Visual Experiences during Paralysis

Rationale: Paralyzed human volunteers (n = 6) participated in several studies the primary one of which required full neuromuscular paralysis while awake. After the primary experiment, while still paralyzed and awake, subjects undertook studies of humor and of attempted eye-movement. The attempted eye-movements tested a central, intentional component to one’s internal visual model and are the subject of this report. Methods: Subjects reclined in a supportive chair and were ventilated after paralysis (cisatracurium, 20 mg intravenously). In illumination, subjects were requested to focus alternately on the faces of investigators standing on the left and the right within peripheral vision. In darkness, subjects were instructed to look away from a point source of light. Subjects were to report their experiences after reversal of paralysis. Results: During attempted eye-movement in illumination, one subject had an illusion of environmental movement but four subjects perceived faces as clearly as if they were in central vision. In darkness, four subjects reported movement of the target light in the direction of attempted eye-movements and three could control the movement of the light at will. Conclusion: The hypothesis that internal visual models receive intended ocular-movement-information directly from oculomotor centers is strengthened by this evidence

Visual Experiences during Paralysis

Rationale: Paralyzed human volunteers (n = 6) participated in several studies the primary one of which required full neuromuscular paralysis while awake. After the primary experiment, while still paralyzed and awake, subjects undertook studies of humor and of attempted eye-movement. The attempted eye-movements tested a central, intentional component to one’s internal visual model and are the subject of this report. Methods: Subjects reclined in a supportive chair and were ventilated after paralysis (cisatracurium, 20 mg intravenously). In illumination, subjects were requested to focus alternately on the faces of investigators standing on the left and the right within peripheral vision. In darkness, subjects were instructed to look away from a point source of light. Subjects were to report their experiences after reversal of paralysis. Results: During attempted eye-movement in illumination, one subject had an illusion of environmental movement but four subjects perceived faces as clearly as if they were in central vision. In darkness, four subjects reported movement of the target light in the direction of attempted eye-movements and three could control the movement of the light at will. Conclusion: The hypothesis that internal visual models receive intended ocular-movement-information directly from oculomotor centers is strengthened by this evidence

Development of functional organization within the sensorimotor network across the perinatal period

In the mature human brain, the neural processing related to different body parts is reflected in patterns of functional connectivity, which is strongest between functional homologs in opposite cortical hemispheres. To understand how this organization is first established, we investigated functional connectivity between limb regions in the sensorimotor cortex in 400 preterm and term infants aged across the equivalent period to the third trimester of gestation (32–45 weeks postmenstrual age). Masks were obtained from empirically derived functional responses in neonates from an independent data set. We demonstrate the early presence of a crude but spatially organized functional connectivity, that rapidly matures across the preterm period to achieve an adult-like configuration by the normal time of birth. Specifically, connectivity was strongest between homolog regions, followed by connectivity between adjacent regions (different limbs but same hemisphere) already in the preterm brain, and increased with age. These changes were specific to the sensorimotor network. Crucially, these trajectories were strongly dependent on age more than age of birth. This demonstrates that during the perinatal period the sensorimotor cortex undergoes preprogrammed changes determining the functional movement organization that are not altered by preterm birth in absence of brain injury

Hand classification of fMRI ICA noise components

We present a practical "how-to" guide to help determine whether single-subject fMRI independent components (ICs) characterise structured noise or not. Manual identification of signal and noise after ICA decomposition is required for efficient data denoising: to train supervised algorithms, to check the results of unsupervised ones or to manually clean the data. In this paper we describe the main spatial and temporal features of ICs and provide general guidelines on how to evaluate these. Examples of signal and noise components are provided from a wide range of datasets (3T data, including examples from the UK Biobank and the Human Connectome Project, and 7T data), together with practical guidelines for their identification. Finally, we discuss how the data quality, data type and preprocessing can influence the characteristics of the ICs and present examples of particularly challenging datasets

Understanding species responses in a changing world by examining the predatory behaviour of southern calamari to changes on temperature

Predator–prey interactions are key drivers in structuring communities, with the potential to substantially impact the whole ecosystem when important predators and prey are involved. Squid are voracious predators and also important prey for other top predators. To date, the available data suggests that under current and projected ocean warming, the behaviour of ectotherms could be modified (for example, through individual movement, predator avoidance and escape speed), yet little is known of the influence of temperature on the predatory behaviour of cephalopods. Here, the predatory behaviour of adult southern calamari (Sepioteuthis australis) under different thermal scenarios was examined demonstrating that squid exhibited different behaviour and performance capabilities across temperature treatments. Overall, attempts of squid to capture prey were faster and more persistent at higher temperature treatments (25°C), suggesting that individuals need to increase their food consumption rate, presumably associated with the higher energetic costs of living at elevated temperatures. However, we also observed a possible decrease in capture efficiency and increased prey handling time at higher temperatures suggesting that implications for energetic balance are not straightforward and that trade-offs need to be carefully explored. As cephalopods are ecologically important species acting as key links in food webs around the world, the results here could have important implications for the dynamics of many marine ecosystems in future

Early prediction of severe retinopathy of prematurity requiring laser treatment using physiological data

Background Early risk stratification for developing retinopathy of prematurity (ROP) is essential for tailoring screening strategies and preventing abnormal retinal development. This study aims to examine the ability of physiological data during the first postnatal month to distinguish preterm infants with and without ROP requiring laser treatment. Methods In this cohort study, preterm infants with a gestational age <32 weeks and/or birth weight <1500 g, who were screened for ROP were included. Differences in the physiological data between the laser and non-laser group were identified, and tree-based classification models were trained and independently tested to predict ROP requiring laser treatment. Results In total, 208 preterm infants were included in the analysis of whom 30 infants (14%) required laser treatment. Significant differences were identified in the level of hypoxia and hyperoxia, oxygen requirement, and skewness of heart rate. The best model had a balanced accuracy of 0.81 (0.72–0.87), a sensitivity of 0.73 (0.64–0.81), and a specificity of 0.88 (0.80–0.93) and included the SpO2/FiO2 ratio and baseline demographics (including gestational age and birth weight). Conclusions Routinely monitored physiological data from preterm infants in the first postnatal month are already predictive of later development of ROP requiring laser treatment, although validation is required in larger cohorts. Impact Routinely monitored physiological data from the first postnatal month are predictive of later development of ROP requiring laser treatment, although model performance was not significantly better than baseline characteristics (gestational age, birth weight, sex, multiple birth, prenatal glucocorticosteroids, route of delivery, and Apgar scores) alone. A balanced accuracy of 0.81 (0.72–0.87), a sensitivity of 0.73 (0.64–0.81), and a specificity of 0.88 (0.80–0.93) was achieved with a model including the SpO2/FiO2 ratio and baseline characteristics. Physiological data have potential to play a significant role for future ROP prediction and provide opportunities for early interventions to protect infants from abnormal retinal development

Analysis of the Macaca mulatta transcriptome and the sequence divergence between Macaca and human

We report the initial sequencing and comparative analysis of the Macaca mulatta transcriptome. Cloned sequences from 11 tissues, nine animals, and three species (M. mulatta, M. fascicularis, and M. nemestrina) were sampled, resulting in the generation of 48,642 sequence reads. These data represent an initial sampling of the putative rhesus orthologs for 6,216 human genes. Mean nucleotide diversity within M. mulatta and sequence divergence among M. fascicularis, M. nemestrina, and M. mulatta are also reported

ICAM-reg: Interpretable Classification and Regression with Feature Attribution for Mapping Neurological Phenotypes in Individual Scans

Feature attribution (FA), or the assignment of class-relevance to different locations in an image, is important for many classification and regression problems but is particularly crucial within the neuroscience domain, where accurate mechanistic models of behaviours, or disease, require knowledge of all features discriminative of a trait. At the same time, predicting class relevance from brain images is challenging as phenotypes are typically heterogeneous, and changes occur against a background of significant natural variation. Here, we present an extension of the ICAM framework for creating prediction specific FA maps through image-to-image translation

ICAM-reg: Interpretable Classification and Regression with Feature Attribution for Mapping Neurological Phenotypes in Individual Scans

An important goal of medical imaging is to be able to precisely detect patterns of disease specific to individual scans; however, this is challenged in brain imaging by the degree of heterogeneity of shape and appearance. Traditional methods, based on image registration to a global template, historically fail to detect variable features of disease, as they utilise population-based analyses, suited primarily to studying group-average effects. In this paper we therefore take advantage of recent developments in generative deep learning to develop a method for simultaneous classification, or regression, and feature attribution (FA). Specifically, we explore the use of a VAE-GAN translation network called ICAM, to explicitly disentangle class relevant features from background confounds for improved interpretability and regression of neurological phenotypes. We validate our method on the tasks of Mini-Mental State Examination (MMSE) cognitive test score prediction for the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort, as well as brain age prediction, for both neurodevelopment and neurodegeneration, using the developing Human Connectome Project (dHCP) and UK Biobank datasets. We show that the generated FA maps can be used to explain outlier predictions and demonstrate that the inclusion of a regression module improves the disentanglement of the latent space. Our code is freely available on Github https://github.com/CherBass/ICAM