Synergy of image analysis for animal and human neuroimaging supports translational research on drug abuse

pre-printThe use of structural magnetic resonance imaging (sMRI) and diffusion tensor imaging (DTI) in animal models of neurophysiology is of increasing interest to the neuroscience community. In this work, we present our approach to create optimal translational studies that include both animal and human neuroimaging data within the frameworks of a study of post-natal neuro-development in intra-uterine cocaine-exposure. We propose the use of non-invasive neuroimaging to study developmental brain structural and white matter pathway abnormalities via sMRI and DTI, as advanced MR imaging technology is readily available and automated image analysis methodology have recently been transferred from the human to animal imaging setting. For this purpose, we developed a synergistic, parallel approach to imaging and image analysis for the human and the rodent branch of our study. We propose an equivalent design in both the selection of the developmental assessment stage and the neuroimaging setup. This approach brings significant advantages to study neurobiological features of early brain development that are common to animals and humans but also preserve analysis capabilities only possible in animal research. This paper presents the main framework and individual methods for the proposed cross-species study design, as well as preliminary DTI cross-species comparative results in the intra-uterine cocaine-exposure study

Synergy of Image Analysis for Animal and Human Neuroimaging Supports Translational Research on Drug Abuse

The use of structural magnetic resonance imaging (sMRI) and diffusion tensor imaging (DTI) in animal models of neuropathology is of increasing interest to the neuroscience community. In this work, we present our approach to create optimal translational studies that include both animal and human neuroimaging data within the frameworks of a study of post-natal neuro-development in intra-uterine cocaine-exposure. We propose the use of non-invasive neuroimaging to study developmental brain structural and white matter pathway abnormalities via sMRI and DTI, as advanced MR imaging technology is readily available and automated image analysis methodology have recently been transferred from the human to animal imaging setting. For this purpose, we developed a synergistic, parallel approach to imaging and image analysis for the human and the rodent branch of our study. We propose an equivalent design in both the selection of the developmental assessment stage and the neuroimaging setup. This approach brings significant advantages to study neurobiological features of early brain development that are common to animals and humans but also preserve analysis capabilities only possible in animal research. This paper presents the main framework and individual methods for the proposed cross-species study design, as well as preliminary DTI cross-species comparative results in the intra-uterine cocaine-exposure study

Aerosolized In Vivo 3D Localization of Nose-to-Brain Nanocarrier Delivery Using Multimodality Neuroimaging in a Rat Model—Protocol Development

The fate of intranasal aerosolized radiolabeled polymeric micellar nanoparticles (LPNPs) was tracked with positron emission tomography/computer tomography (PET/CT) imaging in a rat model to measure nose-to-brain delivery. A quantitative temporal and spatial testing protocol for new radio-nanotheranostic agents was sought in vivo. LPNPs labeled with a zirconium 89 (89Zr) PET tracer were administered via intranasal or intravenous delivery, followed by serial PET/CT imaging. After 2 h of continuous imaging, the animals were sacrificed, and the brain substructures (olfactory bulb, forebrain, and brainstem) were isolated. The activity in each brain region was measured for comparison with the corresponding PET/CT region of interest via activity measurements. Serial imaging of the LPNPs (100 nm PLA–PEG–DSPE+89Zr) delivered intranasally via nasal tubing demonstrated increased activity in the brain after 1 and 2 h following intranasal drug delivery (INDD) compared to intravenous administration, which correlated with ex vivo gamma counting and autoradiography. Although assessment of delivery from nose to brain is a promising approach, the technology has several limitations that require further development. An experimental protocol for aerosolized intranasal delivery is presented herein, which may provide a platform for better targeting the olfactory epithelium

Structural and functional, empirical and modeled connectivity in the cerebral cortex of the rat

[EN] Connectomics data from animal models provide an invaluable opportunity to reveal the complex interplay between structure and function in the mammalian brain. In this work, we investigate the relationship between structural and functional connectivity in the rat brain cortex using a directed anatomical network generated from a carefully curated meta-analysis of published tracing data, along with resting-state functional MRI data obtained from a group of 14 anesthetized Wistar rats. We found a high correspondence between the strength of functional connections, measured as blood oxygen level dependent (BOLD) signal correlations between cortical regions, and the weight of the corresponding anatomical links in the connectome graph (maximum Spearman rank-order correlation rho = 0.48). At the network-level, regions belonging to the same functionally defined community tend to form more mutual weighted connections between each other compared to regions located in different communities. We further found that functional communities in resting-state networks are enriched in densely connected anatomical motifs. Importantly, these higher-order structural subgraphs cannot be explained by lower-order topological properties, suggesting that dense structural patterns support functional associations in the resting brain. Simulations of brain-wide resting-state activity based on neural mass models implemented on the empirical rat anatomical connectome demonstrated high correlation between the simulated and the measured functional connectivity (maximum Pearson correlation rho = 0: 53), further suggesting that the topology of structural connections plays an important role in shaping functional cortical networks.This work was supported in part by the Spanish Ministerio de Economia y Competitividad (MINECO) and FEDER funds under grants BFU2015-64380-C2-1-R (S.C) and BFU2015-64380-C2-2-R (D.M.) and EU Horizon 2020 Program 668863-SyBil-AA grant (S.C.). S.C. acknowledges financial support from the Spanish State Research Agency, through the "Severo Ochoa" Programme for Centres of Excellence in R&D (ref. SEV-2013-0317). A. D.-P., was supported by grant FPU13/01475 from the Spanish Ministerio de Educacion, Cultura y Deporte (MECD). O.S. acknowledges support by the J.S. McDonnell Foundation (#220020387) and the National Institutes of Health (NIH R01 AT009036-01). We are also grateful to Andrea Avena-Koenigsberger and Begona Fernandez for their technical support.Díaz-Parra, A.; Osborn, Z.; Canals Gamoneda, S.; Moratal, D.; Sporns, O. (2017). Structural and functional, empirical and modeled connectivity in the cerebral cortex of the rat. NeuroImage. 159:170-184. https://doi.org/10.1016/j.neuroimage.2017.07.046S17018415

Cyberinfrastructure for the digital brain:spatial standards for integrating rodent brain atlases

Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today’s data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project

Aerosolized In Vivo 3D Localization of Nose-to-Brain Nanocarrier Delivery Using Multimodality Neuroimaging in a Rat Model—Protocol Development

The fate of intranasal aerosolized radiolabeled polymeric micellar nanoparticles (LPNPs) was tracked with positron emission tomography/computer tomography (PET/CT) imaging in a rat model to measure nose-to-brain delivery. A quantitative temporal and spatial testing protocol for new radio-nanotheranostic agents was sought in vivo. LPNPs labeled with a zirconium 89 (89Zr) PET tracer were administered via intranasal or intravenous delivery, followed by serial PET/CT imaging. After 2 h of continuous imaging, the animals were sacrificed, and the brain substructures (olfactory bulb, forebrain, and brainstem) were isolated. The activity in each brain region was measured for comparison with the corresponding PET/CT region of interest via activity measurements. Serial imaging of the LPNPs (100 nm PLA–PEG–DSPE+89Zr) delivered intranasally via nasal tubing demonstrated increased activity in the brain after 1 and 2 h following intranasal drug delivery (INDD) compared to intravenous administration, which correlated with ex vivo gamma counting and autoradiography. Although assessment of delivery from nose to brain is a promising approach, the technology has several limitations that require further development. An experimental protocol for aerosolized intranasal delivery is presented herein, which may provide a platform for better targeting the olfactory epithelium

Characterizing functional and structural brain alterations driven by chronic alcohol drinking: a resting-state fMRI connectivity and voxel-based morphometry analysis

El balance del cerebro se altera a nivel estructural y funcional por el consumo de alcohol y puede causar trastornos por consumo de alcohol (TCA). El objetivo de esta Tesis Doctoral fue investigar los efectos del consumo crónico y excesivo de alcohol en el cerebro desde una perspectiva funcional y estructural, mediante análisis de imágenes multimodales de resonancia magnética (RM). Realizamos tres estudios con objetivos específicos: i) Para entender cómo las neuroadaptaciones desencadenadas por el consumo de alcohol se ven reflejadas en la conectividad cerebral funcional entre redes cerebrales, así como en la actividad cerebral, realizamos estudios en ratas msP en condiciones de control y tras un mes con acceso a alcohol. Para cada sujeto se obtuvieron las señales específicas de sus redes cerebrales tras aplicar análisis probabilístico de componentes independientes y regresión espacial a las imágenes funcionales de RM en estado de reposo (RMf-er). Después, estimamos la conectividad cerebral en estado de reposo mediante correlación parcial regularizada. Para una lectura de la actividad neuronal realizamos un experimento con imágenes de RM realzadas con manganeso. En la condición de alcohol encontramos hipoconectividades entre la red visual y las redes estriatal y sensorial; todas con incrementos en actividad. Por el contrario, hubo hiperconectividades entre tres pares de redes cerebrales: 1) red prefrontal cingulada media y red estriatal, 2) red sensorial y red parietal de asociación y 3) red motora-retroesplenial y red sensorial, siendo la red parietal de asociación la única red sin incremento de actividad. Estos resultados indican que las redes cerebrales ya se alteran desde una fase temprana de consumo continuo y prolongado de alcohol, disminuyendo el control ejecutivo y la flexibilidad comportamental. ii) Para comparar el volumen de materia gris (MG) cortical entre 34 controles sanos y 35 pacientes con dependencia al alcohol, desintoxicados y en abstinencia de 1 a 5 semanas, realizamos un análisis de morfometría basado en vóxel. Las principales estructuras cuyo volumen de MG disminuyó en los sujetos en abstinencia fueron el giro precentral (GPreC), el giro postcentral (GPostC), la corteza motora suplementaria (CMS), el giro frontal medio (GFM), el precúneo (PCUN) y el lóbulo parietal superior (LPS). Disminuciones de MG en el volumen de esas áreas pueden dar lugar a cambios en el control de los movimientos (GPreC y CMS), en el procesamiento de información táctil y propioceptiva (GPostC), personalidad, previsión (GFM), reconocimiento sensorial, entendimiento del lenguaje, orientación (PCUN) y reconocimiento de objetos a través de su forma (LPS). iii) Caracterizar estados cerebrales dinámicos en señales de RMf mediante una metodología basada en un modelo oculto de Markov (HMM en inglés)-Gaussiano en un paradigma con diseño de bloques, junto con distintas señales temporales de múltiples redes: componentes independientes y modos funcionales probabilísticos (PFMs en inglés) en 14 sujetos sanos. Cuatro condiciones experimentales formaron el paradigma de bloques: reposo, visual, motora y visual-motora. Mediante la aplicación de HMM-Gaussiano a los PFMs pudimos caracterizar cuatro estados cerebrales a partir de la actividad media de cada PFM. Los cuatro mapas espaciales obtenidos fueron llamados HMM-reposo, HMM-visual, HMM-motor y HMM-RND (red neuronal por defecto). HMM-RND apareció una vez el estado de tarea se había estabilizado. En un futuro cercano se espera obtener estados cerebrales en nuestros datos de RMf-er en ratas, para comparar dinámicamente el comportamiento de las redes cerebrales como un biomarcador de TCA. En conclusión, las técnicas de neuroimagen aplicadas en imagen de RM multimodal para estimar la conectividad cerebral en estado de reposo, la actividad cerebral y el volumen de materia gris han permitido avanzar en el entendimiento de los mecanismos homeostáticoLa ingesta d'alcohol altera el balanç del cervell a nivell estructural i funcional i pot causar trastorns per consum d' alcohol (TCA). L'objectiu d'aquesta Tesi Doctoral fou estudiar els efectes en el cervell del consum crònic i excessiu d'alcohol, des d'un punt de vista funcional i estructural i per mitjà d'anàlisi d'imatges de ressonància magnètica (RM). Vam realitzar tres anàlisis amb objectius específics: i) Per a entendre com les neuroadaptacions desencadenades pel consum d'alcohol es veuen reflectides en la connectivitat cerebral funcional entre xarxes cerebrals, així com en l'activitat cerebral, vam realitzar estudis en rates msP en les condicions de control i després d'un mes amb accés a alcohol. Per a cada subjecte vam obtindre els senyals de les xarxes cerebrals tras aplicar a les imatges funcionals de RM en estat de repòs una anàlisi probabilística de components independents i regressió espacial. Després, estimàrem la connectivitat cerebral en estat de repòs per mitjà de correlació parcial regularitzada. Per a una lectura de l'activitat cerebral vam adquirir imatges de RM realçades amb manganés. En la condició d'alcohol vam trobar hipoconnectivitats entre la xarxa visual i les xarxes estriatal i sensorial, totes amb increments en activitat. Al contrari, va haver-hi hiperconnectivitats entre tres parells de xarxes cerebrals: 1) xarxa prefrontal cingulada mitja i xarxa estriatal, 2) xarxa sensorial i xarxa parietal d'associació i 3) xarxa motora-retroesplenial i xarxa sensorial, sent la xarxa parietal d'associació l'única xarxa sense increment d'activitat. Aquests resultats indiquen que les xarxes cerebrals ja s'alteren des d'una fase primerenca caracteritzada per consum continu i prolongat d'alcohol, disminuint el control executiu i la flexibilitat comportamental. ii) Per a comparar el volum de MG cortical entre 34 controls sans i 35 pacients amb dependència a l'alcohol, desintoxicats i en abstinència de 1 a 5 setmanes vam emprar anàlisi de morfometria basada en vòxel. Les principals estructures on el volum de MG va disminuir en els subjectes en abstinència van ser el gir precentral (GPreC), el gir postcentral (GPostC), la corteça motora suplementària (CMS), el gir frontal mig (GFM), el precuni (PCUN) i el lòbul parietal superior (LPS). Les disminucions de MG en eixes àrees poden donar lloc a canvis en el control dels moviments (GPreC i CMS), en el processament d'informació tàctil i propioceptiva (GPostC), personalitat, previsió (GFM), reconeixement sensorial, enteniment del llenguatge, orientació (PCUN) i reconeixement d'objectes a través de la seua forma (LPS). iii) Caracterització de les dinàmiques temporals del cervell com a diferents estats cerebrals, en senyals de RMf mitjançant una metodologia basada en un model ocult de Markov (HMM en anglès)-Gaussià en imatges de RMf, junt amb dos tipus de senyals temporals de múltiples xarxes cerebrals: components independents i modes funcionals probabilístics (PFMs en anglès) en 14 subjectes sans. Quatre condicions experimentals van formar el paradigma de blocs: repòs, visual, motora i visual-motora. HMM-Gaussià aplicat als PFMs (senyals de RM funcional de xarxes cerebrals) va permetre la millor caracterització dels quatre estats cerebrals a partir de l'activitat mitjana de cada PFM. Els quatre mapes espacials obtinguts van ser anomenats HMM-repòs, HMM-visual, HMM-motor i HMM-XND (xarxa neuronal per defecte). HMM-XND va aparèixer una vegada una tasca estava estabilitzada. En un futur pròxim s'espera obtindre estats cerebrals en les nostres dades de RMf-er en rates, per a comparar dinàmicament el comportament de les xarxes cerebrals com a biomarcador de TCA. En conclusió, s'han aplicat tècniques de neuroimatge per a estimar la connectivitat cerebral en estat de repòs, l'activitat cerebral i el volum de MG, aplicades a imatges multimodals de RM i s'han obtés resultats que han permés avançar en l'enteniment dels mAlcohol intake alters brain balance, affecting its structure and function, and it may cause Alcohol Use Disorders (AUDs). We aimed to study the effects of chronic, excessive alcohol consumption on the brain from a functional and structural point of view, via analysis of multimodal magnetic resonance (MR) images. We conducted three studies with specific aims: i) To understand how the neuroadaptations triggered by alcohol intake are reflected in between-network resting-state functional connectivity (rs-FC) and brain activity in the onset of alcohol dependence, we performed studies in msP rats in control and alcohol conditions. Group probabilistic independent component analysis (group-PICA) and spatial regression were applied to resting-state functional magnetic resonance imaging (rs-fMRI) images to obtain subject-specific time courses of seven resting-state networks (RSNs). Then, we estimated rs-FC via L2-regularized partial correlation. We performed a manganese-enhanced (MEMRI) experiment as a readout of neuronal activity. In alcohol condition, we found hypoconnectivities between the visual network (VN), and striatal (StrN) and sensory-cortex (SCN) networks, all with increased brain activity. On the contrary, hyperconnectivities were found between three pairs of RSNs: 1) medial prefrontal-cingulate (mPRN) and StrN, 2) SCN and parietal association (PAN) and 3) motor-retrosplenial (MRN) and SCN networks, being PAN the only network without brain activity rise. Interestingly, the hypoconnectivities could be explained as control to alcohol transitions from direct to indirect connectivity, whereas the hyperconnectivities reflected an indirect to an even more indirect connection. These findings indicate that RSNs are early altered by prolonged and moderate alcohol exposure, diminishing the executive control and behavioral flexibility. ii) To compare cortical gray matter (GM) volume between 34 healthy controls and 35 alcohol-dependent patients who were detoxified and remained abstinent for 1-5 weeks before MRI acquisition, we performed a voxel-based morphometry analysis. The main structures whose GM volume decreased in abstinent subjects compared to controls were precentral gyrus (PreCG), postcentral gyrus (PostCG), supplementary motor cortex (SMC), middle frontal gyrus (MFG), precuneus (PCUN) and superior parietal lobule (SPL). Decreases in GM volume in these areas may lead to changes in control of movement (PreCG and SMC), in processing tactile and proprioceptive information (PostCG), personality, insight, prevision (MFG), sensory appreciation, language understanding, orientation (PCUN) and the recognition of objects by touch and shapes (SPL). iii) To characterize dynamic brain states in functional MRI (fMRI) signals by means of an approach based on the Hidden Markov model (HMM). Several parameter configurations of HMM-Gaussian in a block-design paradigm were considered, together with different time series: independent components (ICs) and probabilistic functional modes (PFMs) on 14 healthy subjects. The block-design fMRI paradigm consisted of four experimental conditions: rest, visual, motor and visual-motor. Characterizing brain states' dynamics in fMRI data was possible applying the HMM-Gaussian approach to PFMs, with mean activity driving the states. The four spatial maps obtained were named HMM-rest, HMM-visual, HMM-motor and HMM-DMN (default mode network). HMM-DMN appeared once a task state had stabilized. The ultimate goal will be to obtain brain states in our rs-fMRI rat data, to dynamically compare the behavior of brain RSNs as a biomarker of AUD. In conclusion, neuroimaging techniques to estimate rs-FC, brain activity and GM volume can be successfully applied to multimodal MRI in the advance of the understanding of brain homeostasis in AUDs. These functional and structural alterations are a biomarker of chronic alcoholism to explain impairments in executive control, reward evaluation and visuospatial processing.Pérez Ramírez, MÚ. (2018). Characterizing functional and structural brain alterations driven by chronic alcohol drinking: a resting-state fMRI connectivity and voxel-based morphometry analysis [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/11316

Advanced image-processing techniques in magnetic resonance imaging for the investigation of brain pathologies and tumour angiogenesis

L'imaging a risonanza magnetica (MRI) \ue8 sempre pi\uf9 utilizzato in ambiente medico per la sua abilit\ue0 di produrre in modo non invasivo immagini di alt\ue0 qualit\ue0 dell'interno del corpo umano. Sin dalla sua introduzione nei primi anni 70, techiche di acquisizione via via pi\uf9 complesse sono state proposte, portando l'MRI ad essere utilizzata su uno spettro di applicazioni sempre pi\uf9 ampio. Le tecniche pi\uf9 innovative, tra cui la risonanza magnetica funzionale e di diffusione, richiedono tecniche di analisi ed algoritmi di elaborazione molto complessi per estrarre informazioni utili dai dati acquisiti. Lo scopo di questa tesi \ue8 stato quello di sviluppare e ottimizzare tecniche avanzate di elaborazione per applicarle all'analisi di dati di risonanza magnetica sia in ambiente preclinico che clinico. Durante il corso di dottorato sono stato coinvolto attivamente in diversi progetti di ricerca, ed ogni volta mi sono trovato ad affrontare problematiche diverse. In questa tesi, tuttavia, saranno riportati i risultati ottenuti nei tre progetti pi\uf9 interessanti a cui ho preso parte. Tali progetti avevano come obiettivo (i) l'implementazione di un protocollo sperimentale innovativo per imaging funzionale in animali da laboratorio, (ii) lo sviluppo di nuovi metodi per l'analisi di dati di Dynamic Contrast Enhanced MRI in modelli sperimentali di tumore e (iii) l'analisi di dati di diffusione in pazienti affetti da ischemia cerebrale. Particolare enfasi sar\ue0 posta sugli aspetti tecnici che riguardano gli algoritmi ed i metodi di elaborazione utilizzati nel processo di analisi.Magnetic resonance imaging (MRI) is increasingly being used in medical settings because of its ability to produce, non-invasively, high quality images of the inside of the human body. Since its introduction in early 70\u2019s, more and more complex acquisition techniques have been proposed, raising MRI to be exploited in a wide spectrum of applications. Innovative MRI modalities, such as diffusion and functional imaging, require complex analysis techniques and advanced algorithms in order to extract useful information from the acquired data. The aim of the present work has been to develop and optimize state-of-the-art techniques to be applied in the analysis of MRI data both in experimental and clinical settings. During my doctoral program I have been actively involved in several research projects, each time facing many different issues. In this dissertation, however, I will report the results obtained in three most appealing projects I partecipated to. These projects were devoted (i) to the implementation of an innovative experimental protocol for functional MRI in laboratory animals, (ii) to the development of new methods for the analysis of Dynamic Contrast Enhanced MRI data in experimental tumour models and (iii) to the analysis of diffusion MRI data in stroke patients. Particular emphasis will be given to the technical aspects regarding the algorithms and processing methods used in the analysis of data

Automatic target validation based on neuroscientific literature mining for tractography.

Target identification for tractography studies requires solid anatomical knowledge validated by an extensive literature review across species for each seed structure to be studied. Manual literature review to identify targets for a given seed region is tedious and potentially subjective. Therefore, complementary approaches would be useful. We propose to use text-mining models to automatically suggest potential targets from the neuroscientific literature, full-text articles and abstracts, so that they can be used for anatomical connection studies and more specifically for tractography. We applied text-mining models to three structures: two well-studied structures, since validated deep brain stimulation targets, the internal globus pallidus and the subthalamic nucleus and, the nucleus accumbens, an exploratory target for treating psychiatric disorders. We performed a systematic review of the literature to document the projections of the three selected structures and compared it with the targets proposed by text-mining models, both in rat and primate (including human). We ran probabilistic tractography on the nucleus accumbens and compared the output with the results of the text-mining models and literature review. Overall, text-mining the literature could find three times as many targets as two man-weeks of curation could. The overall efficiency of the text-mining against literature review in our study was 98% recall (at 36% precision), meaning that over all the targets for the three selected seeds, only one target has been missed by text-mining. We demonstrate that connectivity for a structure of interest can be extracted from a very large amount of publications and abstracts. We believe this tool will be useful in helping the neuroscience community to facilitate connectivity studies of particular brain regions. The text mining tools used for the study are part of the HBP Neuroinformatics Platform, publicly available at http://connectivity-brainer.rhcloud.com/