| 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. |
- An, Junghwa, et al.
(författare)
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Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:2, s. 404-408
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Tidskriftsartikel (refereegranskat)abstract
- This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.
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| 3. |
- Jin, Ying-Hui, et al.
(författare)
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Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
- 2020
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Ingår i: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
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| 4. |
- Canesin, Giacomo, et al.
(författare)
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Scavenging of Labile Heme by Hemopexin Is a Key Checkpoint in Cancer Growth and Metastases
- 2020
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Ingår i: Cell Reports. - : Elsevier BV. - 2211-1247. ; 32:12
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Tidskriftsartikel (refereegranskat)abstract
- Canesin et al. describe a role and mechanism for labile heme as a key player in regulating gene expression to promote carcinogenesis via binding to G-quadruplex in the c-MYC promoter. Hemopexin, a heme scavenger, may be used as a strategy to block progression of cancer.
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| 5. |
- Cao, Da-fu, et al.
(författare)
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Evaluation of prestress losses in prestressed concrete specimens subjected to freeze–thaw cycles
- 2016
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Ingår i: Structure and Infrastructure Engineering. - Abington, UK : Taylor & Francis. - 1573-2479 .- 1744-8980. ; 12:2, s. 159-170
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Tidskriftsartikel (refereegranskat)abstract
- Prestressed concrete structures are considered to be reliable and durable. However, their long-term performance when subjected to frost attack is still unclear. In this work, experiments were carried out to evaluate the prestress losses in post-tensioned prestressed concrete specimens subjected to freeze–thaw cycles (FTCs). Two cases were considered: in one case, a series of specimens were prepared and tested in a freeze–thaw chamber; in the second case, the same series of specimens were tested in an indoor environment (outside the chamber). The difference between the prestress losses of the specimens inside the freeze–thaw chamber and those outside the chamber equalled the prestress losses due to FTCs. When using mathematical models to predict the prestress losses due to the FTCs, it was found that they were relatively small when the concrete was slightly damaged. However, they increased rapidly when the FTCs were repeated. The eccentricity of the prestress wires led to larger prestress losses when subjected to FTCs. Moreover, the same cross section and eccentricity resulted in similar prestress losses due to the FTCs, and the relatively high-strength concrete could withstand more FTCs.
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| 6. |
- Cardoso-Moreira, Margarida, et al.
(författare)
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Gene expression across mammalian organ development
- 2019
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Ingår i: Nature. - : NATURE PUBLISHING GROUP. - 0028-0836 .- 1476-4687. ; 571:7766, s. 505-
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Tidskriftsartikel (refereegranskat)abstract
- The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early organogenesis to adulthood for human, rhesus macaque, mouse, rat, rabbit, opossum and chicken. Comparisons of gene expression patterns identified correspondences of developmental stages across species, and differences in the timing of key events during the development of the gonads. We found that the breadth of gene expression and the extent of purifying selection gradually decrease during development, whereas the amount of positive selection and expression of new genes increase. We identified differences in the temporal trajectories of expression of individual genes across species, with brain tissues showing the smallest percentage of trajectory changes, and the liver and testis showing the largest. Our work provides a resource of developmental transcriptomes of seven organs across seven species, and comparative analyses that characterize the development and evolution of mammalian organs.
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| 7. |
- Feng, Tongbao, et al.
(författare)
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miR-124 downregulation leads to breast cancer progression via LncRNA-MALAT1 regulation and CDK4/E2F1 signal activation.
- 2016
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Ingår i: Oncotarget. - : Impact Journals, LLC. - 1949-2553. ; 7:13, s. 16205-16216
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Tidskriftsartikel (refereegranskat)abstract
- The long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been recently shown to be dysregulated in several cancers. However, the mechanisms underlying the role of MALAT1 in breast cancer remain unclear. Herein, we showed that MALAT1 was aberrantly increased in breast cancer tissues and cells. MALAT1-siRNA inhibited breast cancer cell proliferation and cell cycle progression in vitro and in vivo. Furthermore, MALAT1 acted as an endogenous potent regulator by directly binding to miR-124 and down-regulating miR-124 expression. In addition, MALAT1 reversed the inhibitory effect of miR-124 on breast cancer proliferation and was involved in the cyclin-dependent kinase 4 (CDK4) expression. Taken together, our data highlight the pivotal role of MALAT1 in breast cancer tumorigenesis. Moreover, the present study elucidated the MALAT1-miR-124-CDK4/E2F1 signaling pathway in breast cancer, which might provide a new approach for tackling breast cancer.
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| 8. |
- Gao, Hong, et al.
(författare)
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The landscape of tolerated genetic variation in humans and primates
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6648
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Tidskriftsartikel (refereegranskat)abstract
- Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
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| 9. |
- Guangming, Shao, et al.
(författare)
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A novel cooperative platform design for coupled USV-UAV systems
- 2019
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Ingår i: IEEE Transactions on Industrial Informatics. - : IEEE. - 1551-3203 .- 1941-0050. ; 15:9, s. 4913-4922
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents a novel cooperative USV-UAV platform to form a powerful combination, which offers foundations for collaborative task executed by the coupled USV-UAV systems. Adjustable buoys and unique carrier deck for the USV are designed to guarantee landing safety and transportation of UAV. The deck of USV is equipped with a series of sensors, and a multi-ultrasonic joint dynamic positioning algorithm is introduced for resolving the positioning problem of the coupled USV-UAV systems. To fulfill effective guidance for the landing operation of UAV, we design a hierarchical landing guide point generation algorithm to obtain a sequence of guide points. By employing the above sequential guide points, high quality paths are planned for the UAV. Cooperative dynamic positioning process of the USV-UAV systems is elucidated, and then UAV can achieve landing on the deck of USV steadily. Our cooperative USV-UAV platform is validated by simulation and water experiments.
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| 10. |
- Hassanein, M. F., et al.
(författare)
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Small-scale laterally-unrestrained corrugated web girders: (II) Parametric studies and LTB design
- 2022
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Ingår i: Thin-Walled Structures. - : Elsevier BV. - 0263-8231. ; 180
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Tidskriftsartikel (refereegranskat)abstract
- As shown in the companion paper, innovative tests of corrugated web girders (CWGs) were performed followed by validation of the finite element (FE) model. Accordingly, this paper continues investigating the lateral–torsional buckling of small-scale corrugated web girders through parametric studies. This is to expand the available data required to unveil their behaviour and strength. The layout of the tested girders is considered herein, where the webs of small corrugation dimensions are under pure bending moment with symmetrical boundary conditions. This study deals with the linear and nonlinear buckling analyses of the lateral–torsional buckling (LTB) of CWGs using ABAQUS software. Accordingly, 108 models are conducted, considering the effects of the girder length, web overall dimensions, corrugation dimensions, flange dimensions and different steel grades. The results show that increasing the girder length decreases consequently the ultimate flexural strength and stiffness of CWGs. With regard to the web overall dimensions, increasing the web depth is found to have a significant effect on the strength of CWGs in contrast to the effect of the web thickness value, which has insignificant effect on strength. Furthermore, the results revealed that increasing the flange dimensions increases subsequently the strengths of CWGs. In addition, it is noted that the lower the steel grade, the more effectively the material is used especially for girders failing elastically. Additionally, the critical and design LTB strengths of small-scale CWGs with small corrugation dimensions are evaluated. The comparisons show that the critical LTB stress requires modifications to accord well with FE results. Furthermore, comparisons of the ultimate FE strengths with those of Lindner's equation (1990), EC3 (2004) and AISC (2010) are provided. The comparisons exhibit that the predictions of Lindner's equation (1990) are suitable, while the predictions of EC3 (2004) and AISC (2010) are highly conservative. Therefore, modifications are made for EC3 (2004) and AISC (2010) design models to provide more appropriate design strengths for CWGs with small corrugation dimensions for use in buildings.
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