Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated Lung Field Segmentation of Injured Regions and Anatomical Structures from Chest CT Images

Abstract This work proposes a novel functionality for computerized tomography (CT) based investigation of diffuse lung diseases diagnosis that enables the evaluation of the disease with lung anatomical structures. Automated methods for segmenting several anatomy structures in chest CT are proposed: namely the lungs, airway trees and pulmonary vessels trees. The airway and pulmonary vessels trees are segmented using a failure and recovery algorithm. The algorithm checks intermediary results consistence, backtrack to a history position if a failure is detected. The quality of the result is improved while reducing the processing time even for subjects with lung diseases. The pulmonary vessels are segmented through the same algorithm with different seed points. The seed for the airway segmentation is within the tracheal tube, and the seed for the pulmonary vessels segmentation is within the heart. The algorithm is tested with CT images acquired from three distinct types of subjects: healthy, idiopathic interstitial pneumonias (IIPs) and chronic obstructive pulmonary disease (COPD). The main bronchus are found in the segmented airways and the associated lung lobes are determined. Combining the segmented lung lobes and the diffuse lung diseases classification, it is possible to quantify how much and where of each lobe is injured. The proposed algorithm was evaluated to be robust enough to segment the studied cases.
Brain signatures of perceiving a smile: Time course and source localization

Facial happiness is consistently recognized faster than other expressions of emotion. In this study, to determine when and where in the brain such a recognition advantage develops, EEG activity during an expression categorization task was subjected to temporospatial PCA analysis and LAURA source localizations. Happy, angry, and neutral faces were presented either in whole or bottom‐half format (with the mouth region visible). The comparison of part‐ versus whole‐face conditions served to examine the role of the smile. Two neural signatures underlying the happy face advantage emerged. One peaked around 140 ms (left N140) and was source‐located at the left IT cortex (MTG), with greater activity for happy versus non‐happy faces in both whole and bottom‐half face format. This suggests an enhanced perceptual encoding mechanism for salient smiles. The other peaked around 370 ms (P3b and N3) and was located at the right IT (FG) and dorsal cingulate (CC) cortices, with greater activity specifically for bottom‐half happy versus non‐happy faces. This suggests an enhanced recruitment of face‐specific information to categorize (or reconstruct) facial happiness from diagnostic smiling mouths. Additional differential brain responses revealed a specific “anger effect,” with greater activity for angry versus non‐angry expressions (right N170 and P230; right pSTS and IPL); and a coarse “emotion effect,” with greater activity for happy and angry versus neutral expressions (anterior P2 and posterior N170; vmPFC and right IFG). Hum Brain Mapp 36:4287–4303, 2015. © 2015 Wiley Periodicals, Inc.
A critical role of temporoparietal junction in the integration of top‐down and bottom‐up attentional control

Information processing can be biased toward behaviorally relevant and salient stimuli by top‐down (goal‐directed) and bottom‐up (stimulus‐driven) attentional control processes respectively. However, the neural basis underlying the integration of these processes is not well understood. We employed functional magnetic resonance imaging (fMRI) and transcranial direct‐current stimulation (tDCS) in humans to examine the brain mechanisms underlying the interaction between these two processes. We manipulated the cognitive load involved in top‐down processing and stimulus surprise involved in bottom‐up processing in a factorial design by combining a majority function task and an oddball paradigm. We found that high cognitive load and high surprise level were associated with prolonged reaction time compared to low cognitive load and low surprise level, with a synergistic interaction effect, which was accompanied by a greater deactivation of bilateral temporoparietal junction (TPJ). In addition, the TPJ displayed negative functional connectivity with right middle occipital gyrus, which is involved in bottom‐up processing (modulated by the interaction effect), and the right frontal eye field (FEF), which is involved in top‐down control. The enhanced negative functional connectivity between the TPJ and right FEF was accompanied by a larger behavioral interaction effect across subjects. Application of cathodal tDCS over the right TPJ eliminated the interaction effect. These results suggest that the TPJ plays a critical role in processing bottom‐up information for top‐down control of attention. Hum Brain Mapp 36:4317–4333, 2015. © 2015 Wiley Periodicals, Inc.
Multivariate classification of smokers and nonsmokers using SVM‐RFE on structural MRI images

Voxel‐based morphometry (VBM) studies have revealed gray matter alterations in smokers, but this type of analysis has poor predictive value for individual cases, which limits its applicability in clinical diagnoses and treatment. A predictive model would essentially embody a complex biomarker that could be used to evaluate treatment efficacy. In this study, we applied VBM along with a multivariate classification method consisting of a support vector machine with recursive feature elimination to discriminate smokers from nonsmokers using their structural MRI data. Mean gray matter volumes in 1,024 cerebral cortical regions of interest created using a subparcellated version of the Automated Anatomical Labeling template were calculated from 60 smokers and 60 nonsmokers, and served as input features to the classification procedure. The classifier achieved the highest accuracy of 69.6% when taking the 139 highest ranked features via 10‐fold cross‐validation. Critically, these features were later validated on an independent testing set that consisted of 28 smokers and 28 nonsmokers, yielding a 64.04% accuracy level (binomial P = 0.01). Following classification, exploratory post hoc regression analyses were performed, which revealed that gray matter volumes in the putamen, hippocampus, prefrontal cortex, cingulate cortex, caudate, thalamus, pre‐/postcentral gyrus, precuneus, and the parahippocampal gyrus, were inversely related to smoking behavioral characteristics. These results not only indicate that smoking related gray matter alterations can provide predictive power for group membership, but also suggest that machine learning techniques can reveal underlying smoking‐related neurobiology. Hum Brain Mapp 36:4869–4879, 2015. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.
Hippocampal‐DMN disconnectivity in MS is related to WM lesions and depression

The hippocampus is part of the default‐mode network (DMN) and is functionally hit early in multiple sclerosis (MS). Hippocampal and DMN dysfunctions have been associated with depression, both in patients with MS and in major depressive disorders. We hypothesized that white matter lesions may contribute, through a disconnection mechanism, to hippocampal dysfunction. To test this, we assessed the relationship between hippocampal resting‐state (RS) functional connectivity (FC) abnormalities with brain T2 lesion volumes and the presence and severity of depression. Structural and RS fMRI images were acquired from 69 patients with cognitively intact MS and 42 matched healthy controls (HC). Depression was quantified using the Montgomery–Asberg Depression Rating Scale. Seed‐voxel hippocampal RS FC was assessed. SPM8 was used for between‐group comparisons and correlation analysis between RS FC abnormalities with clinical and structural MRI variables. Compared to HC, patients with MS showed a significant atrophy of the whole brain and left hippocampus (P < 0.001), and a distributed pattern of decreased RS FC between the hippocampi and several cortical–subcortical regions, which were mostly located within the DMN. Reduced hippocampal RS FC with regions of the DMN was strongly correlated with higher T2 lesion volume, longer disease duration, and the severity of depression and disability. In patients with cognitively preserved MS, brain focal WM lesions are related to the functional integration of the hippocampus to other brain regions of the DMN, suggesting a disconnection syndrome. Such a disruption of hippocampal RS FC is likely to contribute to the occurrence of depression and to clinical disability. Hum Brain Mapp 36:5051–5063, 2015. © 2015 Wiley Periodicals, Inc.
Selective reduction of fMRI responses to transient achromatic stimuli in the magnocellular layers of the LGN and the superficial layer of the SC of early glaucoma patients

Glaucoma is now viewed not just a disease of the eye but also a disease of the brain. The prognosis of glaucoma critically depends on how early the disease can be detected. However, early glaucomatous loss of the laminar functions in the human lateral geniculate nucleus (LGN) and superior colliculus (SC) remains difficult to detect and poorly understood. Using functional MRI, we measured neural signals from different layers of the LGN and SC, as well as from the early visual cortices (V1, V2 and MT), in patients with early‐stage glaucoma and normal controls. Compared to normal controls, early glaucoma patients showed more reduction of response to transient achromatic stimuli than to sustained chromatic stimuli in the magnocellular layers of the LGN, as well as in the superficial layer of the SC. Magnocellular responses in the LGN were also significantly correlated with the degree of behavioral deficits to the glaucomatous eye. Finally, early glaucoma patients showed no reduction of fMRI response in the early visual cortex. These findings demonstrate that ‘large cells’ in the human LGN and SC suffer selective loss of response to transient achromatic stimuli at the early stage of glaucoma. Hum Brain Mapp 37:558–569, 2016. © 2015 Wiley Periodicals, Inc.
The effects of dexamphetamine on the resting‐state electroencephalogram and functional connectivity

The catecholamines—dopamine and noradrenaline—play important roles in directing and guiding behavior. Disorders of these systems, particularly within the dopamine system, are associated with several severe and chronically disabling psychiatric and neurological disorders. We used the recently published group independent components analysis (ICA) procedure outlined by Chen et al. (2013) to present the first pharmaco‐EEG ICA analysis of the resting‐state EEG in healthy participants administered 0.45 mg/kg dexamphetamine. Twenty‐eight healthy participants between 18 and 41 were recruited. Bayesian nested‐domain models that explicitly account for spatial and functional relationships were used to contrast placebo and dexamphetamine on component spectral power and several connectivity metrics. Dexamphetamine led to reductions across delta, theta, and alpha spectral power bands that were predominantly localized to Frontal and Central regions. Beta 1 and beta 2 power were reduced by dexamphetamine at Frontal ICs, while beta 2 and gamma power was enhanced by dexamphetamine in posterior regions, including the parietal, occipital‐temporal, and occipital regions. Power–power coupling under dexamphetamine was similar for both states, resembling the eyes open condition under placebo. However, orthogonalized measures of power coupling and phase coupling did not show the same effect of dexamphetamine as power‐power coupling. We discuss the alterations of low‐ and high‐frequency EEG power in response to dexamphetamine within the context of disorders of dopamine regulation, in particular schizophrenia, as well as in the context of a recently hypothesized association between low‐frequency power and aspects of anhedonia. Hum Brain Mapp 37:570–588, 2016. © 2015 Wiley Periodicals, Inc.
Material specific lateralization of medial temporal lobe function: An fMRI investigation

The theory of material specific lateralization of memory function posits that left and right MTL regions are asymmetrically involved in mnemonic processing of verbal and nonverbal material respectively. Lesion and functional imaging (fMRI) studies provide robust evidence for a left MTL asymmetry in the verbal memory domain. Evidence for a right MTL/nonverbal asymmetry is not as robust. A handful of fMRI studies have investigated this issue but have generally utilised nonverbal stimuli which are amenable to semantic elaboration. This fMRI study aimed to investigate the neural correlates of recognition memory processing in 20 healthy young adults (mean age = 26 years) for verbal stimuli and nonverbal stimuli that were specifically designed to minimize verbalisation. Analyses revealed that the neural correlates of recognition memory processing for verbal and nonverbal stimuli were differentiable and asymmetrically recruited the left and right MTL respectively. The right perirhinal cortex and hippocampus were preferentially involved in successful recognition memory of items devoid of semantic information. In contrast, the left anterior hippocampus was preferentially involved in successful recognition memory of stimuli which contained semantic meaning. These results suggest that the left MTL is preferentially involved in mnemonic processing of verbal/semantic information. In contrast, the right MTL is preferentially involved in visual/non‐semantic mnemonic processing. We propose that during development, the left MTL becomes specialised for verbal mnemonic processing due to its proximity with left lateralised cortical language processing areas while visual/non‐semantic mnemonic processing gets ‘crowded out’ to become predominantly, but not completely, the domain of the right MTL. Hum Brain Mapp 37:933–941, 2016. © 2015 Wiley Periodicals, Inc.
Behavioural and neurofunctional impact of transcranial direct current stimulation on somatosensory learning

We investigated the effect of repeated delivery of anodal transcranial direct current stimulation (tDCS) on somatosensory performance and long‐term learning. Over the course of five days, tDCS was applied to the primary somatosensory cortex (S1) by means of neuronavigation employing magnetencephalography (MEG). Compared to its sham application, tDCS promoted tactile learning by reducing the two‐point discrimination threshold assessed by the grating orientation task (GOT) primarily by affecting intersessional changes in performance. These results were accompanied by alterations in the neurofunctional organization of the brain, as revealed by functional magnetic resonance imaging conducted prior to the study, at the fifth day of tDCS delivery and four weeks after the last application of tDCS. A decrease in activation at the primary site of anodal tDCS delivery in the left S1 along retention of superior tactile acuity was observed at follow‐up four weeks after the application of tDCS. Thus, we demonstrate long‐term effects that repeated tDCS imposes on somatosensory functioning. This is the first study to provide insight into the mode of operation of tDCS on the brain's response to long‐term perceptual learning, adding an important piece of evidence from the domain of non‐invasive brain stimulation to show that functional changes detectable by fMRI in primary sensory cortices participate in perceptual learning. Hum Brain Mapp 37:1277‐1295, 2016. © 2016 Wiley Periodicals, Inc.
Additional Protein Fortification Is Necessary in Extremely Low-Birth-Weight Infants Fed Human Milk

ABSTRACT In the present study, approximately one in three (49/152, 32.2%) extremely low-birth-weight infants were demonstrated to require additional protein intake to supplement the standard fortification to achieve satisfactory weight gain. This additional protein fortification also resulted in a rapid increase in length-for-age (P < 0.001) and head circumference-for-age (P = 0.02) z scores.
Early silent microstructural degeneration and atrophy of the thalamocortical network in multiple sclerosis

Recent studies on patients with clinically isolated syndrome (CIS) and multiple sclerosis (MS) demonstrated thalamic atrophy. Here we addressed the following question: Is early thalamic atrophy in patients with CIS and relapsing‐remitting MS (RRMS) mainly a direct consequence of white matter (WM) lesions—as frequently claimed—or is the atrophy stronger correlated to “silent” (nonlesional) microstructural thalamic alterations? One‐hundred and ten patients with RRMS, 12 with CIS, and 30 healthy controls were admitted to 3 T magnetic resonance imaging. Fractional anisotropy (FA) was computed from diffusion tensor imaging (DTI) to assess thalamic and WM microstructure. The relative thalamic volume (RTV) and thalamic FA were significantly reduced in patients with CIS and RRMS relative to healthy controls. Both measures were also correlated. The age, gender, WM lesion load, thalamic FA, and gray matter volume‐corrected RTV were reduced even in the absence of thalamic and extensive white matter lesions—also in patients with short disease duration (≤24 months). A voxel‐based correlation analysis revealed that the RTV reduction had a significant effect on local WM FA—in areas next to the thalamus and basal ganglia. These WM alterations could not be explained by WM lesions, which had a differing spatial distribution. Early thalamic atrophy is mainly driven by silent microstructural thalamic alterations. Lesions do not disclose the early damage of thalamocortical circuits, which seem to be much more affected in CIS and RRMS than expected. Thalamocortical damage can be detected by DTI in normal appearing brain tissue. Hum Brain Mapp 37:1866–1879, 2016. © 2016 Wiley Periodicals, Inc.
Connectivity between mPFC and PCC predicts post‐choice attitude change: The self‐referential processing hypothesis of choice justification

Prior research shows that after making a choice, decision makers shift their attitudes in a choice‐congruous direction. Although this post‐choice attitude change effect is robust, the neural mechanisms underlying it are poorly understood. Here, we tested the hypothesis that decision makers elaborate on their choice in reference to self‐knowledge to justify the choice they have made. This self‐referential processing of the choice is thought to play a pivotal role in the post‐choice attitude change. Twenty‐four young American adults made a series of choices. They also rated their attitudes toward the choice options before and after the choices. In support of the current hypothesis, we found that changes in functional connectivity between two putative self‐regions (medial prefrontal cortex and posterior cingulate cortex/precuneus]) during the post‐choice (vs. pre‐choice) rating of the chosen options predicted the post‐choice shift of the attitudes toward the chosen options. This finding is the first to suggest that cognitive integration of various self‐relevant cognitions is instrumental in fostering post‐choice attitude change. Hum Brain Mapp 37:3810–3820, 2016. © 2016 Wiley Periodicals, Inc.
Glucose modulates food‐related salience coding of midbrain neurons in humans

Although early rat studies demonstrated that administration of glucose diminishes dopaminergic midbrain activity, evidence in humans has been lacking so far. In the present functional magnetic resonance imaging study, glucose was intravenously infused in healthy human male participants while seeing images depicting low‐caloric food (LC), high‐caloric food (HC), and non‐food (NF) during a food/NF discrimination task. Analysis of brain activation focused on the ventral tegmental area (VTA) as the origin of the mesolimbic system involved in salience coding. Under unmodulated fasting baseline conditions, VTA activation was greater during HC compared with LC food cues. Subsequent to infusion of glucose, this difference in VTA activation as a function of caloric load leveled off and even reversed. In a control group not receiving glucose, VTA activation during HC relative to LC cues remained stable throughout the course of the experiment. Similar treatment‐specific patterns of brain activation were observed for the hypothalamus. The present findings show for the first time in humans that glucose infusion modulates salience coding mediated by the VTA. Hum Brain Mapp 37:4376–4384, 2016. © 2016 Wiley Periodicals, Inc.
Linezolid in the treatment of drug-resistant tuberculosis: the challenge of its narrow therapeutic index

ABSTRACT Introduction: Linezolid is an oxazolidinone with potent activity against M tuberculosis, and improves culture conversion and cure rates when added to treatment regimens for drug resistant tuberculosis. However, linezolid has a narrow therapeutic window, and the optimal dosing strategy that minimizes the substantial toxicity associated with linezolid’s prolonged use in tuberculosis treatment has not been determined, limiting the potential impact of this anti-mycobacterial agent. Areas covered: This paper aims to review and summarize the current knowledge on linezolid for the treatment of drug-resistant tuberculosis. The focus is on the pharmacokinetic-pharmacodynamic determinants of linezolid’s efficacy and toxicity in tuberculosis, and how this relates to defining an optimal dose. Mechanisms of linezolid toxicity and resistance, and the potential role of therapeutic drug monitoring are also covered. Expert commentary: Prospective pharmacokinetic-pharmacodynamic studies are required to define optimal therapeutic targets and to inform improved linezolid dosing strategies for drug-resistant tuberculosis.
Fatigue in Parkinson's disease: The contribution of cerebral metabolic changes

Fatigue is a common and disabling non‐motor symptom in Parkinson's disease associated with a feeling of overwhelming lack of energy. The aim of this study was to identify the neural substrates that may contribute to the development of fatigue in Parkinson's disease. Twenty‐three Parkinson's disease patients meeting UK Brain Bank criteria for the diagnosis of idiopathic Parkinson's disease were recruited and completed the 2‐[18F]fluoro‐2‐deoxy‐D‐glucose (FDG)‐PET scan. The metabolic activities of Parkinson's disease patients with fatigue were compared to those without fatigue using statistical parametric mapping analysis. The Parkinson's disease group exhibiting higher level of fatigue showed anti‐correlated metabolic changes in cortical regions associated with the salience (i.e., right insular region) and default (i.e., bilateral posterior cingulate cortex) networks. The metabolic abnormalities detected in these brain regions displayed a significant correlation with level of fatigue and were associated with a disruption of the functional correlations with different cortical areas. These observations suggest that fatigue in Parkinson's disease may be the expression of metabolic abnormalities and impaired functional interactions between brain regions linked to the salience network and other neural networks. Hum Brain Mapp 38:283–292, 2017. © 2016 Wiley Periodicals, Inc.