-SCCA has an advantage for incorporating connectivity Loading vector u Maximum imaging biomarkers that depression is information and can handle multi-modal neuroimaging datasets. correlation Brain associated with sleep disorder [2]–[4]. connectivity ··· Prior biological knowledge: The average connectivity matrix computed ··· K samples Y* modalitiesn × Imaging genetics: Many studies adopted imaging from the HCP dataset and linkage disequilibrium obtained from 1,000 q voxels genetics methodology to find associations genome project were used as the prior connectivity information of the K = 2 Loading vector V between imaging and genetic biomarkers. In algorithm. The parameters of the algorithm were tuned jointly by nested K = 1 this study, we examine the imaging genetics five-fold cross-validation. Figure 1. JCB-SCCA association in depression and extract biomarkers for predicting the quality of sleep. Experiments and Results Prediction task: We built a prediction model for the Pittsburgh sleep quality index (PSQI) using the identified biomarkers.
    [Show full text]
  • Polygenic Evidence and Overlapped Brain Functional Connectivities For
    Sun et al. Translational Psychiatry (2020) 10:252 https://doi.org/10.1038/s41398-020-00941-z Translational Psychiatry ARTICLE Open Access Polygenic evidence and overlapped brain functional connectivities for the association between chronic pain and sleep disturbance Jie Sun 1,2,3,WeiYan2,Xing-NanZhang2, Xiao Lin2,HuiLi2,Yi-MiaoGong2,Xi-MeiZhu2, Yong-Bo Zheng2, Xiang-Yang Guo3,Yun-DongMa2,Zeng-YiLiu2,LinLiu2,Jia-HongGao4, Michael V. Vitiello 5, Su-Hua Chang 2,6, Xiao-Guang Liu 1,7 and Lin Lu2,6 Abstract Chronic pain and sleep disturbance are highly comorbid disorders, which leads to barriers to treatment and significant healthcare costs. Understanding the underlying genetic and neural mechanisms of the interplay between sleep disturbance and chronic pain is likely to lead to better treatment. In this study, we combined 1206 participants with phenotype data, resting-state functional magnetic resonance imaging (rfMRI) data and genotype data from the Human Connectome Project and two large sample size genome-wide association studies (GWASs) summary data from published studies to identify the genetic and neural bases for the association between pain and sleep disturbance. Pittsburgh sleep quality index (PSQI) score was used for sleep disturbance, pain intensity was measured by Pain Intensity Survey. The result showed chronic pain was significantly correlated with sleep disturbance (r = 0.171, p-value < 0.001). Their genetic correlation was rg = 0.598 using linkage disequilibrium (LD) score regression analysis. Polygenic score (PGS) association analysis showed PGS of chronic pain was significantly associated with sleep and vice versa. 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Nine shared functional connectivity (FCs) were identified involving prefrontal cortex, temporal cortex, precentral/ postcentral cortex, anterior cingulate cortex, fusiform gyrus and hippocampus.
    [Show full text]
  • Local Connectome Phenotypes Predict Social, Health, and Cognitive Factors
    RESEARCH Local connectome phenotypes predict social, health, and cognitive factors 1 2,3 4,5 Michael A. Powell , Javier O. Garcia , Fang-Cheng Yeh , 2,3,6 7 Jean M. Vettel , and Timothy Verstynen 1Department of Mathematical Sciences, United States Military Academy, West Point, NY, USA 2U.S. Army Research Laboratory, Aberdeen Proving Ground, MD, USA 3Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA 4Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA 5Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA 6Department of Psychological and Brain Sciences, University of California, Santa Barbara, CA, USA 7 an open access journal Department of Psychology and Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA, USA Keywords: Local connectome, White matter, Individual differences, Behavior prediction, Structural connectivity ABSTRACT The unique architecture of the human connectome is defined initially by genetics and subsequently sculpted over time with experience. Thus, similarities in predisposition and experience that lead to similarities in social, biological, and cognitive attributes should also be reflected in the local architecture of white matter fascicles. Here we employ a method known as local connectome fingerprinting that uses diffusion MRI to measure the fiber-wise characteristics of macroscopic white matter pathways throughout the brain. This Citation: Powell, M. A., Garcia, J. O., fingerprinting approach was applied to a large sample (N = 841) of subjects from the Yeh, F.-C., Vettel, J. M., & Verstynen, T. (2017). Local connectome phenotypes Human Connectome Project, revealing a reliable degree of between-subject correlation in predict social, health, and cognitive factors.
    [Show full text]
  • Proteomic Analysis of Postsynaptic Proteins in Regions of the Human Neocortex
    Proteomic analysis of postsynaptic proteins in regions of the human neocortex Marcia Roy1*, Oksana Sorokina2*, Nathan Skene1, Clemence Simonnet1, Francesca Mazzo3, Ruud Zwart3, Emanuele Sher3, Colin Smith1, J Douglas Armstrong2 and Seth GN Grant1. * equal contribution Author Affiliations: 1. Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom 2. School of Informatics, University of Edinburgh, Edinburgh, EH8 9AB, United Kingdom 3. Lilly Research Centre, Eli Lilly & Company, Erl Wood Manor, Windlesham, GU20 6PH, United Kingdom 1 Abstract: The postsynaptic proteome of excitatory synapses comprises ~1,000 highly conserved proteins that control the behavioral repertoire and mutations disrupting their function cause >130 brain diseases. Here, we document the composition of postsynaptic proteomes in human neocortical regions and integrate it with genetic, functional and structural magnetic resonance imaging, positron emission tomography imaging, and behavioral data. Neocortical regions show signatures of expression of individual proteins, protein complexes, biochemical and metabolic pathways. The compositional signatures in brain regions involved with language, emotion and memory functions were characterized. Integrating large-scale GWAS with regional proteome data identifies the same cortical region for smoking behavior as found with fMRI data. The neocortical postsynaptic proteome data resource can be used to link genetics to brain imaging and behavior, and to study the role of postsynaptic proteins in localization of brain functions. 2 Introduction: For almost two centuries, scientists have pursued the study of localization of function in the human cerebral neocortex using diverse methods including neuroanatomy, electrophysiology, imaging and gene expression studies. The frontal, parietal, temporal and occipital lobes of the neocortex have been commonly subdivided into Brodmann areas (BA)1 based on cytoarchitectural features, and specific behavioral functions have been ascribed to these regions.
    [Show full text]
  • A Critical Look at Connectomics
    EDITORIAL A critical look at connectomics There is a public perception that connectomics will translate directly into insights for disease. It is essential that scientists and funding institutions avoid misrepresentation and accurately communicate the scope of their work. onnectomes are generating interest and excitement, both among ­nervous ­system, dubbed the classic connectome because it is ­currently neuroscientists and the public. This September, the first grants the only wiring diagram for an animal’s entire nervous system at the level Cunder the Human Connectome Project, totaling $40 ­million of the synapse. Although major neurobiological insights have been made over 5 years, were awarded by the US National Institutes of Health using C. elegans and its known connectivity and genome, there are still (NIH). In the public arena, striking, colorful pictures of human brains many questions remaining that can only be answered by hypothesis-driven have ­accompanied claims that imply that understanding the complete experiments. For example, we still don’t completely understand the process ­connectivity of the human brain’s billions of neurons by a trillion ­synapses of axon regeneration, relevant to spinal cord injury in humans, in this is not only ­possible, but that this will also directly translate into insights comparatively simple system. Thus, a connectome, at any resolution, is for neurological and psychiatric disorders. Even a press release from only one of several complementary tools necessary to understand nervous the NIH touted that the Human Connectome Project would map the system disease and injury. ­wiring diagram of the entire living human brain and would link these There are substantial efforts aimed at generating connectomes for circuits to the full spectrum of brain function in health and disease.
    [Show full text]
  • Download Download
    NEUROSCIENCE RESEARCH NOTES OPEN ACCESS | EDITORIAL ISSN: 2576-828X From online resources to collaborative global neuroscience research: where are we heading? Pike See Cheah 1,2, King-Hwa Ling 2,3 and Eric Tatt Wei Ho 4,* 1 Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia. 2 NeuroBiology & Genetics Group, Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia. 3 Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia. 4 Center for Intelligent Signal and Imaging Research, Universiti Teknologi PETRONAS, Perak, Malaysia. *Corresponding authors: [email protected]; Tel.: +60-5-368-7899 Published: 21 July 2020 https://doi.org/10.31117/neuroscirn.v3i3.51 Keywords: neuroinformatics; machine learning; bioinformatics; brain project; online resources; databases ©2020 by Cheah et al. for use and distribution in accord with the Creative Commons Attribution (CC BY-NC 4.0) license (https://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. 1.0 INTRODUCTION The most visible contributions from neuroinformatics Neuroscience has emerged as a richly transdisciplinary include the myriad reference atlases of brain anatomy field, poised to leverage potential synergies with (human and other mammals such as rodents, primates information technology. To investigate the complex and pig), gene and protein sequences and the nervous system in its normal function and the disease bioinformatics software tools for alignment, matching state, researchers in the field are increasingly reliant and identification. Other neuroinformatics initiatives on generating, sharing and analyzing diverse data from include the various open-source preprocessing and multiple experimental paradigms at multiple spatial processing software and workflows for data analysis as and temporal scales (Frackowiak & Markram, 2015).
    [Show full text]
  • Genetic and Environmental Influence on the Human Functional Connectome Andrew E
    Cerebral Cortex, 2019;00: 1–15 doi: 10.1093/cercor/bhz225 Original Article Downloaded from https://academic.oup.com/cercor/advance-article-abstract/doi/10.1093/cercor/bhz225/5618752 by guest on 03 March 2020 ORIGINAL ARTICLE Genetic and Environmental Influence on the Human Functional Connectome Andrew E. Reineberg 1, Alexander S. Hatoum2, John K. Hewitt1,2, Marie T. Banich3 and Naomi P. Friedman1,2 1Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, 80309, USA, 2Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, 80309, USA, and 3Institute of Cognitive Science, University of Colorado Boulder, Boulder, CO, 80309, USA Address correspondence to Andrew E. Reineberg, email: [email protected] http://orcid.org/0000-0002-0806-440X Abstract Detailed mapping of genetic and environmental influences on the functional connectome is a crucial step toward developing intermediate phenotypes between genes and clinical diagnoses or cognitive abilities. We analyzed resting-state functional magnetic resonance imaging data from two adult twin samples (Nos = 446 and 371) to quantify genetic and environmental influence on all pairwise functional connections between 264 brain regions (∼35 000 functional connections). Nonshared environmental influence was high across the whole connectome. Approximately 14–22% of connections had nominally significant genetic influence in each sample, 4.6% were significant in both samples, and 1–2% had heritability estimates greater than 30%. Evidence of shared environmental influence was weak. Genetic influences on connections were distinct from genetic influences on a global summary measure of the connectome, network-based estimates of connectivity, and movement during the resting-state scan, as revealed by a novel connectome-wide bivariate genetic modeling procedure.
    [Show full text]
  • National Institute of Mental Health Strategic Plan for Research
    NATIONAL INSTITUTE OF MENTAL HEALTH STRATEGIC PLAN FOR RESEARCH Table of Contents Table of Contents Message from the Director ............................................................................................................................................ 1 Overview of NIMH ......................................................................................................................................................... 3 Serving as an Efficient and Effective Steward of Public Resources ............................................................................... 5 Scientific Stewardship ............................................................................................................................................... 5 Management and Accountability .............................................................................................................................. 7 Accomplishing the Mission ............................................................................................................................................ 9 Challenges and Opportunities ..................................................................................................................................... 10 Suicide Prevention................................................................................................................................................... 10 Early Intervention in Psychosis ...............................................................................................................................
    [Show full text]
  • A Distributed Brain Network Predicts General Intelligence from Resting-State Human Neuroimaging Data
    bioRxiv preprint doi: https://doi.org/10.1101/257865; this version posted January 31, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. A distributed brain network predicts general intelligence from resting-state human neuroimaging data 1,4 5 1,3 1,2,3 Julien Dubois ,​ Paola Galdi ,​ Lynn K. Paul ​ , Ralph Adolphs ​ ​ ​ ​ 1 ​ Division of Humanities and Social Sciences, California Institute of Technology, Pasadena CA 91125, USA 2 ​ Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA 91125, USA 3 ​ Chen Neuroscience Institute, California Institute of Technology, Pasadena CA 91125, USA 4 ​ Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA 5 ​ Department of Management and Innovation Systems, University of Salerno, Fisciano, Salerno, Italy Correspondence: Julien Dubois Department of Neurosurgery Cedars-Sinai Medical Center, Los Angeles, CA 90048 [email protected] bioRxiv preprint doi: https://doi.org/10.1101/257865; this version posted January 31, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Individual people differ in their ability to reason, solve problems, think abstractly, plan and learn. A reliable measure of this general ability, also known as intelligence, can be derived from scores across a diverse set of cognitive tasks. There is great interest in understanding the neural underpinnings of individual differences in intelligence, since it is the single best predictor of long-term life success, and since individual differences in a similar broad ability are found across animal species.
    [Show full text]
  • Cognitive Genomics: Linking Genes to Behavior in the Human Brain
    PERSPECTIVE Cognitive genomics: Linking genes to behavior in the human brain Genevieve Konopka Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA ABSTRACT Correlations of genetic variation in DNA with functional brain activity have already provided a starting point for delving into human cognitive mechanisms. However, these analyses do not provide the specific genes driving the associations, which are complicated by intergenic Downloaded from http://direct.mit.edu/netn/article-pdf/1/1/3/1091843/netn_a_00003.pdf by guest on 30 September 2021 localization as well as tissue-specific epigenetics and expression. The use of brain-derived an open access journal expression datasets could build upon the foundation of these initial genetic insights and yield genes and molecular pathways for testing new hypotheses regarding the molecular bases of human brain development, cognition, and disease. Thus, coupling these human brain gene expression data with measurements of brain activity may provide genes with critical roles in brain function. However, these brain gene expression datasets have their own set of caveats, most notably a reliance on postmortem tissue. In this perspective, I summarize and examine the progress that has been made in this realm to date, and discuss the various frontiers remaining, such as the inclusion of cell-type-specific information, additional physiological measurements, and genomic data from patient cohorts. Progress in understanding the inner workings of the brain has come a long way from the preneu- roscience era of phrenology, when we were limited to conjectures about human behavior Citation: Konopka G. (2017). Cognitive genomics: Linking genes to behavior based on the shape of the skull.
    [Show full text]
  • The Human Gene Connectome As a Map of Short Cuts for Morbid Allele Discovery
    The human gene connectome as a map of short cuts for morbid allele discovery Yuval Itana,1, Shen-Ying Zhanga,b, Guillaume Vogta,b, Avinash Abhyankara, Melina Hermana, Patrick Nitschkec, Dror Friedd, Lluis Quintana-Murcie, Laurent Abela,b, and Jean-Laurent Casanovaa,b,f aSt. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065; bLaboratory of Human Genetics of Infectious Diseases, Necker Branch, Paris Descartes University, Institut National de la Santé et de la Recherche Médicale U980, Necker Medical School, 75015 Paris, France; cPlateforme Bioinformatique, Université Paris Descartes, 75116 Paris, France; dDepartment of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; eUnit of Human Evolutionary Genetics, Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Institut Pasteur, F-75015 Paris, France; and fPediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, 75015 Paris, France Edited* by Bruce Beutler, University of Texas Southwestern Medical Center, Dallas, TX, and approved February 15, 2013 (received for review October 19, 2012) High-throughput genomic data reveal thousands of gene variants to detect a single mutated gene, with the other polymorphic genes per patient, and it is often difficult to determine which of these being of less interest. This goes some way to explaining why, variants underlies disease in a given individual. However, at the despite the abundance of NGS data, the discovery of disease- population level, there may be some degree of phenotypic homo- causing alleles from such data remains somewhat limited. geneity, with alterations of specific physiological pathways under- We developed the human gene connectome (HGC) to over- come this problem.
    [Show full text]
  • Focus on the Neuroscience Toolbox Editorial
    FOCUS ON THE NEUROSCIENCE TOOLBOX EDITORIAL Focus on the neuroscience toolbox We present a special issue on the neuroscience toolbox, highlighting recent technological advances, approaches and collaborative initiatives that are enabling new avenues of research. he pace of technological development in neuroscience is the brain, focusing­ on the instrumental challenges associated with the ­accelerating, providing researchers with powerful new tools to use of ­optical systems. They provide an overview of optimal sampling Tdrive their experiments and ask new questions. Keeping up with ­strategies for rapid imaging in three dimensions and the computational this wave of new technology can be challenging, and decisions about and analytical approaches necessary to handle the size and complexity which tools to use and how best to use them can be difficult. Nature of the resulting datasets. Neuroscience presents a special focus issue on the neuroscience toolbox Simultaneous recordings of activity from hundreds to thousands of aimed at helping researchers take full advantage of available techniques. neurons—optically or electrically—require massively pa­ rallel re­ cordings Researchers and funding agencies across the globe have recognized and sophisticated algorithms, both automatic and manually-curated, that the development of new tools and techniques is central to ad­ vancing operating with sufficient accuracy and selectivity to return high yield basic neuroscience research and the treatment of disorders. On page single units. In our second technical review, on page 1165, Kenneth 1118, we profile six worldwide initiatives involved in this effort: the Allen Harris and colleagues discuss state-of-the-art techniques for inferring Institute for Brain Science, China Brain Project, the European Union’s single spikes from electrophysiology and two-photon ­calcium imaging.
    [Show full text]