| 1. |
- 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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| 2. |
- Su, Changqing, et al.
(författare)
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Gene-Viral Cancer Therapy Using Dual-Regulated Oncolytic Adenovirus with Antiangiogenesis Gene for Increased Efficacy.
- 2008
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Ingår i: Molecular Cancer Research. - 1557-3125. ; 6, s. 568-575
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Tidskriftsartikel (refereegranskat)abstract
- Conditionally replicative adenovirus (CRAD) represents a promising approach for cancer therapy. Several CRADs controlled by the human telomerase reverse transcriptase promoter have been developed. However, because of their replicative capacity, the importance of cancer specificity for CRADs needs to be further emphasized. In this study, we have developed a novel dual-regulated CRAD, CNHK500-mE, which has its E1a and E1b gene controlled by the human telomerase reverse transcriptase promoter and the hypoxia response element, respectively. It also carries a mouse endostatin expression cassette controlled by the cytomegalovirus promoter. These properties allow for increased cancer cell targeting specificity and decreased adverse side effects. We showed that CNHK500-mE preferentially replicated in cancer cells. Compared with a replication-defective vector carrying the same endostatin expression cassette, CNHK500-mE-mediated transgene expression level was markedly increased via viral replication within cancer cells. In the nasopharyngeal tumor xenograft model, CNHK500-mE injection resulted in antitumor efficacy at day 7 after therapy. Three weeks later, it led to significant inhibition of xenograft tumor growth due to the combined effects of viral oncolytic therapy and antiangiogenesis gene therapy. Pathologic examination showed that most cancer cells were positive for adenoviral capsid protein and for apoptotic terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling in the CNHK500-mE-treated tumor tissues, and the microvessels in these tumor tissues were diminished in quantity and abnormal in morphology. These results suggest that, as a potential cancer therapeutic agent, the CNHK500-mE is endowed with higher specificity to cancer cells and low cytotoxicity to normal cells. (Mol Cancer Res 2008;6(4):OF1-8).
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| 3. |
- Wan, Shaohua, et al.
(författare)
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Deep Learning Models for Real-time Human Activity Recognition with Smartphones
- 2020
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Ingår i: Mobile Networks and Applications. - : Springer. - 1383-469X .- 1572-8153. ; 25:2, s. 743-755
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Tidskriftsartikel (refereegranskat)abstract
- With the widespread application of mobile edge computing (MEC), MEC is serving as a bridge to narrow the gaps between medical staff and patients. Relatedly, MEC is also moving toward supervising individual health in an automatic and intelligent manner. One of the main MEC technologies in healthcare monitoring systems is human activity recognition (HAR). Built-in multifunctional sensors make smartphones a ubiquitous platform for acquiring and analyzing data, thus making it possible for smartphones to perform HAR. The task of recognizing human activity using a smartphone's built-in accelerometer has been well resolved, but in practice, with the multimodal and high-dimensional sensor data, these traditional methods fail to identify complicated and real-time human activities. This paper designs a smartphone inertial accelerometer-based architecture for HAR. When the participants perform typical daily activities, the smartphone collects the sensory data sequence, extracts the high-efficiency features from the original data, and then obtains the user's physical behavior data through multiple three-axis accelerometers. The data are preprocessed by denoising, normalization and segmentation to extract valuable feature vectors. In addition, a real-time human activity classification method based on a convolutional neural network (CNN) is proposed, which uses a CNN for local feature extraction. Finally, CNN, LSTM, BLSTM, MLP and SVM models are utilized on the UCI and Pamap2 datasets. We explore how to train deep learning methods and demonstrate how the proposed method outperforms the others on two large public datasets: UCI and Pamap2.
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| 4. |
- Wei, Yanfei, et al.
(författare)
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Stalled oligodendrocyte differentiation in IDH-mutant gliomas.
- 2023
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Ingår i: Genome medicine. - 1756-994X. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Roughly 50% of adult gliomas harbor isocitrate dehydrogenase (IDH) mutations. According to the 2021 WHO classification guideline, these gliomas are diagnosed as astrocytomas, harboring no 1p19q co-deletion, or oligodendrogliomas, harboring 1p19q co-deletion. Recent studies report that IDH-mutant gliomas share a common developmental hierarchy. However, the neural lineages and differentiation stages in IDH-mutant gliomas remain inadequately characterized.Using bulk transcriptomes and single-cell transcriptomes, we identified genes enriched in IDH-mutant gliomas with or without 1p19q co-deletion, we also assessed the expression pattern of stage-specific signatures and key regulators of oligodendrocyte lineage differentiation. We compared the expression of oligodendrocyte lineage stage-specific markers between quiescent and proliferating malignant single cells. The gene expression profiles were validated using RNAscope analysis and myelin staining and were further substantiated using data of DNA methylation and single-cell ATAC-seq. As a control, we assessed the expression pattern of astrocyte lineage markers.Genes concordantly enriched in both subtypes of IDH-mutant gliomas are upregulated in oligodendrocyte progenitor cells (OPC). Signatures of early stages of oligodendrocyte lineage and key regulators of OPC specification and maintenance are enriched in all IDH-mutant gliomas. In contrast, signature of myelin-forming oligodendrocytes, myelination regulators, and myelin components are significantly down-regulated or absent in IDH-mutant gliomas. Further, single-cell transcriptomes of IDH-mutant gliomas are similar to OPC and differentiation-committed oligodendrocyte progenitors, but not to myelinating oligodendrocyte. Most IDH-mutant glioma cells are quiescent; quiescent cells and proliferating cells resemble the same differentiation stage of oligodendrocyte lineage. Mirroring the gene expression profiles along the oligodendrocyte lineage, analyses of DNA methylation and single-cell ATAC-seq data demonstrate that genes of myelination regulators and myelin components are hypermethylated and show inaccessible chromatin status, whereas regulators of OPC specification and maintenance are hypomethylated and show open chromatin status. Markers of astrocyte precursors are not enriched in IDH-mutant gliomas.Our studies show that despite differences in clinical manifestation and genomic alterations, all IDH-mutant gliomas resemble early stages of oligodendrocyte lineage and are stalled in oligodendrocyte differentiation due to blocked myelination program. These findings provide a framework to accommodate biological features and therapy development for IDH-mutant gliomas.
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| 5. |
- Yang, Weizhao, et al.
(författare)
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Transcriptome sequencing provides evidence of genetic assimilation in a toad-headed lizard at high altitude
- 2021
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Ingår i: Asian Herpetological Research. - 2095-0357. ; 12:3, s. 315-322
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Tidskriftsartikel (refereegranskat)abstract
- Understanding how organisms adapt to the environment is a compelling question in modern evolutionary biology. Genetic assimilation provides an alternative hypothesis to explain adaptation, in which phenotypic plasticity is first triggered by environmental factors, followed by selection on genotypes that reduce the plastic expression of phenotypes. To investigate the evidence of genetic assimilation in a high-altitude dweller, the toad-headed agama Phr ynocephalus vlangalii, we conducted a translocation experiment by moving individuals from high-to low-altitude environments. We then measured their gene expression profiles by transcriptome sequencing in heart, liver and muscle, and compared them to two low-altitude species P. axillaris and P. fors ythii. The results showed that the general expression profile of P. vlangalii was similar to its viviparous relative P. fors ythii, however, the differentially expressed genes in the liver of P. vlangalii showed a distinct pattern compared to both the low-altitude species. In particular, several key genes (FASN, ACAA2 and ECI2) within fatty acid metabolic pathway were no longer differentially expressed in P. valgnalii, suggesting the loss of plasticity for this pathway after translocation. This study provides evidence of genetic assimilation in fatty acid metabolism that may have facilitated the adaptation to high-altitude for P. vlangalii.
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| 6. |
- Zhang, Huai, et al.
(författare)
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A global survey on the use of the international classification of diseases codes for metabolic dysfunction-associated fatty liver disease.
- 2024
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Ingår i: Hepatology international. - 1936-0541.
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Tidskriftsartikel (refereegranskat)abstract
- With the implementation of the 11th edition of the International Classification of Diseases (ICD-11) and the publication of the metabolic dysfunction-associated fatty liver disease (MAFLD) nomenclature in 2020, it is important to establish consensus for the coding of MAFLD in ICD-11. This will inform subsequent revisions of ICD-11.Using the Qualtrics XM and WJX platforms, questionnaires were sent online to MAFLD-ICD-11 coding collaborators, authors of papers, and relevant association members.A total of 890 international experts in various fields from 61 countries responded to the survey. We also achieved full coverage of provincial-level administrative regions in China. 77.1% of respondents agreed that MAFLD should be represented in ICD-11 by updating NAFLD, with no significant regional differences (77.3% in Asia and 76.6% in non-Asia, p=0.819). Over 80% of respondents agreed or somewhat agreed with the need to assign specific codes for progressive stages of MAFLD (i.e. steatohepatitis) (92.2%), MAFLD combined with comorbidities (84.1%), or MAFLD subtypes (i.e., lean, overweight/obese, and diabetic) (86.1%).This global survey by a collaborative panel of clinical, coding, health management and policy experts, indicates agreement that MAFLD should be coded in ICD-11. The data serves as a foundation for corresponding adjustments in the ICD-11 revision.
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