In a companion paper by Cohen-Adad et al. we introduce the spine generic quantitative MRI protocol that provides valuable metrics for assessing spinal cord macrostructural and microstructural integrity. This protocol was used to acquire a single subject dataset across 19 centers and a multi-subject dataset across 42 centers (for a total of 260 participants), spanning the three main MRI manufacturers: GE, Philips and Siemens. Both datasets are publicly available via git-annex. Data were analysed using the Spinal Cord Toolbox to produce normative values as well as inter/intra-site and inter/intra-manufacturer statistics. Reproducibility for the spine generic protocol was high across sites and manufacturers, with an average inter-site coefficient of variation of less than 5% for all the metrics. Full documentation and results can be found at https://spine-generic.rtfd.io/ . The datasets and analysis pipeline will help pave the way towards accessible and reproducible quantitative MRI in the spinal cord.
- MeSH
- Adult MeSH
- Humans MeSH
- Magnetic Resonance Imaging * MeSH
- Spinal Cord diagnostic imaging ultrastructure MeSH
- Neuroimaging * MeSH
- Image Processing, Computer-Assisted MeSH
- Reproducibility of Results MeSH
- Check Tag
- Adult MeSH
- Humans MeSH
- Male MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Dataset MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Extramural MeSH
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x
- MeSH
- Bayes Theorem MeSH
- Biomedical Research * methods standards trends MeSH
- Pharmaceutical Research methods trends MeSH
- Clinical Studies as Topic MeSH
- Humans MeSH
- Probability MeSH
- Reproducibility of Results * MeSH
- Statistics as Topic MeSH
- Translational Research, Biomedical methods trends MeSH
- Validation Studies as Topic MeSH
- Scientific Misconduct ethics psychology legislation & jurisprudence MeSH
- Outcome and Process Assessment, Health Care * methods trends utilization MeSH
- Check Tag
- Humans MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
BACKGROUND: Recent advances in data-driven computational approaches have been helpful in devising tools to objectively diagnose psychiatric disorders. However, current machine learning studies limited to small homogeneous samples, different methodologies, and different imaging collection protocols, limit the ability to directly compare and generalize their results. Here we aimed to classify individuals with PTSD versus controls and assess the generalizability using a large heterogeneous brain datasets from the ENIGMA-PGC PTSD Working group. METHODS: We analyzed brain MRI data from 3,477 structural-MRI; 2,495 resting state-fMRI; and 1,952 diffusion-MRI. First, we identified the brain features that best distinguish individuals with PTSD from controls using traditional machine learning methods. Second, we assessed the utility of the denoising variational autoencoder (DVAE) and evaluated its classification performance. Third, we assessed the generalizability and reproducibility of both models using leave-one-site-out cross-validation procedure for each modality. RESULTS: We found lower performance in classifying PTSD vs. controls with data from over 20 sites (60 % test AUC for s-MRI, 59 % for rs-fMRI and 56 % for d-MRI), as compared to other studies run on single-site data. The performance increased when classifying PTSD from HC without trauma history in each modality (75 % AUC). The classification performance remained intact when applying the DVAE framework, which reduced the number of features. Finally, we found that the DVAE framework achieved better generalization to unseen datasets compared with the traditional machine learning frameworks, albeit performance was slightly above chance. CONCLUSION: These results have the potential to provide a baseline classification performance for PTSD when using large scale neuroimaging datasets. Our findings show that the control group used can heavily affect classification performance. The DVAE framework provided better generalizability for the multi-site data. This may be more significant in clinical practice since the neuroimaging-based diagnostic DVAE classification models are much less site-specific, rendering them more generalizable.
We explored the effect of repeated visual stimulation on motion-onset visual evoked potentials (M-VEPs) during 25 min recording sessions in 10 subjects. The aim of the experiment was to determine influence of global motion adaptation (without motion-aftereffect) on intra-individual variability of M-VEPs and to suggest an optimal recording design for clinical examination. In addition to well described middle-time sensory adaptation, we also observed a long-time effect on motion specific N2 peak (155 ms). The N2 peak exhibited a strong relationship between its latency and inter-peak amplitude to the duration of recording in occipito-parietal derivations. In addition to the middle-term adaptation, N2 peak latency was prolonged by 10 ms and amplitude was attenuated by 30% with respect to the start of the experiment. An exponential model was employed to describe the dependency. The model can be used to reduce intra-individual variability during examination. Observed resemblance between the measured electrophysiological values and already published metabolic changes (glucose and oxygen utilization) during brain processing of visual information is discussed.
- MeSH
- Adult MeSH
- Financing, Organized MeSH
- Adaptation, Physiological MeSH
- Habituation, Psychophysiologic physiology MeSH
- Data Interpretation, Statistical MeSH
- Middle Aged MeSH
- Humans MeSH
- Least-Squares Analysis MeSH
- Reaction Time MeSH
- Reproducibility of Results MeSH
- Photic Stimulation MeSH
- Fatigue physiopathology MeSH
- Motion Perception physiology MeSH
- Evoked Potentials, Visual MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Female MeSH
BACKGROUND: Proton magnetic resonance spectroscopy is a non-invasive measurement technique which provides information about concentrations of up to 20 metabolites participating in intracellular biochemical processes. In order to obtain any metabolic information from measured spectra a processing should be done in specialized software, like jMRUI. The processing is interactive and complex and often requires many trials before obtaining a correct result. This paper proposes a jMRUI enhancement for efficient and unambiguous history tracking and file identification. RESULTS: A database storing all processing steps, parameters and files used in processing was developed for jMRUI. The solution was developed in Java, authors used a SQL database for robust storage of parameters and SHA-256 hash code for unambiguous file identification. The developed system was integrated directly in jMRUI and it will be publically available. A graphical user interface was implemented in order to make the user experience more comfortable. The database operation is invisible from the point of view of the common user, all tracking operations are performed in the background. CONCLUSIONS: The implemented jMRUI database is a tool that can significantly help the user to track the processing history performed on data in jMRUI. The created tool is oriented to be user-friendly, robust and easy to use. The database GUI allows the user to browse the whole processing history of a selected file and learn e.g. what processing lead to the results, where the original data are stored, to obtain the list of all processing actions performed on spectra.
Rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) is essential for proper initial antibiotic therapy and timely set up of hygienic measures. Recently, detection of MRSA using MALDI-TOF mass spectrometer mediated by the peptide-phenol-soluble modulin (PSM-mec)-linked to the class A mec gene complex present in SCCmec cassettes types II, III, and VIII of MRSA strains, has been commercially available. We present here a multicentre study on MALDI-TOF MS detection of MRSA evincing a poor repeatability and reproducibility of the assay. The sensitivity of the assay varies between 50 and 90% in strains carrying psmMEC and psmδ genes encoding for PSM-mec and δ-toxin (a member of the PSM peptide family), respectively. No false positive results were found. The very major error calculation was 30% and the major error achieved 0%. Interlaboratory repeatability varies between 0 and 100%. No significant difference was observed with the use of different cultivation media. Our data showed a poor sensitivity of the method excluding it from the use in routine laboratory testing.
- MeSH
- Bacterial Toxins genetics MeSH
- Diagnostic Errors MeSH
- Molecular Diagnostic Techniques * MeSH
- Diagnostic Tests, Routine MeSH
- Humans MeSH
- Methicillin-Resistant Staphylococcus aureus genetics isolation & purification MeSH
- Reproducibility of Results MeSH
- Sensitivity and Specificity MeSH
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization * MeSH
- Staphylococcal Infections diagnosis microbiology MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Multicenter Study MeSH
Intact (whole) cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) is an established method for biotyping in clinical microbiology as well as for revealing phenotypic shifts in cultured eukaryotic cells. Intact cell MALDI-TOF MS has recently been introduced as a quality control tool for long-term cultures of pluripotent stem cells. Despite the potential this method holds for revealing minute changes in cells, there is still a need for improving the ionization efficiency or peak reproducibility. Here we report for the first time that supplementation by fine particles of black phosphorus to the standard MALDI matrices, such as sinapinic and α-cyano-4-hydroxycinnamic acids enhance intensities of mass spectra of particular amino acids and peptides, presumably by interactions with aromatic groups within the molecules. In addition, the particles of black phosphorus induce the formation of small and regularly dispersed crystals of sinapinic acid and α-cyano-4-hydroxycinnamic acid with the analyte on a steel MALDI target plate. Patterns of mass spectra recorded from intact cells using black phosphorus-enriched matrix were more reproducible and contained peaks of higher intensities when compared to matrix without black phosphorus supplementation. In summary, enrichment of common organic matrices by black phosphorus can improve discrimination data analysis by enhancing peak intensity and reproducibility of mass spectra acquired from intact cells.
- MeSH
- Amino Acids analysis chemistry MeSH
- Cell Culture Techniques methods MeSH
- Cell Line MeSH
- Phosphorus chemistry MeSH
- Humans MeSH
- Human Embryonic Stem Cells MeSH
- Peptides analysis chemistry MeSH
- Reproducibility of Results MeSH
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization methods standards MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The distribution of data presented in many electrophysiological studies is presumed to be normal without any convincing evidence. To test this presumption, the cell membrane capacitance and magnitude of inward rectifier potassium currents were recorded by the whole-cell patch clamp technique in rat atrial myocytes. Statistical analysis of the data showed that these variables were not distributed normally. Instead, a positively skewed distribution appeared to be a better approximation of the real data distribution. Consequently, the arithmetic mean, used inappropriately in such data, may substantially overestimate the true mean value characterizing the central tendency of the data. Moreover, a large standard deviation describing the variance of positively skewed data allowed 95% confidence interval to include unrealistic negative values. We therefore conclude that the normality of the electrophysiological data should be tested in every experiment and, if rejected, the positively skewed data should be more accurately characterized by the median and interpercentile range or, if justified (namely in the case of log-normal and gamma data distribution), by the geometric mean and the geometric standard deviation.
- MeSH
- Algorithms MeSH
- Cell Membrane pathology physiology MeSH
- Electric Capacitance MeSH
- Electrodes MeSH
- Electrophysiology methods MeSH
- Data Interpretation, Statistical MeSH
- Rats MeSH
- Membrane Potentials MeSH
- Normal Distribution * MeSH
- Rats, Wistar MeSH
- Reproducibility of Results MeSH
- Heart Atria pathology MeSH
- Muscle Cells physiology MeSH
- Models, Theoretical MeSH
- Animals MeSH
- Check Tag
- Rats MeSH
- Male MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The diagnosis of Sleep disorders, highly prevalent in the western countries, typically involves sophisticated procedures and equipments that are intrusive to the patient. Wrist actigraphy, on the contrary, is a non-invasive and low cost solution to gather data which can provide valuable information in the diagnosis of these disorders. The acquired data may be used to infer the Sleep/Wakefulness (SW) state of the patient during the circadian cycle and detect abnormal behavioral patterns associated with these disorders. In this paper a classifier based on Autoregressive (AR) model coefficients, among other features, is proposed to estimate the SW state. The real data, acquired from 23 healthy subjects during fourteen days each, was segmented by expert medical personal with the help of complementary information such as light intensity and Sleep e-Diary information. Monte Carlo tests with a Leave-One-Out Cross Validation (LOOCV) strategy were used to assess the performance of the classifier which achieves an accuracy of 96%.
- MeSH
- Actigraphy methods MeSH
- Automation MeSH
- Electronic Data Processing methods MeSH
- Bayes Theorem MeSH
- Wakefulness physiology MeSH
- Humans MeSH
- Sleep Wake Disorders diagnosis physiopathology MeSH
- Reproducibility of Results MeSH
- Sleep physiology MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Úvod: Optická koherentní tomografie (OCT) je neinvazivní zobrazovací metoda používaná pro vyšetření makuly a peripapilární vrstvy nervových vláken sítnice (RNFL), jejíž výsledek může být ovlivněn kvalitou snímaného obrazu. Cílem práce bylo posoudit vliv nekomplikované extrakce katarakty na měření tloušťky makuly a RNFL pomocí OCT a zjistit reprodukovatelnost této metody před a po operaci katarakty v souboru zdravých osob. Rovněž byl hodnocen vliv implantované nitrooční čočky (IOL bez žlutého filtru / se žlutým filtrem) na reprodukovatelnost OCT vyšetření. Metodika: Do studovaného souboru bylo zařazeno 51 očí 51 pacientů, u kterých byla provedena operace katarakty standardní technikou fakoemulzifikace s implantací zadněkomorové IOL do čočkového pouzdra. Jeden týden před operací a pooperačně za jeden a šest měsíců byla změřena tloušťka makuly a RNFL pomocí SD-OCT (spectral domain) (Optovue, model RT 100). Pro posouzení reprodukovatelnosti byly při každé návštěvě provedeny vždy tři OCT skeny. Získaná data byla statisticky zpracována. Výsledky: Analýza změn tloušťky makuly a RNFL ukázala nárůst tloušťky sítnice ve všech sledovaných oblastech, s maximem jeden měsíc po operaci a regresí ztluštění šest měsíců po operaci. Reprodukovatelnost OCT vyšetření se po operaci katarakty významně zlepšila, přesto již před operací byly hodnoty koeficientu rozptylu nízké a tedy přesnost metody vysoká. Vliv typu implantované nitrooční čočky na reprodukovatelnost OCT vyšetření nebyl prokázán. Závěr: Přítomnost katarakty ovlivňuje měření tloušťky makuly a vrstvy nervových vláken pomocí OCT. Po operaci katarakty se reprodukovatelnost metody významně zlepšuje. Je pravděpodobné, že nárůst tloušťky makuly a vrstvy nervových vláken po odstranění zkalené čočky je částečně způsoben zlepšením kvality snímaného obrazu a větší přesností OCT vyšetření. Klíčová slova: optická koherentní tomografie, glaukom, katarakta, tloušťka sítnice, tloušťka vrstvy nervových vláken
Introduction: Optical coherence tomography (OCT) is a non-invasive imaging technique used for the examination of the macula and peripapillary retinal nerve fibre layer (RNFL), the result of which may be affected by the quality of the scanned image. The aim of our study was to assess the influence of uncomplicated cataract extraction on the measurement of macular and RNFL thickness with OCT and to determine the reproducibility of this method before and after cataract surgery in a group of healthy people. We also evaluated the effect of different intraocular lenses (IOL) (with/without yellow filter) on the reproducibility of the OCT examination. Methods: The study group included 51 eyes of 51 patients who underwent cataract surgery with posterior chamber IOL implantation. Macular and RNFL thickness were measured with spectral domain OCT (Optovue, Model RT 100) one week before surgery, and postoperatively after one and six months. Three OCT scans were performed at each visit to assess the reproducibility of the measurement. Data were statistically processed. Results: Analysis of the changes in macular and RNFL thickness showed a significant increase in retinal thickness, with the maximum increase one month after surgery, and regression of this thickening six months after surgery. Reproducibility of OCT examination improved significantly after cataract surgery, even though the preoperative values were of low coefficient of variance and therefore of high accuracy. No difference was found in the use of different intraocular lenses on the reproducibility of the OCT examination. Conclusion: The presence of cataract affects the OCT measurement of macular and RNFL thickness. The reproducibility of the method significantly improves after cataract surgery. It is likely that the increase in macular and RNFL thickness after cataract removal is partly due to improvement in the quality of the scanned image and thus to the greater accuracy of the OCT examination. Key words: optical coherence tomography, glaucoma, cataract, macular thickness, retinal nerve fibre layer thickness
- MeSH
- Cataract Extraction * statistics & numerical data utilization MeSH
- Cataract therapy MeSH
- Middle Aged MeSH
- Humans MeSH
- Nerve Fibers physiology MeSH
- Ophthalmologic Surgical Procedures MeSH
- Tomography, Optical Coherence * statistics & numerical data utilization MeSH
- Reproducibility of Results MeSH
- Retinal Ganglion Cells physiology MeSH
- Aged, 80 and over MeSH
- Aged MeSH
- Check Tag
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Aged, 80 and over MeSH
- Aged MeSH
- Female MeSH
