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| 2. |
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| 3. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 4. |
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| 5. |
- Ge, Q., et al.
(författare)
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Active contour evolved by joint probability classification on Riemannian manifold
- 2016
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Ingår i: Signal, Image and Video Processing. - : Springer London. - 1863-1703 .- 1863-1711. ; 10:7, s. 1257-1264
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we present an active contour model for image segmentation based on a nonparametric distribution metric without any intensity a priori of the image. A novel nonparametric distance metric, which is called joint probability classification, is established to drive the active contour avoiding the instability induced by multimodal intensity distribution. Considering an image as a Riemannian manifold with spatial and intensity information, the contour evolution is performed on the image manifold by embedding geometric image feature into the active contour model. The experimental results on medical and texture images demonstrate the advantages of the proposed method.
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| 6. |
- Ge, Qi, et al.
(författare)
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Structure-Based Low-Rank Model With Graph Nuclear Norm Regularization for Noise Removal
- 2017
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Ingår i: IEEE Transactions on Image Processing. - : Institute of Electrical and Electronics Engineers (IEEE). - 1057-7149 .- 1941-0042. ; 26:7, s. 3098-3112
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Tidskriftsartikel (refereegranskat)abstract
- Nonlocal image representation methods, including group-based sparse coding and block-matching 3-D filtering, have shown their great performance in application to low-level tasks. The nonlocal prior is extracted from each group consisting of patches with similar intensities. Grouping patches based on intensity similarity, however, gives rise to disturbance and inaccuracy in estimation of the true images. To address this problem, we propose a structure-based low-rank model with graph nuclear norm regularization. We exploit the local manifold structure inside a patch and group the patches by the distance metric of manifold structure. With the manifold structure information, a graph nuclear norm regularization is established and incorporated into a low-rank approximation model. We then prove that the graph-based regularization is equivalent to a weighted nuclear norm and the proposed model can be solved by a weighted singular-value thresholding algorithm. Extensive experiments on additive white Gaussian noise removal and mixed noise removal demonstrate that the proposed method achieves a better performance than several state-of-the-art algorithms.
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| 7. |
- Ge, Yue, et al.
(författare)
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Environmental OMICS: Current Status and Future Directions
- 2013
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Ingår i: JOURNAL OF INTEGRATED OMICS. - : Proteomass Scientific Society. - 2182-0287. ; 3:2, s. 75-87
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Tidskriftsartikel (refereegranskat)abstract
- Applications of OMICS to high throughput studies of changes of genes, RNAs, proteins, metabolites, and their associated functionsin cells or organisms exposed to environmental chemicals has led to the emergence of a very active research field: environmental OMICS.This developing field holds an important key for improving the scientific basis for understanding the potential impacts of environmentalchemicals on both health and the environment. Here we describe the state of environmental OMICS with an emphasis on its recent accomplishmentsand its problems and potential solutions to facilitate the incorporation of OMICS into mainstream environmental and healthresearch.Data sources: We reviewed relevant and recently published studies on the applicability and usefulness of OMICS technologies to the identificationof toxicity pathways, mechanisms, and biomarkers of environmental chemicals for environmental and health risk monitoring andassessment, including recent presentations and discussions on these issues at The First International Conference on Environmental OMICS(ICEO), held in Guangzhou, China during November 8-12, 2011. This paper summarizes our review.Synthesis: Environmental OMICS aims to take advantage of powerful genomics, transcriptomics, proteomics, and metabolomics tools toidentify novel toxicity pathways/signatures/biomarkers so as to better understand toxicity mechanisms/modes of action, to identify/categorize/prioritize/screen environmental chemicals, and to monitor and predict the risks associated with exposure to environmental chemicalson human health and the environment. To improve the field, some lessons learned from previous studies need to be summarized, aresearch agenda and guidelines for future studies need to be established, and a focus for the field needs to be developed.Conclusions: OMICS technologies for identification of RNA, protein, and metabolic profiles and endpoints have already significantly improvedour understanding of how environmental chemicals affect our ecosystem and human health. OMICS breakthroughs are empoweringthe fields of environmental toxicology, chemical toxicity characterization, and health risk assessment. However, environmental OMICS is stillin the data generation and collection stage. Important data gaps in linking and/or integrating toxicity data with OMICS endpoints/profilesneed to be filled to enable understanding of the potential impacts of chemicals on human health and the environment. It is expected thatfuture environmental OMICS will focus more on real environmental issues and challenges such as the characterization of chemical mixturetoxicity, the identification of environmental and health biomarkers, and the development of innovative environmental OMICS approachesand assays. These innovative approaches and assays will inform chemical toxicity testing and prediction, ecological and health risk monitoringand assessment, and natural resource utilization in ways that maintain human health and protects the environment in a sustainable manner.
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| 8. |
- Hu, Xian-Ge, et al.
(författare)
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De Novo Transcriptome Assembly and Characterization for the Widespread and Stress-Tolerant Conifer Platycladus orientalis
- 2016
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:2
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Tidskriftsartikel (refereegranskat)abstract
- Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species' genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28% of all unigenes), 42,158 (28.32%), and 23,179 (15.57%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs.
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| 9. |
- Hu, Xian-Ge, et al.
(författare)
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Predicting Impacts of Future Climate Change on the Distribution of the Widespread Conifer Platycladus orientalis
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:7
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Tidskriftsartikel (refereegranskat)abstract
- Chinese thuja (Platycladus orientalis) has a wide but fragmented distribution in China. It is an important conifer tree in reforestation and plays important roles in ecological restoration in the arid mountains of northern China. Based on high-resolution environmental data for current and future scenarios, we modeled the present and future suitable habitat for P. orientalis, evaluated the importance of environmental factors in shaping the species' distribution, and identified regions of high risk under climate change scenarios. The niche models showed that P. orientalis has suitable habitat of ca. 4.2x10(6) km(2) across most of eastern China and identified annual temperature, monthly minimum and maximum ultraviolet-B radiation and wet-day frequency as the critical factors shaping habitat availability for P. orientalis. Under the low concentration greenhouse gas emissions scenario, the range of the species may increase as global warming intensifies; however, under the higher concentrations of emissions scenario, we predicted a slight expansion followed by contraction in distribution. Overall, the range shift to higher latitudes and elevations would become gradually more significant. The information gained from this study should be an useful reference for implementing long-term conservation and management strategies for the species.
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| 10. |
- Jiao, Xiang, et al.
(författare)
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Comparative analysis of nonlinear growth curve models for Arabidopsis thaliana rosette leaves
- 2018
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Ingår i: Acta Physiologiae Plantarum. - : Springer. - 0137-5881 .- 1861-1664. ; 40:6
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Tidskriftsartikel (refereegranskat)abstract
- As a model organism, modeling and analysis of the phenotype of Arabidopsis thaliana (A. thaliana) leaves for a given genotype can help us better understand leaf growth regulation. A. thaliana leaves growth trajectories are to be nonlinear and the leaves contribute most to the above-ground biomass. Therefore, analysis of their change regulation and development of nonlinear growth models can better understand the phenotypic characteristics of leaves (e.g., leaf size) at different growth stages. In this study, every individual leaf size of A. thaliana rosette leaves was measured during their whole life cycle using non-destructive imaging measurement. And three growth models (Gompertz model, logistic model and Von Bertalanffy model) were analyzed to quantify the rosette leaves growth process of A. thaliana. Both graphical (plots of standardized residuals) and numerical measures (AIC, R2 and RMSE) were used to evaluate the fitted models. The results showed that the logistic model fitted better in describing the growth of A. thaliana leaves compared to Gompertz model and Von Bertalanffy model, as it gave higher R2 and lower AIC and RMSE for the leaves of A. thaliana at different growth stages (i.e., early leaf, mid-term leaf and late leaf).
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| 11. |
- Jin, Yuqing, et al.
(författare)
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Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)
- 2016
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average H-e = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.
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| 12. |
- Li, WM, et al.
(författare)
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Plasma metabolomics and lipidomics signatures of motoric cognitive risk syndrome in community-dwelling older adults
- 2022
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Ingår i: Frontiers in aging neuroscience. - : Frontiers Media SA. - 1663-4365. ; 14, s. 977191-
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Tidskriftsartikel (refereegranskat)abstract
- Motoric cognitive risk syndrome (MCR) is characterized by subjective cognitive complaints (SCCs) and slow gait (SG). Metabolomics and lipidomics may potentiate disclosure of the underlying mechanisms of MCR.MethodsThis was a cross-sectional study from the West China Health and Aging Trend cohort study (WCHAT). The operational definition of MCR is the presence of SCCs and SG without dementia or mobility disability. The test and analysis were based on untargeted metabolomics and lipidomics, consensus clustering, lasso regression and 10-fold cross-validation.ResultsThis study enrolled 6,031 individuals for clinical analysis and 577 plasma samples for omics analysis. The overall prevalence of MCR was 9.7%, and the prevalence of MCR-only, assessed cognitive impairment-only (CI-only) and MCR-CI were 7.5, 13.3, and 2.1%, respectively. By consensus clustering analysis, MCR-only was clustered into three metabolic subtypes, MCR-I, MCR-II and MCR-III. Clinically, body fat mass (OR = 0.89, CI = 0.82–0.96) was negatively correlated with MCR-I, and comorbidity (OR = 2.19, CI = 1.10–4.38) was positively correlated with MCR-III. Diabetes mellitus had the highest ORs above 1 in MCR-II and MCR-III (OR = 3.18, CI = 1.02–9.91; OR = 2.83, CI = 1.33–6.04, respectively). The risk metabolites of MCR-III showed relatively high similarity with those of cognitive impairment. Notably, L-proline, L-cystine, ADMA, and N1-acetylspermidine were significantly changed in MCR-only, and PC(40:3), SM(32:1), TG(51:3), eicosanoic acid(20:1), methyl-D-galactoside and TG(50:3) contributed most to the prediction model for MCR-III.InterpretationPre-dementia syndrome of MCR has distinct metabolic subtypes, and SCCs and SG may cause different metabolic changes to develop MCR.
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| 13. |
- Liang, Jiamin, et al.
(författare)
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Synthesis of Zr2Al3C4 coatings on zirconium-alloy substrates with Al-C/Si interlayers as diffusion barriers
- 2019
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Ingår i: Vacuum. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0042-207X .- 1879-2715. ; 160, s. 128-132
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Tidskriftsartikel (refereegranskat)abstract
- Zr2Al3C4 coatings are potential candidates to prevent claddings of traditional Zr-based alloys from severe oxidation in water steam at high temperature. However, the diffusion of aluminum between coating and substrates at high temperature results in a coating composition deviating from the compositional domain for formation of the Zr2Al3C4 phase. Thus, synthesis of Zr2Al3C4 coatings on zirconium-alloy substrates is challenging. Here, we report that the Zr2Al3C4 phase can be obtained on zirconium alloy (ZIRLO) substrates where an Al-C/Si interlayer deposited by magnetron sputtering is introduced. The Al-C/Si interlayer prevented elemental diffusion of aluminum between the Zr-Al-C coating and the substrates during a post-annealing process at 800 degrees C for 3 h. The Al/Zr ratio of the Zr-Al-C coating after annealing was 0.96 and 0.59 in the cases of with and without Al-C/Si interlayer, respectively. Hence, the Al-C/Si interlayer acts as diffusion barrier and greatly decreases the deviation from the standard stoichiometric ratio of the Zr2Al3C4 phase, which facilitates the formation of the Zr2Al3C4 phase in the final coating.
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| 14. |
- Shao, Wen-Ze, et al.
(författare)
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DeblurGAN plus : Revisiting blind motion deblurring using conditional adversarial networks
- 2020
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Ingår i: Signal Processing. - : ELSEVIER. - 0165-1684 .- 1872-7557. ; 168
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Tidskriftsartikel (refereegranskat)abstract
- This work studies dynamic scene deblurring (DSD) of a single photograph, mainly motivated by the very recent DeblurGAN method. It is discovered that training the generator alone of DeblurGAN will result in both regular checkerboard effects and irregular block color excursions unexpectedly. In this paper, two aspects of endeavors are made for a more effective and robust adversarial learning approach to DSD. On the one hand, a kind of opposite-channel -based discriminative priors is developed, improving the deblurring performance of DeblurGAN without additional computational burden in the testing phase. On the other hand, a computationally more efficient while architecturally more robust auto -encoder is developed as a substitute of the original generator in DeblurGAN, promoting DeblurGAN to a new state-of-the-art method for DSD. For brevity, the proposed approach is dubbed as DeblurGAN+. Experimental results on the benchmark GoPro dataset validate that DeblurGAN+ achieves more than 1.5 dB improvement than DeblurGAN in terms of PSNR as trained utilizing the same amount of data. More importantly, the results on realistic non -uniform blurred images demonstrate that DeblurGAN+ is really more effective than DeblurGAN as well as most of variational model-based methods in terms of both blur removal and detail recovery.
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| 15. |
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The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
- 2022
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Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
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Tidskriftsartikel (refereegranskat)abstract
- This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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| 16. |
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| 17. |
- Wang, Sainan, et al.
(författare)
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Second-line antituberculosis drug exposure thresholds predictive of adverse events in multidrug-resistant tuberculosis treatment
- 2024
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Ingår i: International Journal of Infectious Diseases. - : ELSEVIER SCI LTD. - 1201-9712 .- 1878-3511. ; 140, s. 62-69
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: This study aimed to investigate the association between drug exposure and adverse events (AEs) during the standardized multidrug-resistant tuberculosis (MDR -TB) treatment, as well as to identify predictive drug exposure thresholds. Methods: We conducted a prospective, observational multicenter study among participants receiving standardized MDR -TB treatment between 2016 and 2019 in China. AEs were monitored throughout the treatment and their relationships to drug exposure (e.g., the area under the drug concentration -time curve from 0 to 24 h, AUC0-24 h ) were analyzed. The thresholds of pharmacokinetic predictors of observed AEs were identified by boosted classification and regression tree (CART) and further evaluated by external validation. Results: Of 197 study participants, 124 (62.9%) had at least one AE, and 15 (7.6%) experienced serious AEs. The association between drug exposure and AEs was observed including bedaquiline, its metabolite M2, moxifloxacin and QTcF prolongation (QTcF > 450 ms), linezolid and mitochondrial toxicity, cycloserine and psychiatric AEs. The CART -derived thresholds of AUC0-24 h predictive of the respective AEs were 3.2 mg <middle dot>h/l (bedaquiline M2); 49.3 mg <middle dot>h/l (moxifloxacin); 119.3 mg <middle dot>h/l (linezolid); 718.7 mg <middle dot>h/l (cycloserine). Conclusions: This study demonstrated the drug exposure thresholds predictive of AEs for key drugs against MDR -TB treatment. Using the derived thresholds will provide the knowledge base for further randomized clinical trials of dose adjustment to minimize the risk of AEs.
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| 18. |
- Wei, Peng, et al.
(författare)
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Charactering the Peak-to-Average Power Ratio of OTFS Signals : A Large System Analysis
- 2022
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Ingår i: IEEE Transactions on Wireless Communications. - : Institute of Electrical and Electronics Engineers (IEEE). - 1536-1276 .- 1558-2248. ; 21:6, s. 3705-3720
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Tidskriftsartikel (refereegranskat)abstract
- Orthogonal time frequency space (OTFS) system constitutes an effective structure conceived for efficiently utilizing the channel information, which is capable of achieving a promising transmission performance in high-mobility environment. To extract enough channel diversity, a two-dimensional Fourier transformation combined with a pulse shape is designed at the OTFS transmitter. Consequently, the amplitude of OTFS signals may fluctuate drastically, owing to the combined dependency of the OTFS transformation and the pulse shape. To quantify the amplitude fluctuation, we investigate the peak-to-average power ratio (PAPR) of OTFS signals, for a large amount of data in the delay-Doppler domain. We first reveal that when the number of data points approaches to infinity, based on central limit theorems for dependent variables, the complexvalued OTFS signals weakly converge to a Gaussian distribution. Then, according to the extremal theory of the Chi-squared process for stationary OTFS signals, an accurate expression of the PAPR distribution is derived, depending on the transmit pulse and the number of data points. It is also demonstrated that upon modifying the exponential factor, the analytical PAPR expression is applicable for the non-stationary Gaussian distribution caused by the bandlimited pulse with a large roll-off factor. Simulation results confirm the accuracy of the analytical PAPR probability for practical conditions.
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| 19. |
- Wu, ZC, et al.
(författare)
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Tumor suppressor ZHX2 inhibits NAFLD-HCC progression via blocking LPL-mediated lipid uptake
- 2020
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Ingår i: Cell death and differentiation. - : Springer Science and Business Media LLC. - 1476-5403 .- 1350-9047. ; 27:5, s. 1693-1708
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Tidskriftsartikel (refereegranskat)abstract
- Non-alcoholic fatty liver disease (NAFLD) leads to hepatocellular carcinoma (HCC). However, the underlying mechanism remains largely unclear. Here, we investigated the role of the tumor suppressor Zinc fingers and homeoboxes 2 (ZHX2) in the progression of NAFLD to HCC. ZHX2 expression was significantly decreased in fatty liver tissues, especially in the liver with NAFLD–HCC. ZHX2 overexpression disturbed lipid homeostasis of cultured HCC cells, and inhibited lipid deposition in hepatocytes both in vitro and in vivo. Moreover, ZHX2 inhibited uptake of exogenous lipids through transcriptional suppression of lipid lipase (LPL), leading to retarded proliferation of HCC cells. Importantly, LPL overexpression significantly reversed ZHX2-mediated inhibition of HCC cell proliferation, xenograft tumor growth, lipid deposition, and spontaneous liver tumor formation. Consistently, IHC staining demonstrated a negative correlation of ZHX2 with LPL in an HCC cohort. Collectively, ZHX2 protects hepatocytes from abnormal lipid deposition in NAFLD through transcriptional repression of LPL, which subsequently retards cell growth and NAFLD–HCC progression. These findings illustrate a novel mechanism of NAFLD progression into HCC.
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