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Yu Y, Xu H, Jiang S, Gao C. Predictors for mortality and recovery in patients with acute renal injury receiving continuous renal replacement therapy. Int J Artif Organs 2022; 45:455-461. [PMID: 35356829 DOI: 10.1177/03913988221086301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Despite continuous renal replacement therapy (CRRT) has been widely used in critically ill patients with acute kidney injury (AKI), the prognosis and recovery of renal function in these patients are still poor. Therefore, we aimed to identify the prognostic factors for the mortality and recovery of renal function in patients with AKI receiving CRRT. METHODS A total of 125 patients with AKI, treated with CRRT in the emergency intensive care unit (EICU) in an academic teaching hospital from January 2014 to December 2018 were enrolled in this retrospective study. The clinical data of these patients were collected. Univariate regression analysis and multivariate regression analysis were conducted to identify the predictors for the mortality and recovery of renal function. RESULTS The median age was 68.0 (56.5-79.0) years old, and from which 69.6% were males. Sixty-four patients (51.2%) survived and 50 patients (40%) recovered their renal function. Multivariate regression analysis showed that the independent risk factors for mortality were male (odds ratio [OR]:3.771, 95% confidence interval [CI]:1.063-13.372, p = 0.04), Acute Physiology and Chronic Health Evaluation (APACHE) II score (OR: 1.187, 95% CI: 1.050-1.341, p = 0.006), mechanical ventilation (OR: 6.266, 95% CI: 1.771-22.167, p = 0.004) and vasopressor use (OR: 5.224, 95% CI: 1.546-17.657, p = 0.008). Moreover, the independent predictors for not recovering of renal function were male (OR: 3.440, 95% CI: 1.271-9.311, p = 0.015), pre-existing comorbidity of hypertension (OR: 4.207, 95% CI: 1.609-11.000, p = 0.003) and vasopressor use (OR: 5.280, 95% CI: 2.018-13.811, p = 0.001). CONCLUSIONS Male, high APACHE II score, mechanical ventilation and vasopressor use were closely associated with the increased mortality, while male, pre-existing history of hypertension, and vasopressor use were the independent predictors for non-recovery of renal function.
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Zou XY, Zhang M, Tu WJ, Zhang Q, Jin ML, Fang RD, Jiang S. Bacillus subtilis inhibits intestinal inflammation and oxidative stress by regulating gut flora and related metabolites in laying hens. Animal 2022; 16:100474. [PMID: 35220172 DOI: 10.1016/j.animal.2022.100474] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/18/2022] Open
Abstract
Bacillus subtilis is one of the most popular commercial probiotics used in farm animal production. However, its potential mechanisms are not very clear. The aim of this study was to investigate the effects of dietary Bacillus subtilis on intestinal histomorphology, innate immunity, microbiota composition, transcriptomics, and related metabolomics. Twenty-four 48-week-old Lohman Pink-shell laying hens were randomly divided into two groups: a basic diet and the basic diet supplemented with Bacillus subtilis (0.5 g/kg) for a 9-week experiment. At the end of the experiment, tissues of the duodenum, ileum, and jejunum as well as cecal content of each bird were collected for microstructure, PCR, transcriptome, metabolome, and 16S rRNA analyses. The results showed that dietary Bacillus subtilis supplement had no effect on the intestinal microstructure. However, Bacillus subtilis increased mRNA expression of tight junction protein occludin (P < 0.05), while reduced mRNA expression of lipopolysaccharide-induced TNF factor (P < 0.01) in the duodenum. Moreover, transcriptomic results indicated that most of Bacillus subtilis supplement-induced differential genes were associated with inflammation and immunity, including cytochrome b-245 beta chain, transferrin, and purinergic receptor P2X 7, resulting in a decrease in Malondialdehyde level (P < 0.05) in the duodenum. In addition, at the genus level, Bacillus subtilis supplement enriched the potential beneficial bacteria, Candidatus_Soleaferrea (P = 0.02) but inhibited the harmful bacteria including Lachnospiraceae_FCS020_group, Ruminiclostridium, Lachnospiraceae_UCG-010, and Oxalobacter. Metabolomic results revealed that N-Acetylneuraminic acid and ADP were increased by fed Bacillus subtilis. These results suggest that dietary Bacillus subtilis could inhibit gut inflammation and improve antioxidative status and barrier integrity of the duodenum via regulating gut microbial composition in laying hens.
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Han S, Jiang S, Xiong R, Shafique K, Zahid KR, Wang Y. Response and tolerance mechanism of food crops under high temperature stress: a review. BRAZ J BIOL 2022; 82:e253898. [PMID: 35107484 DOI: 10.1590/1519-6984.253898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 11/23/2021] [Indexed: 01/15/2023] Open
Abstract
High temperature stress events are critical factors inhibiting crop yield. Meanwhile, world population is growing very rapidly and will be reached up to 9 billion by 2050. To feed increasing world population, it is challenging task to increase about 70% global food productions. Food crops have significant contribution toward global food demand and food security. However, consequences from increasing heat stress events are demolishing their abilities to survive and sustain yield when subjected to extreme high temperature stress. Therefore, there is dire need to better understand response and tolerance mechanism of food crops following exposure to heat stress. Here, we aimed to provide recent update on impact of high temperature stress on crop yield of food crops, pollination, pollinators, and novel strategies for improving tolerance of food crop under high temperature stress. Importantly, development of heat-resistant transgenic food crops can grant food security through transformation of superior genes into current germplasm, which are associated with various signaling pathways as well as epigenetic regulation in response to extreme high temperature stress.
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JIAO Y, Jiang S, Li W. POS-199 Transcriptomics and Clinical analysis of prognostic value of Glomerular C1q and C3 deposition in diabetic nephropathy. Kidney Int Rep 2022. [DOI: 10.1016/j.ekir.2022.01.217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Yu H, Azzam M, Wang Y, Lin X, Alqhtani A, Al-Abdullatif A, Alhidary I, Jiang S. Dietary requirements of sodium and chloride for slow-growing broiler breeds during finisher phase of production. J APPL POULTRY RES 2022. [DOI: 10.1016/j.japr.2022.100243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Jiang S, Guo C, Bian Z, Wang R, Zhu J, Song P, Hu P, Hu D, Zhang Z, Hoshino K, Feng B, Zheng G. Ptychographic sensor for large-scale lensless microbial monitoring with high spatiotemporal resolution. Biosens Bioelectron 2022; 196:113699. [PMID: 34653716 DOI: 10.1016/j.bios.2021.113699] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/30/2021] [Accepted: 10/08/2021] [Indexed: 01/19/2023]
Abstract
Traditional microbial detection methods often rely on the overall property of microbial cultures and cannot resolve individual growth event at high spatiotemporal resolution. As a result, they require bacteria to grow to confluence and then interpret the results. Here, we demonstrate the application of an integrated ptychographic sensor for lensless cytometric analysis of microbial cultures over a large scale and with high spatiotemporal resolution. The reported device can be placed within a regular incubator or used as a standalone incubating unit for long-term microbial monitoring. For longitudinal study where massive data are acquired at sequential time points, we report a new temporal-similarity constraint to increase the temporal resolution of ptychographic reconstruction by 7-fold. With this strategy, the reported device achieves a centimeter-scale field of view, a half-pitch spatial resolution of 488 nm, and a temporal resolution of 15-s intervals. For the first time, we report the direct observation of bacterial growth in a 15-s interval by tracking the phase wraps of the recovered images, with high phase sensitivity like that in interferometric measurements. We also characterize cell growth via longitudinal dry mass measurement and perform rapid bacterial detection at low concentrations. For drug-screening application, we demonstrate proof-of-concept antibiotic susceptibility testing and perform single-cell analysis of antibiotic-induced filamentation. The combination of high phase sensitivity, high spatiotemporal resolution, and large field of view is unique among existing microscopy techniques. As a quantitative and miniaturized platform, it can improve studies with microorganisms and other biospecimens at resource-limited settings.
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Jiang S, Ma J, Ye S, Meaney C, Moore TE, Pan S, Gao C. Associations Among Disseminated Intravascular Coagulation, Thrombocytopenia Cytokines/Chemokines and Genetic Polymorphisms of Toll-Like Receptor 2/4 in Chinese Patients with Sepsis. J Inflamm Res 2022; 15:1-15. [PMID: 35018107 PMCID: PMC8742598 DOI: 10.2147/jir.s337559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/20/2021] [Indexed: 02/06/2023] Open
Abstract
Objectives(s) Toll-like receptors (TLRs) on platelets have been extensively studied. Both TLR2 and TLR4 have been shown to augment platelet activation and alter its function from a hemostatic regulator to an immune sentinel. However, few studies have investigated the relationship between genetic polymorphisms in TLR2, TLR4 and platelets. We investigated whether genetic polymorphisms of TLR2 and TLR4 were related to thrombocytopenia and coagulation failure in Chinese patients with sepsis. Basic Methods Adult Chinese patients with sepsis in the intensive care unit of a university medical center were monitored for up to 28 days. Thrombocytopenia and disseminated intravascular coagulation (DIC), diagnosed using Japanese Association for Acute Medicine (JAAM) criteria, were observed as the primary outcomes. Single-nucleotide polymorphisms (SNPs) in TLR2 (rs111200466, rs5743708) and TLR4 (rs11536889, rs145801336, rs11536896, rs7869402) in patients with sepsis were detected by polymerase chain reaction. The data were analyzed using chi-square and rank sum tests. Results The genotype of TLR2 (rs111200466) (Del/Del) was associated with the initial DIC. The genotype of TLR4 (rs11536889) (C/C&C/G) was associated with initial DIC, DIC onset during hospitalization and platelet counts. Furthermore, both DIC and platelet counts were associated with cytokines and chemokines, especially the IL10. Conclusion Our results demonstrate that in Chinese sepsis patients, the rs111200466 SNP in TLR2 and rs11536889 SNP in TLR4 are associated with thrombocytopenia and DIC, with potential effects on the TLR4 pathways of platelets.
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Li Q, Jiang S, Li HJ, Gan YD, Liu M, Zhang L. [Epstein-Barr virus-positive inflammatory follicular dendritic cell sarcoma of the colon: report of a case]. ZHONGHUA BING LI XUE ZA ZHI = CHINESE JOURNAL OF PATHOLOGY 2022; 51:56-58. [PMID: 34979757 DOI: 10.3760/cma.j.cn112151-20210702-00475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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Huang Y, Jiang S, Li W, Fan Y, Leng Y, Gao C. Establishment and Effectiveness Evaluation of a Scoring System-RAAS (RDW, AGE, APACHE II, SOFA) for Sepsis by a Retrospective Analysis. J Inflamm Res 2022; 15:465-474. [PMID: 35082513 PMCID: PMC8786358 DOI: 10.2147/jir.s348490] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/25/2021] [Indexed: 01/19/2023] Open
Abstract
Background Methods Results Conclusion
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Zhou Y, Ren Y, Dai G, Li X, Xiang Y, Zhang J, Jiang Y, Jiang S, Hou X, Zhu Z, Wu R. Genetic characterization and clinical characteristics of bovine viral diarrhea viruses in cattle herds of Heilongjiang province, China. IRANIAN JOURNAL OF VETERINARY RESEARCH 2022; 23:69-73. [PMID: 35782353 PMCID: PMC9238938 DOI: 10.22099/ijvr.2021.38650.5625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/24/2021] [Accepted: 12/12/2021] [Indexed: 06/15/2023]
Abstract
BACKGROUND Heilongjiang province is the main cattle-producing area in China, and molecular epidemiological studies of bovine viral diarrhea viruses (BVDV) in cattle have not been performed in the province. AIMS The objective of this research was to determine the genetic and clinical characteristics of BVDV in cattle. METHODS Fifty-three BVDV-positive clinical samples were collected from 22 cattle farms in Heilongjiang, and the 5´-untranslated region (5´-UTR) was used to carry out a phylogenetic analysis of the viruses. RESULTS The similarity of the 5´-UTR sequences among these BVDVs was 84.2%-100%, and the phylogenetic analysis showed that all viruses belong to the BVDV-1 species, which is classified into five subtypes: BVDV-1b (47.17%, n=25), 1c (15.09%, n=8), 1d (16.98%, n=9), 1 m (3.77%, n=2), and 1o (16.98%, n=9). The statistical results showed that the BVDV-1b subtype had a positive correlation with gastrointestinal disease (P<0.05; 95% CI: 1.19 to 3.34). There were up to three or four BVDV-1 subtypes in some dairy cattle farms, but farms with a single subtype were prevalent (5/10). CONCLUSION BVDV-1b is predominant in cattle herds of Heilongjiang province, China, and shows a positive correlation with gastrointestinal disease. BVDV-1o was found for the first time in Chinese cattle, which increased the complex distribution of BVDV-1 subtypes in cattle herds of China.
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Song P, Guo C, Jiang S, Wang T, Hu P, Hu D, Zhang Z, Feng B, Zheng G. Optofluidic ptychography on a chip. LAB ON A CHIP 2021; 21:4549-4556. [PMID: 34726219 DOI: 10.1039/d1lc00719j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report the implementation of a fully on-chip, lensless microscopy technique termed optofluidic ptychography. This imaging modality complements the miniaturization provided by microfluidics and allows the integration of ptychographic microscopy into various lab-on-a-chip devices. In our prototype, we place a microfluidic channel on the top surface of a coverslip and coat the bottom surface with a scattering layer. The channel and the coated coverslip substrate are then placed on top of an image sensor for diffraction data acquisition. Similar to the operation of a flow cytometer, the device utilizes microfluidic flow to deliver specimens across the channel. The diffracted light from the flowing objects is modulated by the scattering layer and recorded by the image sensor for ptychographic reconstruction, where high-resolution quantitative complex images are recovered from the diffraction measurements. By using an image sensor with a 1.85 μm pixel size, our device can resolve the 550 nm linewidth on the resolution target. We validate the device by imaging different types of biospecimens, including C. elegans, yeast cells, paramecium, and closterium sp. We also demonstrate a high-resolution ptychographic reconstruction at a video framerate of 30 frames per second. The reported technique can address a wide range of biomedical needs and engenders new ptychographic imaging innovations in a flow cytometer configuration.
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Guo C, Jiang S, Yang L, Song P, Wang T, Shao X, Zhang Z, Murphy M, Zheng G. Deep learning-enabled whole slide imaging (DeepWSI): oil-immersion quality using dry objectives, longer depth of field, higher system throughput, and better functionality. OPTICS EXPRESS 2021; 29:39669-39684. [PMID: 34809325 DOI: 10.1364/oe.441892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/04/2021] [Indexed: 05/18/2023]
Abstract
Whole slide imaging (WSI) has moved the traditional manual slide inspection process to the era of digital pathology. A typical WSI system translates the sample to different positions and captures images using a high numerical aperture (NA) objective lens. Performing oil-immersion microscopy is a major obstacle for WSI as it requires careful liquid handling during the scanning process. Switching between dry objective and oil-immersion lens is often impossible as it disrupts the acquisition process. For a high-NA objective lens, the sub-micron depth of field also poses a challenge to acquiring in-focus images of samples with uneven topography. Additionally, it implies a small field of view for each tile, thus limiting the system throughput and resulting in a long acquisition time. Here we report a deep learning-enabled WSI platform, termed DeepWSI, to substantially improve the system performance and imaging throughput. With this platform, we show that images captured with a regular dry objective lens can be transformed into images comparable to that of a 1.4-NA oil immersion lens. Blurred images with defocus distance from -5 µm to +5 µm can be virtually refocused to the in-focus plane post measurement. We demonstrate an equivalent data throughput of >2 gigapixels per second, the highest among existing WSI systems. Using the same deep neural network, we also report a high-resolution virtual staining strategy and demonstrate it for Fourier ptychographic WSI. The DeepWSI platform may provide a turnkey solution for developing high-performance diagnostic tools for digital pathology.
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Li W, Liu Y, Huang X, Jiang S, Zhao C, Mai W. Interfacial Gradient-Energy-Band-Alignment Modulation via a Vapor-Phase Anion-Exchange Reaction toward Lead-Free Perovskite Photodetectors with Excellent UV Imaging Capability. ACS APPLIED MATERIALS & INTERFACES 2021; 13:53194-53201. [PMID: 34719922 DOI: 10.1021/acsami.1c15635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bi-based inorganic perovskites have attracted great attention in optoelectronics, as they feature similar photoelectric properties but have high stability and lead-free merits. Unfortunately, due to the high exciton binding energy and small Bohr radius, their photodetection performance still largely lags behind that of Pb-based counterparts. Herein, using a vapor-phase chloride ion-substitution strategy, Cs3Bi2Br9 photodetectors (PDs) with gradient energy band alignment were delicately modulated, contributing to a high carrier separation/collection efficiency. The optimized Bi-based perovskite ACCT (Al2O3/Cs3Bi2Br9/Cs3Bi2ClxBr9-x/TiO2) PDs exhibit outstanding performance, the ON/OFF ratio and linear dynamic range (LDR) are significantly improved by 20 and 2.6 times, respectively. Significantly, we further demonstrate the high-SNR (signal-to-noise ratio) UV imaging based on the optimized device, which shows 21.887 dB higher than that of the pristine device. Finally, the vapor-phase anion-exchange modified perovskite PDs show long-term stability and high UV resistance. Vapor-phase ion-substitution is a promising approach for the synergistic effect of matched energy band alignment and interface passivation, which can be applied to other perovskite-based optoelectronic devices.
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Huang Y, Jiang S, Wang R, Song P, Zhang J, Zheng G, Ji X, Zhang Y. Ptychography-based high-throughput lensless on-chip microscopy via incremental proximal algorithms. OPTICS EXPRESS 2021; 29:37892-37906. [PMID: 34808853 DOI: 10.1364/oe.442530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Ptychography-based lensless on-chip microscopy enables high-throughput imaging by retrieving the missing phase information from intensity measurements. Numerous reconstruction algorithms for ptychography have been proposed, yet only a few incremental algorithms can be extended to lensless on-chip microscopy because of large-scale datasets but limited computational efficiency. In this paper, we propose the use of accelerated proximal gradient methods for blind ptychographic phase retrieval in lensless on-chip microscopy. Incremental gradient approaches are adopted in the reconstruction routine. Our algorithms divide the phase retrieval problem into sub-problems involving the evaluation of proximal operator, stochastic gradient descent, and Wirtinger derivatives. We benchmark the performances of accelerated proximal gradient, extended ptychographic iterative engine, and alternating direction method of multipliers, and discuss their convergence and accuracy in both noisy and noiseless cases. We also validate our algorithms using experimental datasets, where full field of view measurements are captured to recover the high-resolution complex samples. Among these algorithms, accelerated proximal gradient presents the overall best performance regarding accuracy and convergence rate. The proposed methods may find applications in ptychographic reconstruction, especially for cases where a wide field of view and high resolution are desired at the same time.
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Guo C, Jiang S, Song P, Wang T, Shao X, Zhang Z, Zheng G. Quantitative multi-height phase retrieval via a coded image sensor. BIOMEDICAL OPTICS EXPRESS 2021; 12:7173-7184. [PMID: 34858708 PMCID: PMC8606130 DOI: 10.1364/boe.443528] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 06/01/2023]
Abstract
Multi-height phase retrieval introduces different object-to-detector distances for obtaining phase diversity measurements. In the acquisition process, the slow-varying phase information, however, cannot be converted to intensity variations for detection. Therefore, the low-frequency contents of the phase profile are lost during acquisition and cannot be properly restored via phase retrieval. Here, we demonstrate the use of a coded image sensor for addressing this challenge in multi-height phase retrieval. In our scheme, we add a coded layer on top of the image sensor for encoding the slow-varying complex wavefronts into intensity variations of the modulated patterns. Inspired by the concept of blind ptychography, we report a reconstruction scheme to jointly recover the complex object and the unknown coded layer using multi-height measurements. With both simulation and experimental results, we show that the recovered phase is quantitative and the slow-varying phase profiles can be properly restored using lensless multi-height measurements. We also show that the image quality using the coded sensor is better than that of a regular image sensor. For demonstrations, we validate the reported scheme with various biospecimens and compare the results to those of regular lensless multi-height phase retrieval. The use of a coded image sensor may enable true quantitative phase imaging for the lensless multi-height, multi-wavelength, and transport-of-intensity equation approaches.
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Chen Y, Qian W, Lin L, Cai L, Yin K, Jiang S, Song J, Han RPS, Yang C. Mapping Gene Expression in the Spatial Dimension. SMALL METHODS 2021; 5:e2100722. [PMID: 34927963 DOI: 10.1002/smtd.202100722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/25/2021] [Indexed: 06/14/2023]
Abstract
The main function and biological processes of tissues are determined by the combination of gene expression and spatial organization of their cells. RNA sequencing technologies have primarily interrogated gene expression without preserving the native spatial context of cells. However, the emergence of various spatially-resolved transcriptome analysis methods now makes it possible to map the gene expression to specific coordinates within tissues, enabling transcriptional heterogeneity between different regions, and for the localization of specific transcripts and novel spatial markers to be revealed. Hence, spatially-resolved transcriptome analysis technologies have broad utility in research into human disease and developmental biology. Here, recent advances in spatially-resolved transcriptome analysis methods are summarized, including experimental technologies and computational methods. Strengths, challenges, and potential applications of those methods are highlighted, and perspectives in this field are provided.
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Jiang S, Guo C, Hu P, Hu D, Song P, Wang T, Bian Z, Zhang Z, Zheng G. High-throughput lensless whole slide imaging via continuous height-varying modulation of a tilted sensor. OPTICS LETTERS 2021; 46:5212-5215. [PMID: 34653155 DOI: 10.1364/ol.437832] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
We report a new, to the best of our knowledge, lensless microscopy configuration by integrating the concepts of transverse translational ptychography and defocus multi-height phase retrieval. In this approach, we place a tilted image sensor under the specimen for introducing linearly increasing phase modulation along one lateral direction. Similar to the operation of ptychography, we laterally translate the specimen and acquire the diffraction images for reconstruction. Since the axial distance between the specimen and the sensor varies at different lateral positions, laterally translating the specimen effectively introduces defocus multi-height measurements while eliminating axial scanning. Lateral translation further introduces sub-pixel shift for pixel super-resolution imaging and naturally expands the field of view for rapid whole slide imaging. We show that the equivalent height variation can be precisely estimated from the lateral shift of the specimen, thereby addressing the challenge of precise axial positioning in conventional multi-height phase retrieval. Using a sensor with 1.67 µm pixel size, our low-cost and field-portable prototype can resolve the 690 nm linewidth on the resolution target. We show that a whole slide image of a blood smear with a 120mm2 field of view can be acquired in 18 s. We also demonstrate accurate automatic white blood cell counting from the recovered image. The reported approach may provide a turnkey solution for addressing point-of-care and telemedicine-related challenges.
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Yue Y, Chen Y, Du X, Jin Y, Hu M, Jiang X, Wang C, Chen Z, Su L, Chen C, Jiang S, Tuo X. A survey of a COVID-19 cluster of charter flight importation. Public Health 2021; 199:107-109. [PMID: 34601152 PMCID: PMC8435375 DOI: 10.1016/j.puhe.2021.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 09/03/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVES Although a number of cases of importation with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection have been reported, there are still no data available concerning the characteristics in the coronavirus disease 2019 (COVID-19) cluster of charter flight importation. Here, we provide an analysis of COVID-19 cases and their close contacts who worked for the same company on a project in Karbala, Iraq, and returned back to Chengdu, China, by a charter flight. METHODS The data of imported COVID-19 cases and their close contacts were obtained from National Notifiable Disease Report System of Chinese Center for Disease Control and Prevention and field epidemiological investigation reports by Centers for Disease Control and Prevention (CDCs) in Chengdu. The information of general characteristics and laboratory findings of this cluster were collected and summarized. RESULTS One hundred and six (66.67%) of 159 charter flight passengers tested positive for COVID-19 before entry. Through treatment, all 159 people tested negative and meet the requirements of taking flights bound for China before boarding. However, there has been still 36 (22.64%) of them tested positive after entry. The median time from entry to confirmation was 1.0 day (Interquartile Range (IQR): 0-4.3). The Cycle threshold value (Ct value) of 36 patients' positive samples are all above 30 and most values are above 35. CONCLUSIONS In conclusion, there is still a risk that a number of COVID-19 cases can be imported through charter flight. However, the infectivity of confirmed patients of the charter flight was considered to be low.
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Liu Z, Zhou Y, Feng WN, Chen MY, Han G, Zou GR, Yang S, He Y, Zou X, Tang J, Zhang L, Cui L, Chen H, Li G, Jiang S, Gao J, Xiao L, Zhang Q, Yi W, Huang C. LBA64 Olanzapine, an alternative to dexamethasone for preventing nausea and vomiting induced by cisplatin-based doublet highly emetogenic chemotherapy: A non-inferiority, prospective, multi-centered, randomized, controlled, phase III clinical trial. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.2145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Xin K, Jiang S, Chen X, He Y, Zhang J, Wang H, Liu H, Peng Q, Zhang Y, Ji X. Low-cost whole slide imaging system with single-shot autofocusing based on color-multiplexed illumination and deep learning. BIOMEDICAL OPTICS EXPRESS 2021; 12:5644-5657. [PMID: 34692206 PMCID: PMC8515991 DOI: 10.1364/boe.428655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Recent research on whole slide imaging (WSI) has greatly promoted the development of digital pathology. However, accurate autofocusing is still the main challenge for WSI acquisition and automated digital microscope. To address this problem, this paper describes a low cost WSI system and proposes a fast, robust autofocusing method based on deep learning. We use a programmable LED array for sample illumination. Before the brightfield image acquisition, we turn on a red and a green LED, and capture a color-multiplexed image, which is fed into a neural network for defocus distance estimation. After the focus tracking process, we employ a low-cost DIY adaptor to digitally adjust the photographic lens instead of the mechanical stage to perform axial position adjustment, and acquire the in-focus image under brightfield illumination. To ensure the calculation speed and image quality, we build a network model based on a 'light weight' backbone network architecture-MobileNetV3. Since the color-multiplexed coherent illuminated images contain abundant information about the defocus orientation, the proposed method enables high performance of autofocusing. Experimental results show that the proposed method can accurately predict the defocus distance of various types of samples and has good generalization ability for new types of samples. In the case of using GPU, the processing time for autofocusing is less than 0.1 second for each field of view, indicating that our method can further speed up the acquisition of whole slide images.
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Guo C, Bian Z, Alhudaithy S, Jiang S, Tomizawa Y, Song P, Wang T, Shao X. Brightfield, fluorescence, and phase-contrast whole slide imaging via dual-LED autofocusing. BIOMEDICAL OPTICS EXPRESS 2021; 12:4651-4660. [PMID: 34513215 PMCID: PMC8407850 DOI: 10.1364/boe.428196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/10/2021] [Accepted: 06/20/2021] [Indexed: 05/20/2023]
Abstract
Whole slide imaging (WSI) systems convert the conventional biological samples into digital images. Existing commercial WSI systems usually require an expensive high-performance motorized stage to implement the precise mechanical control, and the cost is prohibitive for most individual pathologists. In this work, we report a low-cost WSI system using the off-the-shelf components, including a computer numerical control (CNC) router, a photographic lens, a programmable LED array, a fluorescence filter cube, and a surface-mount LED. To perform real-time single-frame autofocusing, we exploited two elements of a programmable LED array to illuminate the sample from two different incident angles. The captured image would contain two copies of the sample with a certain separation determined by the defocus distance of the sample. Then the defocus distance can be recovered by identifying the translational shift of the two copies. The reported WSI system can reach a resolution of ∼0.7 µm. The time to determine the optimal focusing position for each tile is only 0.02 s, which is about an 83% improvement compared to our previous work. We quantified the focusing performance on 1890 different tissue tiles. The mean focusing error is ∼0.34 µm, which is well below the ± 0.7 µm depth of field range of our WSI system. The reported WSI system can handle both the semitransparent and the transparent sample, enabling us to demonstrate the implementation of brightfield, fluorescence, and phase-contrast WSI. An automatic digital distortion correction strategy is also developed to avoid the stitching errors. The reported prototype has an affordable cost and can make it broadly available and utilizable for individual pathologists as well as can promote the development of digital pathology.
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Zou T, Jiang S, Zhang Y, Liu J, Yi B, Qi Y, Dissanayaka WL, Zhang C. In Situ Oxygen Generation Enhances the SCAP Survival in Hydrogel Constructs. J Dent Res 2021; 100:1127-1135. [PMID: 34328028 DOI: 10.1177/00220345211027155] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Prolonged and severe hypoxia is the main cause of death of transplanted cells prior to the establishment of functional circulation. In situ generation of oxygen by oxygen-producing scaffolds-a unique solution that could produce and deliver oxygen to the adjacent cells independently of blood perfusion-has attracted considerable attention to enhance the survivability of the transplanted cells. However, the application of oxygen-generating scaffolds for facilitating cell survival in pulp-like tissue regeneration is yet to be explored. In this study, gelatin methacryloyl (GelMA)-a biocompatible scaffolding material that closely mimics the native extracellular matrix and is conducive to cell proliferation and differentiation-was used to fabricate oxygen-generating scaffolds by loading various concentrations of CaO2. The CaO2 distribution, topography, swelling, and pore size of CaO2-GelMA hydrogels were characterized in detail. The release of O2 by the scaffold and the viability, spreading, and proliferation of stem cells from apical papilla (SCAPs) encapsulated in the GelMA hydrogels with various concentrations of CaO2 under hypoxia were evaluated. In addition, cellular constructs were engineered into root canals, and cell viability within the apical, middle, and coronal portions was assessed. Our findings showed that 0.5% CaO2-GelMA was sufficient to supply in situ oxygen for maintaining the embedded SCAP viability for 1 wk. Furthermore, the 0.5% CaO2-GelMA hydrogels improved the survivability of SCAPs within the coronal portion of the engineered cellular constructs within the root canals. This work demonstrated that 0.5% CaO2-GelMA hydrogels offer a potential promising scaffold that enhances survival of the embedded SCAPs in endodontic regeneration.
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Xu J, Zhang L, Jiang R, Hu K, Hu D, Liao C, Jiang S, Yang Y, Huang J, Tang L, Li L. Nicotinamide improves NAD + levels to protect against acetaminophen-induced acute liver injury in mice. Hum Exp Toxicol 2021; 40:1938-1946. [PMID: 33949241 DOI: 10.1177/09603271211014573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Acetaminophen (APAP) overdose causes acute liver injury (ALI). Nicotinamide adenine dinucleotide (NAD) is an essential coenzyme, and NAD+ is oxidized type which synthesized from nicotinamide (NAM). The present study aimed to investigate the role of NAD+ in ALI and protective property of NAM. The mice were subjected to different doses APAP. After 8 hours, the serum activities of alaninetransaminase (ALT) and aspartate aminotransferase (AST), the hepatic NAD+ level and nicotinamide phosphoribosyltransferase (NAMPT) expression were determined. Then, the mice were pretreated with NAM (800 mg/kg), the hepatoprotective effects and the key antioxidative molecules were evaluated. Our findings indicated that APAP resulted in remarkable NAD+ depletion in a dose-dependent manner accompanied by NAMPT downregulation, and NAM pretreatment significantly elevated the NAD+ decline due to upregulation of NAMPT. Moreover, the downregulated Kelch-like ECH-associated protein-1 (Keap1), upregulated nuclear factor erythroid 2-related factor 2 (Nrf2) and its translocation activation after NAM administration were confirmed, which were in accordance with improved superoxide dismutase (SOD) and glutathione (GSH) levels. Finally, NAM dramatically exhibited hepatoprotective effects by reducing the liver index and necrotic area. This study has suggested that APAP impairs liver NAD+ level and NAM is able to improve hepatic NAD+ to activate antioxidant pathway against APAP-induced ALI.
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Ma J, Wang R, Chen T, Jiang S, Xu A. Protective effects of baicalin in a Caenorhabditis elegans model of Parkinson's disease. Toxicol Res (Camb) 2021; 10:409-417. [PMID: 34141154 DOI: 10.1093/toxres/tfaa107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/01/2020] [Accepted: 12/07/2020] [Indexed: 12/29/2022] Open
Abstract
Parkinson's disease (PD) is a common neurodegenerative disorder of the central nervous system. However, the pathogenetic mechanisms of PD are far from understood. The aim of this study was to determine the protective effect of baicalin in a Caenorhabditis elegans model of PD. C. elegans worms were stimulated for 24 h with 6-hydroxydopamine (6-OHDA, 50 mM) and treated with or without baicalin (1, 10, or 100 μM). At all tested concentrations, baicalin improved the reversal and omega turn behavioral phenotypes, as well as the survival, of 6-OHDA-stimulated worms. It also inhibited 6-OHDA-induced oxidative stress by decreasing malondialdehyde levels, increasing superoxide dismutase, glutathione reductase, catalase, and glutathione levels and up-regulating mRNA expression of the antioxidant-related genes sod-1, sod-2, sod-3, daf-2, and daf-16. Additionally, it significantly decreased the expression of the apoptosis-related gene ced-3 and increased that of the anti-apoptosis-related gene ced-9. The expression levels of cleaved caspase-3 and B-cell lymphoma 2 in 6-OHDA-treated worms were reversed by baicalin. Apoptosis was suppressed by 6-OHDA in loss-of-function strains via the p38 mitogen-activated protein kinase (MAPK) signaling pathway. Furthermore, the apoptotic effects of 6-OHDA were blocked in sek-1 and pmk-1 mutants. Finally, the mRNA expression of sek-1 and pmk-1 and the protein expression of p38 MAPK and stress-activated protein kinase/extracellular signal-regulated kinase 1 were up-regulated by 6-OHDA and reversed by baicalin. Baicalin may protect against 6-OHDA injury by inhibiting apoptosis and decreasing oxidative stress through the p38 MAPK signaling pathway.
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Lu C, Zhou Y, Guo Y, Jiang S, Zhang Z, Zheng G, Zhong J. Mask-modulated lensless imaging via translated structured illumination. OPTICS EXPRESS 2021; 29:12491-12501. [PMID: 33985007 DOI: 10.1364/oe.421228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Lensless microscopy technique enables high-resolution image recovery over a large field of view. By integrating the concept of phase retrieval, it can also retrieve the lost phase information from intensity-only measurements. Here we report a mask-modulated lensless imaging platform based on translated structured illumination. In the reported platform, we sandwich the object in-between a coded mask and a naked image sensor for lensless data acquisition. An LED array is used to provide angle-varied illumination for projecting a translated structured pattern without involving mechanical scanning. For different LED elements, we acquire the lensless intensity data for recovering the complex-valued object. In the reconstruction process, we employ the regularized ptychographic iterative engine and implement an up-sampling process in the reciprocal space. As demonstrated by experimental results, the reported platform is able to recover complex-valued object images with higher resolution and better quality than previous implementations. Our approach may provide a cost-effective solution for high-resolution and wide field-of-view ptychographic imaging without involving mechanical scanning.
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