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3,739 results for “RePAIR”
Active repair of a dinuclear photocatalyst for visible light-driven hydrogen production
<p>The peer-reviewed publication for this dataset has been published in <em>Nature Chemistry</em> and can be accessed <em>via</em> <strong><a href="https://doi.org/10.1038/s41557-021-00860-6"> DOI 10.1038/s41557-021-00860-6</a></strong>. Please cite this when using the data.</p>
Using CSA Cement for Novel Waterway Repair Materials
<p>Many maritime structures (e.g., locks, dams, ports) in the US are either reaching or are past their design lives, and there are limited funds for necessary maintenance activities which can often lead to closures. These structures are not easy to detour and often require dewatering before repairs can be made. Closures can cause delays and business-related losses which can have a large economic effect. Thus, it is advantageous to reduce the repair time for maritime structures. BCSA (belitic calcium sulfoaluminate) cement is a promising repair material due to its properties. BCSA cement is a fast-setting hydraulic cement capable of reaching compressive strengths greater than 4000 psi (27.6 MPa) in less than 2 hours. BCSA also has low shrinkage and good long-term strengths. This research consisted of developing an optimal rapid-setting underwater repair mortar mixture design using BCSA cement. Properties such as compressive strength and workability were tested to select the best mix design. Additionally, soil-cements made with BCSA cement were compared to portland cement-based soil-cements. These soil cements have applications for the rapid repair of levees and earthen dams, but also for rapid soil stabilization. The results obtained proved that BCSA cement is a promising material for rapid underwater repairs and repairs of soil-based waterway structures.</p>
Reliable Paintless Dent Repair Shop in Sydney
<p>The repair relies on the experience and knowledge of the technician to ensure the panel can withstand the preferred method of repair. This mostly refers to the pulling technique where the quality of the paint on the car is the main factor to consider, if factory paint, it’s more resistant than a panel that is repainted. Auto Dent Care in Sydney is the reliable <a href="https://www.autodentcare.com.au/services/paintless-dent-removal/">Paintless Dent Repair shop in Sydney</a> with premier service to guarantee the best high-end repair for your vehicle.</p>
Rapid Repair of Cracks on the Embankment Slopes Using Bio-Cement
<p>This research explored the feasibility of using Microbially Induced Carbonate Precipitation (MICP) to improve fine-grained soil mechanical properties, seal the soil cracks, and assess the improvement of MICP on slope stability. The conducted research tasks include (1) direct shear tests to investigate the mechanical behavior and biogeochemical reactions of low-plasticity silt treated by MICP, (2) cyclic wetting-drying tests to assess the feasibility of using MICP to seal and waterproof the soil cracks, and (3) SLOPE/W modeling of a slope treated by MICP. Direct shear tests were used to evaluate the shear responses of the low-plasticity silt under different overburden pressures (12, 25, and 35 kPa) and different bio-cement treatments. A series of cyclic wetting-drying tests were used to assess the effectiveness of MICP treatment on healing soil cracks. Crack lengths, area, width, and area percentage were measured and compared before and after the MICP treatment. SLOPE/W analysis was performed to assess the factor of safety of a slope under MICP treatment. The direct shear tests results show that the peak shear strengths increased by an average of 30% from the untreated to the MICP-treated soil samples. The wetting-drying cycle tests results show that MICP treatment can heal desiccation cracks, reducing crack length, crack width, and crack area. The results of the SLOPE/W modeling show that the MICP treatment had a positive effect on the improvement of slope stability, but more field tests are needed for optimizing the treatment solutions and procedures and assessing the long-term effect and ecological impacts.</p>
Applying an Inconsistency Repair Mechanism for clone-and-own Code Smell Analysis: the Apo-games Case Study (Evaluation Data)
<p>This is a repository containing the artifacts and the results of the evaluation of the solution paper "Applying an Inconsistency Repair Mechanism for <em>clone-and-own</em> Code Smell Analysis: the Apo-games Case Study"</p>
Microscopy data from: Identification of genetic interactions with priB links the PriA/PriB DNA replication restart pathway to double-strand DNA break repair in Escherichia coli
<p>Collisions between DNA replication complexes (replisomes) and impediments such as damaged DNA or proteins tightly bound to the chromosome lead to premature dissociation of replisomes at least once per cell cycle in <em>Escherichia coli</em>. Left unrepaired, these events produce incompletely replicated chromosomes that cannot be properly partitioned into daughter cells. DNA replication restart, the process that reloads replisomes at prematurely terminated sites, is therefore essential in <em>E. coli</em> and other bacteria. Three replication restart pathways have been identified in <em>E. coli</em>: PriA/PriB, PriA/PriC, and PriC/Rep. A limited number of genetic interactions between replication restart and other genome maintenance pathways have been defined, but a systematic study placing replication restart reactions in a broader cellular context has not been performed. We have utilized transposon insertion sequencing to identify new genetic interactions between DNA replication restart pathways and other cellular systems. Known genetic interactors with the <em>priB</em> replication restart gene (uniquely involved in the PriA/PriB pathway) were confirmed and several novel <em>priB </em>interactions were discovered. Far fewer connections were found with the PriA/PriC or PriC/Rep pathways, suggesting a primacy role for the PriA/PriB pathway in <em>E. coli</em>. Targeted genetic and imaging-based experiments with <em>priB</em> and its genetic partners revealed significant double-strand DNA break (DSB) accumulation in strains with mutations in <em>dam</em>, <em>rep</em>, <em>rdgC</em>, <em>lexA</em>, or <em>polA</em>. Modulating the activity of the RecA recombinase partially suppressed the detrimental effects of <em>rdgC</em> or <em>lexA</em> mutations in Δ<em>priB</em> cells. Taken together, our results highlight roles for several genes in DSB homeostasis and define a genetic network that facilitates DNA repair/processing upstream of PriA/PriB-mediated DNA replication restart in <em>E. coli</em>.</p>
RBBP4 regulates the expression of Mre11-Rad50-NBS1(MRN)complex and promotes DNA double-strand breaks repair to mediate glioblastoma Chemoradiotherapy resistance
<p>Article <a>related</a> SUPPLEMENTARY data.</p> <p> </p>
Distinct mechanisms of mismatch repair deficiency delineate two modes of response to PD-1 immunotherapy in endometrial carcinoma
<p>Responses to immune checkpoint blockade (ICB) are variable even among mismatch repair deficient (MMRd) cancers. We completed a phase 2 clinical trial of the PD-1 inhibitor pembrolizumab in 24 patients with MMRd endometrial cancer (NCT02899793). Patients with mutational MMRd tumors (6 patients) had higher response rates and longer survival than those with epigenetic MMRd tumors (18 patients). Mutation burden was higher in tumors with mutational MMRd compared to epigenetic MMRd; however, within each category of MMRd, mutation burden was not associated with ICB response. Notably, JAK1 mutations did not confer resistance to pembrolizumab. Longitudinal single-cell RNA-seq of circulating immune cells revealed contrasting modes of anti-tumor immunity against mutational and epigenetic MMRd tumors. Whereas effector CD8+ T cell responses correlated with mutational MMRd, highly active CD16+ NK cells were associated with epigenetic MMRd tumors responsive to ICB. These data highlight factors beyond neoantigen burden that influence ICB response.</p>
The effect of presence and absence of DNA repair genes on the rate and pattern of mutation in bacteria
<p>This repository contains the code, data, and outputs used in the manuscript "The effect of presence and absence of DNA repair genes on the rate and pattern of mutation in bacteria".</p> <ul> <li><strong>Script.py:</strong> This is a Python script for estimating the number of polymorphisms and mutation rates of bacterial clusters of orthologous genes found in ATGC_data.zip. It produces individual strain outputs to<em> Polymorphism_Results/</em> and<em> Rate_Results/ </em>directories.</li> <li><strong>ATGC_data.zip: </strong>This is a data set of bacterial clusters of orthologous genes downloaded from the ATGC database by Kristensen et al. (2017). The fasta files are utilised by <em>Script.py</em> and should be extracted to the same working directory, under <em>ATGC_data/.</em></li> <li><strong>mutation_rate_data.csv: </strong>This file contains the outputs of <em>Script.py </em>merged into a single file, alongside additional information regarding the presence and absence of particular repair genes, and the calculation of overall mutation rate and Watterson's corrected mutation rate.</li> <li><strong>Phylogenetic_Comparisons.xlsx:</strong> This file contains the averages of overall mutation rate, transition/transversion ratio, and GC-AT bias, for 50 phylogenetic comparisons under presence and absence of repair enzymes. </li> </ul>
Dynamic interplay of cNHEJ and MMEJ pathways of DNA double-strand break repair during embryonic development in zebrafish.
<p><span>Fastq sequences from zebrafish embryos corresponding to 9 amplicons sequenced by </span><span>Illumina MiSeq. DNA sample were obtained from non-treated wildtype controls (ctrl) or from wildtype (WT), polq mutants, lig3 mutant or lig4 mutant injected with Cas9 protein and a pool of 5 or 4 different sgRNA (numbered from 1#1 to 5#2). Each target site corresponds to one amplicon. </span></p>
Comparing developer-provided to user-provided tests for fault localization and automated program repair: Artifacts
<p>Artifacts for the paper <em>Comparing developer-provided to user-provided tests for fault localization and automated program repair.</em></p> <p>Note that the artifacts are maintained in the following repositories:</p> <ul> <li>https://github.com/rjust/defects4j</li> <li>https://bitbucket.org/rjust/tests-tested-data</li> <li>https://bitbucket.org/rjust/fault-localization-data</li> </ul>
Confocal microscopy of gH2AX and 53BP1 DNA repair foci of cells exposed to gamma-irradiation, pt. 2/3
<p><strong>Summary</strong></p> <p>Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1.</p> <ul> <li><strong>Part 1/3: </strong>Head and neck primocultures immunostained with gH2AX/53BP1, Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2564980">10.5281/zenodo.2564980</a></li> <li><strong>Part 2/3 (this dataset)</strong>: U-87 and NHDF Cells exposed to 1-4 Gy confocal microscopy data of head and neck tumor primocultures immunostained with gH2AX/53BP1. Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2572450">10.5281/zenodo.2572450</a>. 174 TIFFs</li> <li><strong>Part 3/3</strong>: training dataset for nuclei and gH2AX foci with ground truth annotation masks, head and neck primocultures (head and neck non-tumor and spinocellular tumor cells). DOI <a href="https://doi.org/10.5281/zenodo.2576241">10.5281/zenodo.2576241</a>. 150 TIFFs for nuclei learning incl 150 png nuclei masks + 99 TIFFs for DNA repair foci training</li> <li><strong>Code</strong>: the code is available at <a href="https://github.com/tomasvicar/LearnFoci">https://github.com/tomasvicar/LearnFoci</a></li> </ul> <p><strong>Materials and methods</strong></p> <p><em>Dataset</em></p> <p>Following cells were used: (1) patient primocultures of patients with spinocellular head and neck tumors (histologically verified tumor and tumor-adjacent tissues), isolation protocol descibed in <em>Svobodova et al, 2017</em>, (2) primary glioblastoma cell line U-87 (ATCC HTB-14, LGC Standards, United Kingdom), (3) primary normal human dermal fibroblasts (NHDF, PromoCell, Hedelberg, Germany) isolated from the dermis of juvenile foreskin or adult skin.<br> The study was conducted in accord with the Helsinki Declaration of 1964 and all subsequent revisions thereof. It was approved by the ethical committee of St. Anne’s Faculty Hospital, Brno. Primoculture cells were cultivated in Pen/Strep antibiotic solution (PAA Laboratories GmbH, Austria) in RPMI-1640 medium with 10% FBS (Biochrom, USA) at 37 °C and 50% CO2 in humidified atmosphere up to 50% confluence. U-87 were grown in Eagle's MEM with 10% FBS.</p> <p><em>Gamma irradiation</em></p> <p>The cells were irradiated at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic in a following schemes: (a) patient-derived primoculture was irradiated with a single dose of 2 Gy (D = 1 Gy/min) of gamma-rays (60Co, Chisostat, Chirana, CR) , (b) U-87 and NHDF cells were irradiated with doses 1, 2, and 4 Gy (D = 1 Gy/min). Cells were irradiated in RPMI 1640 medium (37 °C, normal atmosphere). Confocal microscopy of gammaH2AX and 53BP1 foci immunodetection was consequently performed.</p> <p><em>Fluorescent staining </em></p> <p>DNA double strand breaks (DSBs) were quantified in different periods of time post-irradiation (30 min, 8h and 24h post irradiation) by means of $\gamma$H2AX and 53BP1 foci immunodetection combined with confocal microscopy. For details see \cite{falk2007chromatin}.</p> <p><em>Confocal microscopy</em></p> <p>The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm.</p> <p><strong>File description</strong></p> <p>all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification</p> <ul> <li>Confocal_NHDF_cells_IR_1-4Gy.zip: Human fibroblast NHDF cell line, exposed to gamma irradiation doses 1, 2, and 4 Gy, 64 TIFFs</li> <li>Confocal_U-87_cells_IR_1-4Gy.zip: Human glioblastoma U-87 cell line, exposed to gamma irradiation doses 1, 2, and 4 Gy, 108 TIFFs</li> </ul>
Confocal microscopy of gH2AX and 53BP1 DNA repair foci of cells exposed to gamma-irradiation, pt. 1/3
<p><strong>Summary</strong></p> <p>Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1.</p> <ul> <li><strong>Part 1/3 (this dataset): </strong>Head and neck primocultures immunostained with gH2AX/53BP1, Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2564980">10.5281/zenodo.2564980</a></li> <li><strong>Part 2/3</strong>: U-87 and NHDF Cells exposed to 1-4 Gy confocal microscopy data of head and neck tumor primocultures immunostained with gH2AX/53BP1. Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2572450">10.5281/zenodo.2572450</a>. 174 TIFFs</li> <li><strong>Part 3/3</strong>: training dataset for nuclei and gH2AX foci with ground truth annotation masks, head and neck primocultures (head and neck non-tumor and spinocellular tumor cells). DOI <a href="https://doi.org/10.5281/zenodo.2576241">10.5281/zenodo.2576241</a>. 150 TIFFs for nuclei learning incl 150 png nuclei masks + 99 TIFFs for DNA repair foci training</li> <li><strong>Code</strong>: the code is available at <a href="https://github.com/tomasvicar/LearnFoci">https://github.com/tomasvicar/LearnFoci</a></li> </ul> <p><strong>Materials and methods</strong></p> <p><em>Dataset</em></p> <p>Following cells were used: (1) patient primocultures of patients with spinocellular head and neck tumors (histologically verified tumor and tumor-adjacent tissues), isolation protocol descibed in <em>Svobodova et al, 2017</em>, (2) primary glioblastoma cell line U-87 (ATCC HTB-14, LGC Standards, United Kingdom), (3) primary normal human dermal fibroblasts (NHDF, PromoCell, Hedelberg, Germany) isolated from the dermis of juvenile foreskin or adult skin.<br> The study was conducted in accord with the Helsinki Declaration of 1964 and all subsequent revisions thereof. It was approved by the ethical committee of St. Anne’s Faculty Hospital, Brno. Primoculture cells were cultivated in Pen/Strep antibiotic solution (PAA Laboratories GmbH, Austria) in RPMI-1640 medium with 10% FBS (Biochrom, USA) at 37 °C and 50% CO2 in humidified atmosphere up to 50% confluence. U-87 were grown in Eagle's MEM with 10% FBS.</p> <p><em>Gamma irradiation</em></p> <p>The cells were irradiated at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic in a following schemes: (a) patient-derived primoculture was irradiated with a single dose of 2 Gy (D = 1 Gy/min) of gamma-rays (60Co, Chisostat, Chirana, CR) , (b) U-87 and NHDF cells were irradiated with doses 1, 2, and 4 Gy (D = 1 Gy/min). Cells were irradiated in RPMI 1640 medium (37 °C, normal atmosphere). Confocal microscopy of gammaH2AX and 53BP1 foci immunodetection was consequently performed.</p> <p><em>Fluorescent staining </em></p> <p>DNA double strand breaks (DSBs) were quantified in different periods of time post-irradiation (30 min, 8h and 24h post irradiation) by means of $\gamma$H2AX and 53BP1 foci immunodetection combined with confocal microscopy. For details see \cite{falk2007chromatin}.</p> <p><em>Confocal microscopy</em></p> <p>The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm.</p> <p><strong>File description</strong></p> <p>all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification</p> <ul> <li>Confocal_HN_tumor_primocultures.zip: dataset of patient-derived primocultures (gamma-irradiated with 2 Gy and controls), for description see file below, 100 FOVs,</li> <li>Confocal_HN_tumor_primocultures_description.xlsx: description of confocal dataset files and patient tumor characteristics</li> <li>Confocal_HN_tumor_primocultures_train_nuclei.zip: annotated training subset 1 of dataset of patient-derived primocultures (gamma-irradiated with 2 Gy and controls) used for nuclei segmentation training, 150 FOVs, includes TIFF and manually annotated binary mask for nuclei (data_###.tif and respective mask_###.png)</li> <li>Confocal_HN_tumor_primocultures_train_nuclei_description.xlsx: description of above-mentioned files (tissue type, TNM stage, grade, time post irradiation)</li> </ul>
A Comprehensive Reliability-Based Framework for Corrosion Damage Monitoring and Repair Design of Reinforced Concrete Structures
<p>Corresponding data set for Tran-SET Project No. 17STLSU03. Abstract of the final report is stated below for reference:</p> <p>"In this work, we developed a comprehensive framework for corrosion management of reinforced concrete (RC) structures. This framework includes critical steps of an effective approach to quantify the damage evolution as well as providing the timeframe for effective maintenance/repair strategies for corrosion assessment in RC structures. The framework included several activities including the use of indirect and direct inspection tools, theoretical development for damage prediction, experimental measurements and theoretical development of repair time based on reliability. The uniqueness of the framework is the integration of deterministic modeling of corrosion damage evolution by using mechanistic analysis with statistical modeling on corrosion of RC structures by using measurements from the field (or natural environment) and experimental testing (in the laboratory). The framework includes a simple algorithm that relies in each development and task generated from this work to monitor and estimate the status of the reinforced concrete structures and the most suitable strategy to extend the life of the system while maximizing the reliability."</p>
Use of Ultra‐High‐Performance Fiber‐Reinforced Concrete (UHP‐FRC) for Fast and Sustainable Repair of Pavements
<p>Corresponding data set for Tran-SET Project No.17STUTA03. Abstract of the final report is stated below for reference:</p> <p>"This research presents a new methodology, which enables streets, roads, highways, bridges, and airfields to use an advanced fiber-reinforced concrete material, which can delay or prevent the deterioration of these transportation infrastructure when subjected to traffic and environmental loadings. The major problem of concrete is its considerable deterioration and limited service life due to its brittleness and limited durability. As a result, it requires frequent repair and eventual replacement, which consumes more natural resources. Ultra-high-performance fiber-reinforced concrete (UHP-FRC) introduces significant enhancement in the sustainability of concrete structures due to its dense microstructure and damage-tolerance characteristics. These characteristics can significantly reduce the amount of repair, rehabilitation, and maintenance work, thereby giving the transportation infrastructure a longer service life. This research addresses the strong need to develop fast and sustainable UHP-FRC materials for pavement repair that can be easily cast onsite without special treatments. This avoids any major changes to current concrete production practice and accelerates the use of UHP-FRC materials. This research investigated a new method for concrete repair by combining precast UHP-FRC panels with a small quantity of cast-in-place UHP-FRC for pavement repair without any dowel bars. In this method, a precast UHP-FRC panel is used along with cast-in-place UHP-FRC. The vertical repair surfaces of the existing concrete are roughened on site. The outer edges of the UHP-FRC precast panel are roughened before they are brought to the site (no dowel bars are needed). The depth of the precast UHP-FRC panel is the same as the existing pavement thickness. Only a small cast-in-place UHP-FRC joint (one to two inches wide) is done onsite. The roughened precast UHP-FRC panel is placed in the repair area and cast-in-place UHP-FRC is cast into the joint. Experimental results showed that using a roughened surface (up to about CSP 5) provides a very large bond resistance, which is enough to prevent faulting."</p>
Bigwig files for paper "STK19 is a transcription-coupled repair factor that participates in UVSSA ubiquitination and TFIIH loading"
<p>Bigwig files for paper "STK19 is a transcription-coupled repair factor that participates in UVSSA ubiquitination and TFIIH loading". </p>
Vascular Damage and Repair - Are Small-diameter Vascular Grafts Still the "Holy Grail" of Tissue Engineering?
Open the record for dataset details and reuse information.
The role of TAp63g and p53 point mutations in regulating DNA repair, mutational susceptibility and invasion of bladder cancer cell
<p>Raw data set for the manuscript submitted to e-Life (10-06-2021-RA-eLife-71184 ) for peer-review. </p>
Processed data from Repair-seq screens of double-strand breaks
<p>Processed data from Repair-seq screens of double-strand breaks induced by SpCas9 and AsCas12a in the presence or absence of oligonucleotide homology donors.</p>
Impact of Code Language Models on Automated Program Repair (Dataset)
<p>This is the fine-tuning dataset used in the paper Impact of Code Language Models on Automated Program Repair</p>
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