Evaluation of atlas-based segmentation of hippocampi in healthy humans

Introduction and aim: Region of interest (ROI)-based functional magnetic resonance imaging (fMRI) data analysis relies on extracting signals from a specific area which is presumed to be involved in the brain activity being studied. The hippocampus is of interest in many functional connectivity studies for example in epilepsy as it plays an important role in epileptogenesis. In this context, ROI may be defined using different techniques. Our study aims at evaluating the spatial correspondence of hippocampal ROIs obtained using three brain atlases with hippocampal ROI obtained using an automatic segmentation algorithm dedicated to the hippocampus. Material and methods: High-resolution volumetric T1-weighted MR images of 18 healthy volunteers (five females) were acquired on a 3T scanner. Individual ROIs for both hippocampi of each subject were segmented from the MR images using an automatic hippocampus and amygdala segmentation software called SACHA providing the gold standard ROI for comparison with the atlas-derived results. For each subject, hippocampal ROIs were also obtained using three brain atlases: PickAtlas available as a commonly used software toolbox; automated anatomical labeling (AAL) atlas included as a subset of ROI into PickAtlas toolbox and a frequency-based brain atlas by Hammers et al. The levels of agreement between the SACHA results and those obtained using the atlases were assessed based on quantitative indices measuring volume differences and spatial overlap. The comparison was performed in standard Montreal Neurological Institute space, the registration being obtained with SPM5 (http://www.fil.ion.ucl.ac.uk/spm/). Results: The mean volumetric error across all subjects was 73% for hippocampal ROIs derived from AAL atlas; 20% in case of ROIs derived from the Hammers atlas and 107% for ROIs derived from PickAtlas. The mean false-positive and false-negative classification rates were 60% and 10% respectively for the AAL atlas; 16% and 32% for the Hammers atlas and 6% and 72% for the PickAtlas. Conclusion: Though atlas-based ROI definition may be convenient, the resulting ROIs may be poor representations of the hippocampus in some studies critical to under- or oversampling. Performance of the AAL atlas was inferior to that of the Hammers atlas. Hippocampal ROIs derived from PickAtlas are highly significantly smaller, and this results in the worst performance out of three atlases. It is advisable that the defined ROIs should be verified with knowledge of neuroanatomy before using it for further data analysis

Drug related problems and pharmacist interventions in a geriatric unit employing electronic prescribing

Background Computerised physician order entry (CPOE) and the integration of a pharmacist in clinical wards have been shown to prevent drug related problems (DRPs). Objectives The primary objective was to make an inventory of the DRPs and resident pharmacist on-ward interventions (PIs) identified in a geriatric acute care unit using CPOE system. The secondary objective was to evaluate the physicians\u27 acceptance of the proposed interventions. Setting A 26-bed geriatric ward of a 1,300-bed teaching hospital. Method A 6-month descriptive study with prescription analysis and recommendations to physicians by a resident pharmacist during five half days a week. Main outcome measures Patients\u27 characteristics, number of prescribed drugs per patient, nature and frequency of DRPs and PIs, physicians\u27 acceptance and drugs questioned. Results Resident pharmacist reviewed 311 patients and identified 241 DRPs. One hundred and fifty-two patients (49 %) had at least one DRP (mean +/- A SD age 87 +/- A 6 years, mean +/- A SD number of prescribed drugs 10.7 +/- A 3.4). Most frequent DRPs were: untreated indication (n = 58, 24.1 %), dose too high (n = 46, 19.1 %), improper administration (n = 31, 12.9 %) and drug interactions (n = 23, 9.5 %). The rate of physicians\u27 acceptance was 90.0 % (7.5 % refusals, 2.5 % not assessable). DRPs related to CPOE system misuse (n = 35, 14.5 %) appeared as a worrying phenomenon (e.g., errors in selecting dosage or unit, or duplication of therapy). Conclusion A resident pharmacist detected various DRPs. Most PIs were accepted. DRPs related to the misuse of the CPOE system appeared potentially dangerous and need particular attention by healthcare professionals. The description of the DRPs is an essential step for implementation of targeted clinical pharmacy services in order to optimize pharmacists\u27 job time

Metabolomics and Lipidomics Profiling of a Combined Mitochondrial Plus Endoplasmic Reticulum Fraction of Human Fibroblasts: A Robust Tool for Clinical Studies

Mitochondria and endoplasmic reticulum (ER) are physically and functionally connected. This close interaction, via mitochondria-associated membranes, is increasingly explored and supports the importance of studying these two organelles as a whole. Metabolomics and lipidomics are powerful approaches for the exploration of metabolic pathways that may be useful to provide deeper information on these organelles\u27 functions, dysfunctions, and interactions. We developed a quick and simple experimental procedure for the purification of a mitochondria-ER fraction from human fibroblasts. We applied combined metabolomics and lipidomics analyses by mass spectrometry with excellent reproducibility. Seventy-two metabolites and 418 complex lipids were detected with a mean coefficient of variation around 12%, among which many were specific to the mitochondrial metabolism. Thus this strategy based on robust mitochondria-ER extraction and "omics" combination will be useful for investigating the pathophysiology of complex diseases

Nouméa: a new multi-mission calibration and validation site for past and future altimetry missions?

Today, monitoring the evolution of sea level in coastal areas is of importance, since almost 11 % of the world's population lives in low-lying areas. Reducing uncertainties in sea level estimates requires a better understanding of both altimetry measurements and local sea level dynamics. In New Caledonia, the Nouméa lagoon is an example of this challenge, as altimetry, coastal tide gauge, and vertical land motions from global navigation satellite systems (GNSSs) do not provide consistent information. The GEOCEAN-NC 2019 field campaign addresses this issue with deployments of in situ instruments in the lagoon (GNSS buoy, pressure gauge, etc.), with a particular focus on the crossover of one Jason-series track and two Sentinel-3A missions tracks. In this study, we propose a method to virtually transfer the Nouméa tide gauge at the altimetry crossover point, using in situ data from the field campaign. Following the philosophy of calibration and validation (Cal/Val) studies, we derive absolute altimeter bias time series over the entire Jason and Sentinel-3A periods. Overall, our estimated altimeter mean biases are slightly larger by 1–2 cm compared to Corsica and Bass Strait results, with inter-mission biases in line with those of Bass Strait site. Uncertainties still remain regarding the determination of our vertical datum, only constrained by the three days of the GNSS buoy deployment. With our method, we are able to re-analyse about 20 years of altimetry observations and derive a linear trend of −0.2 ± 0.1 mm yr−1 over the bias time series. Compared to previous studies, we do not find any significant uplift in the area, which is more consistent with the observations of inland permanent GNSS stations. These results support the idea of developing Cal/Val activities in the lagoon, which is already the subject of several experiments for the scientific calibration phase of the SWOT wide-swath altimetry mission.</p

Metabo-lipidomics of Fibroblasts and Mitochondrial-Endoplasmic Reticulum Extracts from ALS Patients Shows Alterations in Purine, Pyrimidine, Energetic, and Phospholipid Metabolisms

Amyotrophic lateral sclerosis (ALS) is characterized by a wide metabolic remodeling, as shown by recent metabolomics and lipidomics studies performed in samples from patient cohorts and experimental animal models. Here, we explored the metabolome and lipidome of fibroblasts from sporadic ALS patients (n = 13) comparatively to age- and sex-matched controls (n = 11), and the subcellular fraction containing the mitochondria and endoplasmic reticulum (mito-ER), given that mitochondrial dysfunctions and ER stress are important features of ALS patho-mechanisms. We also assessed the mitochondrial oxidative respiration and the mitochondrial genomic (mtDNA) sequence, although without yielding significant differences. Compared to controls, ALS fibroblasts did not exhibit a mitochondrial respiration defect nor an increased proportion of mitochondrial DNA mutations. In addition, non-targeted metabolomics and lipidomics analyses identified 124 and 127 metabolites, and 328 and 220 lipids in whole cells and the mito-ER fractions, respectively, along with partial least-squares-discriminant analysis (PLS-DA) models being systematically highly predictive of the disease. The most discriminant metabolomic features were the alteration of purine, pyrimidine, and energetic metabolisms, suggestive of oxidative stress and of pro-inflammatory status. The most important lipidomic feature in the mito-ER fraction was the disturbance of phosphatidylcholine PC (36:4p) levels, which we had previously reported in the cerebrospinal fluid of ALS patients and in the brain from an ALS mouse model. Thus, our results reveal that fibroblasts from sporadic ALS patients share common metabolic remodeling, consistent with other metabolic studies performed in ALS, opening perspectives for further exploration in this cellular model in ALS

Lipidomics Reveals Triacylglycerol Accumulation Due to Impaired Fatty Acid Flux in Opa1-Disrupted Fibroblasts

OPA1 is a dynamin GTPase implicated in mitochondrial membrane fusion. Despite its involvement in lipid remodeling, the function of OPA1 has never been analyzed by whole-cell lipidomics. We used a nontargeted, reversed-phase lipidomics approach, validated for cell cultures, to investigate OPA1-inactivated mouse embryonic fibroblasts ( Opa1 MEFs). This led to the identification of a wide range of 14 different lipid subclasses comprising 212 accurately detected lipids. Multivariate and univariate statistical analyses were then carried out to assess the differences between the Opa1 and Opa1 genotypes. Of the 212 lipids identified, 69 were found to discriminate between Opa1 MEFs and Opa1 MEFs. Among these lipids, 34 were triglycerides, all of which were at higher levels in Opa1 MEFs with fold changes ranging from 3.60 to 17.93. Cell imaging with labeled fatty acids revealed a sharp alteration of the fatty acid flux with a reduced mitochondrial uptake. The other 35 discriminating lipids included phosphatidylcholines, lysophosphatidylcholines, phosphatidylethanolamine, and sphingomyelins, mainly involved in membrane remodeling, and ceramides, gangliosides, and phosphatidylinositols, mainly involved in apoptotic cell signaling. Our results show that the inactivation of OPA1 severely affects the mitochondrial uptake of fatty acids and lipids through membrane remodeling and apoptotic cell signaling

Warburg-like effect is a hallmark of complex I assembly defects

Due to its pivotal role in NADH oxidation and ATP synthesis, mitochondrial complex I (CI) emerged as a crucial regulator of cellular metabolism. A functional CI relies on the sequential assembly of nuclear- and mtDNA-encoded subunits; however, whether CI assembly status is involved in the metabolic adaptations in CI deficiency still remains largely unknown. Here, we investigated the relationship between CI functions, its structure and the cellular metabolism in 29 patient fibroblasts representative of most CI mitochondrial diseases. Our results show that, contrary to the generally accepted view, a complex I deficiency does not necessarily lead to a glycolytic switch, i.e. the so-called Warburg effect, but that this particular metabolic adaptation is a feature of CI assembly defect. By contrast, a CI functional defect without disassembly induces a higher catabolism to sustain the oxidative metabolism. Mechanistically, we demonstrate that reactive oxygen species overproduction by CI assembly intermediates and subsequent AMPK-dependent Pyruvate Dehydrogenase inactivation are key players of this metabolic reprogramming. Thus, this study provides a two-way-model of metabolic responses to CI deficiencies that are central not only in defining therapeutic strategies for mitochondrial diseases, but also in all pathophysiological conditions involving a CI deficiency

Automatic ROI Selection in Structural Brain MRI Using SOM 3D Projection

This paper presents a method for selecting Regions of Interest (ROI) in brain Magnetic Resonance Imaging (MRI) for diagnostic purposes, using statistical learning and vector quantization techniques. The proposed method models the distribution of GM and WM tissues grouping the voxels belonging to each tissue in ROIs associated to a specific neurological disorder. Tissue distribution of normal and abnormal images is modelled by a Self-Organizing map (SOM), generating a set of representative prototypes, and the receptive field (RF) of each SOM prototype defines a ROI. Moreover, the proposed method computes the relative importance of each ROI by means of its discriminative power. The devised method has been assessed using 818 images from the Alzheimer's disease Neuroimaging Initiative (ADNI) which were previously segmented through Statistical Parametric Mapping (SPM). The proposed algorithm was used over these images to parcel ROIs associated to the Alzheimer's Disease (AD). Additionally, this method can be used to extract a reduced set of discriminative features for classification, since it compresses discriminative information contained in the brain. Voxels marked by ROIs which were computed using the proposed method, yield classification results up to 90% of accuracy for controls (CN) and Alzheimer's disease (AD) patients, and 84% of accuracy for Mild Cognitive Impairment (MCI) and AD patients.This work was partly supported by the MICINN under the TEC2012-34306 project and the Consejería de Innovación, Ciencia y Empresa (Junta de Andalucía, Spain) under the Excellence Projects P09-TIC-4530 and P11-TIC-7103. Data collection and sharing for this project was funded by the Alzheimer's Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904) and DOD ADNI (Department of Defense award number W81XWH-12-2-0012). ADNI is funded by the National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following: Alzheimer's Association; Alzheimer's Drug Discovery Foundation; BioClinica, Inc.; Biogen Idec Inc.; Bristol-Myers Squibb Company; Eisai Inc.; Elan Pharmaceuticals, Inc.; Eli Lilly and Company; F. Hoffmann-La Roche Ltd and its affiliated company Genentech, Inc.; GE Healthcare; Innogenetics, N.V.; IXICO Ltd.; Janssen Alzheimer Immunotherapy Research & Development, LLC.; Johnson & Johnson Pharmaceutical Research & Development LLC.; Medpace, Inc.; Merck & Co., Inc.; Meso Scale Diagnostics, LLC.; NeuroRxResearch; Novartis Pharmaceuticals Corporation; Pfizer Inc.; Piramal Imaging; Servier; Synarc Inc.; and Takeda Pharmaceutical Company. The Canadian Institutes of Health Research is providing funds to support ADNI clinical sites in Canada. Private sector contributions are facilitated by the Foundation for the National Institutes of Health (www.fnih.org). The grantee organization is the Northern California Institute for Research and Education, and the study is coordinated by the Alzheimer's Disease Cooperative Study at the University of California, San Diego. ADNI data are disseminated by the Laboratory for Neuro Imaging at the University of Southern California

Anopheles Gambiae PRS1 Modulates Plasmodium Development at Both Midgut and Salivary Gland Steps

Background: Invasion of the mosquito salivary glands by Plasmodium is a critical step for malaria transmission. From a SAGE analysis, we previously identified several genes whose expression in salivary glands was regulated coincident with sporozoite invasion of salivary glands. To get insights into the consequences of these salivary gland responses, here we have studied one of the genes, PRS1 (Plasmodium responsive salivary 1), whose expression was upregulated in infected glands, using immunolocalization and functional inactivation approaches. Methodology/Principal Findings: PRS1 belongs to a novel insect superfamily of genes encoding proteins with DM9 repeat motifs of uncharacterized function. We show that PRS1 is induced in response to Plasmodium, not only in the salivary glands but also in the midgut, the other epithelial barrier that Plasmodium has to cross to develop in the mosquito. Furthermore, this induction is observed using either the rodent parasite Plasmodium berghei or the human pathogen Plasmodium falciparum. In the midgut, PRS1 overexpression is associated with a relocalization of the protein at the periphery of invaded cells. We also find that sporozoite invasion of salivary gland cells occurs sequentially and induces intra-cellular modifications that include an increase in PRS1 expression and a relocalization of the corresponding protein into vesicle-like structures. Importantly, PRS1 knockdown during the onset of midgut and salivary gland invasion demonstrates that PRS1 acts as an agonist for the development of both parasite species in the two epithelia, highlighting shared vector/parasite interactions in both tissues. Conclusions/Significance: While providing insights into potential functions of DM9 proteins, our results reveal that PRS1 likely contributes to fundamental interactions between Plasmodium and mosquito epithelia, which do not depend on the specific Anopheles/P. falciparum coevolutionary history

Mitochondrial complex I defect resulting from exercise-induced lower limb ischemia in patients with peripheral arterial disease

This study aims to compare the structural and mitochondrial alterations between muscle segments affected by exercise-induced ischemia and segments of the same muscle without ischemia, in the same subject. In a prospective analysis, 34 patients presenting either peripheral arterial disease or chronic coronary syndrome without any evidence of peripheral arterial disease were eligible for inclusion based on findings indicating a need for either a femoro-popliteal bypass or a saphenous harvesting for coronary bypass. Before surgery, we assessed the level of exercise-induced ischemia in proximal and distal sections of the thigh by the measurement of transcutaneous oxygen pressure during an exercise treadmill test. Distal and proximal biopsies of the sartorius muscle were procured during vascular surgical procedures to assess mitochondrial function and morphometric parameters of the sartorius myofibers. Comparisons were made between the distal and proximal biopsies, with respect to these parameters. Thirteen of the study patients that initially presented with peripheral arterial disease had evidence of an isolated distal thigh exercise-induced ischemia, associated with a 35% decrease in the mitochondrial complex I enzymatic activity in the distal muscle biopsy. This defect was also associated with a decreased expression of the manganese superoxide dismutase enzyme and with alterations of the shapes of the myofibers. No functional or structural alterations were observed in the patients with coronary syndrome. We validated a specific model ischemia in peripheral arterial disease characterized by muscular alterations. This "Distal-Proximal-Sartorius Model" would be promising to explore the physiopathological consequences specific to chronic ischemia. NEW &amp; NOTEWORTHY We compared proximal versus distal biopsies of the sartorius muscle in patients with superficial femoral artery stenosis or occlusion and proof of, distal only, regional blood flow impairment with exercise oximetry. We identified a decrease in the mitochondrial complex I enzymatic activity and antioxidant system impairment at the distal level only. We validate a model to explore the physiopathological consequences of chronic muscle ischemia