Amplification and sequencing conserved sequence. Medical search. Frequent questions

Degenerate primers-based polymerase chain reaction (PCR) are commonly used for isolation of unidentified gene sequences in related organisms. (ac.ir)
For designing the degenerate primers, we propose the use of local alignment search method for searching the conserved regions long enough to design an acceptable primer pair. (ac.ir)
The retrieved sequences from Genbank amino acid sequence databases were analyzed for designing degenerate primers. (ac.ir)
The Multiple allignments of the selected sequences revealed two highly conserve motif regions of amino acids that enabled us to design a degenerate primers. (ac.ir)
Forward and reverse degenerate primers for amplification of the related WD40 repeat-containing domain gene were designed from an alignment of the translated sequences from some other fungi. (ac.ir)
We opted for conserved sequences between species, presenting enough sequence heterogeneities to be considered for the design of species- specific LAMP primers: such primers would allow the selective amplification of the DNA targets. (who.int)
The sequences identified in the previous section of the work were used to design a combinations of 6 primers in 8 distinct regions of the target sequences for the amplification of a selection of reference DNAs belonging to the different Old World Leishmania species. (who.int)
The highly conserved sequences of HSV II are selected to design specific primers and Taqman probes. (mmtegypt.com)
Ultra-degenerate primers with 3' termini overlapping the probe-binding site adapt the target through site-directed mutagenesis during qPCR to replace DRM-proximal sequence variation. (nature.com)
PCR amplification was carried out as explained by Downes (2005), with the conserved bacterial primers 8F (Wilmotte within the phylum 158T (95? (woofahs.com)
First, RT-PCR amplification of total RNA was performed using degenerate primers that were designed based on the conserved sequences of known group 2 allergens. (mergullo.net)
Subsequently, specific primers were designed based on sequence of this short fragment to amplify the 5 and 3 ends of the Etidronate (Didronel) full-length open reading framework by RACE. (mergullo.net)
Two pairs of primers have been designed: one for the amplification of your entire sequence and one other one for the amplification of essentially the most conserved area of this peroxisomal protein. (genomeboy.com)
Using primers designed based mostly on the conserved area of the Asp n three encoding gene allowed us to establish the presence of the intently associated fungal species Aspergillus fumigatus by detecting Asp n three homologous protein, which could be cross-reactive. (genomeboy.com)
This single set of primers and reaction conditions were used for the amplification of the 16s-23s spacer regions for 61 strains of standard bacteria and corresponding clinical isolates belonging to 20 genera and 27 species, including Listeria , Staphylococcus and Salmonella species, et al. (zju.edu.cn)
In order to increase the amount of sequence derived from these lesions, direct PCR was performed using the primary primers of the nested PCR. (vin.com)
Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. (frontiersin.org)
In this study, we aimed to validate archaeal primers suitable for high throughput next generation sequencing. (frontiersin.org)
Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. (frontiersin.org)
Here, we propose new primers and protocols that allow the amplification of medium-sized DNA fragments (∼500 bp) from herbarium samples. (bioone.org)
This document describes some of the target genes and primers that can be used for DNA sequence-based identification of fungi and the PCR conditions with which to use those primers. (cdc.gov)
There is a special set of ITS primers specifically for amplification of the ITS region of dermatophytes, especially Trichophyton (Gräser, 2000). (cdc.gov)
We designed primers for each segment in most conserved regions after aligning available CCHFV sequences from all genotypes retrieved from GenBank ( Table ). (blogspot.com)
We directly sequenced purified amplicons by using additional internal primers (data not shown). (blogspot.com)
Based on the the conserved sequences of antimicrobial peptides of insects (mainly Diptera) from different antimicrobial peptide databases, thirty-seven pairs of degenerate primers were designed, and the antimicrobial peptide genes from Hermetia illucens L were screened using these primers. (ukessays.com)
In this study, the potential use of PCR was investigated using the primers Pt8-Pt9 based on the insertion sequence IS 6110 of the Mycobacterium tuberculosis complex (Kolk etal, 1992). (who.int)

Here, we identified mcr gene-harboring ESBL-producing Escherichia coli isolates during whole-genome sequencing of ESBL-producing E. coli isolates from a dog and a cat in Osaka, Japan. (bvsalud.org)
Right here we suggest a novel strategy named DISMIR, which might present ultrasensitive and sturdy most cancers detection by integrating DNA sequence and methylation data in plasma cfDNA whole-genome bisulfite sequencing (WGBS) knowledge. (genomeboy.com)
For contact tracing or inquiries related to antibiotic resistance, whole genome sequencing (WGS) of bacterial isolates is offered. (folkhalsomyndigheten.se)
Whole genome sequencing can also provide insights into the specific genes or mutations that may be linked to antibiotic resistance. (folkhalsomyndigheten.se)
It is a platform and database for the automated analysis of whole genome sequencing data. (folkhalsomyndigheten.se)

Sequencing of a 2.5-kb chromosomal Sma I- Pst I fragment containing the structural gene revealed an open reading frame encoding 537 amino acids, homologous to known pckA genes. (asm.org)
The FeSOD-A and FeSOD-B genes of 35 T. cruzi strains, belonging to six discrete typing units (Tcl-TcVI), from different hosts and geographical regions were amplified by PCR and sequenced using the Sanger method. (biomedcentral.com)
Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. (biomedcentral.com)
Regions of the L. killicki ( L. tropica ) and L. major genes sequences were scanned using BLAST program and subsequently compared using appropriate bioinformatic tools Chromas and MEGA. (who.int)
A generic pair of priming sequences was selected from highly conserved sequences in the 16s and 23s genes occurring adjacent to these polymorphic regions. (zju.edu.cn)
Current diagnostic PCR assays target a variety of SARS CoV-2 genes and the vast majority target sequences in regions of the SARS CoV-2 genome that are highly conserved. (who.int)
While the size of the introns, number of introns per gene and the number of intron-containing genes can vary greatly between sequenced eukaryotic genomes, the structure of a gene with reference to intron presence and positions is typically conserved in closely related species. (biomedcentral.com)
Primer development - Selected sequences of the plastid ndhF and nuclear PepC genes for Bignonieae from Lohmann ( 2006 ) were combined with newly generated sequences for the plastid rpl32-trnL intergenic spacer region following Shaw et al. (bioone.org)
Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. (cdc.gov)
DNA sequence alignment analysis and the forecast-analysis of protein structure indicated that these seven antimicrobial peptide genes were not homologous to any other antimicrobial peptide genes in GenBank. (ukessays.com)
In addition, IGS sequencing (e.g., sequencing of intergenic regions between the 16S and 23S rRNA genes) has been used to taxonomy studies, while partial sequencing of the gene gtfB , which encodes the enzyme glucosyltransferase B, has been used to investigate enzymatic activity and virulence 11-12 . (bvsalud.org)

Sequence alignment showed the isolates to be most closely related to Salmonella enterica. (researchsquare.com)
When the spacer amplification products were resolved by electrophoresis, the resulting patterns could be used to distinguish most of the bacteria species within the test group, and the amplification products of the clinical isolates clustered at the standard species level. (zju.edu.cn)
However, these proteins are conserved not only in multiple ETEC isolates, but also in commensal bacteria. (biomedcentral.com)
Next, the isolates were differentiated by sequencing a specific region of the gene encoding the enzyme glucosyltransferase B ( gtfB ). (bvsalud.org)
By sequencing the 16S-23S intergenic region, it was found that all of the isolates belonged to the species S. mutans . (bvsalud.org)
Based on the genetic similarity of the isolates and pattern of amino acid variations identified by partial sequencing of the gtfB gene, base-pair changes were identified and correlated with different virulence patterns among the isolates. (bvsalud.org)

In both scenarios, overlaps between sequences (Sanger or next-generation sequencing, NGS) have been used to assemble full-length mitogenomes. (biomedcentral.com)
However, traditional Sanger sequencing-based DNA barcoding protocols can be prohibitively expensive and laborious when large community samples have to be processed. (springer.com)

Primer extension and polymerase chain reaction amplification were used to obtain additional 5' protein coding sequences. (rupress.org)
Dust-mite sensitized individuals living in SHH these countries display varying examples of pores and skin prick reactivity to crude protein extracts Etidronate (Didronel) of using a combination of two techniques, reverse transcription polymerase chain reaction (RT-PCR) and RACE (Random Amplification of cDNA Etidronate (Didronel) Ends). (mergullo.net)
Actual-time polymerase chain response (RT-PCR) was used for the amplification of Asp n three gene. (genomeboy.com)
The all-electronic Single Molecule Break Junction (SMBJ) methodology is an rising different to conventional polymerase chain response (PCR) strategies for genetic sequencing and identification. (genomeboy.com)
2,3 The targeted sequence corresponded to a region of the DNA polymerase gene containing multiple conserved amino acid motifs. (vin.com)
1 Interestingly, the amino acid sequence deduced from the short DNA polymerase fragment of one of the two alphaherpesviruses from our study was 96.8% identical to one of the viruses associated with generalized lethal infection. (vin.com)
The amino acid sequences of the alphaherpesviruses small DNA polymerase fragments from the skin lesions shared 77.2% identity. (vin.com)
The amino acid sequences deduced from the four long DNA polymerase fragments of these viruses were between 88.1 and 96.3% similar and between 84.8 and 93.8% identical. (vin.com)
These viruses were rapidly characterized after sequencing of DNA polymerase gene fragments, multiple sequence alignments and phylogeny. (vin.com)

Additionally, once a transgenic event is obtained, molecular studies required for a commercial release by regulatory authorities, which include transgene insertion site, number of transgenes and gene expression levels, are all hindered by the genomic complexity and the lack of a complete sequenced reference genome for this crop. (frontiersin.org)
By sequencing the entire genome, a comprehensive understanding of the genetic composition is obtained. (folkhalsomyndigheten.se)

2007 ). Vouchers and GenBank accessions of the sequences used and/or generated in this paper are presented in Appendix 1 . (bioone.org)
The betA gene sequence reported in this study contains several base substitutions with that of reported sequences in GenBank, resulting in the altered amino acid sequences of the translated proteins. (scialert.net)
Moreover, the sequence analysis of choline dehydrogenase from our isolate shows several base substitutions with that of reported sequences in GenBank, resulting in the altered amino acid sequences of the translated proteins. (scialert.net)

In contrast, the 16S rRNA gene sequences from 158T and 78-1T were only 95 and 90? (woofahs.com)
Some species presenting similar pattern were further analyzed by HinfI or AluI digestion or DNA clone and sequences analysis in order to establish the specific 16s-23s rRNA gene spacer regions map. (zju.edu.cn)
The 16S rRNA gene is highly conserved with certain variable regions. (folkhalsomyndigheten.se)
The laboratory procedure is based on amplifying and sequencing four variable regions of the 16S rRNA gene with two amplicons. (folkhalsomyndigheten.se)

This is facilitated by directing primer and probe design to evolutionarily conserved regions identified through multiple sequence alignments that portray geographical and temporal genomic variability. (nature.com)

We further demonstrated that intron 7 carried two motifs that were highly conserved across the monocot-dicot divide. (biomedcentral.com)

However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. (frontiersin.org)
16S sequencing is performed to determine which bacterial species are present in a clinical sample or isolate. (folkhalsomyndigheten.se)
The method uses an internal control sequence (spike) which is amplified and sequenced simultaneously with the sample to facilitate the assessment of the bacterial content and to detect amplification-inhibiting factors in the sample that may lead to a negative result. (folkhalsomyndigheten.se)

Mediated Isothermal Amplification based assays for the selective and/or specific identification of, and discrimination among the two (2) Leishmania species encountered in Tunisia. (who.int)

4) Nucleic acid amplification test. (mmtegypt.com)
A synthetic non-competitive sequence is designed as an internal control template in this kit, which has no interference with the target gene of HSV II, then BLAST ratio analysis is performed for this sequence on NCBI website, confirmed that it cannot be found in the NCBI nucleic acid library, no interfere with each other. (mmtegypt.com)
[ 27 ] A voided urine sample, whether midstream or first-void, effectively captures the chlamydial organism for nucleic acid amplification testing (NAAT). (medscape.com)
All nucleic acid in the clinical sample is sequenced and the resulting data is analysed by experienced bioinformaticians. (folkhalsomyndigheten.se)

A cDNA clone coding for a membrane proteoglycan core protein was isolated from a neonatal rat Schwann cell cDNA library by screening with an oligonucleotide based on a conserved sequence in cDNAs coding for previously described proteoglycan core proteins. (rupress.org)
Analysis of the cDNA and deduced amino acid sequences revealed a high degree of identity with the transmembrane and cytoplasmic domains of previously described proteoglycans but a unique extracellular domain sequence. (rupress.org)
In this case, the basic principle is to detect specific DNA and RNA sequences via hybridization of a probe, detecting any complementary sequence on the cDNA of this bacterium. (australiaessays.com)
The ESTs sequences of caffeic acid O-methyltransferase from Larix kaempferi transcriptome database, an cDNA clone encoding COMT, was isolated from L. kaempferi by gene-specific PCR amplification. (lykxyj.com)
to acheive this aim the stomoxyn-zy gene was amplified by rapid amplification of cDNA ends (RACE) from Hermetia illucens L larvae stimulated with S. aureus , and cloned into the pPICZαA vector. (ukessays.com)

Metagenomic sequencing engables a thorough mapping of the genetic material in the clinical sample, providing a broader understanding of the microbiological profile. (folkhalsomyndigheten.se)
In contrast to metagenomic detection of unknown pathogens which sequences all available genetic material, 16S sequencing specifically targets the small ribosomal subunit. (folkhalsomyndigheten.se)
In epidemiological contact tracing, this technology enables the mapping of infection spread and identification of sources of infection through the comparison of genetic sequences. (folkhalsomyndigheten.se)

Primer extension analysis identified a transcriptional start site 72 bp upstream of the pckA initiation codon and an upstream sequence similar to ς 70 promoters. (asm.org)
The probes can specifically bind to a DNA template in the middle of the primer amplification region. (mmtegypt.com)
Sequence divergence within oligonucleotide-binding sites creates primer-template duplex instability and lowers T m . (nature.com)

We systematically violated canonical qPCR design principles to develop a Pan-Degenerate Amplification and Adaptation (PANDAA), a point mutation assay that mitigates the impact of sequence variation on probe-based qPCR performance. (nature.com)

In the last two decades, DNA barcoding, the sequencing of short species-specific amplicons, has considerably simplified community analyses (Hebert et al. (springer.com)
The procedure's high sequence depth allows for these amplicons to be analysed separetely so different bacteria from the same sample can be identified. (folkhalsomyndigheten.se)

Methods: S. mutans samples were isolated from the saliva of 30 children with varying histories of dental caries, and they were characterized according to morphological and biochemical markers and the sequences of their 16S-23S intergenic spacer region. (bvsalud.org)

Detecting most cancers indicators in cell-free DNA (cfDNA) high-throughput sequencing knowledge is rising as a novel noninvasive most cancers detection methodology. (genomeboy.com)
DISMIR exhibited excessive accuracy and robustness on hepatocellular carcinoma detection by plasma cfDNA WGBS knowledge even at ultralow sequencing depths. (genomeboy.com)
The objective of this document is to outline the available methods and tools for screening and sequencing patient specimens for the detection of VOC or VOI, with a focus on those that offer a rapid turn-around time so as to support rapid implementation of public health actions for COVID 19 control. (who.int)
laboratories that can perform pan coronavirus detection and A single negative test result, particularly if this is from an directed sequencing. (who.int)
In conclution, DNA amplification is a rapid, reliable and accurate method with a high degree of sensitivity and specificity for the detection of Mycobacterium tuberculosis DNA sequences and it can replace the conventional culture method in the diagnosis of extra pulmonary tuberculosis and tuberculosis meningitis except in the situation when antibiotic sensitivity results are required. (who.int)

According to a procedure that has been previously validated for the identification of species - specific targets among which some fragments would fit into the second category of sequences expected. (who.int)
Sequence analysis of the small DNA fragments indicated that alpha or gamma herpesviruses were present in the lesions. (vin.com)
This assay resulted in the amplification of fragments 731-bp in length in the case of four of the five gammaherpesvirus contained in the mucosal lesions. (vin.com)
The first molecular phylogenetic study for the tribe ( Lohmann, 2006 ) was mainly based on recently collected samples that did not present any problems for the amplification of large DNA fragments. (bioone.org)

To date, mtDNA sequences have been generated for hundreds of thousands of specimens in many vertebrate species [ 8 ]. (biomedcentral.com)
Sequences from 6 clones of both specimens were identical. (blogspot.com)

Human HEV sequences are classified into genotypes 1-4, which are subdivided into subtypes. (blogspot.com)

Phylogenetic analysis with DNA amplification technologies. (who.int)
allow proceeding to the in silico comparative genomics analysis of Leishmania DNAs and annotating the sequences identified. (who.int)
Sequence analysis of DNA from formalin-fixed, paraffin-embedded samples revealed S. commune infection. (bvsalud.org)
The samples, collected in 2000-2007, were analyzed using PCR amplification of a 173-206 bp (depending on HPV type) conserved region in the L1 open reading frame, restriction endonuclease analysis and, where required, sequence analysis for type determination. (biomedcentral.com)
The amplified gene was sequenced and phylogeny analysis was done. (scirp.org)
Sequence comparison and phylogenetic analysis showed striking conservations among insect ecdysone receptors, especially between P. xylostella and other lepidopterans. (biomedcentral.com)
The application of next-generation sequencing technology in microbial community analysis increased our knowledge and understanding of the complexity and diversity of a variety of ecosystems. (frontiersin.org)
The result of of metagenomic sequencing is the outcome of a collaborative effort between bioinformaticians and clinical microbiologists, where the clinical interpretation confirms and complements the technical analysis. (folkhalsomyndigheten.se)
Sequence variations between different bacteria provide a unique identity, and the analysis of these sequence enables taxonomic placement. (folkhalsomyndigheten.se)

The basis of the GENSAM project is the joint national management of clinical microbial sequencing data. (folkhalsomyndigheten.se)

The Committee concluded that additional work may be needed to assess the viability of the stocks held in VECTOR, and that further molecular characterization of additional strains may be valuable in helping to identify strains from which further DNA sequences could be determined. (who.int)
However, MipA, Skp, and ETEC_2479 are conserved not only among pathogenic ETEC strains, but also among the commensal Proteobacteria . (biomedcentral.com)
More than 68 percent had less than 5 copies of the IS sequence suggesting that our local M.tuberculosis strains have a fewer number of copies compared to data shown in most countries. (who.int)

Highly conserved regions are less likely to mutate, therefore there is a high likelihood that the diagnostic test will remain accurate in the presence of variants. (who.int)
The ABCB1 gene structure is highly dynamic, while the structure of ABCB19 remained largely conserved through evolution. (biomedcentral.com)
The C domain, the central DNA-binding domain (DBD), contains two highly conserved zinc finger motifs that are characteristic of the nuclear receptor superfamily (NRs). (biomedcentral.com)
The sequence indicated that the deduced amino acid contained five highly conserved regions of COMT family, and shared 94% identity with PpCOMT from Pinus pinaster. (lykxyj.com)

Despite the reliance of clinical virology on qPCR, technical challenges persist that compromise their reliability for sustainable epidemic containment as sequence instability in probe-binding regions produces false-negative results. (nature.com)
Spacer regions within these loci showed a significant level of length and sequence polymorphism across most of the species lines. (zju.edu.cn)

Current work signifies that the present spectra recorded from SMBJ experimentations comprise distinctive signatures to establish identified sequences from a dataset. (genomeboy.com)

Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. (biomedcentral.com)
Based on the nucleotide sequence of the mitochondrial cytochrome b gene, the voles from the Krasnaya Polyana and Pslukh station were attributed to Robert's snow vole (Chionomys roberti), whereas the animals from the Utrish nature reserve belong to the Eastern-European vole (Microtus rossiaemeridionalis). (sgu.ru)

To test this method, a WD40 repeat-containing domain protein from Beauveria bassiana was used as reference sequence to find out a group of homologous gene sequences similar to some closely related to Verticillium dahliae. (ac.ir)

The pckA gene, encoding the gluconeogenic enzyme phosphoenolpyruvate carboxykinase (PEPCK), was cloned by PCR amplification from the purple nonsulfur bacterium Rhodopseudomonas palustris No. 7. (asm.org)

Evolutionary loss and gain of introns in genomic sequence data may provide a mechanism by which organisms diversify gene expression and gene function. (biomedcentral.com)
We obtained the virus from a patient sample and characterized its full genomic sequence. (blogspot.com)
Here, we report the complete genomic sequence of the virus from 1 of these case-patients and show the phylogenetic relationships among the 3 segments. (blogspot.com)

Metagenomic sequencing is offered in cases where infection is suspected but other methods have failed to identify a pathogen. (folkhalsomyndigheten.se)

One of the techniques that has consistently been transversal in specifically detecting sequences of target pathogens in humans, plants and animals, including fish, is real-time PCR because of its sensitivity, specificity, speed, throughput and reproducibility. (thefishsite.com)

The objective of the study was to develop a rapid method to detect Mycobacterium tuberculosis from clinical samples and the applicability of DNA amplification techniques to a developing country like Sri Lanka. (who.int)

First of all we proceeded to an alignment using the CLUSTAL W program to each Leishmania species and for the selected gene (cysteine protase b) (the alignment use published sequences and sequences which were sequenced in our laboratory). (who.int)

The full-length clone acquired was sequenced to confirm its identity. (mergullo.net)

A homology search was performed using the sequence acquired against the non-redundant database in NCBI using the BLAST-X algorithm24, which showed a match to group 2 dust mite allergens, with the closest homology becoming to Ale o 2 (from and varieties which are predominant in the interior environment of Singapore3. (mergullo.net)
There were 9 amino acid insertions and an amino acid substitution in this transcript compared with the validated reference sequence in NCBI. (hindawi.com)

Molecular diagnostic methods for amplification have been used to diagnose influenza but considering it is caused by a virus that replicate fast the use of accurate diagnostic procedures should be used. (australiaessays.com)
MERS-CoV) via next generation sequencing (NGS) from found in Wuhan, but it would appear samples prepared for cultured virus or directly from samples received from molecular testing could be handled as would samples of several pneumonia patients. (who.int)

Our results showed that the coding sequence of EZH2 was 2241 bp, encoding 746 amino acids. (hindawi.com)

Two approaches were developed to identify unique sequences to L. major in the first case and to L. tropica in the second. (who.int)

Conclusions: The partial sequencing of the gtfB gene can be a useful tool for elucidating the colonization patterns of S. mutans . (bvsalud.org)

The sequence lengths vary greatly from approximately 200 basepairs to up to 700 basepairs depending on the species. (cdc.gov)

qPCR probe design is more averse to similar modifications because increasing probe T m through nucleotide degeneracy or sequence lengthening may lead to high T m variations that reduce specific target discrimination. (nature.com)

sequence similarity) and 78-1T (90? (woofahs.com)

In previous studies, we have identified cysteine protease b sequences, which are specific to L. infantum . (who.int)

By using two rounds of Touchdown Semi-Nested RT- PCR, a partial 249 bp PCR products were isolated and sequenced. (ac.ir)

Anatomy15

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Analytical, Diagnostic and Therapeutic Techniques and Equipment64

Phenomena and Processes117

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Anthropology, Education, Sociology and Social Phenomena2

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Primers26

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Multiple sequence alignments1

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Assays1

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Amplicons2

Intergenic spacer region1

Detection5

Fragments4

Specimens2

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Analysis9

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