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Identifies Fumarate Reductase as a Determinant of Virulence. Infect Immun 2008,76(6):2284–2295.CrossRefPubMed 26. Ge Z, Feng Y, Dangler C, Xu S, Taylor N, Fox J: Fumarate reductase is essential for Helicobacter pylori colonization of the mouse stomach. Microb Pathog 2000,29(5):279–287.CrossRefPubMed 27. Connolly JP, Comerci D, Alefantis TG, Walz A, Quan M, Chafin R, Grewal this website P, Mujer CV, Ugalde RA, DelVecchio VG:

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Table 1 Proteins #this website randurls[1|1|,|CHEM1|]# differentially expressed in ovariectomized rat livers after isoflavone intake and exercise

using MALDI-TOF MS/MS Spot number Accession number Official symbol Protein identification Theoretical MW(kDa)/pI Measured MW(kDa)/pI Score a Coverage 8203 NP_058797 PPIA Peptidyl-prolyl cis-trans isomerase A 18.1/8.34 17.5/9.0 86 71 9401 P81178 ALDH2 Aldehyde dehydrogenase, mitochondrial 54.8/5.83 46.4/6.6 298 12 3607 NP_001101972 BUCS1 Butyryl Coenzyme A synthetase 1 27.8/5.57 50.1/5.1 39 13 5701 BAA08207 PSME2 Proteasome activator rPA28 subunit beta 27.1/5.52 30.1/5.3 75 13 8002 AAB19918 AKR1C3 3 alpha-hydroxysteroid dehydrogenase 37.6/7.03 36.1/7.4 121 9 9801 AAA41769 OTC Ornithine carbamoyltransferase 39.9/9.1 52.1/7.8 220 14 5503 NP_001102492 INMT Indolethylamine N-methyltransferase 30/5.7 29.3/5.4 99 12 6601 NP_036925 GAMT Guanidinoacetate N-methyltransferase 26.7/5.69 28.2/5.8 48 16 a Score is −10xlog(P), where P is the probability that the observed match is a random event, based on the NCBInr database using the MASCOT searching program as MS/MS data. Comparison of hepatic protein expressions between sham-operated and ovariectomized rats Hepatic protein profiles for each SHAM and OVX group are shown in Figure  1A and B. Spot number 5503 (INMT)

was detected in the SHAM but not in any of the other ovariectomized groups (Figure  2). On the other hand, when compared to the SHAM, ovariectomized rats demonstrated an increase in protein levels, which were spot

numbers 8203 (PPIA, 2.83 fold up), 3607 (BUCS1, 5.86 fold CBL0137 price up), 5701 (PSME2, 3.93 fold up), 8002 (AKR1C3, 3.61 fold up), and 6601 (GAMT, 2.57 fold up). Two protein spots were down-regulated in ovariectomized rats when compared to the SHAM group, which include spot numbers 9401 (ALDH2, 1.54 fold down) and 9801 (OTC, 5.26 fold down). Effects of isoflavone supplementation on the levels of hepatic protein expression in ovariectomized rats We also determined if isoflavone supplementation could affect protein expression patterns in ovariectomized rats. The expression of hepatic proteins in ovariectomized rats on an isoflavone-supplemented diet (ISO) was compared with that of the OVX group (Figure  1B and C). Isoflavone-supplementation resulted in the down-regulation of spot number 3607 (BUCS1, a 1.82 fold down) and the up-regulation of spot numbers 8203 Immune system (PPIA, 1.61 fold up), 8002 (AKR1C3, a 1.57 fold up), and 9801 (OTC, 2.95 fold up) compared to the rats without isoflavone supplementation (Figure  2). Spot numbers 9401 (ALDH2), 5701 (PSME2), 6601 (GAMT), and 5503 (INMT) did not change after isoflavone supplementation (Figure  2). Effects of exercise on the levels of hepatic protein expressions in ovariectomized rats The influence of physical exercise was also examined in ovariectomized rats (Figure  1B and D). The animals that underwent regular exercise (EXE) demonstrated an up-regulation of spot numbers 5701 (PSME2, 2.

Genome Res 22(3):421–428PubMedCentralPubMedCrossRef Check Hayden E (2014) Is the $1,000 genome for real? Nature.com http://​www.​nature.​com/​news/​GSK690693 molecular weight is-the-1-000-genome-for-real-1.​14530. Accessed 19 June 2014 Clarke A, Richards M, Kerzin-Storrar L, Halliday J, Young MA, Simpson SA, Featherstone PF-6463922 concentration K, Forrest K, Lucassen A, Morrison PJ, Quarrell OW, Stewart H (2005) Genetic professionals’ reports of nondisclosure of genetic risk information within families. Eur J Hum Genet 13(5):556–562PubMedCrossRef Couzin-Frankel J (2013) Return of unexpected DNA results urged. Science 339(6127):1507–1508PubMedCrossRef

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S, Biesecker LG, Biesecker BB (2011) Motivators for participation Nintedanib (BIBF 1120) in a whole-genome sequencing study: implications for translational genomics research. Eur J Hum Genet 19(12):1213–1217PubMedCentralPubMedCrossRef Facio FM, Eidem H, Fisher T, Brooks S, Linn A, Kaphingst KA, Biesecker LG, Biesecker BB (2013) Intentions to receive individual results from whole-genome sequencing among participants in the ClinSeq study. Eur J Hum Genet 21(3):261–265PubMedCentralPubMedCrossRef GenomeWeb (2013) Reconsidering incidental findings http://​www.​genomeweb.​com/​blog/​reconsidering-incidental-findings. Accessed 26 Jul 2013 Goddard KA, Whitlock EP, Berg JS, Williams MS, Webber EM, Webster JA, Lin JS, Schrader KA, Campos-Outcalt D, Offit K, Feigelson HS, Hollombe C (2013) Description and pilot results from a novel method for evaluating return of incidental findings from next-generation sequencing technologies. Genet Med. doi:10.​1038/​gim.​2013.​37 PubMedCentral Goldman RE, Kingdon C, Wasser J, Clark MA, Goldberg R, Papandonatos GD, Hawrot E, Koren G (2008) Rhode Islanders attitudes towards the development of a statewide genetic biobank.

Considering that those fragments may contain part of the additional IS copies plus their surrounding sequences, we cloned and sequenced the 3.3 kb and 2.5 kb DNA amplicons of B12 and B16, respectively, and designed flanking primers (Table

2) to confirm the position of the new IS copy. As predicted for the insertion of complete IS711 copies of 842 bp in length, specific PCR products of 1077 bp (B12) and 1142 bp (B16) were amplified (Figure 2C and 2D). We believe that an IS replicative transposition is the most plausible explanation for these results. In fact, the sequence analysis suggested that transposition had occurred by a canonical TA duplication at YTAR site (R, purine; Y, pirimidine). In strain B12, this site was in an

intergenic region between a lactate permease gene (lldP) and BruAb1_0736 (hypothetical protein) (Figure 3, upper panel) corresponding to a 103 bp Bru-RS1 element, a palindromic repeat sequence VE-822 research buy that represents a putative insertion site for IS711 [14]. In contrast, the IS711 extra copy in B16, B49 and B50 was interrupting an ORF encoding a transcriptional regulator of the MarR family (BruAb2_0461, Figure 3 lower panel). Similarity searches showed that the B12 and B16 sites did not match with any of the IS711 loci previously reported for B. abortus or even with the novel IS711 sites recently described for Brucella marine PARP inhibitor mammal strains [6], although the B16 site was found in B. ovis. To confirm these findings and to investigate whether these sites were also present in the genomes (not available in databases) of the Brucella species carrying a high-copy number of IS711, we carried out PCR assays with B. ovis, B. ceti and B. pinnipedialis DNAs. For the B12-specific IS711, PCR amplifications with flanking primers yielded an IS-empty locus fragment (not shown). In contrast, the PCR amplifying PAK5 the B16 fragment yielded the predicted 1142 bp fragment in B. ovis but not in B. ceti or B. pinnipedialis (Additional file 1). Table 2 Primers used in this work Name Sequence (5′-3′) Reference 711d CATATGATGGGACCAAACACCTAGGG [19] 711u CACAAGACTGCGTTGCCGACAGA [19] RB51

CCCCGGAAGATATGCTTCGATCC [12] IS711out CAAGTTGAAACGCTATCGTCGC This work P5 CGGCCCCGGT [20] BruAb1_0736F TTGGTTTCCTTGCGACAGAT This work BruAb1_0737R AACCTTGCCTTTAGTTGCTCA This work BruAb2_0461F ATCAGGCTTTGCTGGCAATC This work BruAb2_0461R TCGTTTGCCATCTTGTTCAG This work marR-F1 GACGTGGTGGAGGAAACCTA This work marR-R2 ACTCGGCCAAACCTGATAA This work marR-F3 TTATCAGGTTTTGGCCGAGTCACATTGGAGTTGACCATCG This work marR-R4 EPZ015938 supplier CGCTTCGTGGTACGCTATTT This work Figure 2 PCR identification and characterization of new IS 711 insertion sites in B. abortus B12 and B16 field isolates. IS711-anchored PCR with: (A), primers IS711out-P5; or (B), RB51-P5. Site-specific PCR with: (C), primers BruAb1_0736F and BruAb1_0737R; or (D), forward and reverse primers of BruAb2_0461. For each lane, the number refers to the B. abortus strain used in the amplification.

71 and 4.01 ppm #find more randurls[1|1|,|CHEM1|]# were the characteristic resonances of the coterminous two methylene protons of -CH2CH2- in DEA unit, and

the signals at 1.05 and 2.59 ppm belonged respectively to the end methyl and methylene protons of -CH2CH3 in DEA unit. The characteristic PEGMA peaks at 3.40, 3.65, and 4.35 ppm attributed to -OCH3, −OCH2-CH2O-, and -COO-CH2- protons, respectively. The degree of polymerization of PCL (x), PDEA (y) and PPEGMA (z) and the molecular weights (M n,NMR) were calculated from the integration ratio values of signal (g) to (a) (I g/I a), signal (n) to (g) (I n/I g), and signal (r) to (g) (I r/I g), respectively, as summarized in Table 1. Figure 2 1 H NMR spectra of (PCL) 2 -Br 2 (A) and (PCL) 2 (PDEA- b -PPEGMA) 2 (B) in CDCl 3 . Table 1 GPC and 1 H NMR data of (PCL) 2 (PDEA- b -PPEGMA) 2 polymers Entry Samplea M n, GPC b M w/M n b M n,

NMR c M n, RealIR d 1 (PCL24)2(PDEA16-b-PPEGMA19)2 14,888 1.28 29,617 28,200 2 (PCL24)2(PDEA37-b-PPEGMA15)2 12,692 1.19 33,977 34,300 3 (PCL38)2(PDEA26-b-PPEGMA11)2 18,302 1.19 29,530 28,524 4 (PCL38)2(PDEA17-b-PPEGMA9)2 13,586 1.35 24,480 24,614 5 (PCL32)2(PDEA25-b-PPEGMA22)2 19,389 1.41 37,766 38,114 6 (PCL32)2(PDEA20-b-PPEGMA19)2 18,707 1.37 32,907 32,120 aThe subscripts check details of PCL, PDEA and PPEGMA were the DP of PCL (x), PDEA (y) and PPEGMA (z) calculated from 1H NMR spectrum; bmeasured by GPC in THF; ccalculated by the equations M n, NMR = (114 × x +185 × y + 475 × z ) × 2 + 434; dcalculated by monomer conversion from the ReactIR. Figure 3 showed that the reaction process could be easily in situ monitored by ReactIR iC10 via detecting the change of absorbance at 938 cm−1 (=CH2 wags of the DEA and PEGMA) [36, 37]. It

could be seen that the absorbance at 938 cm−1 decreased as the polymerization of DEA proceeded. Since the absorbance of DEA almost kept constant at 5 h, the second monomer PEGMA was added to continue the polymerization for another 20 h until the absorbance remained unchanged again in Figure 3A. From the change of absorbance at 938 cm−1 in situ monitored by react infrared spectroscopy, we could calculate the conversions of DEA and PEGMA PtdIns(3,4)P2 during the ARGET ATRP presented in Figure 3B. And thus the molecular weights (M n, ReactIR) of the (PCL)2(PDEA-b-PPEGMA)2 could be calculated from the conversions of DEA and PEGMA, which was seldom reported before. The M n, ReactIR listed in Table 1 were in good agreement with the M n,NMR, suggesting that (PCL)2(PDEA-b-PPEGMA)2 with different PCL/PDEA/PPEGMA contents were well-defined. The semilogarithmic plots of ln([M]o/[M]) vs. time from Figure 3C showed linear time dependency for both DEA and PEGMA during their polymerization, indicating that a good control of the polymerization process was achieved in the current work.

Genes GSK1120212 clinical trial colored geen have greater than 2-fold higher expression and genes colored red have a greater than 2-fold lower expression in the PM than the WT in standard

media. 10     ML LL ML LL ML LL ML LL ML LL glucose-6-phosphate to PEP Cthe_0347 Phosphofructokinase 1.77 2.59 2.97 2.13 −1.35 −1.31 −1.14 −1.49 −2.27 −1.07 Cthe_0349 fructose-1,6-bisphosphate BVD-523 cost aldolase, class II 1.60 2.49 3.31 2.50 −1.52 −1.41 −1.49 −2.03 −3.14 −1.42 Cthe_2449 Phosphoglycerate mutase

−2.46 −1.85 1.42 −1.74 −1.48 −1.90 −2.01 −2.88 −5.18 −2.03 Cthe_3153 alpha-ribazole phosphatase 2.11 2.33 1.40 1.40 1.21 1.23 1.42 selleck products −1.14 1.82 2.04 Cthe_0143 Enolase −1.23 −1.04 1.63 −1.02 −1.11 −1.13 −1.05 −2.96 −2.22 −1.16 Non-oxidative Pentose Phosphate pathway Cthe_2443 Transketolase domain-containing protein −3.24 −4.70 1.02 −3.00 1.14 −1.75 −1.90 −1.52 −2.88 −2.74 Cthe_2444 Transketolase domain-containing protein −3.47 −4.63 −1.15 −3.39 1.26 −1.72 −1.63 −1.57 −2.41 −2.36 Cthe_2705 Transketolase central region −1.44 −1.33 2.25 1.19 1.24 1.21 1.17 −1.81 −2.60 −1.32 PEP to Pyruvate Cthe_2874 Phosphoenolpyruvate carboxykinase [GTP] 1.39 2.46 1.43 2.09 −1.05 −1.04 1.30 1.38 −1.07 1.14 Cthe_0344

malic protein NAD-binding −1.68 1.06 1.26 −1.10 −1.01 −1.14 1.20 −1.27 −2.13 1.02 Cthe_1308 pyruvate, phosphate dikinase 1.64 2.29 −1.30 1.65 −1.05 1.07 1.30 1.10 2.03 1.49 Pyruvate to Lactate/Formate/Acetyl-CoA Cthe_1053 L-lactate dehydrogenase −1.78 −1.25 1.32 −1.02 −1.41 −1.27 −1.33 −1.16 −3.30 −1.55 Cthe_2794 pyruvate/ketoisovalerate oxidoreductase, gamma subunit 4.30 1.48 5.15 3.99 1.92 2.56 2.45 2.78 1.61 −1.05 Cthe_2796 pyruvate flavodoxin/ferredoxin oxidoreductase domain protein 3.13 1.47 4.16 2.94 1.98 2.05 1.88 1.94 1.49 1.02 Cthe_0505 formate acetyltransferase −1.95 −1.91 1.46 −1.04 1.24 1.04 1.11 −1.81 −2.31 −1.76 Acetyl-CoA to Ethanol/Acetate Cthe_1028 Acetate kinase 1.67 2.57 3.63 3.05 2.12 1.26 2.76 1.50 −1.02 1.06 Cthe_1029 phosphate acetyltransferase 1.54 1.79 4.01 filipin 3.83 2.42 1.33 2.73 1.63 −1.08 −1.61 Cthe_2238 Aldehyde Dehydrogenase 1.06 1.04 −1.81 −1.29 1.20 1.36 1.36 1.02 2.30 1.83 Cthe_0101 iron-containing alcohol dehydrogenase −1.35 −1.19 2.19 1.20 1.22 −1.04 −1.18 −1.82 −2.43 −1.48 Cthe_0423 iron-containing alcohol dehydrogenase 1.12 1.07 4.75 5.02 1.26 1.06 1.28 1.45 −3.36 −4.42 Bold values indicate significantly different levels of expression as determined by ANOVA.

Similarly, proteome data revealed a consistent expression of 64 and 60 proteins

by the cattle and sheep MAP strains respectively. A comparison of these consistently detected transcripts and proteins revealed that, in the presence of iron, one third of the differentially regulated genes (P < 0.05) were represented both in the respective transcriptome and the proteomes of the two strains (Figure 1). Figure 1 Transcriptome and selleck chemicals llc proteome comparisons: Venn diagram showing the comparison of transcripts and proteins that were differentially expressed at a fold change of 1.5 or greater in cattle or sheep MAP strains in response to iron. One third of the genes differentially expressed in response to iron were represented in both the transcriptome and the proteome. Transcript profiles under iron-limiting conditions Under iron-limiting conditions both the MAP strains showed increased transcription of genes belonging to mycobactin synthesis

and esx-3, an essential secretory system of mycobactin biosynthesis (Additional file 1, Tables S2 – S5) [30]. C MAP showed increased transcription of genes belonging to ABC type transporter proteins, suf operon involved in Fe-S cluster assembly proteins GSK690693 research buy (MAP1187-MAP1192), fatty acid biosynthesis operon (MAP3188-MAP3190) and a pyruvate dehydrogenase operon (MAP2307c-MAP2309c) (Table 1 and Additional file 1, Table S5) suggesting that the transcriptional machinery is used to mobilize iron to maintain intracellular homeostasis. CMAP also upregulated expression of an enhanced intracellular survival gene (eis) (MAP2325), which was described as “”deletion 3″” in sheep strains of MAP [16]. Table 1 Transcript and protein expression in

cattle MAP under iron-limiting (LI) conditions   MAP ORF ID Predicted function aFold change       Protein Transcript Metabolism           MAP1587c alpha amylase 2.03 ± 0.2 2.87 ± 0.7   MAP1554c FadE33_2 (acyl-coA synthase) 1.79 ± 0.5 1.88 ± 0.8   MAP2307c pdhC alpha-keto acid dehydrogenase 1.68 ± 0.3 2.52 ± 0.4   MAP3189 FadE23 (acyl-CoA dehydrogenase) 2.41 ± 0.2 3.51 ± 1.0   MAP3694c FadE5 (acyl-CoA dehydrogenase) 1.87 ± 0.8 3.15 D-malate dehydrogenase ± 0.2 Cellular processes           MAP3701c heat shock protein 2.18 ± 0.6 2.48 ± 0.3   MAP1188 FeS assembly protein SufD 2.23 ± 1.0 2.73 ± 0.2   MAP1189 FeS assembly ATPase SufC 1.78 ± 0.5 2.03 ± 0.1   MAP4059 heat shock protein HtpX 1.48 ± 0.1 1.66 ± 0.5 Poorly characterized pathways           MAP1012c patatin-like phospholipase 1.67 ± 0.3 1.56 ± 0.3   MAP1944c iron suphur cluster biosynthesis 1.56 ± 0.9 1.66 ± 0.2   MAP2482 Glyoxalase/Bleomycin resistance 1.84 ± 0.3 2.19 ± 0.8   MAP3838c RES Milciclib chemical structure domain containing protein 1.50 ± 0.7 2.40 ± 0.2 aMAP oligoarray was used to measure gene expression whereas iTRAQ was used to quantitate protein expression in the cultures of cattle MAP strain grown in iron-replete (HI) or iron-limiting (LI) medium. Fold change for each target was calculated and represented as a log2 ratio of LI/HI.

The results showed that 50% of the https://www.selleckchem.com/products/Cyt387.html sequences are encoded within IGRs, 90% of which are situated between 16S and 23S rRNA (shown on the right), 31% are tRNA sequences, 6% are part of rRNA sequences, 9% completely overlap with ORFs, and 4% partially overlap with ORFs. Analyses of the INCB28060 research buy cDNA sequences encoding partial ORFs indicated which genes were expressed in the presence of tigecycline. As stated above, 9% of the sequences identified matched to rRNAs, in addition to a further

sequence which was found to overlap the 30S ribosomal protein and another mapped to elongation factor tu. This is perhaps not surprising, given that the specific target for tigecycline is the ribosome [19]. On the other hand, sequences overlapping known stress-response genes were also captured in the cDNA library, e.g. dinF and a gene encoding a putative outer membrane protein (SL1344_1151). The dinF gene is a member of the SOS response family and encodes an efflux pump which belongs to the multidrug and toxic compound extrusion (MATE) family [31], and SL1344_1151, encoding a putative outer membrane protein homologous to ycfR in E. coli, which influences biofilm formation through stress response and surface hydrophobicity [32]. The expression of these genes supports our hypothesis that challenge at half the MIC of tigecycline triggers a stress response. Of note, the cDNA library also contained

sequences of different lengths that mapped to open reading frames, which we postulate to be a result of mRNA degradation, Semaxanib order rather than a representation of bona fide sRNA regulators. Meanwhile, 4% of all sequences that partially overlap ORFs, all do so at the 5’ end of the ORFs. This suggests that these sequences might be 5’ selleck chemicals llc untranslated regions, or encode riboswitches and/or control the expression of the downstream genes. Northern blot verification

Northern blot analysis was performed on RNA extracted from SL1344 that were either unchallenged or challenged with half the MIC of tigecycline. Since most sRNAs are produced from IGRs [30], only sequences from these regions (100 out of 200 in total) were selected for further validation by northern blot analysis. As 90% of the IGR sequences are located between 16S and 23S rRNA coding sequences, most of which are identical, there were 20 unique IGR sequences (including those located between 16S and 23S rRNA) that were assayed, of which four (encoding sYJ5, sYJ20, sYJ75 and sYJ118) were found to consistently show elevated expression with tigecycline challenge (Figure 2A). The remaining sRNA candidates were either not detectable by northern blots, or did not show differential levels of transcription. Correspondingly all further analyses focused on these four sRNAs. The relative fold increase in sRNA expression was determined by northern blots in challenged versus unchallenged cells.

Conservationists already use flagship species to promote conservation actions (e.g. Krauss 2005; Smith and Sutton 2008; Veríssimo et al. 2009; Barua et al. 2010; Barua et al. 2011; Veríssimo et al. 2011; Root-Bernstein and Armesto 2013), and though anthropomorphic traits such as forward facing eyes are often key in flagship selection (Smith et al. 2012), little attention has been given to the role of anthropomorphized flagships. Commercial marketers have long established that anthropomorphism can be an effective way to connect people to products and services. This has led to the use of anthropomorphism in campaigns dealing

with products ranging from flavored fruit drinks to condoms to car parts (Spears et al. 1996; Waytz et al. 2010). Nonetheless, marketers have Belnacasan realized anthropomorphism is not universal, with its impact influenced by the social, economic and cultural profile of the target audience. As such, anthropomorphism has been used largely in a strategic way for particular product and service categories and linked to specific animal groups (Epley et al. 2008; Waytz et al. 2010). For example, representations of animals are mainly associated with the selling of food and drink (nondurables), pet foods, and services, with wild animals more frequently shown in an anthropomorphic state than domesticated animals (Spears et al. 1996). Social marketers

have also used anthropomorphism to improve the impact of conservation messages. For example, in the United States, Smokey the Bear, a black bear shown AZD6738 in a Forest Ranger’s uniform, is one of the most buy MCC950 popular conservation icons, branded with his message “only you can prevent wildfires.” As would be expected, anthropomorphism is common in Tyrosine-protein kinase BLK marketing campaigns that associate animals to the brands they are promoting as a

means to influence their target audience (Spears et al. 1996). This influence occurs both through the symbolic meanings that have been culturally assigned to particular animal species as well as the species physical attractiveness and likability (Lancendorfer et al. 2008). In this context, anthropomorphism gives marketers ample flexibility to move away from or reinforce the symbolic meanings associated with a species and in this way construct brand personalities that more effectively resonate with their target audience (Kotler and Armstrong 2012). Nevertheless, we still do not understand many of the dimensions of this use such as what aspects of animals (e.g. behavior, physical) are most often anthropomorphized and how these different aspects impact different socio-economic groups. Anthropomorphism is thus likely to motivate conservation support by highlighting commonalities between the human and non-human conditions. Anthropomorphism is based on at least three primary engagements with other species, including egomorphism, charisma and empathy, but it can develop through different experiences and take many forms.

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