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IScience Sep 2020Autophagy is an intracellular degradation process that is mediated by formation of autophagosomes. Autophagosome formation involves dynamic morphological changes; a...
Autophagy is an intracellular degradation process that is mediated by formation of autophagosomes. Autophagosome formation involves dynamic morphological changes; a disk-shaped membrane cisterna grows, bends to become a cup-shaped structure, and finally develops into a spherical autophagosome. We have constructed a theoretical model that integrates the membrane morphological change and entropic partitioning of putative curvature generators, which we have used to investigate the autophagosome formation process quantitatively. We show that the membrane curvature and the distribution of the curvature generators stabilize disk- and cup-shaped intermediate structures during autophagosome formation, which is quantitatively consistent with observations. These results suggest that various autophagy proteins with membrane curvature-sensing properties control morphological change by stabilizing these intermediate structures. Our model provides a framework for understanding autophagosome formation.
PubMed: 32891055
DOI: 10.1016/j.isci.2020.101466 -
LIPIcs : Leibniz International... Sep 2023A colored de Bruijn graph (also called a set of k-mer sets), is a set of k-mers with every k-mer assigned a set of colors. Colored de Bruijn graphs are used in a variety...
A colored de Bruijn graph (also called a set of k-mer sets), is a set of k-mers with every k-mer assigned a set of colors. Colored de Bruijn graphs are used in a variety of applications, including variant calling, genome assembly, and database search. However, their size has posed a scalability challenge to algorithm developers and users. There have been numerous indexing data structures proposed that allow to store the graph compactly while supporting fast query operations. However, disk compression algorithms, which do not need to support queries on the compressed data and can thus be more space-efficient, have received little attention. The dearth of specialized compression tools has been a detriment to tool developers, tool users, and reproducibility efforts. In this paper, we develop a new tool that compresses colored de Bruijn graphs to disk, building on previous ideas for compression of k-mer sets and indexing colored de Bruijn graphs. We test our tool, called ESS-color, on various datasets, including both sequencing data and whole genomes. ESS-color achieves better compression than all evaluated tools and all datasets, with no other tool able to consistently achieve less than 44% space overhead.
PubMed: 38712341
DOI: 10.4230/LIPIcs.WABI.2023.17 -
Current Microbiology May 2024Antimicrobial susceptibility testing (AST) by disk diffusion provides an accurate image of bacterial growth, enabling the detection of culture purity, heterogeneous...
Antimicrobial susceptibility testing (AST) by disk diffusion provides an accurate image of bacterial growth, enabling the detection of culture purity, heterogeneous growth, and antibiotic interactions. However, this manual method is time-consuming and visual interpretation is prone to errors. To overcome these disadvantages, the Radian® In-Line Carousel (Copan, Brescia, Italy) was launched, which is a WASPLab® module dedicated to full automation of (pre)-analytical steps as well as interpretation of disk diffusion AST. However, until now, no evaluation of Radian® against manual disk diffusion has been performed. We assessed the categorical agreement (CA) between standardized disk diffusion (reference method) and Radian® using EUCAST 2021 breakpoints. We tested 135 non-duplicate strains, selected from the National EUCAST challenge panel, clinical strains, and external quality controls. The strains included Enterobacterales (n = 63), Enterococcus faecalis (n = 3), Enterococcus faecium (n = 10), Pseudomonas aeruginosa (n = 16), Staphylococcus aureus (n = 19), coagulase-negative staphylococci (n = 4), and Streptococcus spp. (n = 20). Furthermore, we explored antibiotic disk thermolability in the WASP Radian® carousel by testing 10 ATCC® strains up to 7 days. The observed CA was 95.3%, 96.3%, 93.8%, 97.3% and 98.0% for Enterobacterales, Enterococcus spp., P. aeruginosa, Staphylococcus spp. and Streptococcus spp., respectively, resulting in an acceptable overall CA for all groups. (Very) major error rates were ≤ 5% for all antibiotics. Antibiotic disk thermostability was confirmed up to 4 days in the WASP Radian® In-Line Carousel. The Radian® In-Line Carousel provides a fully automated solution for accurate disk diffusion AST, reducing workload and improving standardization and traceability. In addition, our study demonstrated the thermostability of antibiotic disks up to 4 days in the WASP Radian® In-Line Carousel.
Topics: Anti-Bacterial Agents; Disk Diffusion Antimicrobial Tests; Bacteria; Humans; Microbial Sensitivity Tests; Automation, Laboratory
PubMed: 38816509
DOI: 10.1007/s00284-024-03710-z -
Micromachines Dec 2021Swarming robotic systems, which stem from insect swarms in nature, exhibit a high level of environmental adaptability and enhanced tasking capabilities for targeted...
Swarming robotic systems, which stem from insect swarms in nature, exhibit a high level of environmental adaptability and enhanced tasking capabilities for targeted delivery and micromanipulation. Here, we present a strategy that reconfigures paramagnetic nanoparticles into microswarms energized by a sawtooth magnetic field. A rotary-stepping magnetic-chain mechanism is proposed to address the forming principle of disk-like swarms. Based on programming the sawtooth field, the microswarm can perform reversible transformations between a disk, an ellipse and a ribbon, as well as splitting and merging. In addition, the swarms can be steered in any direction with excellent maneuverability and a high level of pattern stability. Under accurate manipulation of a magnetic microswarm, multiple microparts with complicated shapes were successfully combined into a complete assembly. This reconfigurable swarming microrobot may shed light on the understanding of complex morphological transformations in living systems and provide future practical applications of microfabrication and micromanipulation.
PubMed: 34945379
DOI: 10.3390/mi12121529 -
Optics Express Jul 2023A compact Kerr-lens mode-locked thin-disk oscillator reproducibly delivering 110 MW output peak power, the highest among all oscillators, is reported. This simple and...
A compact Kerr-lens mode-locked thin-disk oscillator reproducibly delivering 110 MW output peak power, the highest among all oscillators, is reported. This simple and stable femtosecond oscillator delivering a unique combination of high average power (202 W) and peak power, is an ideal driver and an important milestone for the development of extreme ultraviolet transportable frequency comb sources.
PubMed: 37710469
DOI: 10.1364/OE.491938 -
Microbiology Spectrum Feb 2022The objective of this research was to evaluate the correlation between inhibitory zones and MIC when testing ceftazidime-avibactam using disk diffusion, Etest, and broth... (Comparative Study)
Comparative Study
The objective of this research was to evaluate the correlation between inhibitory zones and MIC when testing ceftazidime-avibactam using disk diffusion, Etest, and broth microdilution method established by the Clinical and Laboratory Standards Institute (CLSI). Four-hundred and 58 isolates of isolated from 54 medical centers from the China Antimicrobial Surveillance Network (CHINET) in 2016 to 2020 were collected. Antimicrobial susceptibility testing using broth microdilution, Etest, and disk diffusion were performed according to the CLSI. Of the 458 , 17.2% (79/458) and 82.8%(379/458) were resistant or susceptible to ceftazidime-avibactam by broth microdilution, respectively. Compared with the broth microdilution method, the categorical agreement (CA) and essential agreement (EA) of the Etest were 99.6% (456/458) and 94.8% (434/458), respectively; the major error (ME) and very major error (VME) were both 0.2% (1/458). For disk diffusion, the CA and VME were 99.8% (457/458) and 0.2% (1/458), respectively. For Escherichia coli, the CA and EA of the Etest were 100% and 97.1% (135/139), respectively. The CA of the disk diffusion was 100%. For Klebsiella pneumoniae, the CA and EA of the Etest were 99.3% (288/290) and 93.4% (271/290), respectively, the ME and VME were both 0.3% (1/290). The CA and VME of disk diffusion were 99.7% (289/290) and 0.3% (1/290), respectively. For other , the CA and EA of the Etest were 100% and 96.6% (28/29), respectively. The CA of the disk diffusion was 100%. Ceftazidime-avibactam disk diffusion (30/20-μg disks) and Etest demonstrated good performance for ceftazidime-avibactam susceptibility testing against clinical isolates. Multidrug-resistant Gram-negative bacteria, especially for extended-spectrum β-lactamases-producing and carbapenemase-producing , are disseminating rapidly around the world. Treatment options for these infections are limited, which prompt the development of novel or combinational therapies to combat the infections caused by multidrug-resistant pathogens. The newly available β-lactam combination agent ceftazidime-avibactam has been demonstrated good and activity against ESBL, AmpC, KPC-2, or OXA-48-like-producing isolates and has shown promise in treating carbapenem-resistant infections. Concerningly, there are few available automated systems for ceftazidime-avibactam susceptibility testing, and the broth microdilution method is hard to perform in most routine laboratories. Therefore, we urgently need an economical and practical method for the accurate detection of ceftazidime-avibactam activity against Gram-negative bacilli. Here, we evaluate the performance of the disk diffusion and Etest compared with the reference broth microdilution method against clinical strains.
Topics: Anti-Bacterial Agents; Azabicyclo Compounds; Ceftazidime; Disk Diffusion Antimicrobial Tests; Drug Combinations; Drug Resistance, Multiple, Bacterial; Enterobacteriaceae; Enterobacteriaceae Infections; Humans
PubMed: 35019685
DOI: 10.1128/spectrum.01092-21 -
Frontiers in Neurology 2023Over the years, most back pain-related biological studies focused on the pathogenesis of disk degeneration. It is known that nerve distributions at the outer layer of...
INTRODUCTION
Over the years, most back pain-related biological studies focused on the pathogenesis of disk degeneration. It is known that nerve distributions at the outer layer of the annulus fibrosus (AF) may be an important contributor to back pain symptoms. However, the types and origins of sensory nerve terminals in the mouse lumbar disks have not been widely studied. Using disk microinjection and nerve retrograde tracing methods, the current study aimed to characterize the nerve types and neuropathway of the lumbar 5/6 (L5/6) disk in mice.
METHODS
Using an anterior peritoneal approach, the L5/6 disk of adult C57BL/6 mice (males, 8-12 weeks) disk microinjection was performed. Fluorogold (FG) was injected into the L5/6 disk using the Hamilton syringe with a homemade glass needle driven by a pressure microinjector. The lumbar spine and bilateral thoracic 13 (Th13) to L6 DRGs were harvested at 10 days after injection. The number of FG neurons among different levels was counted and analyzed. Different nerve markers, including anti-neurofilament 160/200 (NF160/200), anti-calcitonin gene-related peptide (CGRP), anti-parvalbumin (PV), and anti-tyrosine hydroxylase (TH), were used to identify different types of nerve terminals in AF and their origins in DRG neurons.
RESULTS
There were at least three types of nerve terminals at the outer layer of L5/6 AF in mice, including NF160/200 (indicating Aβ fibers), CGRP (Aδ and C fibers), and PV (proprioceptive fibers). No TH fibers (sympathetic nerve fibers and some C-low threshold mechanoreceptors) were noticed in either. Using retrograde tracing methods, we found that nerve terminals in the L5/6 disk were multi-segmentally from Th13-L6 DRGs, with L1 and L5 predominately. An immunofluorescence analysis revealed that FG neurons in DRGs were co-localized with NF160/200, CGRP, and PV, but not TH.
CONCLUSION
Intervertebral disks were innervated by multiple types of nerve fibers in mice, including Aβ, Aδ, C, and proprioceptive fibers. No sympathetic nerve fibers were found in AF. The nerve network of the L5/6 disk in mice was multi-segmentally innervated by the Th13-L6 DRGs (mainly L1 and L5 DRGs). Our results may serve as a reference for preclinical studies of discogenic pain in mice.
PubMed: 37077575
DOI: 10.3389/fneur.2023.1084209 -
Sport Sciences For Health 2022Information about comparing the effectiveness of exercise methods on management of disk herniation is limited. The aim of this study was to compare the effect of two...
Information about comparing the effectiveness of exercise methods on management of disk herniation is limited. The aim of this study was to compare the effect of two programs of suspension and core stability exercises on some electromyography (EMG) coordinates, pain and range of motion of patients with disk herniation. Thirty-two men with disk herniation participated in this clinical trial study which was randomly divided into three groups of suspension exercises (: 12, age: 34.25 ± 8.81, BMI: 24.01 ± 2.7), core stability exercises (: 10, age: 35 ± 10.3, BMI: 25 ± 2.27) and control (: 10, age: 34.4 ± 6.67, BMI: 23.76 ± 1.45). Electrical activity of rectus abdominis, internal and external oblique and erector spinae muscles was masured by superficial EMG, back pain by McGill Pain Questionnaire and range of motion by Modified Schober test, one day before and immediately after of intervention period. The experimental groups performed an 8-week training period while the control group was only followed up. Data were analyzed using paired sample test and analysis of covariance test and statistical significance was set at 0.05. Suspension group showed significant improvement in EMG of rectus abdominis, internal and external oblique muscles (respectively, = 0.030, = 0.017, = 0.022) and pain ( = 0.001) compared to core stability group; but there was no significant difference between two groups in EMG of erector spinae muscle and range of motion. Changes in both training groups were significant in all variables compared to control groups ( ˂ 0.05). Our findings showed that although both exercises were effective in patients with lumbar disk herniation, but the effectiveness of suspension exercises in increasing muscle activation and reducing pain was more pronounced than core stability exercises. Iranian Registry of Clinical Trials (IRCT): IRCT20191016045136N1.
PubMed: 34691266
DOI: 10.1007/s11332-021-00848-2 -
BMC Microbiology Jun 2020Ceftazidime-avibactam was approved in China in 2019 for treating complicated intra-abdominal infections, hospital-acquired pneumonia, ventilator-associated pneumonia,... (Comparative Study)
Comparative Study
BACKGROUND
Ceftazidime-avibactam was approved in China in 2019 for treating complicated intra-abdominal infections, hospital-acquired pneumonia, ventilator-associated pneumonia, and infections caused by Enterobacterales and Pseudomonas aeruginosa for which treatment options are limited. However, no currently available commercial systems have been approved for antimicrobial susceptibility testing of ceftazidime-avibactam in China. Here, we evaluated the Etest and disk diffusion method for detecting the activity of ceftazidime-avibactam against Enterobacterales and P. aeruginosa in China.
RESULTS
In total, 194 Enterobacterales and 77 P. aeruginosa isolates, which were divided into a random selection group (140 Enterobacterales and 46 P. aeruginosa isolates) and stock group (54 Enterobacterales and 31 P. aeruginosa isolates), were assessed by the Etest, disk diffusion and broth microdilution methods. Minimum inhibitory concentrations and zone diameters were interpreted according to the CLSI supplement M100 30th edition. For all 271 tested isolates, no very major errors were found by using Etest, whereas the overall major error rate was 2.0% (4/203). The overall categorical agreement rates of Etest for Enterobacterales and P. aeruginosa were 99.5% (193/194) and 96.1% (74/77), respectively, and the essential agreement rates were 95.9% (186/194) and 94.8% (73/77), respectively. The disk diffusion method showed that the very major error and major error rates were 1.5% (3/204) and 2.5% (5/203), respectively. Overall categorical agreement rates values of the disk diffusion method for Enterobacterales and P. aeruginosa were 98.5% (191/194) and 93.5% (72/77) compared with broth microdilution, respectively.
CONCLUSIONS
For Enterobacterales and P. aeruginosa, both the Etest and disk diffusion method showed acceptable performance as alternatives to the standard broth microdilution method for clinical treatment interpretation. Application of the disk diffusion method in Enterobacterales was slightly better than that in P. aeruginosa.
Topics: Azabicyclo Compounds; Ceftazidime; China; Disk Diffusion Antimicrobial Tests; Drug Combinations; Enterobacteriaceae; Humans; Microbial Sensitivity Tests; Microbial Viability; Pseudomonas aeruginosa; Sensitivity and Specificity
PubMed: 32600252
DOI: 10.1186/s12866-020-01870-z -
Arquivos Brasileiros de Oftalmologia 2022In glaucoma, initial visual field scotomas can be peripheral or central, whereas central scotomas are more severe and can disrupt daily activities. Individual anatomical...
PURPOSE
In glaucoma, initial visual field scotomas can be peripheral or central, whereas central scotomas are more severe and can disrupt daily activities. Individual anatomical features may influence the distribution of retinal nerve fibers and the starting site of visual field defects in glaucoma. In this study, we aimed to correlate myopia and hyperopia or anatomical variation of the disk-fovea angle with initial central or peripheral lesions in the visual field.
METHODS
This cross-sectional study included patients with primary open-angle glaucoma divided into a group of isolated central or peripheral scotomas in the visual field with MD > or equal to -6 dB, correlating with the degree of ametropia and anatomical variations, such as the disk-fovea angle.
RESULTS
We included 52 patients with glaucoma. Of 20 myopic patients, 6 (30%) had central scotomas, and 14 (70%) had peripheral scotomas. Of 32 hyperopic patients, 12 (37.5%) had central scotomas, and 20 (63.5%) had peripheral scotomas. Regarding the disk-fovea angle, 25 eyes had the disk-fovea angle of < -7°, with 9 (36%) eyes presenting with central scotoma, and 27 eyes presented with the disk-fovea angle of > -7°, with 9 (33.3%) eyes presenting with a central scotoma.
CONCLUSION
This study showed an association between ametropia and scotomas on the perimetry in patients with glaucoma. Patients had a higher incidence of peripheral scotomas, but hyperopic patients had a greater number of central scotomas than myopic patients, and myopic patients had more peripheral scotomas than hyperopic patients. The disk-fovea angle was not correlated with scotomas in initial glaucoma.
Topics: Humans; Scotoma; Visual Fields; Visual Field Tests; Glaucoma, Open-Angle; Cross-Sectional Studies; Intraocular Pressure; Vision Disorders; Glaucoma; Myopia
PubMed: 36169425
DOI: 10.5935/0004-2749.2021-0042