X-PloRat: Software para o Registro do Comportamento em Espaços Confinados

The present technical note introduces the X-PloRat, a software for the scoring of animal location, displacement, and other behavioral properties, in enclosed spaces. The X-PloRat offers a variety of data reports and can be used for training students in behavioral observation and in validating other kinds of scoring procedures.A presente nota técnica apresenta o X-PloRat, um software que permite o registro da localização, deslocamento e outras propriedades do comportamento animal em espaços confinados. O X-PloRat oferece uma grande variedade de relatórios e pode ajudar no treinamento de estudantes em observação do comportamento e também na validação de outros tipos de registros

GESTÃO DE PROJETO APLICADA À PESQUISA: EXPERIÊNCIA EM INSTITUIÇÃO PÚBLICA UNIVERSITÁRIA DE GRANDE PORTE

Pesquisadores dos departamentos de Patologia e de Radiologia da Faculdade de Medicina da USP (FMUSP) conceberam o projeto Plataforma de Imagens na Sala de Autópsia (PISA) para investigar possibilidades de pesquisa, ensino e assistência à saúde utilizando diferentes técnicas de imagens associadas à autópsia. Em seu desenvolvimento, o projeto envolveu diversas instituições do Sistema Acadêmico da FMUSP e de seu Hospital das Clínicas, além da Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP). As dimensões alcançadas rapidamente pelo projeto exigiram a adoção de um modelo de gestão que leva em conta as peculiaridades de um projeto de pesquisa mas adota as ferramentas modernas de gestão, além de um modelo de governança que permite a transparência e a comunicação entre os diversos interessados na Plataforma. O objetivo deste trabalho é mostrar a interface entre a vertente científica que o projeto aborda e o modelo de gestão adotado para seu gerenciamento. Além disso, expor sua estrutura organizacional, desde sua concepção até a formatação que possui nos dias de hoje. Para se chegar ao modelo de gestão atual, foram usadas técnicas e práticas consagradas de gerenciamento de projetos

Evaluation of Glaucomatous Damage via Functional Magnetic Resonance Imaging, and Correlations Thereof with Anatomical and Psychophysical Ocular Findings

PurposeTo evaluate the functional magnetic resonance imaging (fMRI) response to binocular visual stimulation and the association thereof with structural ocular findings and psychophysical test results in patients with glaucoma, and controls.MethodsCross-sectional study. Participants underwent a complete ophthalmic examination, including Humphrey 24-2 visual field (VF) testing and optical coherence tomography. Binocular VF in each quadrant was determined using an integrated method. Patients with glaucoma were assigned to three subgroups: initial, asymmetrical and severe glaucoma. Regions of interest (ROIs) were determined anatomically. fMRI (3 T) was performed using a bilaterally presented polar angle stimulus, and the accompanying changes in blood oxygen level-dependent (BOLD) signals were obtained from the occipital poles and calcarine ROIs. We used generalized estimation equation models to compare anatomical and functional data between the groups.ResultsA total of 25 subjects were enrolled, of whom 17 had glaucoma and 8 were controls. Significant associations between quadrant binocular VF sensitivities and fMRI responses were found in the occipital pole ROIs (p = 0.033) and the calcarine ROIs (p = 0.045). in glaucoma severity subgroup analysis, retinal nerve fiber layer (RNFL) thickness was associated with the BOLD response of the calcarine and occipital pole ROIs (p = 0.002 and 0.026, respectively). the initial and asymmetrical glaucoma subgroups had similar binocular VF sensitivities and RNFL thicknesses, but distinct BOLD responses.ConclusionsThe response of the visual cortex to binocular stimulation was associated with binocular VF sensitivity. RNFL thickness was associated with the BOLD response of the calcarine and occipital pole ROIs.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Universidade Federal de São Paulo, Dept Ophthalmol, São Paulo, BrazilHosp Israelita Albert Einstein, São Paulo, BrazilUniv São Paulo, Inst Psychol, Dept Expt Psychol, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Ophthalmol, São Paulo, BrazilFAPESP: 2007/07339-2Web of Scienc

Functional Magnetic Resonance Imaging for Memory Mapping in Epilepsy

O lobo temporal mesial (LTM) é essencial para tarefas de memória e possui muitas conexões com diferentes áreas do cérebro. Pacientes com epilepsia do LTM, refratários ao tratamento medicamentoso, são candidatos à cirurgia para remoção do foco das crises. Portanto, antes da cirurgia, é essencial avaliar eventuais riscos de declínio das funções de memória, por meio de uma série de testes clínicos. Recentemente, abriu-se a possibilidade de estudar certos aspectos do funcionamento cerebral, de modo não invasivo, utilizando Imagens funcionais por Ressonância Magnética (fMRI). O objetivo deste trabalho foi desenvolver métodos que possibilitem a aplicação de protocolos de memória em estudos de fMRI, com vistas a pacientes com epilepsia. Para a manutenção da atenção durante os estudos de fMRI foi confeccionado um dispositivo infravermelho para registrar as respostas obtidas. Além disso, foi desenvolvido um programa (VOI Analyser) para a otimização das análises dos exames de fMRI. Tanto o dispositivo infravermelho como o programa foram amplamente utilizados em vários projetos de pesquisa permitindo o estudo de tarefas complexas. Neste estudo, a tarefa visava identificar as redes funcionais que participam do processo de codificação e recuperação de memória episódica utilizando tarefas visuais de identificação de cenas complexas. Foram estudados nesse estudo 12 voluntários assintomáticos e 7 pacientes com epilepsia do LTM. O estudo de grupo evidenciou o envolvimento de estruturas do LTM. A tarefa demonstrou ter um nível de dificuldade alta, em especial para pacientes, baseando-se na avaliação do tempo de resposta e nível de acertos. Além do estudo dos grupos, foi realizada uma análise por região de interesse (ROI), com ênfase no complexo amídala-hipocampo. Em seguida, o foco do estudo foi voltado para a assimetria hemisférica funcional, por meio do cálculo do índice de lateralização (IL). Além de rever os resultados obtidos pelo IL convencional, resultados preliminares levaram à proposta de um segundo índice corrigido, considerando a quantidade de voxels e a assimetria das ROI. A utilização do índice corrigido tornou a análise mais estável por diminuir a dependência do limiar estatístico considerado. A seguir, foi realizada uma subdivisão do hipocampo em porção anterior, central e posterior a qual indicou uma maior participação da região posterior na tarefa de codificação e da anterior na tarefa de recuperação, tanto entre os voluntários como em pacientes.Medial temporal lobe (MTL) is essential for memory tasks and has many connections with different areas of the brain. Patients with MTL epilepsy refractory to medical treatment are candidates for surgery to remove the epileptiform tissue. Therefore, before surgery, it is essential to assess the risk of memory function decrease caused by the procedure, through a series of clinical trials. Recently, there is the possibility of studying certain aspects of brain functioning by using a non-invasive technique: functional Magnetic Resonance Imaging (fMRI). The aim of this work was to implement memory protocols in fMRI studies of epilepsy patients. For attention maintenance during the fMRI study an infrared device was built, in order to record the response times. In addition, a software was developed (VOI Analyser) to optimize the analysis of the fMRI examinations. Both have been widely used in several research projects enabling the study of complex tasks. In this study, the task was intended to identify the functional networks involved in the process of encoding and retrieving of episodic memory using a visual task involving complex scenes. 19 subjects were studied: 12 controls and 7 patients with refractory epilepsy. Group study showed the involvement of structures in MTL. The task has demonstrated a high level of difficulty, especially for patients, based on the analysis of response times and correct hits. In addition to the study of groups, an individual analysis was performed by region of interest (ROI), with emphasis on amigdala-hippocampus complex. Then, functional hemispheric asymmetry was studied, by means of the lateralization index (LI). In addition to the computation of conventional LI, an alternative LI was proposed, which considers voxels occupancy and ROI asymmetry. The use of such modified index tuned the analysis more stable by decreasing the dependence on considered statistical threshold. Moreover, LI was also computed on 3 portions of the hippocampus: anterior, middle and posterior. The results indicated a greater involvement of the posterior portion on the encoding task and anterior one in the recovery task, both for volunteers and patients

X-PloRat: A Software for Scoring Animal Behavior in Enclosed Spaces

ABSTRACT The present technical note introduces the X-PloRat, a software for the scoring of animal location, displacement, and other behavioral properties, in enclosed spaces. The X-PloRat offers a variety of data reports and can be used for training students in behavioral observation and in validating other kinds of scoring procedures

Time-perception network and default mode network are associated with temporal prediction in a periodic motion task

The updating of prospective internal models is necessary to accurately predict future observations. Uncertainty-driven internal model updating has been studied using a variety of perceptual paradigms, and have revealed engagement of frontal and parietal areas. In a distinct literature, studies on temporal expectations have also characterized a time-perception network, which relies on temporal orienting of attention. However, the updating of prospective internal models is highly dependent on temporal attention, since temporal attention must be reoriented according to the current environmental demands. In this study we used fMRI to evaluate to what extend the continuous manipulation of temporal prediction would recruit update-related areas and the time-perception network areas. We developed an exogenous temporal task that combines rhythm cueing and time-to-contact principles to generate implicit temporal expectation. Two patterns of motion were created: periodic (simple harmonic oscillation) and non-periodic (harmonic oscillation with variable acceleration). We found that non-periodic motion engaged the exogenous temporal orienting network, which includes the ventral premotor and inferior parietal cortices, and the cerebellum, as well as the presupplementary motor area, which has previously been implicated in internal model updating, and the motion-sensitive area MT+. Interestingly, we found a right-hemisphere preponderance suggesting the engagement of explicit timing mechanisms. We also show that the periodic motion condition, when compared to the non-periodic motion, activated a particular subset of the default-mode network (DMN) midline areas, including the left dorsomedial prefrontal cortex, anterior cingulate cortex, and bilateral posterior cingulate cortex/precuneus. It suggests that the DMN plays a role in processing contextually expected information and supports recent evidence that the DMN may reflect the validation of prospective internal models and predictive control. Taken together, our findings suggest that continuous manipulation of temporal predictions engages representations of temporal prediction as well as task-independent updating of internal models

Decompose quantitative susceptibility mapping (QSM) to sub-voxel diamagnetic and paramagnetic components based on gradient-echo MRI data

PurposeA method named DECOMPOSE-QSM is developed to decompose bulk susceptibility measured with QSM into sub-voxel paramagnetic and diamagnetic components based on a three-pool complex signal model.MethodsMulti-echo gradient echo signal is modeled as a summation of three weighted exponentials corresponding to three types of susceptibility sources: reference susceptibility, diamagnetic and paramagnetic susceptibility relative to the reference. Paramagnetic component susceptibility (PCS) and diamagnetic component susceptibility (DCS) maps are constructed to represent the sub-voxel compartments by solving for linear and nonlinear parameters in the model.ResultsNumerical forward simulation and phantom validation confirmed the ability of DECOMPOSE-QSM to separate the mixture of paramagnetic and diamagnetic components. The PCS obtained from temperature-variant brainstem imaging follows the Curie's Law, which further validated the model and the solver. Initial in vivo investigation of human brain images showed the ability to extract sub-voxel PCS and DCS sources that produce visually enhanced contrast between brain structures comparing to threshold QSM

Evaluation of multi-channel phase reconstruction methods for quantitative susceptibility mapping on postmortem human brain

Quantitative Susceptibility Mapping (QSM) is an established Magnetic Resonance Imaging (MRI) technique with high potential in brain iron studies associated to several neurodegenerative diseases. Unlike other MRI techniques, QSM relies on phase images to estimate tissue's relative susceptibility, therefore requiring a reliable phase data. Phase images from a multi-channel acquisition should be reconstructed in a proper way. On this work it was compared the performance of combination of phase matching algorithms (MCPC3D-S and VRC) and phase combination methods based on a complex weighted sum of phases, considering the magnitude at different powers (k = 0 to 4) as the weighting factor. These reconstruction methods were applied in two datasets: a simulated brain dataset for a 4-coil array and data of 22 postmortem subjects acquired at a 7T scanner using a 32 channels coil. For the simulated dataset, differences between the ground truth and the Root Mean Squared Error (RMSE) were evaluated. For both simulated and postmortem data, the mean (MS) and standard deviation (SD) of susceptibility values of five deep gray matter regions were calculated. For the postmortem subjects, MS and SD were statistically compared across all subjects. A qualitative analysis indicated no differences between methods, except for the Adaptive approach on postmortem data, which showed intense artifacts. In the 20% noise level case, the simulated data showed increased noise in central regions. Quantitative analysis showed that both MS and SD were not statistically different when comparing k=1 and k=2 on postmortem brain images, however visual inspection showed some boundaries artifacts on k=2. Furthermore, the RMSE decreased (on regions near the coils) and increased (on central regions and on overall QSM) with increasing k. In conclusion, for reconstruction of phase images from multiple coils with no reference available, alternative methods are needed. In this study it was found that overall, the phase combination with k=1 is preferred over other powers of k

Experimental and numerical investigations of a small animal coil for ultra-high field magnetic resonance imaging (7T)

The purpose of this work was to develop and investigate a radiofrequency (RF) coil to perform image studies on small animals using the 7T magnetic resonance imaging (MRI) system, installed in the imaging platform in the autopsy room (Portuguese acronym PISA), at the University of Sao Paulo, Brazil, which is the unique 7T MRI scanner installed in South America. Due to a high demand to create new specific coils for this 7T system, it is necessary to carefully assess the distribution of electromagnetic (EM) fields generated by the coils and evaluate the patient/object safety during MRI procedures. To achieve this goal 3D numerical methods were used to design and analyse a 8-rungs transmit/receive linearly driven birdcage coil for small animals. Calculated magnetic field (B1) distributions generated by the coil were crosschecked with measured results, indicating good confidence in the simulated results. Electric field results were post-processed and predictions of local specific absorption rate (SAR) values were achieved for a spherical phantom filled with muscle-like tissue, indicating that the sample would not suffer any unsafe deposition of energy. Post mortem abdomen images obtained from a rat presented good image quality and no artifacts related to field non-homogeneity were observed