7 research outputs found
Altered Urinary Amino Acids in Children With Autism Spectrum Disorders
Autism spectrum disorders (ASD) affect 1% of children. Although there is no cure, early diagnosis and behavioral intervention can relieve the symptoms. The clinical heterogeneity of ASD has created a need for improved sensitive and specific laboratory diagnostic methods. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based analysis of the metabolome has shown great potential to uncover biomarkers for complex diseases such as ASD. Here, we used a two-step discovery–validation approach to identify potential novel metabolic biomarkers for ASD. Urine samples from 57 children with ASD and 81 matched children with typical development (TD) were analyzed by LS-MS/MS to assess differences in urinary amino acids and their metabolites (referred to as UAA indicators). A total of 63 UAA indicators were identified, of which 21 were present at significantly different levels in the urine of ASD children compared with TD children. Of these 21, the concentrations of 19 and 10 were higher and lower, respectively, in the urine of ASD children compared with TD children. Using support vector machine modeling and receiver operating characteristic curve analysis, we identified a panel of 7 UAA indicators that discriminated between the samples from ASD and TD children (lysine, 2-aminoisobutyric acid, 5-hydroxytryptamine, proline, aspartate, arginine/ornithine, and 4-hydroxyproline). Among the significantly changed pathways in ASD children were the ornithine/urea cycle (decreased levels of the excitatory amino acid aspartate [p = 2.15 × 10-10] and increased arginine/ornithine [p = 5.21 × 10-9]), tryptophan metabolism (increased levels of inhibitory 5-hydroxytryptamine p = 3.62 × 10-9), the methionine cycle (increased methionine sulfoxide [p = 1.46 × 10-10] and decreased homocysteine [p = 2.73 × 10-7]), and lysine metabolism (reduced lysine [p = 7.8 × 10-9], α-aminoadipic acid [p = 1.16 × 10-9], and 5-aminovaleric acid [p = 1.05 × 10-5]). Collectively, the data presented here identify a possible imbalance between excitatory and inhibitory amino acid metabolism in ASD children. The significantly altered UAA indicators could therefore be potential diagnostic biomarkers for ASD
CloudBrain-MRS: An Intelligent Cloud Computing Platform for in vivo Magnetic Resonance Spectroscopy Preprocessing, Quantification, and Analysis
Magnetic resonance spectroscopy (MRS) is an important clinical imaging method
for diagnosis of diseases. MRS spectrum is used to observe the signal intensity
of metabolites or further infer their concentrations. Although the magnetic
resonance vendors commonly provide basic functions of spectra plots and
metabolite quantification, the widespread clinical research of MRS is still
limited due to the lack of easy-to-use processing software or platform. To
address this issue, we have developed CloudBrain-MRS, a cloud-based online
platform that provides powerful hardware and advanced algorithms. The platform
can be accessed simply through a web browser, without the need of any program
installation on the user side. CloudBrain-MRS also integrates the classic
LCModel and advanced artificial intelligence algorithms and supports batch
preprocessing, quantification, and analysis of MRS data from different vendors.
Additionally, the platform offers useful functions: 1) Automatically
statistical analysis to find biomarkers for diseases; 2) Consistency
verification between the classic and artificial intelligence quantification
algorithms; 3) Colorful three-dimensional visualization for easy observation of
individual metabolite spectrum. Last, both healthy and mild cognitive
impairment patient data are used to demonstrate the functions of the platform.
To the best of our knowledge, this is the first cloud computing platform for in
vivo MRS with artificial intelligence processing. We have shared our cloud
platform at MRSHub, providing free access and service for two years. Please
visit https://mrshub.org/software_all/#CloudBrain-MRS or
https://csrc.xmu.edu.cn/CloudBrain.html.Comment: 11 pages, 12 figure
Physics-informed Deep Diffusion MRI Reconstruction with Synthetic Data: Break Training Data Bottleneck in Artificial Intelligence
Diffusion magnetic resonance imaging (MRI) is the only imaging modality for
non-invasive movement detection of in vivo water molecules, with significant
clinical and research applications. Diffusion MRI (DWI) acquired by multi-shot
techniques can achieve higher resolution, better signal-to-noise ratio, and
lower geometric distortion than single-shot, but suffers from inter-shot
motion-induced artifacts. These artifacts cannot be removed prospectively,
leading to the absence of artifact-free training labels. Thus, the potential of
deep learning in multi-shot DWI reconstruction remains largely untapped. To
break the training data bottleneck, here, we propose a Physics-Informed Deep
DWI reconstruction method (PIDD) to synthesize high-quality paired training
data by leveraging the physical diffusion model (magnitude synthesis) and
inter-shot motion-induced phase model (motion phase synthesis). The network is
trained only once with 100,000 synthetic samples, achieving encouraging results
on multiple realistic in vivo data reconstructions. Advantages over
conventional methods include: (a) Better motion artifact suppression and
reconstruction stability; (b) Outstanding generalization to multi-scenario
reconstructions, including multi-resolution, multi-b-value,
multi-undersampling, multi-vendor, and multi-center; (c) Excellent clinical
adaptability to patients with verifications by seven experienced doctors
(p<0.001). In conclusion, PIDD presents a novel deep learning framework by
exploiting the power of MRI physics, providing a cost-effective and explainable
way to break the data bottleneck in deep learning medical imaging.Comment: 23 pages, 16 figure
One for Multiple: Physics-informed Synthetic Data Boosts Generalizable Deep Learning for Fast MRI Reconstruction
Magnetic resonance imaging (MRI) is a principal radiological modality that
provides radiation-free, abundant, and diverse information about the whole
human body for medical diagnosis, but suffers from prolonged scan time. The
scan time can be significantly reduced through k-space undersampling but the
introduced artifacts need to be removed in image reconstruction. Although deep
learning (DL) has emerged as a powerful tool for image reconstruction in fast
MRI, its potential in multiple imaging scenarios remains largely untapped. This
is because not only collecting large-scale and diverse realistic training data
is generally costly and privacy-restricted, but also existing DL methods are
hard to handle the practically inevitable mismatch between training and target
data. Here, we present a Physics-Informed Synthetic data learning framework for
Fast MRI, called PISF, which is the first to enable generalizable DL for
multi-scenario MRI reconstruction using solely one trained model. For a 2D
image, the reconstruction is separated into many 1D basic problems and starts
with the 1D data synthesis, to facilitate generalization. We demonstrate that
training DL models on synthetic data, integrated with enhanced learning
techniques, can achieve comparable or even better in vivo MRI reconstruction
compared to models trained on a matched realistic dataset, reducing the demand
for real-world MRI data by up to 96%. Moreover, our PISF shows impressive
generalizability in multi-vendor multi-center imaging. Its excellent
adaptability to patients has been verified through 10 experienced doctors'
evaluations. PISF provides a feasible and cost-effective way to markedly boost
the widespread usage of DL in various fast MRI applications, while freeing from
the intractable ethical and practical considerations of in vivo human data
acquisitions.Comment: 22 pages, 9 figures, 1 tabl
Robust estimation of bacterial cell count from optical density
Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data
An MPI parallel DEM-IMB-LBM framework for simulating fluid-solid interaction problems
The high-resolution DEM-IMB-LBM model can accurately describe pore-scale fluid-solid interactions, but its potential for use in geotechnical engineering analysis has not been fully unleashed due to its prohibitive computational costs. To overcome this limitation, a message passing interface (MPI) parallel DEM-IMB-LBM framework is proposed aimed at enhancing computation efficiency. This framework utilises a static domain decomposition scheme, with the entire computation domain being decomposed into multiple subdomains according to predefined processors. A detailed parallel strategy is employed for both contact detection and hydrodynamic force calculation. In particular, a particle ID re-numbering scheme is proposed to handle particle transitions across sub-domain interfaces. Two benchmarks are conducted to validate the accuracy and overall performance of the proposed framework. Subsequently, the framework is applied to simulate scenarios involving multi-particle sedimentation and submarine landslides. The numerical examples effectively demonstrate the robustness and applicability of the MPI parallel DEM-IMB-LBM framework
Characterization and ohmic contact of hydrothermally synthesized vertical ZnO and Ag/ZnO nanowires
Vertically aligned ZnO nanowire arrays were synthesized by two-step hydrothermal method. ZnO seed layers were prepared on substrate by using anhydrous ethanol and zinc acetate dihydrate solution, followed by the generation of ZnO nanowire arrays by low-temperature liquid-phase hydrothermal methods. The ZnO nanowire arrays were prepared under different conditions to compare the effects of growth conditions on the morphology of ZnO nanowires, in order to explore the optimal growth conditions for ZnO nanowire arrays used in semiconductor device. The morphological changes of ZnO nanowire arrays grown under different conditions were systematically analyzed by SEM, XRD and other characterization means. The results show that the seed solution concentration, growth solution concentration, doping concentration and growth time all have certain effects on the morphology of ZnO nanowire arrays. Besides, the Ag/ZnO ohmic contact were investigated, the optimal annealing temperatures of 450 °C was obtained