| 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. |
- Liu, Jian, et al.
(författare)
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Quantitative proteomics approach reveals novel biomarkers and pathological mechanism of keloid
- 2022
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Ingår i: PROTEOMICS - Clinical Applications. - : John Wiley & Sons. - 1862-8346 .- 1862-8354. ; 16:4
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Tidskriftsartikel (refereegranskat)abstract
- Background Keloid is a pathological skin scar formation with complex and unclear molecular pathology mechanism. Novel biomarkers and associated mechanisms are needed to improve current therapies.Objectives To identify novel biomarkers and underlying pathological mechanisms of keloids.MethodsSix pairs of keloid scar tissues and corresponding normal skin tissues were quantitatively analyzed by a high-resolution label-free mass spectrometry-based proteomics approach. Differential protein expression data was further analyzed by a comprehensive bioinformatics approach to identify novel biomarkers and mechanistic pathways for keloid formation. Candidate biomarkers were validated experimentally.Results In total, 1359 proteins were identified by proteomic analysis. Of these, 206 proteins exhibited a significant difference in expression between keloid scar and normal skin tissues. RCN3 and CALU were significantly upregulated in keloids. RCN1 and PDGFRL were uniquely expressed in keloids. Pathway analysis suggested that the XBP1-mediated unfolded protein response (UPR) pathway was involved in keloid formation. Moreover, a PDGFRL centric gene coexpression network was constructed to illustrate its function in skin.Conclusions and Clinical Relevance Our study proposed four novel biomarkers and highlighted the role of XBP1-mediated UPR pathway in the pathology of keloids. It provided novel biological insights that contribute to develop novel therapeutic strategies for keloids.
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| 3. |
- Guo, Jingqiu, et al.
(författare)
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Characteristics of Mixed Traffic Flow in Two-lane Scenario Based on Cooperative Gaming Method
- 2019
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Ingår i: Tongji Daxue Xuebao/Journal of Tongji University. - 0253-374X. ; 47:7, s. 976-983
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Tidskriftsartikel (refereegranskat)abstract
- This paper aims to explore the impacts of connected and automated vehicles (CAV) on traffic flow efficiency based on in-depth microscopic simulation studies using cooperative gaming method. First, the Gipps car-following models were integrated into an improved cellular automata model to mimic the regular vehicle's driving behavior. Then, cooperative gaming method integrated with enhanced Q-learning was employed as the modeling platform for CAV, to strengthen the capability of the simulation system in realistically reproducing CAV lane changing and car following behavior. Finally, a 2-lane freeway stretch was applied to our simulations, and with extensive simulation studies we obtained some promising results. The study results suggest that the impacts of CAV are quite positive. The inclusion of CAV considerably improves traffic flow, mean speed, and traffic capacity. Such understanding is essential for research concerning CAV as well as the CAV implication for future traffic management and control.
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| 4. |
- Gupta, Vikas, et al.
(författare)
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Fast and robust adaptation of organs-at-risk delineations from planning scans to match daily anatomy in pre-treatment scans for online-adaptive radiotherapy of abdominal tumors
- 2018
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Ingår i: Radiotherapy and Oncology. - : ELSEVIER IRELAND LTD. - 0167-8140 .- 1879-0887. ; 127:2, s. 332-338
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To validate a novel deformable image registration (DIR) method for online adaptation of planning organ-at-risk (OAR) delineations to match daily anatomy during hypo-fractionated RT of abdominal tumors. Materials and methods: For 20 liver cancer patients, planning OAR delineations were adapted to daily anatomy using the DIR on corresponding repeat CTs. The DIRs accuracy was evaluated for the entire cohort by comparing adapted and expert-drawn OAR delineations using geometric (Dice Similarity Coefficient (DSC), Modified Hausdorff Distance (MHD) and Mean Surface Error (MSE)) and dosimetric (D-max and D-mean) measures. Results: For all OARs, DIR achieved average DSC, MHD and MSE of 86%, 2.1 mm, and 1.7 mm, respectively, within 20 s for each repeat CT. Compared to the baseline (translations), the average improvements ranged from 2% (in heart) to 24% (in spinal cord) in DSC, and 25% (in heart) to 44% (in right kidney) in MHD and MSE. Furthermore, differences in dose statistics (D-max, D-mean and D-2%) using delineations from an expert and the proposed DIR were found to be statistically insignificant (p amp;gt; 0.01). Conclusion: The validated DIR showed potential for online-adaptive radiotherapy of abdominal tumors as it achieved considerably high geometric and dosimetric correspondences with the expert-drawn OAR delineations, albeit in a fraction of time required by experts. (C) 2018 The Authors. Published by Elsevier B.V.
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| 5. |
- Labiran, Clare, et al.
(författare)
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Genotyping markers used for multi locus VNTR analysis with ompA (MLVA-ompA) and multi sequence typing (MST) retain stability in Chlamydia trachomatis
- 2012
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Ingår i: Frontiers in Cellular and Infection Microbiology. - : Frontiers Media SA. - 2235-2988. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- We aimed to evaluate the stability of the Chlamydia trachomatis multi locus VNTR analysis (MLVA-ompA) and multi sequence typing (MST) systems through multiple passages in tissue culture. Firstly, we analyzed the stability of these markers through adaptation of C. trachomatis to tissue culture and secondly, we examined the stability of a four-locus MLVA-ompA and a five-locus MST system after multiple passages in tissue culture. Marker sequences were monitored through successive chlamydial developmental cycles to evaluate the stability of the individual DNA markers through many bacterial divisions and this, in turn, informed us of the usefulness of using such typing systems for short and long-term molecular epidemiology. Southampton genitourinary medicine (GUM) clinic isolates from endocervical swabs collected from C. trachomatis positive women were passaged through tissue culture. MLVA-ompA typing was applied to primary swab samples and to the same samples after C. trachomatis had been passaged through cell culture (eight passages). Sequence data from time-zero and passage-eight isolates were aligned with reference sequences to determine the stability of the markers. The Swedish new variant (nvCT) underwent 72 passages in cell culture and the markers of the two schemes were similarly analyzed. Analysis of genetic markers of the MLVA-ompA typing system before and after the isolates were introduced to tissue culture showed no change in the dominant sequence. The nvCT that had been passaged 72 times over the duration of a year also showed no variation in the dominant sequence for both the genotyping schemes. MLVA-ompA and MST markers are stable upon adaptation of C. trachomatis to tissue culture following isolation of strains from primary endocervical swab samples. These markers remain stable throughout multiple rounds of cell-division in tissue culture, concomitant with the incubation period and appearance of symptoms normally associated with host-infection. Both genotyping schemes are, therefore, suitable for epidemiology of C. trachomatis.
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| 6. |
- Lai, En Yin, et al.
(författare)
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Pressure induces intracellular calcium changes in juxtaglomerular cells in perfused afferent arterioles
- 2011
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Ingår i: Hypertension Research. - : Springer Science and Business Media LLC. - 0916-9636 .- 1348-4214. ; 34:8, s. 942-948
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Tidskriftsartikel (refereegranskat)abstract
- Calcium (Ca(2+)) has an important role in nearly all types of cellular secretion, with a particularly novel role in the juxtaglomerular (JG) cells in the kidney. In JG cells, Ca(2+) inhibits renin secretion, which is a major regulator of blood pressure and renal hemodynamics. However, whether alterations in afferent arteriolar (Af-Art) pressure change intracellular Ca(2+) concentration ([Ca(2+)](i)) in JG cells and whether [Ca(2+)](i) comes from extracellular or intracellular sources remains unknown. We hypothesize that increases in perfusion pressure in the Af-Art result in elevations in [Ca(2+)](i) in JG cells. We isolated and perfused Af-Art of C57BL6 mice and measured changes in [Ca(2+)](i) in JG cells in response to perfusion pressure changes. The JG cells' [Ca(2+)](i) was 93.3 +/- 2.2 nM at 60 mm Hg perfusion pressure and increased to 111.3 +/- 13.4, 119.6 +/- 7.3, 130.3 +/- 2.9 and 140.8 +/- 12.1 nM at 80, 100, 120 and 140 mm Hg, respectively. At 120 mm Hg, increases in [Ca(2+)](i) were reduced in mice receiving the following treatments: (1) the mechanosensitive cation channel blocker, gadolinium (94.6 +/- 7.5 nM); (2) L-type calcium channel blocker, nifedipine (105.8 +/- 7.5 nM); and (3) calcium-free solution plus ethylene glycol tetraacetic acid (96.0 +/- 5.8 nM). Meanwhile, the phospholipase C inhibitor, inositol triphosphate receptor inhibitor, T-type calcium channel blocker, N-type calcium channel blocker and Ca(2+)-ATPase inhibitor did not influence changes in [Ca(2+)](i) in JG cells. In summary, JG cell [Ca(2+)](i) rise as perfusion pressure increases; furthermore, the calcium comes from extracellular sources, specifically mechanosensitive cation channels and L-type calcium channels.
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| 7. |
- Li, Xixing, et al.
(författare)
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Flexible Job Shop Composite Dispatching Rule Mining Approach Based on an Improved Genetic Programming Algorithm
- 2024
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Ingår i: Tsinghua Science and Technology. - : Tsinghua University. - 1007-0214 .- 1878-7606. ; 29:5, s. 1390-1408
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Tidskriftsartikel (refereegranskat)abstract
- To obtain a suitable scheduling scheme in an effective time range, the minimum completion time is taken as the objective of Flexible Job Shop scheduling Problems (FJSP) with different scales, and Composite Dispatching Rules (CDRs) are applied to generate feasible solutions. Firstly, the binary tree coding method is adopted, and the constructed function set is normalized. Secondly, a CDR mining approach based on an Improved Genetic Programming Algorithm (IGPA) is designed. Two population initialization methods are introduced to enrich the initial population, and a superior and inferior population separation strategy is designed to improve the global search ability of the algorithm. At the same time, two individual mutation methods are introduced to improve the algorithm’s local search ability, to achieve the balance between global search and local search. In addition, the effectiveness of the IGPA and the superiority of CDRs are verified through comparative analysis. Finally, Deep Reinforcement Learning (DRL) is employed to solve the FJSP by incorporating the CDRs as the action set, the selection times are counted to further verify the superiority of CDRs.
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| 8. |
- Li, Yibing, et al.
(författare)
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Digital twin-based job shop anomaly detection and dynamic scheduling
- 2023
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Ingår i: Robotics and Computer-Integrated Manufacturing. - : Elsevier BV. - 0736-5845 .- 1879-2537. ; 79
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Tidskriftsartikel (refereegranskat)abstract
- Scheduling scheme is one of the critical factors affecting the production efficiency. In the actual production, anomalies will lead to scheduling deviation and influence scheme execution, which makes the traditional job shop scheduling methods are not sufficient to meet the needs of real-time and accuracy. By introducing digital twin (DT), further convergence between physical and virtual space can be achieved, which enormously reinforces real-time performance of job shop scheduling. For flexible job shop, an anomaly detection and dynamic scheduling framework based on DT is proposed in this paper. Previously, a multi-level production process monitoring model is proposed to detect anomaly. Then, a real-time optimization strategy of scheduling scheme based on rolling window mechanism is explored to enforce dynamic scheduling optimization. Finally, the improved grey wolf optimization algorithm is introduced to solve the scheduling problem. Under this framework, it is possible to monitor the deviation between the actual processing state and the planned processing state in real time and effectively reduce the deviation. An equipment manufacturing job shop is taken as a case study to illustrate the effectiveness and advantages of the proposed framework.
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| 9. |
- Seth-Smith, Helena M. B., et al.
(författare)
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Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain
- 2009
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Background: Chlamydia trachomatis is the most common cause of sexually transmitted infections globally and the leading cause of preventable blindness in the developing world. There are two biovariants of C trachomatis: 'trachoma', causing ocular and genital tract infections, and the invasive 'lymphogranuloma venereum' strains. Recently, a new variant of the genital tract C trachomatis emerged in Sweden. This variant escaped routine diagnostic tests because it carries a plasmid with a deletion. Failure to detect this strain has meant it has spread rapidly across the country provoking a worldwide alert. In addition to being a key diagnostic target, the plasmid has been linked to chlamydial virulence. Analysis of chlamydial plasmids and their cognate chromosomes was undertaken to provide insights into the evolutionary relationship between chromosome and plasmid. This is essential knowledge if the plasmid is to be continued to be relied on as a key diagnostic marker, and for an understanding of the evolution of Chlamydia trachomatis. Results: The genomes of two new C trachomatis strains were sequenced, together with plasmids from six C trachomatis isolates, including the new variant strain from Sweden. The plasmid from the new Swedish variant has a 377 bp deletion in the first predicted coding sequence, abolishing the site used for PCR detection, resulting in negative diagnosis. In addition, the variant plasmid has a 44 bp duplication downstream of the deletion. The region containing the second predicted coding sequence is the most highly conserved region of the plasmids investigated. Phylogenetic analysis of the plasmids and chromosomes are fully congruent. Moreover this analysis also shows that ocular and genital strains diverged from a common C trachomatis progenitor. Conclusion: The evolutionary pathways of the chlamydial genome and plasmid imply that inheritance of the plasmid is tightly linked with its cognate chromosome. These data suggest that the plasmid is not a highly mobile genetic element and does not transfer readily between isolates. Comparative analysis of the plasmid sequences has revealed the most conserved regions that should be used to design future plasmid based nucleic acid amplification tests, to avoid diagnostic failures.
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| 10. |
- Sigar, Ira M., et al.
(författare)
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Plasmid deficiency in urogenital isolates of Chlamydia trachomatis reduces infectivity and virulence in a mouse model
- 2014
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Ingår i: Pathogens and Disease. - : Wiley-Blackwell. - 2049-632X. ; 70:1, s. 61-69
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Tidskriftsartikel (refereegranskat)abstract
- We hypothesized that the plasmid of urogenital isolates of Chlamydia trachomatis would modulate infectivity and virulence in a mouse model. To test this hypothesis, we infected female mice in the respiratory or urogenital tract with graded doses of a human urogenital isolate of C.trachomatis, serovar F, possessing the cognate plasmid. For comparison, we inoculated mice with a plasmid-free serovar F isolate. Following urogenital inoculation, the plasmid-free isolate displayed significantly reduced infectivity compared with the wild-type strain with the latter yielding a 17-fold lower infectious dose to yield 50% infection. When inoculated via the respiratory tract, the plasmid-free isolate exhibited reduced infectivity and virulence (as measured by weight change) when compared to the wild-type isolate. Further, differences in infectivity, but not in virulence were observed in a C.trachomatis, serovar E isolate with a deletion within the plasmid coding sequence 1 when compared to a serovar E isolate with no mutations in the plasmid. We conclude that plasmid loss reduces virulence and infectivity in this mouse model. These findings further support a role for the chlamydial plasmid in infectivity and virulence in vivo.
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| 11. |
- Wang, Yibing, et al.
(författare)
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An individualized strategy to estimate the effect of deformable registration uncertainty on accumulated dose in the upper abdomen
- 2018
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Ingår i: Physics in Medicine and Biology. - : IOP PUBLISHING LTD. - 0031-9155 .- 1361-6560. ; 63:12
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Tidskriftsartikel (refereegranskat)abstract
- In the abdomen, it is challenging to assess the accuracy of deformable image registration (DIR) for individual patients, due to the lack of clear anatomical landmarks, which can hamper clinical applications that require high accuracy DIR, such as adaptive radiotherapy. In this study, we propose and evaluate a methodology for estimating the impact of uncertainties in DIR on calculated accumulated dose in the upper abdomen, in order to aid decision making in adaptive treatment approaches. Sixteen liver metastasis patients treated with SBRT were evaluated. Each patient had one planning and three daily treatment CT-scans. Each daily CT scan was deformably registered 132 times to the planning CT-scan, using a wide range of parameter settings for the registration algorithm. A subset of realistic registrations was then objectively selected based on distances between mapped and target contours. The underlying 3D transformations of these registrations were used to assess the corresponding uncertainties in voxel positions, and delivered dose, with a focus on accumulated maximum doses in the hollow OARs, i.e. esophagus, stomach, and duodenum. The number of realistic registrations varied from 5 to 109, depending on the patient, emphasizing the need for individualized registration parameters. Considering for all patients the realistic registrations, the 99th percentile of the voxel position uncertainties was 5.6 +/- 3.3 mm. This translated into a variation (difference between 1st and 99th percentile) in accumulated Dmax in hollow OARs of up to 3.3 Gy. For one patient a violation of the accumulated stomach dose outside the uncertainty band was detected. The observed variation in accumulated doses in the OARs related to registration uncertainty, emphasizes the need to investigate the impact of this uncertainty for any DIR algorithm prior to clinical use for dose accumulation. The proposed method for assessing on an individual patient basis the impact of uncertainties in DIR on accumulated dose is in principle applicable for all DIR algorithms allowing variation in registration parameters.
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| 12. |
- Wang, Yibing, et al.
(författare)
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Genetic Transformation of a Clinical (Genital Tract), Plasmid-Free Isolate of Chlamydia trachomatis: Engineering the Plasmid as a Cloning Vector
- 2013
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:3
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Tidskriftsartikel (refereegranskat)abstract
- Our study had three objectives: to extend the plasmid-based transformation protocol to a clinical isolate of C. trachomatis belonging to the trachoma biovar, to provide "proof of principle'' that it is possible to "knock out'' selected plasmid genes (retaining a replication competent plasmid) and to investigate the plasticity of the plasmid. A recently developed, plasmid-based transformation protocol for LGV isolates of C. trachomatis was modified and a plasmid-free, genital tract C. trachomatis isolate from Sweden (SWFP-) was genetically transformed. Transformation of this non-LGV C. trachomatis host required a centrifugation step, but the absence of the natural plasmid removed the need for plaque purification of transformants. Transformants expressed GFP, were penicillin resistant and iodine stain positive for accumulated glycogen. The transforming plasmid did not recombine with the host chromosome. A derivative of pGFP::SW2 carrying a deletion of the plasmid CDS5 gene was engineered. CDS5 encodes pgp3, a protein secreted from the inclusion into the cell cytoplasm. This plasmid (pCDS5KO) was used to transform C. trachomatis SWFP-, and established that pgp3 is dispensable for plasmid function. The work shows it is possible to selectively delete segments of the chlamydial plasmid, and this is the first step towards a detailed molecular dissection of the role of the plasmid. The 3.6 kb beta-galactosidase cassette was inserted into the deletion site of CDS5 to produce plasmid placZ-CDS5KO. Transformants were penicillin resistant, expressed GFP and stained for glycogen. In addition, they expressed b-galactosidase showing that the lacZ cassette was functional in C. trachomatis. An assay was developed that allowed the visualisation of individual inclusions by X-gal staining. The ability to express active beta-galactosidase within chlamydial inclusions is an important advance as it allows simple, rapid assays to measure directly chlamydial infectivity without the need for plaquing, fluorescence or antibody staining.
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| 13. |
- Wang, Yibing, et al.
(författare)
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Transformation of a plasmid-free, genital tract isolate of Chlamydia trachomatis with a plasmid vector carrying a deletion in CDS6 revealed that this gene regulates inclusion phenotype
- 2013
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Ingår i: Pathogens and Disease. - 2049-632X. ; 67:2, s. 100-103
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Tidskriftsartikel (refereegranskat)abstract
- The development of a plasmid-based genetic transformation protocol for Chlamydia trachomatis provides the basis for the detailed investigation of the function of the chlamydial plasmid and its individual genes or coding sequences (CDS). In this study we constructed a plasmid vector with CDS6 deleted (pCDS6KO) from the original Escherichia coli/C. trachomatis shuttle vector pGFP::SW2. pCDS6KO was transformed into a clinical isolate of C. trachomatis from Sweden that is plasmid-free (C. trachomatis SWFP-). Penicillin-resistant transformants expressing the green fluorescent protein were selected. These transformants did not stain with iodine, indicating that this property is regulated by CDS6 or its gene product. In addition, mature inclusions of C. trachomatis SWFP-transformed by pCDS6KO displayed an identical morphological phenotype to the untransformed plasmid-free recipient host. In this phenotype the morphology of inclusions was altered with the chlamydiae lining the periphery of the inclusion leaving a 'hole' in the centre. These green fluorescent inclusions appear 'doughnut-shaped' with an empty centre when examined under blue light, giving rise to a characteristic 'black hole' phenotype. Our study demonstrates the power of the new genetic system for investigating chlamydial gene function using gene deletion technology.
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| 14. |
- Xu, Xiaobao, et al.
(författare)
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Efficient p-type dye-sensitized solar cells based on disulfide/thiolate electrolytes
- 2013
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 5:17, s. 7963-7969
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Tidskriftsartikel (refereegranskat)abstract
- Herein, an organic redox couple 1-methy-1H-tetrazole-5-thiolate (T-) and its disulfide dimer (T-2) redox shuttle, as an electrolyte, is introduced in a p-type dye-sensitized solar cell (DSC) on the basis of an organic dye (P1) sensitizer and nanocrystal CuCrO2 electrode. Using this iodide-free transparent redox electrolyte in conjunction with the sensitized heterojunction, we achieve a high open-circuit voltage of over 300 mV. An optimal efficiency of 0.23% is obtained using a CoS counter electrode and an optimized electrolyte composition under AM 1.5 G 100 mW cm(-2) light illumination which, to the best of our knowledge, represents the highest efficiency that has so far been reported for p-type DSCs using organic redox couples.
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