Input: Task: corroborate the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: Impact factor12. 4 ISSN: 1838-7640Aims and scope Editorial board Author info Submit manuscript Manuscript login issue 2024 2023 2022 2021 2020 534. Full text PDF Nanotheranostics 2024; 8(4): 506-520. Full text of of Journal of reach, higher impact PDF Theranostics 2020; 10(14):6310-6321. doi:10. 7150/thno. 42573 This issue Paper Phage-delivered sensitisation with subsequent antibiotic treatment reveals sustained effect against antimicrobial resistant bacteria Hongbo Liu1,2,†, Hao Li3,†, Yuan Liang2,†, Xinying Du2,†, Chaojie Yang2,†, Lang Yang1, Jing Xie2, Rongtao Zhao2, Yigang Tong4, Shaofu Qiu2, Hongbin Song1,2, 1. Academy of Sciences, 27 Taiping Road, Haidian District, Beijing 100850, China2. for for and Prevention, 20 Dongda Street, Fengtai District, Beijing 100071, China3. Laboratory of Pathogen and Biosecurity, of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing 100071, China4. for Science and Engineering (BAIC-SM), College of and Technology, of Chemical Technology, Beijing 100029, China†These authors contributed equally to this 6321. doi:10. 7150/thno. 42573. styles go to File – Import. Select the file that you have just downloaded and select import option (RIS). Click on Import. File import instruction phages integrated with clustered regularly interspaced short palindromic repeat ()/Cas systems have been gaining attention as potential strategies for combating bacteria resistant to antimicrobials. To further advance this technology, phage recombination procedure should be improved, and the bactericidal effect should be examined in detail and compared with conventional lytic phage strategy. The possibility of the emergence of mutational resistance, a phenomenon commonly observed with lytic phage therapy, should be illustrated. Methods: Here, we developed a novel one-step cloning method to fulfil the recombination ofCas9 system within the genome of a new isolated lysogenic Escherichia coli phage. [SEP] Justify:

Output: The text supports the claim that phage therapy is an effective treatment for antibiotic-resistant bacteria by discussing phages integrated with CRISPR/Cas systems as potential strategies for combating these bacteria. It emphasizes the need to improve phage recombination procedures and to examine the bactericidal effects of phages, which suggests a focus on developing and validating phage therapy as a viable treatment option against antimicrobial resistance.


Input: Task: contrast the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: The phage-resistant mutants become predominant under the selection pressure of phage activity, which leads to a rapid loss of the bactericidal effectiveness of lytic phages [13-15]. Thus, particular lytic phages cannot provide long-term and stable bactericidal effectiveness [16]. In recent years, temperate phage-delivered clustered regularly interspaced short palindromic repeat ()/Cas (PDC) strategies have been developed to combat bacteria resistant to antimicrobials. /Cas cassettes are integrated in the genome of temperate phages to eradicate resistant bacteria by lethal chromosomal DNA cleavage or resistance-encoding plasmid removal [17-20]. Although the idea of combating antibiotic-resistant bacteria via RNA-guided nuclease targeting is intriguing, previous studies of chromosome targeting strategies have shown limited therapeutic effects; only a 102 to 103-fold decrease in bacterial load has been observed [17, 18]. Essentially, modified temperate phages that cause lethal double strand breaks (DSBs) in the bacterial chromosome can be considered as a type of lytic phage. However, they are far less effective than native lytic phages since lytic phage therapies require no genome recombination process and have shown reliable therapeutic potential [15, 21]. A resistance-encoding plasmid targeting strategy has been shown to sensitise resistant bacteria in vitro [20]. However, whether this strategy can be utilised to eradicate resistant bacteria is yet to be evaluated, especially using in vivo assays. Eradication of bacterial resistance can restore sensitivity to common antibiotics. In this study, we used aCas9 system for targeting and eliminating resistance-encoding plasmids and presented a PDC-based strategy with potent antimicrobial efficacy. For efficient delivery, we designed a one-step engineering method to integrate theCas9 system, capable of efficiently destroying NDM-1-encoding plasmids that mediate resistance against carbapenems within the genome of a novel temperate phage. The plasmid elimination and bacterial sensitising efficacy of PDC were then determined using both in vitro and in vivo assays. Next, the efficacy of this phage-delivered resistance eradication with subsequent antibiotic treatment (PRESA) strategy for eradicating resistant bacteria was evaluated. targets resistant bacteria without phage-induced cell lysing activity, it has the potential to prevent the rapid development of bacterial phage resistance. [SEP] Justify:

Output: The text contrasts the claim by discussing the limitations of phage therapy in treating antibiotic-resistant bacteria. It mentions that 'phage-resistant mutants become predominant' under phage activity, leading to a 'rapid loss of the bactericidal effectiveness of lytic phages.' Although some strategies are highlighted, such as the use of temperate phages and RNA-guided nuclease targeting, the overall effectiveness of these methods remains limited, with previous studies showing only a 102 to 103-fold decrease in bacterial load. This suggests that while phage therapy might be used, its effectiveness is questionable and not consistently reliable.


Input: Task: pass the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: Therefore, the long-term antimicrobial effectiveness of PRESA was observed in vitro and in vivo to determine whether new bacterial resistance against PRESA occurred during treatment. To highlight the value of PRESA, a lytic phage was examined in parallel as a direct killing strategy comparison. Finally, bacterial clones receiving PRESA or other parallel treatment strategies were analysed for the emergence of bacterial antibiotic or phage resistance-related mutations. By eradicating plasmid-encoding resistance and preventing the development of antibiotic or phage resistance, the efficacy of low-cost antibiotics can be restored for the treatment of bacterial infections. could be developed as a potential solution for the problem of bacterial antimicrobial resistance. and strain constructionplasmids were constructed based on pCas9 (plasmid 42876; ). Specific spacer oligo pairs were synthesised and inserted into pCas9 according to the manufacturer's protocol. All spacers in the reengineered systems were verified by sequencing with the spacer-F/R primers (for all primers see Table S1). E. coli J53 pNDM-1 and E. coli J53 pmcr-1 were generated by bacterial conjugation. The donor plasmids were obtained from clinical isolates. pEGFPlac-ndm was constructed from pEGFP-N1 (Gen#U55762; ). The prokaryotic lac promoter was added to the upstream region of EGFP, and blaNDM-1 was amplified from pNDM-1 (primers NDM1001-F/R) and inserted into pEGFP-N1 between the XbaI and SalI restriction sites. Recombinant plasmid pEGFPlac-ndm was transformed into E. coli DH5α competent cells to generate the fluorescent model strain E. coli DH5α pEGFPlac-ndm. The sucrose-induced suicide plasmid pSTK was constructed by inserting sacB into the NdeI restriction site in pUC-19 and integration of a kanamycin-selectable marker sequence between the SalI and BamHI sites in the same pUC19. The kanamycin-selectable marker was amplified using primers (N1Kana-F/R), containing the target-PAM sequence from blaNDM-1 at the 5′ end of primer N1Kana-F. [SEP] Justify:

Output: The text provided does not directly address the claim regarding phage therapy as a treatment for antibiotic-resistant bacteria. Instead, it describes experiments involving plasmid construction and bacterial strain generation without explicitly discussing the effectiveness of phage therapy.


Input: Task: corroborate the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: Then, we proposed and developed a phage-delivered resistance eradication with subsequent antibiotic treatment (PRESA) strategy. The removal efficiency and antimicrobial effect of the plasmids were analysed. Long-term antimicrobial effect was evaluated by continued OD600 monitoring for 240 hours to illustrate the potential mutational resistance, compared with the lytic phage strategy. The treatment effect of PRESA was evaluated in vivo by determining bacterial loads in the skin and intestine of infected mice, in contrast with lytic phage therapy. Genome sequencing was performed to identify mutations in bacterial cells treated with phage strategies. Results: Phage-delivered targeting efficiently eradicated and blocked the transfer of the antibiotic resistance plasmid. PRESA decreased the bacterial load by over 6- and 5-logs in vitro and in vivo, respectively. Importantly, while lytic phages induced mutational phage resistance at 24 h in vitro and 48 hours in vivo, PRESA demonstrated a constant effect and revealed no resistant mutants. Genes involved in DNA mismatch repair were upregulated in cells undergoing Cas9-based plasmid cleavage, which may reduce the development of mutations. Conclusion: strategy for eradicating resistant bacteria showed high bactericidal efficacy and a sustained inhibition effect against resistant bacteria. By restoring the efficacy of low-cost antibiotics, PRESA could be developed as an efficient and economical therapy for infections of antibiotic resistant bacteria. Keywords: Antimicrobial resistance, Phage delivery system,Cas, Phage genome recombination, Phage therapy antibiotic resistance has become a serious threat to human health [1-3]. Superbugs, such as blaNDM- or mcr-possessing pathogens, have developed resistance against carbapenems or polymyxins, which are considered antibiotics of last resort [4-9]. Unfortunately, the development of new classes of antibiotics has not kept pace with clinical demand. Thus, novel antimicrobial techniques defending against bacterial drug resistance are urgently needed. Lytic phages are considered a promising strategy for combating antibiotic resistant bacteria as they are natural and effective predators of bacteria. The use of lytic phages against bacteria resistant to antimicrobials has revealed potent treatment effects [10, 11]. However, phages that kill bacteria directly by cell lysis or cytotoxicity always result in bacterial phage-resistance. This resistance develops because of the emergence of mutant bacterial clones [10, 12]. [SEP] Justify:

Output: The text corroborates the claim by detailing the effectiveness of phage therapy, specifically the PRESA strategy, in eradicating antibiotic-resistant bacteria. It highlights that PRESA demonstrated a significant decrease in bacterial load both in vitro and in vivo, showing 'high bactericidal efficacy and a sustained inhibition effect against resistant bacteria.' Moreover, it mentions that lytic phages have potent treatment effects against bacteria resistant to antimicrobials, thus supporting the idea that phage therapy is a viable option for treating antibiotic-resistant infections.


Input: Task: pass the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: The fur on the mice backs was carefully shaved and removed with an 8% Na2S solution. Next, the denuded mice were sterilised. A 1. 5 cm × 1. 5 cm burn wound on mice backs was made by exposing this area at 95 °C for 10 s. Wounded skin was immediately challenged with inoculation of 10 µL PBS containing 105 E. coli MG1655 pUCtargetk cells. After 1 h, 20 µL of either vB_Cas9 or the wild-type phage solution (~107 PFU) were subcutaneously injected under the infected skin. An additional 50 µL of the phage lysate was applied by direct spread on the wound. The wounded skin was covered with a moisturising dressing, and the activity of the mice was restricted to protect the wound. Kanamycin treatment was administered by tail vein injection. Wounded skin was homogenised to recover the colonised bacterial cells on MacConkey medium agar. Separated MG1655 cells were confirmed using 16S sequencing. E. coli clones were counted (by estimated CFUs) to calculate the bacterial load on burned skin tissue. A mouse model of the intestine was prepared by the administration of 50 µL of PBS containing ~105 cells of E. coli MG1655 pUCtargetk into the mouse intestine via an enema. Phages were also delivered by administration of 100 µL of a lysate containing ~107 of either vB_Cas9 or the wild-type control. DNA was extracted from fresh stool samples using the (Qiagen, Hilden, Germany). Concentration of pUCtargetk was quantified using qPCR with a standard curve as a reference. MG1655 cells in stool samples were isolated on MacConkey agar and identified using 16S sequencing. Number of colonies in each group were counted. Sequence analysisIn total, seven vB_253-resistant clones and four kanamycin-resistant clones were isolated from the in vitro experiment and subjected to genome sequencing, along with three clones isolated from the combined treatment group and one wildtype MG1655 strain. The genomic DNA of all MG1655 strains was extracted using the. A DNA library was constructed using the for Illumina. Genome sequencing was performed with an Illumina MiSeq sequencing platform, and annotation was obtained using RAST. [SEP] Justify:

Output: The text does not directly address the effectiveness of phage therapy against antibiotic-resistant bacteria. Instead, it describes experimental procedures involving phage treatment in a mouse model without explicitly confirming or contrasting the claim regarding its effectiveness.


Input: Task: pass the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: Plasmids pUCk and pUCtargetk were constructed based on pUC-19, with the insertion of a kanamycin-selectable marker using primers Kana-F/R and N1kana-F/R, respectively. Resistant E. coli model strains used for the analysis of plasmid eradication by vB_Cas9 were constructed by transforming pUCtargetk into wild-type E. coli strains. Determination of the plasmid-eradication effectThe PCR primers targeting pNDM-1 were ndm300-F/R and the primers for pMCR were clr-F/R. The relative fold change values of the plasmids in bacterial cells were determined using qPCR; 16S was used as the reference gene (primers 16s-F/R). Quantitative PCR was performed using primers ndm300-F/R with (Tli RPlus; Takara, Beijing, China) and a Bio-Rad qPCR instrument (). Amplification conditions were set according to the instructions provided with the qPCR reagents. Phage preparation and genome modification assaysTemperate phage vB_EcoM-IME365 was a novel lambda-like phage, which whole genome sequence length is 47. 175 kb (Text S1). The host strain of this phage includes E. coli strains like MG1655, DH5α, J53. The entire length of lytic phage vB_Ecos-IME253 (referred to as vB_253) (GenBank Accession: KX130960) is 46. 17 kb. It can infect and lyse the MG1655, DH5α, J53 strains. The methods for phage purification were similar to those in a previously reported study [20]. Phage titre was determined using plaque-forming assays or qPCR with primers Phage200-F/R. Modification of the phage genome was performed using our one-step method. This method based on traditional bacterial homologous recombination method, but without introducing of the resistance-selective marker. First, the E. coli MG1655 strain was infected with temperate phage vB_365. Next, pKD46 and pSTk were transformed into lysogenic cells. [SEP] Justify:

Output: The text does not directly address the claim regarding phage therapy as an effective treatment for antibiotic-resistant bacteria. It discusses technical aspects of plasmid construction, qPCR methods, and phage properties, but does not provide information on the effectiveness of phage therapy itself.


Input: Task: corroborate the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: Sequence alignment analysis was performed using CLC 9. 0 (CLC). The on-line version of the MG1655 genome was set as the reference (GenBank Accession: NC_000913. 3). All reads of each clone were aligned with the reference sequence to determine the position and type of mutations and indicate gene annotations in the genome. Phage resistance-associated genes, including ompA, ompC, ompF, phoE, lamB, fhuA, tonB, waaB, and btuB, were screened. Transcription analysis of mismatch repair genesA volume of 1 mL MG1655 pUCtargetk cells (OD600 ≈ 0. 3) was treated with the modified phage strategy (vB_Cas9) or lytic phage strategy (vB_253) separately (MOI ≈ 50). An equal amount of MG1655 cells was treated with kanamycin (final concentration 50 μg/mL); MG1655 pUCtargetk cells were treated with saline as the blank control. Bacterial cells were collected after 24 h, and bacterial RNA was extracted using the. cDNA was prepared using the PrimeScript RT reagent Kit with gDNA Eraser (TaKaRa). Following reverse transcription, the cDNA level of mutS, mutT, polB and dnaE was determined using relative quantitative PCR. Statistical analysisGraphs were obtained using GraphPad Prism. Statistical analyses were performed with unpaired t-test. P < 0. 05 was considered statistically significant. Error bars represent the standard deviation of at least three independent experiments. Results One-step integration of theCas9 system into a lysogenic phagePlasmid pCas9-N1 possessing aCas9 system targeting blaNDM-1 was constructed based on pCas9. Quantitative PCR results proved that target NDM-harbouring plasmids could be efficiently eradicated by pCas9-N1 in 8 h in E. coli cells, independent of plasmid copy number (Figure S1, S2). This highly functionalCas9 cassette was then inserted into temperate phage vB_EcoM-IME365 (vB_365). To integrate theCas9 sequence of pCas9-N1 into the phage genome, we designed and implemented a novel seamless recombination procedure. [SEP] Justify:

Output: The text supports the claim by discussing the application of a modified phage therapy strategy (vB_Cas9) to efficiently eradicate target plasmids (like blaNDM-1) in antibiotic-resistant E. coli cells. It describes how notable results were achieved using quantitative PCR, demonstrating the effectiveness of the phage treatment over an 8-hour period, implying the potential for phage therapy against antibiotic resistance.


Input: Task: contrast the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: In contrast, the E. coli vB_253 was used as a lytic phage strategy. The lytic phage resulted in a decrease in OD600 values during the initial 24 h but soon lost its inhibitory effect. The surviving bacterial cells in PRESA and lytic phage groups were separated at 96, 144, 192, and 240 h. A phage plaque test was used to confirm that the MG1655 cells in the vB_253 group had acquired phage-resistance after receiving the lytic phage strategy while cells in the combinatory treatment group had not (Figure S6). In addition, the wild-type MG1655 strain treated with kanamycin was used as a parallel experiment group, to determine induced kanamycin-resistance mutant. The OD600 results showed that bacterial growth was inhibited by kanamycin during the first 84 h, but subsequently, resistant mutants emerged and the OD600 value increased until the end of experiment. This result indicates that the combinatory strategy of PDC and kanamycin prevented both the rapid development of phage resistance and the emergence of kanamycin-resistant mutant clones. Figure 2 The phage deliveredCas9 was applied to eliminate resistance plasmids. Plasmids with or without the target site were treated with the modified vB_Cas9 phage or the wild-type temperate phage (WT) at a MOI of ~20 for 8 h. (A) Data represent the colony counts of resistance plasmid-possessing bacteria following different phage treatment (n = 3, mean ± SD). (B) Time-course analysis of the MG1655 pUCtargetk strain treated with vB_Cas9 or the wild-type control. The relative fold change of pUCtargetk copy number was determined at various time points using qPCR (n = 3, mean ± SD). (C) Kanamycin-resistant strains containing the targeted plasmid were cultured with vB_Cas9 or the wild-type control at various MOIs for 8 h. Surviving bacterial cells were determined by colony counts (n = 3, mean ± SD). (D) MG1655 pUCtargetk cells was treated with combined use of modified phage and kanamycin, lytic vB_253 phage or wild-type vB_365 control. [SEP] Justify:

Output: The text contrasts the claim by describing results from experiments involving phage therapy that show a lack of long-term effectiveness. Specifically, it states that the lytic phage treatment led to a decrease in bacterial load initially but ultimately lost its inhibitory effect, which indicates that the bacteria can develop resistance to the phage over time. Furthermore, it highlights that resistant mutants emerged during treatment with kanamycin, suggesting challenges in effectively using phage therapy against resistant bacteria.


Input: Task: pass the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: The linear dsDNA donor was amplified and fusion PCR with primers phageup-F/R, spCas9-F/R and phagedown-F/R and purified using the (). Then, the E. coli MG1655 pKD46 pSTk prophage strain was grown in LB medium at 30 °C and 200 rpm, and the expression of the λ-Red system was induced by the addition of 0. 02 mol/mL L-arabinose when the OD600 reached 0. 1. When the OD600 reached 0. 6, competent cells were obtained, and the dsDNA was electro-transformed. Transformant colonies were screened with LB agar containing ampicillin and sucrose, and then verified using PCR detection with primers phicas-F/R. Determination of the bacterial sensitising effect in vitroE. coli containing the targeted plasmid was cultured at 30 °C until mid-exponential phase. The bacterial culture was then aliquoted into a 96-well plate (100 μL per well), and phages were added to each well at a MOI as indicated in each assay. Bacteria in the plate were incubated at 30 °C for 4 h and cells were cultured on LB medium plates to yield single colonies. Intracellular plasmids of bacterial colonies were determined by qPCR following the same method described above. The time course of plasmid eradication by the modified phage was determined by culturing resistant bacteria, adding the vB_Cas9 to bacterial liquid cultures for different time periods, and quantifying the relative fold change of the plasmid in the bacterial cells at the indicated time. In the PRESA strategy assays, cells were treated with phages together with kanamycin (25 μg/mL). In vivo assaysAll animal experiments were supervised and approved by the of Chinese PLA Centre for and Prevention. All in vivo assays were conducted using 6- to 8-week-old female BALB/c mice. In this study, the mouse model used for superficial infection assays was modified from the thermal injury model of Stieritz and Holder [22]. All mice were initially anesthetised with 4% pentobarbital sodium (4 µL/g of weight) by intraperitoneal injection. [SEP] Justify:

Output: The text describes a detailed experimental protocol involving the use of phage therapy but does not explicitly support or contradict the claim about its effectiveness in treating antibiotic-resistant bacteria. It primarily focuses on methodologies and procedures without present evidence demonstrating successful outcomes or results related to antibiotic resistance.


Input: Task: corroborate the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: First, we designed a counter-selection system and constructed plasmid pSTk, which contained the sucrose-induced suicide gene sacB and a 30 bp target sequence (with PAM) from blaNDM-1 (Figure 1A). Subsequently, the vB_365 prophage, pSTk plasmid and pKD46 plasmid were successively introduced into the E. coli MG1655 host strain, providing the necessary enzymes for homologous recombination. Next, the dsDNA donor, containing the specificCas9 cassette from pCas9-N1 and homologous arms, was transformed into the cells by electro-transformation. /Cas9 system integrated within the prophage genome could be directed to the target-PAM sequence and eliminate the suicide plasmid via an RNA-guided nuclease, enabling cell survival. In contrast, bacterial transformants that failed to integrate theCas9 system were killed by the suicide gene (Figure 1B). /Cas9-positive recombinants were further identified by PCR screening, which revealed a recombination rate of 28. 1% (Figure S3). Finally, the genetically modified phage vB_EcoM-IME365_Cas9 (referred to as vB_Cas9) was induced from the recombinant host strain. The modified phage was shown to beCas9-positive by PCR analysis (Figure S4). In addition, a 6. 542 kb DNA fragment flanking the full length of theCas9 sequence within the modified phage genome was examined to verify the integration of the specificCas9 cassette (Figure S5). In comparison with previous methods (Table S2), ourCas9 integration process does not leave resistance marker residues in the phage p9. Bacterial cells were continually recovered on LB agar and analysed for the presence of intracellular plasmids using colony PCR. The results indicated that vB_Cas9 decreased the number of resistance plasmid-possessing bacteria by over 5 logs (Figure 2A). Additionally, the efficiency of intracellular plasmid elimination was analysed by qPCR (Figure 2B). Nearly 99% of the intracellular resistance plasmids were eradicated in 4 h, over 99. 99% of the plasmids were eradicated in 8 h and the elimination effect continued through 32 h. [SEP] Justify:

Output: The text corroborates the claim by detailing a method where a genetically modified phage (vB_Cas9) successfully eliminates antibiotic resistance plasmids in bacteria. It states that nearly 99% of intracellular resistance plasmids were eradicated in 4 hours, and over 99.99% were eliminated in 8 hours, demonstrating the effectiveness of phage therapy against antibiotic-resistant bacteria.


Input: Task: contrast the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: In addition, false positive recombination, such as mutations in theCas9 cassette [18], could be precluded. Then the highly functionalCas9 system was efficiently delivered to the target and destroyed the bacterial resistance plasmid, yielding > 99. 99% clearance rate of the target plasmid in 8 h. Plasmid removal not only eradicated the antibiotic resistance of E. coli cells, but also prevented the spread of bacterial antibiotic resistance. Plasmid-mediated horizontal gene transfer of drug-resistance was blocked by PDC. In contrast, lytic phages killed the bacterial cells but led to the dissemination of intracellular antibiotic resistance plasmids in the bacterial environment. These plasmids are possible to be taken up by co-harboured strains, resulting in the emergence of new resistant strains [27-31]. Therefore, direct killing of resistant cells might increase the risk of horizontal transfer of resistance factors in bacteria-rich environments, such as the human intestine, hospital surfaces, and livestock farms [32, 33]. Thus, plasmid targeting by PDC is not only expected to offer a novel alternative for resistant bacterial infections but will also aid in blocking the transfer of antibiotic resistance. Owing to efficient target plasmid elimination and bacterial sensitisation, kanamycin sensitivity was restored and could be used to treat resistant E. coli. strategy yielded a potent antimicrobial effect against resistant E. coli and the bacterial load decreased by 6 logs in vitro and 5 - 6 logs in the mouse skin or intestine infection models, showing a greater bactericidal effect than in previous studies [17, 18]. Our results indicate that plasmid targeting strategy has the potential to facilitate antibiotic treatment of resistant bacteria in the future. Some antibiotic resistance genes are located in the bacterial chromosome, which is not suitable for using the PRESA strategy. However, according to previous studies, our modified phage can also be utilised to cleave chromosome-encoded antibiotic resistance genes, leading to bacterial cell death. There were concerns about the possibility that the temperate phage-based strategy could spread antibiotic resistance or virulence genes by phage delivery [34]. In our assessment, the risk is low because when treating bacterial infections, the combined use of antibiotics can eradicate the strains receiving phage-induced transduction and sensitisation. [SEP] Justify:

Output: The text contrasts with the claim by indicating that while lytic phages can kill bacterial cells, they can also lead to the spread of antibiotic resistance plasmids in the environment. It discusses the potential risks associated with using phages in terms of increasing the emergence of new resistant strains, which suggests that phage therapy may not be a straightforward effective treatment for antibiotic-resistant bacteria due to these implications.


Input: Task: pass the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: The fur on the mice backs was carefully shaved and removed with an 8% Na2S solution. Next, the denuded mice were sterilised. A 1. 5 cm × 1. 5 cm burn wound on mice backs was made by exposing this area at 95 °C for 10 s. Wounded skin was immediately challenged with inoculation of 10 µL PBS containing 105 E. coli MG1655 pUCtargetk cells. After 1 h, 20 µL of either vB_Cas9 or the wild-type phage solution (~107 PFU) were subcutaneously injected under the infected skin. An additional 50 µL of the phage lysate was applied by direct spread on the wound. The wounded skin was covered with a moisturising dressing, and the activity of the mice was restricted to protect the wound. Kanamycin treatment was administered by tail vein injection. Wounded skin was homogenised to recover the colonised bacterial cells on MacConkey medium agar. Separated MG1655 cells were confirmed using 16S sequencing. E. coli clones were counted (by estimated CFUs) to calculate the bacterial load on burned skin tissue. A mouse model of the intestine was prepared by the administration of 50 µL of PBS containing ~105 cells of E. coli MG1655 pUCtargetk into the mouse intestine via an enema. Phages were also delivered by administration of 100 µL of a lysate containing ~107 of either vB_Cas9 or the wild-type control. DNA was extracted from fresh stool samples using the (Qiagen, Hilden, Germany). Concentration of pUCtargetk was quantified using qPCR with a standard curve as a reference. MG1655 cells in stool samples were isolated on MacConkey agar and identified using 16S sequencing. Number of colonies in each group were counted. Sequence analysisIn total, seven vB_253-resistant clones and four kanamycin-resistant clones were isolated from the in vitro experiment and subjected to genome sequencing, along with three clones isolated from the combined treatment group and one wildtype MG1655 strain. The genomic DNA of all MG1655 strains was extracted using the. A DNA library was constructed using the for Illumina. Genome sequencing was performed with an Illumina MiSeq sequencing platform, and annotation was obtained using RAST. [SEP] Justify:

Output: The text does not directly address the effectiveness of phage therapy against antibiotic-resistant bacteria. Instead, it describes experimental procedures involving phage treatment in a mouse model without explicitly confirming or contrasting the claim regarding its effectiveness.


Input: Task: corroborate the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: These results demonstrate the high efficacy of the Cas9 nuclease against resistance plasmids. Next, a combined strategy against resistant E. coli, involving phage-induced sensitisation and kanamycin treatment, was tested (Figure 2C). The bactericidal efficiency of this strategy increased with increasing multiplicity of infection (MOI); > 6-log reduction in colony forming units (CFUs) was detected at a MOI of 102. In total, nine E. coli host strains were transformed with pUCtargetk to test the plasmid elimination effect of the modified phage. The bacterial sensitisation effect was confirmed for all of these host strains. Furthermore, the combined strategy could block the spread of resistance by preventing the distribution of the responsible plasmids. Specifically, the transfer of pNDM-1 from Acinetobacter XM1750 to E. coli J53 was inhibited by the intervention of the modified phage. We further analysed the accumulation of resistance genes in the bacterial supernatant during the killing of the resistant strain. To highlight the advantages of PDC, the modified phage was compared with lytic E. coli phage clone vB_ 253. The bacterial supernatant of each group (5 μL) was filtered. Plasmid contained in the supernatant was transformed into E. coli DH5α competent cells. According to result of colony counts, the accumulation of resistance plasmids in the supernatant was slower in the modified phage group than in the lytic phage and control groups; the modified phage group yielded fewer transformant colonies compared with the lytic phage group at 6 and 8 h (Figure 2D; unpaired t-test, n = 3, P < 0. 0001). PRESA sustained inhibition effect to the growth of antibiotic resistant bacteria in vitroE. coli cells with plasmid pUCtargetk mediated Kanamycin-resistance were killed using PRESA. As mutational resistance can be triggered by phage or antibiotic strategies and compromise the antimicrobial effect, we determined the OD600 every 12 h to analyse the inhibition of bacterial growth using different strategies until 240 h (Figure 3). The modified phage and kanamycin (25 μg/mL) combination demonstrated continued efficacy against resistant strain E. coli MG1655 pUCtargetk. New resistance to PRESA was not observed until 240 h. [SEP] Justify:

Output: The text corroborates the claim by detailing a study that shows the efficacy of a modified phage in treating antibiotic-resistant E. coli. It describes a combined strategy involving phage treatment and kanamycin that resulted in a significant reduction in colony forming units, indicating effective treatment against antibiotic-resistant bacteria. Furthermore, it notes sustained inhibition of bacterial growth by the modified phage over an extended period, further supporting the claim of phage therapy's effectiveness.


Input: Task: contrast the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: Most importantly, eradication of bacteria using PRESA did not lead to mutational resistance, which is always observed using lytic phage treatment. In addition to acquired antibiotic resistance mediated by mobile plasmids, emergence of mutational antimicrobial resistance is another threat during bacterial infection treatment. Direct killing strategies are more likely to result in the selection of resistant mutants [34]. Various studies have demonstrated that the efficacy of phage antimicrobials is rapidly compromised because of the development of bacterial resistance against the phage [35-38]. In most cases, phage resistance arises owing to changes in receptors on the bacterial cell membrane, resulting in the absence or modification of phage receptors [15]. Selection pressure exerted by lytic phages leads to the predominance of resistant mutants and the recovery of bacterial growth [39]. Our results demonstrate that new bacterial resistance against lytic phage vB_253 rapidly developed by 12 h in vitro. Genome sequence analysis revealed that the occurrence of mutations in the fepA gene was closely related to this phage resistance. The outer membrane protein, FepA, participates in the adsorption of ferric enterobactin and also functions as the receptor of some phages [23, 40]. exhibited persistent efficacy against antibiotic resistant bacteria. No mutations were found in fepA or other phage receptor-associated genes. In fact, our engineered temperate phage did not kill bacterial cells through repeated lytic life cycles but efficiently disarmed bacterial cells following infection. Thus, temperate phages carrying theCas9 system do not trigger the selection of phage resistance and can sustain longer effectiveness compared with lytic phages. Antibiotic often lost sensitivity because of the occurrence of mutational antibiotic resistance [41]. Our results indicated that even the sensitive MG1655 strain developed new resistance against kanamycin after treating with kanamycin for three days in vitro. Sequence analysis discovered mutations in the fusA gene in the genome of kanamycin-resistant mutant clones. The fusA gene encodes the translation elongation factor EF-G; mutations in this gene are responsible for the development of kanamycin-resistance [42, 43]. Surprisingly, our results suggest that the PRESA strategy prevents the formation of mutational kanamycin-resistance. This phenomenon might be associated with the nuclease activity ofCas9. [SEP] Justify:

Output: The text contrasts the claim by discussing the shortcomings of phage therapy, especially related to lytic phage treatment. It explains that lytic phages can lead to the emergence of mutational resistance in bacteria, ultimately compromising their efficacy. It notes that various studies have demonstrated that phages may quickly lose their effectiveness due to the development of bacterial resistance. Furthermore, it highlights the rapid development of resistance against lytic phage vB_253 and underscores that, unlike lytic phages, the engineered temperate phage carrying the Cas9 system does not trigger the selection of phage resistance, indicating that conventional phage therapy may not be as effective against antibiotic-resistant bacteria as suggested by the claim.


Input: Task: pass the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: 2018ZX10301407, 2018ZX10101003-001-002) and the of China (nos. 81873968, 81673237). and YT designed the experiments; and XD performed the experiments; CY, LY, and LJ analysed the data; PL, LW, and RZ prepared the tables and figures; and YT prepared the manuscript. All authors read and approved the final manuscript. Supplementary figures and tables. The authors have declared that no competing interest exists. 1. -Solano L. et al. A global view of antibiotic resistance. . 2009;33:44-65 2. Johnson AP, Woodford N. Global spread of antibiotic resistance: the example of metallo-beta-lactamase (NDM)-mediated carbapenem resistance. J Med Microbiol. 2013;62:499-513 3. . Global prevalence of antibiotic resistance in paediatric urinary tract infections caused by Escherichia coli and association with routine use of antibiotics in primary care: systematic review and meta-analysis. BMJ. 2016;352:i939 4. . et al. Acinetobacter calcoaceticus from a fatal case of pneumonia harboring bla(NDM-1) on a widely distributed plasmid. BMC Infect Dis. 2015;15:131 5. . et al. Coproduction of MCR-1 and NDM-1 by colistin-resistant Escherichia coli isolated from a healthy individual. Chemother. 2017 61 6. . et al. Emergence of extensively drug-resistant proteus mirabilis harboring a conjugative NDM-1 plasmid and a novel Salmonella genomic island 1 variant, SGI1-Z. Chemother. 2015;59:6601-4 7. . Worldwide dissemination of the NDM-type carbapenemases in gram-negative bacteria. BioInt. 2014;2014:249856 8. Matamoros S, van. et al. Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction. Sci Rep. 2017;7:15364 9. . Widespread distribution of mcr-1-bearing bacteria in the ecosystem, 2015 to 2016. Eurosurveillance. 2017 22 10. -. et al. [SEP] Justify:

Output: The text does not address the claim regarding phage therapy as a treatment for antibiotic-resistant bacteria. Instead, it primarily discusses antibiotic resistance and various studies related to the global impact and prevalence of such resistance, lacking any mention or relevance of phage therapy. Therefore, it is deemed irrelevant.


Input: Task: corroborate the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: The concentration of plasmid in the bacterial supernatant was quantified by qPCR (n = 3, mean ± SD). Figure 3 Solid curves represent the growth of the MG1655 pUCtargetk strain treated with PRESA, lytic phage vB_253, kanamycin, vB_Cas9 and the PBS control. Phages added in each group were at a MOI of 10. The dashed curve represents the growth of MG1655 strain treated with kanamycin. Each dot represents the OD600 value (n = 3, mean ± SD) at the indicated time point relative to 0 h. PRESA eradicated resistant E. coli in a mouse skin infection modelWe next investigated the therapeutic benefit of the bacteria-sensitising effect of the modified phage in a mouse skin infection model. As E. coli is a common species identified in burn wounds, we tested the sensitisation effect in a mouse model of infected skin. An area on the mouse back was depilated and superficially wounded. Next, the burned area was colonised with 107 CFU of E. coli MG1655 pUCtargetk. Then the burned area was treated with the modified phage or wild type vB_365. Then the sensitising effect of the modified phage on mouse skin was examined using PCR. Twelve hours after the modified phage treatment, only 6. 67% bacterial cells isolated from the wounded skin were positive for the pUCtargetk, which was significantly lower than in the control group, i. e. , 98. 33% (unpaired t-test, P < 0. 0001; Figure 4A). To demonstrate the advantages of the modified phage strategy, a combination of modified phage administration and kanamycin injection was used to kill MG1655 pUCtargetk cells in mouse skin infection model, in comparison with the lytic phage strategy. The treatments were implemented every 24 h and the bacterial load in the infected skin was determined for the next seven days. The results showed that the lytic phage strategy decreased the bacterial load during the first two days (Figure 4B). However, the inhibition effect of the lytic phage ceased on the third day, and the bacterial load recovered from the fourth day. The developed lytic phage resistance was confirmed using a phage plaque test (Figure S7). [SEP] Justify:

Output: The text corroborates the claim by providing evidence of the effectiveness of phage therapy in treating antibiotic-resistant E. coli in a mouse skin infection model. It discusses how the modified phage reduced the presence of resistant bacterial cells significantly compared to the control group. It also mentions the combination of modified phage and kanamycin administration, which highlights the potential therapeutic benefit of using phages against antibiotic-resistant bacteria.


Input: Task: pass the claim using the given text. Claim: Bioinformatics is crucial for analyzing genomic data. [SEP] Text: As data production and research are a constantly moving target, any tools provided to mine the data must be developed as quickly as the data is being produced. As creating entirely new tools is a time and developer intensive process, using rapid application development (RAD) techniques, appropriate visual analytics can be quickly provided. By adapting tools and using appropriate frameworks, rather than creating entirely new ones, it becomes practical to create views that are specific to a particular task or research direction. For the work discussed in this paper we adopted a number of standard software frameworks. A number of web-based frameworks for both data and visual development were used that enable both rapid application development and rapid data delivery. These include: the Source libraries for simple, standard data access using SQL database-like language; ExtJS and GXTJS (JavaScript frameworks) for quickly creating intuitive, web-based user interfaces; and web-based visual libraries such as Protovis [52]. Well-known and understood desktop tools such as Cytoscape are also adopted and integrated where appropriate. The use of existing libraries and visual tools has enabled the development of interactive, usable tools (see Figures 4, 5, and 6) within days or weeks rather than months or more. Nested task specific viewsWhile it is necessary to enable general exploration, researchers often need to explore the data from a particular starting point. Our visualizations are generally dedicated to a limited set of tasks however, so providing multiple levels of linked visualization for the data becomes necessary (e. g. cross-population, whole genome, chromosomal location). Information visualization has advocated common workflows and scopes for the development of visualizations which are useful when accessing massive data sets. The macro and micro view [53] ideas have more recently evolved into the information seeking mantra [54] workflow (overview, filter, data on demand). Such a workflow offers a practical approach to the delivery of visualizations, so that they can be accessed using desktop and web based tools. However, development of initial "overview" or macro visualizations is not straightforward with large research data sets, and depends largely on the task that is going to be undertaken. For this reason we have typically provide a number of macro views which can be used to start filtering or analyzing the data. In the PeptideAtlas project the visual tools provide three different "overview" starting points to explore the underlying data. [SEP] Justify:

Output: The text does not directly address the claim about bioinformatics being crucial for analyzing genomic data. Instead, it discusses the development of tools and frameworks for data visualization and management in a broader context, which may indirectly relate to bioinformatics but does not explicitly corroborate or contrast with the claim.


Input: Task: pass the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: 2009;11:1971-82 38. . Impact of a single phage and a phage cocktail application in broilers on reduction of Campylobacter jejuni and development of resistance. PloS One. 2013;8:e78543 39. Drulis-Kawa Z, Majkowska-. Learning from bacteriophages - advantages and limitations of phage and phage-encoded protein applications. Pept Sc. 2012;13:699-722 40. . Bacterial phage receptors, versatile tools for display of polypeptides on the cell surface. J Bacteriol. 2001;183:6924-35 41. . et al. Bacterial evolution of antibiotic hypersensitivity. Biol. 2013;9:700 42. . Genomic analysis reveals distinct concentration-dependent evolutionary trajectories for antibiotic resistance in Escherichia coli. DNA Res. 2014;21:711-26 43. . Modulation of global transcriptional regulatory networks as a strategy for increasing kanamycin resistance of the translational elongation factor-G mutants in Escherichia coli. G3. 2017;7:3955-66 44. Khil PP, Camerini-Otero RD. Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol Microbiol. 2002;44:89-105 45. . et al. Novel self-assembled organic nanoprobe for molecular imaging and treatment of gram-positive bacterial infection. Theranostics. 2018;8:1911-22 46. Radaic A, de. Bacterial anti-microbial peptides and nano-sized drug delivery systems: The state of the art toward improved bacteriocins. J Control Release. 2020;321:100-18 Author contact Corresponding authors: hongbinsongnet (H. S. ); qiushf0613com (S. Q. ); tong. yigangcom (Y. T. ). Received 2019-11-29 Accepted 2020-4-25 Published 2020-5-15Citation styles. , Li, H. , Liang, Y. , Du, X. , Yang, C. , Yang, L. , Xie, J. , Zhao, R. , Tong, Y. , Qiu, S. , Song, H. (2020). [SEP] Justify:

Output: The text does not provide any direct information or evidence regarding phage therapy as a treatment for antibiotic-resistant bacteria. Instead, it includes citations related to various topics concerning bacteria and phages, without addressing the efficacy of phage therapy.


Input: Task: corroborate the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: The modified phage and kanamycin combination yielded a constant bacterial growth inhibition effect. New resistance to the combinatory treatment and recovery of bacterial growth were not observed. PRESA eradicated resistant E. coli in a mouse intestine infection modelE. coli colonises the lower digestive tract and harbours resistance plasmids that can be transferred to Enterobacteriaceae strains. Accordingly, we tested the effectiveness of plasmid eradication using the phage deliveredCas9 system in the mouse intestine. The mouse intestine model was prepared by administration of an E. coli MG1655 pUCtargetk inoculum into the mouse intestine. After 4 h, either vB_Cas9 or wild-type phage was applied to the mouse intestine by enema. Next, mouse stool samples were collected, and the concentration of pUCtargetk in the stool samples was determined. Treatment with the modified phage resulted in a reduction in the target plasmid concentration in the stool samples to 3. 45 ± 0. 76 × 10-3 ng/g at 24 h and 1. 79 ± 0. 73 × 10-3 ng/g at 48 h; these concentrations were significantly different from the plasmid concentrations in the wild-type control-treated samples, i. e. , 14. 72 ± 4. 27 × 10-2 ng/g at 24 h and 10. 50 ± 1. 68 × 10-2 ng/g at 48 h (Figure 5A; unpaired t-test, P < 0. 0001). These results indicate that the phage deliveredCas9 system could effectively reduce antibiotic resistance gene levels in the mouse intestine. Next, different strategies were used to treat kanamycin-resistant E. coli MG1655 pUCtargetk in a mouse intestine model (Figure 5B). Lytic phage vB_253 treatment reduced the E. coli cell count in stool samples on the first and second day. This inhibition effect was lost from the third day. However, treatment using the combinatory strategy showed persistent efficacy until the final day of the experiment. Figure 4 PRESA eradicated resistant E. coli in a mouse skin infection model. (A) The proportion of MG1655 cells containing pUCtargetk in infected skin was determined 12 h after treatment with vB_Cas9 or WT temperate phage. [SEP] Justify:

Output: The text corroborates the claim by detailing the effectiveness of phage therapy against antibiotic-resistant bacteria. It mentions that 'the modified phage and kanamycin combination yielded a constant bacterial growth inhibition effect' and highlights that 'PRESA eradicated resistant E. coli in a mouse intestine infection model.' Furthermore, it provides data showing the reduction of antibiotic resistance gene levels in the mouse intestine when treated with a phage delivered Cas9 system, indicating the potential efficacy of phage therapy in combating antibiotic resistance.


Input: Task: contrast the claim using the given text. Claim: Bioinformatics is crucial for analyzing genomic data. [SEP] Text: Then PCA is performed on X perm to get the singular values. We perform P = 1000 permutations, from which we can compute the p-values of the observed d k 's. The number of principal components, k0, is such that the p-value of d k 's is less than 0. 001 when k ≤ k0. For NCI data, we get k0 = 8 (eight significant principal components). The numbers of nonzero elements in the eight loading vectors (v1…v8) are given in Table 5. We also report the adjusted variance and cumulative adjusted variance as suggested by [7] to get the explained variance properly when the principal component scores are correlated. Note that the adjusted variance is equal to the variance in the ordinary PCA because the principal components of PCA are uncorrelated. Despite the sparsity, in comparison with the ordinary PCA, both of SPCA and SSPCA method give higher cumulative adjusted variance. In fact the SSPCA method gives extremely sparse results, with only 1,260, 681 and 375 nonzero loadings for the first 3 principal components, compared to 13,259, 4,086 and 15,362 for the SPCA method. Up to the third principal component the latter has only slightly larger cumulative variance. Table 5 Analysis of NCI data: number of zero loadingsFull size tableFigure 2 in the Additional file 1 shows the scatterplot matrix of the first 3 SSPCA scores. Except for breast cancer, the different cancer types appear in recognizable clusters in the plot. This means that the sparse vector loadings capture some underlying biological differences between the cancers. To find biological explanation, Table 6 shows the (GO) [12] biological processes enrichment analyses of the nonzero loadings from the first 3 principal components from SSPCA. Only the top 20 most enriched categories with P-values < 10-5 are shown. The results indicate that the greatest variation in gene expression are associated with structure development, cell proliferation and cell death (apoptosis), and cell adhesion. These processes are closely related to the hallmarks of cancer progression such as angiogenesis (development of blood vessels), abnormal cell growth and eventually metastasis (cell migration made possible by abnormally low cell adhesion). Table 6 analysisFull size tableComparative GO analyses from the ordinary PCA are given in the Additional file 1. [SEP] Justify:

Output: The text contrasts the claim by focusing on specific statistical methods (PCA, SPCA, and SSPCA) used in analyzing genomic data rather than directly emphasizing the overall importance of bioinformatics. While it does highlight the analyses performed on genomic data and discusses results related to biological processes, it does not substantiate the claim about bioinformatics being 'crucial' as it primarily details the analytical methods and their outcomes.


Input: Task: pass the claim using the given text. Claim: Bioinformatics is crucial for analyzing genomic data. [SEP] Text: Studies have confirmed that the clustering coefficient in TRNs depends only on the degree of the nodes and it is distributed again as a power-law C(k)≈k −1 [8,13,14]. Both these two properties specify that genes with low degree have a higher clustering coefficient than nodes highly connected leading to a hierarchical network of separated modules of genes interconnected by high-degree genes. On a local scale genes organize in modules. The most significantly frequent patterns of connections between genes of a module are called motifs [15] each with different dynamical proprieties, such as self-regulation, feed-forward and feed-back loops and dense overlapping regulons [15,16] (Figure 1). The most frequent motifs that comprehend miRNAs and TFs interactions are the feedback and feed forward loops [17-19]. Figure 1Motifs of interactions. Graphical representation of the interactions between genes and miRNAs. Arrows are for activation, blunt edges are for repression. Full size image MethodsIntuitively, network construction is based on an iterative procedure. The key idea is to construct a regulatory network starting from a graph without edges in which each node represent a gene or a miRNA and to add connections between nodes imitating some well known motif randomly chosen. Every time a motif is constructed into the network, all the participating nodes are removed from the graph. Regulating genes of the constructed motifs are kept in a separate set of nodes, namely, H. When the graph remains without nodes, a new graph is constructed with the nodes stored in H again with no edges. The procedure then restarts. This iterative method goes on until there are no nodes. The reinsertion of the regulating genes ensures the creation of a modular hierarchy of nodes. The methods here proposed have been implemented as an R [20] package freely available from (Additional file 1) topologyThe idea of creating a modular hierarchical network by replicating the same module at different scales was proposed in [8]. In [7] this replication procedure was extended by constructing a network using a set of motifs instead of a single one replicated at different scales. In this work, this idea is further extended with the addition of the interactions among TFs and miRNAs with the objective of synthesizing multi-view biological data. [SEP] Justify:

Output: The text does not address the claim that bioinformatics is crucial for analyzing genomic data. Instead, it focuses on specific properties of gene regulatory networks and the iterative methods used to construct a modular hierarchy of nodes, which is only tangentially related to the broader claim about the importance of bioinformatics in genomic analysis.


Input: Task: corroborate the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: Each value represents the percentage of plasmid-positive cells in each isolated mouse skin sample (n = 4, mean ± SD). (B) Infected mouse skin was treated with PRESA, lytic phage vB_253, kanamycin, vB_Cas9, or a PBS control. Data represent the logarithm value of bacterial cell counts per gram of skin (n = 3, mean ± SD). Figure 5 PRESA eradicated resistant E. coli in a mouse intestine infection model. (A) MG1655 pUCtargetk cells in the mouse intestine were treated with vB_Cas9 or the WT temperate phage. Data represent the concentration of pUCtargetk per gram of stool sample collected from each mouse (n = 6, mean ± SD). (B) The mouse intestine was treated with PRESA, lytic phage vB_253, kanamycin, vB_Cas9 or the PBS control. Data represent the logarithm value of bacterial cell counts per gram stool sample (n = 3, mean ± SD). PRESA eradicated bacteria without the development of resistant mutantLytic phage-resistant E. coli clones were induced during treatment using phage vB_253. The emergence of phage resistance compromises the phage therapy efficacy. The vB_253-resistant MG1655 clones that emerged in the in vitro assay were isolated and subjected to genome sequence analysis. Five of the seven sequenced clones (253R1, 253R2, 253R3, 253R4, and 253R5) contained mutations in fepA (Figure 6A), including SNV (253R1: 943A>G, 253R3: 2197G>T), insertion (253R2: 844_845insT), and deletion (253R4: 462_477del253R5: 512delG). The fepA gene encodes the FepA protein, which is the ferric enterobactin outer membrane transporter involved in phage absorption as a recognition receptor [23]. The kanamycin-resistant mutant showed a unique mutation in fusA (Figure 6B), which encodes protein chain elongation factor EF-G. [SEP] Justify:

Output: The text corroborates the claim by providing evidence that phage therapy, specifically with the use of PRESA and lytic phages, was effective in eradicating resistant E. coli in a mouse intestine infection model and did so without the development of resistant mutants. It emphasizes that phage therapy may serve as a viable treatment against antibiotic-resistant bacteria, as demonstrated by the data presented regarding the reduction of bacterial cell counts.


Input: Task: pass the claim using the given text. Claim: Bioinformatics is crucial for analyzing genomic data. [SEP] Text: The fact that only one source might provide a gene does not mean that the second source has evidence against the inclusion of the gene in the combined list. Rather this situation indicates no evidence for inclusion. However, if two future web sources do conflict, DST manages disbelief as well. When combining conflicting evidence, the strength of the belief and disbelief are combined, with the stronger evidence having a greater effect. Multiple belief functions may be combined by applying DST iteratively for each basic confidence measurement assignment. When multiple web services return the same gene, DST increases confidence in that gene's inclusion in the results list. The visualization module addresses the problem of p-value conversion without distribution information. For DST to be used, one must have beliefs assigned to each of the values representing the data. Sidekick's visualization and clustering methodology gives the user the ability to manage the conversion from p-value to credibility measures, reflecting prior knowledge in the credibility scores. Once credibility scores are assigned, either as a result of a computation or by the user, Sidekick uses DST for combining these scores into an overall result credibility. A detailed example of combining credibility using Theory is provided in the supplemental materials file. file 1 supplemental. pdfProvenance and version tracking are incorporated into Sidekick to facilitate repetition of experiments and evaluation of data quality. Given the rate which data is updated, a key aspect to Sidekick's strength is ensuring up-to-date data at the time of downloads. Within Sidekick, provenance information is included in the saved workflows and results. Sidekick currently supports six genomes, however the framework was constructed with the goal of extending to a variety of other genomes. When an additional genome is added, the developer adds the pertinent information to the species specific lists. Currently this includes the taxonomy id, the formal and informal species names, and the genome sequence group label to use for chromosomal information. If any specific genome is not covered by a particular data source, the lack of information will appear as lack of results in the query or enrichment. This lack of information can be mitigated through the use of Query: genes → orthologous pair list. By finding orthologous genes that are covered by existing data sources, the user is able to transfer annotations to the unannotated genome. ConclusionsSidekick offers an easy-to-use web-based, flexible alternative to current research tools. [SEP] Justify:

Output: The text does not directly address the significance of bioinformatics in analyzing genomic data. Instead, it discusses the operation of the Sidekick tool for managing data quality and results, without explicitly supporting or contrasting the claim regarding the importance of bioinformatics.


Input: Task: pass the claim using the given text. Claim: Bioinformatics is crucial for analyzing genomic data. [SEP] Text: 5566\) with R 2=0. 9362. Full size image We then verified the scale-invariance of the clustering coefficient. For this, we generated 100 networks with size randomly sampled from the interval [10,1000]. 4 the estimated scale parameter of the distribution of the clustering coefficient in relation with network size is shown. Together these results show that generated networks have the hierarchical modularity property of the real regulatory networks. Figure 4Scale invariance of clustering coefficient. Simulation of 100 networks of random size in [10,1000] shows that the estimated scaling parameter of the clustering coefficient is independent from the network size and approximates the value found in real networks. Full size image In the rest of this section we report four cases of analysis that can be performed on the generated datasets: two examples try to explore the topology of the network and are based on network reconstruction methods and on clustering methods. The other two are methods of feature relevance: a filter method based on t-tests and a wrapper method based on the Boruta method. For the experiments we generated three regulatory networks from which we generated different simulated dataset of increasing complexity: GRN1 1000 genes, 100 miRNAs and 10 controlling signals GRN2 1000 genes, 300 miRNAs and 35 controlling signals GRN3 500 genes, 100 miRNAs and 20 controlling signalsIn all cases the synthetic datasets are obtained by simulating the regulatory network for an amount of 100 time points. The resulting dataset is obtained by taking the expression values at the last simulated time point. Reverse engineeringWe wanted to test if the synthetic networks generated with the proposed model can be reconstructed with commonly used tools for this task. From GRN1 we generated a dataset of 75 samples by assigning to each of the 10 controlling signals a constant value randomly sampled from a uniform distribution in [0,1]. We estimated the significance of each connection for both gene-only expression dataset and genes+miRNAs dataset with PANDA [28]. PANDA is a message-passing network prediction method based on interactions among TFs and regulated genes. Information for each type of interaction is propagated to the others iteratively, resulting in a prediction score for each interaction. For both types of regulatory networks we provided different numbers of a priori connections. [SEP] Justify:

Output: The text does not provide any direct information or evidence regarding the importance of bioinformatics in analyzing genomic data. Instead, it details methods and simulations related to regulatory networks and various analytical techniques but does not explicitly support or refute the claim about bioinformatics' crucial role.


Input: Task: corroborate the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: Three of the four mutant clones (KanR1, KanR2, and KanR3) contained mutations in fusA, including SNV (KanR1: 105A>G, KanR2: 1979C>T, KanR3: 572T>A) and a deletion (KanR1: 4_6delATT). These phage- or kanamycin-resistance related mutations above, as well as other mutations in several common phage receptor genes and membrane protein genes (lamb, ompA, ompC, ompF, phoE, phuA, tonB, waaB, btuB), were not observed in the sequence of E. coli clones treated with PRESA. The expression of DNA mismatch repair genes at the mRNA level was examined using RT-qPCR (Figure 6C). Transcription of a number of genes (mutS, mutT, polB and dnaE) was upregulated in MG1655 cells receiving Cas9-based plasmid eradication, compared with phage- or kanamycin- resistant clones. Figure 6 Sequence alignments of resistant mutant clones treated with wild-type MG1655, including clones with emerged resistance following treatment with the lytic phage (A) and with kanamycin (B). (C) Expression of genes involved in DNA mismatch repair (mutS, mutT, polB and dnaE; n = 3, mean ± SD). concept of utilising genetic technology to combat antibiotic resistant bacteria has attracted substantial attention [24, 25]. In this study, we evaluated a strategy for combating resistant bacteria using a combination of -based sensitisation and conventional antibiotic treatment. This strategy restored the efficacy of low-cost drugs and efficiently eradicated resistant E. coli cells without the emergence of new resistance against PRESA. Temperate E. coli phage was engineered using our novel method to integrate the -Cas9 system within its genome. A negative screening system was designed based on combining the suicide gene sacB and the target sequence. This screening system was introduced into homologous recombination to replace the traditional screening system based on resistance markers [26]. It guaranteed that temperate phages can integrate with a functionalCas9 system within one recombination step without any resistance residue in its genome. [SEP] Justify:

Output: The text supports the claim by discussing a strategy to combat antibiotic-resistant bacteria through the use of engineered phages. It describes how 'this strategy restored the efficacy of low-cost drugs and efficiently eradicated resistant E. coli cells without the emergence of new resistance.' This illustrates the effectiveness of phage therapy in addressing antibiotic resistance, aligning directly with the claim that phage therapy can be effective.


Input: Task: pass the claim using the given text. Claim: Bioinformatics is crucial for analyzing genomic data. [SEP] Text: Structure sectionThe protein structure section is adapted from the PDB data model [20] to describe experimentally determined protein structures as well as theoretical models. Each monomer is stored as a single structure entry (Structures). The table PDB holds the information on the source of the structure entries. Data on atoms, heteroatoms, coordinates and connectivities is stored in Atoms,Hetatms, Coords and Connectivities, respectively. The sequence corresponding to each structure data set is stored as separate sequence entry. Thus structure-derived properties like secondary structure information (DSSP) are mapped on the sequence and consistently annotated structure data sets are generated. This approach also overcomes the problem of sequence length inconsistencies caused by unresolved residues. ArchitectureThe data warehouse was developed on Linux (3) and is built as a server-client architecture. Scripts for the back-end and query interface were developed in Perl. For the web-based query interface the Apache web server [21] is used. Since the query interface was build as a set of CGI (common gateway interface) scripts, each Internet browser can be used as client software. The usage of the standard Perl CGI modules [22] ensures a high compatibility between scripts and Internet browsers. Some tasks (highlighting or selection of features) have been developed in Javascript. Besides the web-based query interface, the access on SQL level allows to query the underlying data directly. Thus, assisted by the position-specific sequence description, complex queries can be easily performed. Data loadersFor the population of the DWARF data tables, data loaders were developed to parse, transform, and load information form the original source data sets. The data loaders are separated into two main categories: (1) sequence specific data loaders for information derived from GenBank [17] and (2) a data loader for protein structure information on coordinates derived from ExPDB [18] and secondary structure information calculated by DSSP [23]. The sequence specific data loaders extract selected information from the GenBank data sets. These data sets have been represented in the. 1 format, but since recently also XML-formatted GenBank data sets are available. Data loaders for either the ASN. 1 or the XML Genpept format are provided in DWARF. [SEP] Justify:

Output: The text is largely focused on technical aspects of protein structure data and the infrastructure for querying and handling data in bioinformatics, without directly addressing the importance of bioinformatics in analyzing genomic data. Therefore, it does not corroborate or contrast the claim; instead, it is irrelevant to it.


Input: Task: pass the claim using the given text. Claim: Bioinformatics is crucial for analyzing genomic data. [SEP] Text: We executed PANDA with prior information covering the 10%, 25%, 50%, 75% and 100% of all actual connections among the gene-gene network (1656 edges) and full network interactions (3969 edges). In addition, we introduced noisy prior information in the form of false connections. Different quantities of incorrect edges have been tested, namely 10%, 25%, 50%, 75%, 100% of incorrect edges. Since the PANDA scores can be interpreted as z-scores, we set a p-value threshold to 0. 05 for both nominal and Bonferroni corrected p-values. We also set a threshold of 0. 05 to false discovery rate (FDR). For each significant connection we calculated the length of the path in the actual synthetic network. 1, 2, 3 and 4 are reported the results of the analysis (where 1 signifies direct interaction, >1 signifies indirect interaction, Inf signifies no interaction). When given correct prior information PANDA is able to mark as significant almost 100% of true interactions, whereas when noisy (false) prior information is passed, none of it is marked as significant. Table 1 Gene-only path length Full size table Table 2 Gene-only path length with false information Full size table Table 3 Whole-network path length Full size table Table 4 Whole-network path length with false information Full size table We carried out additional tests using [29], which estimates pairwise interactions by the degree of mutual information shared among the nodes in exam. Indirect connections that may stem are removed applying the data processing inequality. Starting from the expression dataset we estimated the mutual information matrix for both gene-only interactions and for the full regulatory network. We set a threshold of 0. 05 on the weights of the reconstructed connections and checked how many of them are actual connections in the synthetic network. 5 are listed the path lengths for the interactions predicted by on the synthetic network. In the gene-only network, most of the interactions found do not actually exist, whereas in the full network, comprising both genes and miRNAs, about half of the interactions found exist in the network but have an average path length of 4. 38. Table 5 Whole-network path length with size table The high rate of erroneous interactions may be due to the fact that works well when the role of the loops in the regulatory network is negligible [29], whereas the networks produced by the proposed simulator involve both feedback and feed-forward loops on different scales (i. e. [SEP] Justify:

Output: The text does not directly address the importance of bioinformatics in analyzing genomic data. Instead, it provides a detailed explanation of the PANDA method and its application in assessing gene interactions and connections in networks. While it involves data analysis aspects, it does not explicitly confirm or deny the claim regarding the general necessity of bioinformatics.


Input: Task: corroborate the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: It has been reported that double stand breaks in bacterial DNA result in the activation of the DNA repair mechanisms [44]. Indeed, RT-qPCR analysis showed that the transcription of DNA mismatch repair-related genes was increased after E. coli cells underwent targeted plasmid cleavage. The rise of gene mutations associated with drug resistance could be suppressed due to the activation of DNA mismatch repair mechanisms. Further research is still needed to reveal the underlying mechanism of this phenomenon. strategy exhibited a potent effect against resistant bacteria and prevented the re-emergence of new antibiotic or phage resistance. Further development and application of this strategy could provide a solution for the antibiotic resistance crisis. Also, this research illustrated the benefit of the combined use of novel phage strategy and conventional antibiotics. Previous studies have shown that phage-resistance often leads to a decrease of bacterial fitness or antibiotic resistance [36, 37]. These findings provide increasing evidence that phage-based therapy may become a solution for bacterial resistance. A limitation that needs to be addressed is the narrow host range of phage. Utilising broad-host range phages or a cocktail strategy may solve this problem. Advances in nano-materials may also provide new solutions toCas9 delivery [45, 46]. With better delivery systems, a -based bacterial sensitisation strategy could be extensively applied in clinical treatment, and well-established antibiotic therapies could become effective once again in treating drug-resistant infections. this study, we demonstrated that the PRESA strategy effectively eradicated resistant bacteria by restoring the efficacy of conventional antibiotics. This strategy shows higher efficacy than previously reported -based antimicrobials. Importantly, unlike the lytic phage strategy, PRESA exhibited a continuous inhibitory effect against resistant bacteria, without the emergence of new mutational resistance. Thus, the efficacy of low-cost antibiotics could be restored in bacterial infection treatment. Finally, we believe that PRESA can be further developed as a promising therapy to address the antibiotic resistance issue. thank Jiang W. , Bikard D. , Cox D. , Zhang F. , and Marraffini L. A. for sharing the prokaryotic gRNA/Cas9 co-expressing vector pCas9. FundingThis study was supported by funding from the R&D Program of China (no. 2017YFC1600105), the Mega-Projects of Science and (nos. [SEP] Justify:

Output: The text corroborates the claim by discussing how the 'PRESA strategy' effectively eradicated resistant bacteria and restores the efficacy of conventional antibiotics, indicating that phage-based therapy may become a solution for bacterial resistance. It highlights the potential of phage therapy and mentions that it has a continuous inhibitory effect against resistant bacteria without the emergence of new mutational resistance, supporting the idea that phage therapy can be an effective treatment for antibiotic-resistant bacteria.


Input: Task: pass the claim using the given text. Claim: Bioinformatics is crucial for analyzing genomic data. [SEP] Text: It is not developed in any phase of the software development process, but rather it originates during the execution of an implemented system. It consists of instances of classes from the operational model, which use type attributes. The names "operational model" and "knowledge model" are inspired by the terms "operational level" and "knowledge level," used by Fowler in [22]. Beale used the terms "knowledge level" and "information level" in [12]; the latter term was the inspiration behind the naming of the "information model. "Properties of knowledge model conceptsConcrete concepts usually define properties. For example, double-stranded DNA has a melting temperature and a GC ratio, and proteins can have annotations describing their function. In our approach, properties cannot be modeled as instance attributes of the typed class. This is because properties are not shared by all kinds of concepts; every concept has its own set of properties. To meet this challenge, we integrated properties using a generic property model (Figure 3). The basis of this model is the "Property" pattern [23]. Figure 3Modeling properties. Properties of concrete concepts are held by the typed class Property. Instances of its type definition class PropertyType (gcType, mtType, and funcType) specify the meaning of properties with their attribute name. The attributes valueType and cardinality restrict the data type and number of hold values. PropertyHolder and PropertyRegistry support the handling and definition of property sets. The PropertyHolder aDnaMol holds the Property gcProp of type gcType; the optional Property of type mtType is not set. Full size imageThe property model defines kinds of properties by instances of the type definition class PropertyType. These instances are elements of the knowledge model (the object diagram at the bottom right of Figure 3) and represent concrete kinds of properties (mtType, gcType, and funcType). Instances of the typed class Property (mtProp and funcProp) represent property values according to its PropertyType. Domain concepts usually have several properties; they have a property set. These sets are defined by instances of the type definition class PropertyRegistry (dnaPropReg and proteinPropReg in Figure 3). These instances define property sets for concrete concepts, they are also elements of the knowledge model. [SEP] Justify:

Output: The text does not address the claim directly or provide any information that supports or contrasts it. Instead, it discusses the modeling of properties in a knowledge model and the operational aspects of a property model without mentioning bioinformatics or its role in genomic data analysis.


Input: Task: pass the claim using the given text. Claim: Bioinformatics is crucial for analyzing genomic data. [SEP] Text: For this more complex dataset we used the wrapper method of Boruta [33]. This method relies on the random forest classifier. The significance of each feature is assessed comparing its importance given by the random forest to the importance of a randomly computed version of the same feature. Features that are significantly more important than their random permutations are marked as relevant. The procedure marked as relevant 59 genes: 9 are signalling genes, 28 are directly connected to (at least) a signalling gene, 20 are at distance 2 from a signalling gene and the remaining 3 genes are at distance 3 from a signalling gene. Of the 6 relevant miRNAs, 5 are at distance 2 from a signalling gene and only 1 is at distance 1 from a signalling gene. From these experiments it is to be noted that almost all signalling genes which have been set to different values for each experimental condition are recognised as significant. The remaining signalling genes that are not marked as significant may have been set to values too similar between different conditions or the amount of noise is such to deteriorate the pattern. It should be also noted that both feature relevance procedures marked as significant nodes directly connected to at least a signalling gene or in the same pathway. This shows the capability of the proposed model of propagating information through modules of locally connected genes. ConclusionsHere we proposed a multi-view biological data simulator based on ordinary differential equations with the objective of benchmarking multi-view learning methods. We ensured that the generated data is biologically relevant for the features need to follow patterns of interaction that are similar to those observed in real biological networks. We showed different cases of analysis where the simulated datasets can complement real datasets in the assessment of novel methods for data analysis. At the same time the sample analysis further validated the proposed approach since information coherent with the regulatory network is extracted from the synthetic dataset. It will be possible to implement additional layers of complexity (e. g. , including DNA methylation or copy number variations) as more comprehensive and systematic knowledge on the biological interactions arises. AbbreviationsTRN: Transcriptional regulatory network ODE: Ordinary differential equations TF: Transcription factor miRNA: micro: False discovery rate 3801. Berlin, Heidelberg: Springer; 2005, 14. doi:10. 1007/11596448. 2011. p. 121–125. . A mathematical model for the validation of gene selection methods. IEEE/; 8(5):1385–92. doi:10. [SEP] Justify:

Output: The text discusses the use of a specific method for feature selection in a biological dataset, but does not address or support the broader claim that bioinformatics is crucial for analyzing genomic data. While it provides details on a method, it does not explicitly link this to the importance or role of bioinformatics in genomic analysis.


Input: Task: corroborate the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection. Chemother. 2017 61 11. Fox A. Engineered phages stymie drug-resistant infection. Science. 2019;364:518-9 12. . Molecular basis for lytic bacteriophage resistance in Enterococci. mBio. 2016;7:e01304-16 13. Summers WC. Bacteriophage therapy. Microbiol. 2001;55:437-51 14. Hagens S, Blasi U. Genetically modified filamentous phage as bactericidal agents: a pilot study. Microbiol. 2003;37:318-23 15. Maciejewska B, Olszak T, Drulis-Kawa Z. Applications of bacteriophages versus phage enzymes to combat and cure bacterial infections: an ambitious and also a realistic application? . Biotechnol. 2018;102:2563-81 16. . A genetic approach to the development of new therapeutic phages to fight pseudomonas aeruginosa in wound infections. Viruses. 2012;5:15-53 17. . et al. -Cas nucleases to produce sequence-specific antimicrobials. Nature Biotechnol. 2014;32:1146-50 18. . Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nature Biotechnol. 2014;32:1141-5 19. . Genetic engineering of a temperate phage-based delivery system forCas9 antimicrobials against Staphylococcus aureus. Sci Rep. 2017;7:44929 20. . Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria. . 2015;112:7267-72 21. . Phage therapy: An alternative to antibiotics in the age of multi-drug resistance. Ther. 2017;8:162-73 22. . Experimental studies of the pathogenesis of infections due to Pseudomonas aeruginosa: description of a burned mouse model. J Infect Dis. 1975;131:688-91 23. . et al. FepA- and TonB-dependent bacteriophage H8: receptor binding and genomic sequence. [SEP] Justify:

Output: The text provides multiple references to the development and use of personalized bacteriophage therapies to treat infections caused by antibiotic-resistant bacteria, such as Acinetobacter baumannii. Statements like 'Phage therapy: An alternative to antibiotics in the age of multi-drug resistance' explicitly support the claim that phage therapy can effectively treat such infections. The mention of engineered phages and studies discussing their efficacy against resistant strains further corroborates the claim.


Input: Task: contrast the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: For instance, some yeasts perform respiro-fermentation to enhance ATP production (Pfeiffer and Morley, 2014). Another example is the electron bifurcating mechanism used by some fermentative microorganisms such as Clostridium spp. (Herrmann et al. , 2008; Li et al. , 2008). Through that energy conservation strategy, cells can generate extra ATP through oxidative phosphorylation (Buckel and Thauer, 2013; Müller et al. , 2018). Along with other examples that are not fully understood (Hunt et al. , 2010Kracke et al. , 2018), these observations suggest metabolisms that combine aspects of fermentation and respiration may exist. We recently discovered that Listeria monocytogenes, a facultative anaerobic pathogen known to rely on respiratory metabolism, uses EET to reduce Fe3+ or an anode through a flavin-based extracellular electron transfer pathway (Light et al. , 2018). Use of this pathway allowed L. monocytogenes to maintain intracellular redox balance via NADH oxidation. This capacity was associated with the presence of a gene locus, called a flavin-based EET (FLEET) locus, that was identified in many Gram-positive species in the Firmicutes phylum, including LAB. Studies in individual species of LAB such as Lactococcus lactis (Freguia et al. , 2009; Masuda et al. , 2010), Enterococcus faecalis (Hederstedt et al. , 2020; Keogh et al. , 2018), and Lactiplantibacillus pentosus (et al. , 2015) show that they can perform EET with an anode endogenously, that is without addition of molecules foreign to their native niches. These observations are quite surprising because endogenous EET has been mainly associated with respiratory organisms, even though some of these organisms also possess fermentative-type metabolism (Glasser et al. , 2014). Those observations also raise the question of whether the FLEET locus is functional in LAB and what, if any, role it plays in energy conservation and metabolism. [SEP] Justify:

Output: The text contrasts the claim by discussing various metabolic processes in different microorganisms, including yeasts and Clostridium spp., without specifically emphasizing the importance of lactic acid bacteria (LAB) in fermentation. Although it mentions LAB's capacity for extracellular electron transfer (EET) and briefly touches on their metabolic capabilities, it primarily highlights the surprising nature of LAB engaging in pathways typically associated with respiratory organisms. Thus, while LAB are mentioned, the emphasis on respiratory metabolism rather than fermentation challenges the claim's assertion on the importance of LAB specifically for fermentation.


Input: Task: pass the claim using the given text. Claim: Bioinformatics is crucial for analyzing genomic data. [SEP] Text: 1109/TCBB. 2010. 83. . Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics. 2003; 19(Suppl 2):122–9. doi:10. 1093/bioinformatics/btg1069. 43. doi:10. 1186/1471-2105-7-43. . GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods. Bioinformatics (Oxford, England). 2011; 27(16):2263–70. doi:10. 1093/bioinformatics/btr373. 42. doi:10. 1111/j. 1749-6632. 2008. 03756. x. 5. doi:10. 1126/science. 1073374. 74. doi:10. 1038/nature11247. 5. doi:10. 1038/nature02871. 7. doi:10. 1126/science. 298. 5594. 824. 0. doi:10. 1002/(SICI)1521-1878(199805)20:5<433::AID-BIES10>3. 0. CO;2-2. Barabási AL, Oltvai ZN. Network biology: understanding the cell’s functional organization. Genet. 2004; 5(2):101–13. doi:10. 1038/nrg1272. 8. CAS PubMed 61. doi:10. 1038/nrg2102. 8. doi:10. 1038/ng881. 131. doi:10. 1371/journal. pcbi. 0030131. -Stamm L, et al. A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev. 2008; 22(18):2535–49. doi:10. 1101/gad. 1678608. 2488. doi:10. 1371/journal. pcbi. 1002488. R Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria; 2014. M, Lambeck S, Töepfer S, van Someren E, Guthke R. Gene regulatory network inference: data integration in dynamic models-a review. Biosystems. [SEP] Justify:

Output: The text provided is primarily a list of references and does not contain any substantive content that directly addresses the claim about the importance of bioinformatics in genomic data analysis. While the references appear to be associated with bioinformatics, they do not confirm or refute the claim; instead, they lack context that would clarify their relevance to the statement about bioinformatics.


Input: Task: corroborate the claim using the given text. Claim: Phage therapy can be an effective treatment for antibiotic-resistant bacteria. [SEP] Text: J Bacteriol. 2007;189:5658-74 24. . Programmable removal of bacterial strains by use of genome-targeting -Cas systems. mBio. 2014;5:e00928-13 25. . Sensitizing pathogens to antibiotics using the -Cas system. Update: reviews and commentaries in antimicrobial and anticancer chemotherapy. 2017;30:1-6 26. . Gene replacement and transposon delivery using the negative selection marker sacB. Med. 2001;54:59-75 27. . Bacillus subtilis develops competence for uptake of plasmid DNA when growing in milk products. Microbiol. 1998;21:28-32 28. . Studying plasmid horizontal transfer in situ: a critical review. Microbiol. 2005;3:700-10 29. . Natural plasmid transformation in Escherichia coli. Sci. 2002;9:246-52 30. . Intergeneric natural plasmid transformation between E. coli and a marine Vibrio species. Mol Ecol. 1992;1:37-46 31. Zhu B. Degradation of plasmid and plant DNA in water microcosms monitored by natural transformation and real-time polymerase chain reaction (PCR). Water Res. 2006;40:3231-8 32. . et al. Fate of antibiotic resistance genes and their associations with bacterial community in livestock breeding wastewater and its receiving river water. Water Res. 2017;124:259-68 33. . Antimicrobial-resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste. PloS One. 2015;10:e0132586 34. . Bacteriophage therapy: a potential solution for the antibiotic resistance crisis. J Ctries. 2014;8:129-36 35. . Adsorption of temperate phages of Lactobacillus delbrueckii strains and phage resistance linked to their cell diversity. J App Microbiol. 2011;110:935-42 36. Sanchez C. Bacterial evolution: phage resistance comes at a cost. Microbiol. 2011;9:398 37. . Bacteriophages drive strain diversification in a marine Flavobacterium: implications for phage resistance and physiological properties. Environ Microbiol. [SEP] Justify:

Output: The text corroborates the claim by referencing bacteriophage therapy as a potential solution for the antibiotic resistance crisis, indicating its effectiveness against antibiotic-resistant bacterial populations.


Input: Task: pass the claim using the given text. Claim: Lactic acid bacteria are important for fermentation processes. [SEP] Text: 1 and NCIMB700965 were aligned to the NCIMB8826 genome in Meg(). Insoluble iron reduction assays Request a detailed protocol Cells were collected by centrifugation at 10,000 g for 3 min, washed twice in phosphate-buffered saline (PBS), pH 7. 2 ( and adjusted to an optical density (OD) at 600 nm (OD600nm) of 2 in the presence of 2. 2 mM ferrihydrite (Schwertmann and Fischer, 1973; Stookey, 2002) and 2 mM ferrozine (Sigma-Aldrich). Where indicated, 55 mM glucose or mannitol, 20 μg/mL DHNA, and riboflavin were added. After 3 hr incubation at 30 °C, the cells were collected by centrifugation at 10,000 g for 5 min and the absorbance of the supernatant was measured at 562 nm with a Synergy 2 spectrophotometer (). Quantities of ferrihydrite reduced were determined using a standard curve containing a 2-fold range of FeSO4 (Sigma-Aldrich) (0. 25 mM to 0. 016 mM) and 2 mM ferrozine. The FeSO4 was dissolved in 10 mM cysteine-HCl () to prevent environmental re-oxidation of Fe2+ to Fe3+ in the standard curve. For testing iron reduction activity of cells with a DHNA concentration of 0. 01 μg/mL in the medium, iron(III) oxide nanop5. Splicing-by-overlap extension (SOEing) PCR was used to combine PCR products as previously described (Heckman and Pease, 2007). PCR products were digested with restriction enzymes or SalI () for plasmid ligation and transformation into E. coli DH5α. The resulting plasmids were then introduced to L. plantarum NCIMB8826 by electroporation. Erythromycin-resistant mutants were selected and confirmed for plasmid integration by PCR (see Supplementary file 5 for primer sequences). Subsequently, deletion mutants were identified by a loss of resistance to erythromycin, PCR (see Supplementary file 5 for primer sequences) confirmation, and DNA sequencing ( Bioelectrochemical reactors (BES) construction, operation, and electrochemical techniques Request a detailed protocol L. [SEP] Justify:

Output: The text is largely irrelevant to the claim as it discusses protocols and experimental methods related to iron reduction assays and genetic manipulation of E. coli, without mentioning lactic acid bacteria or fermentation processes. As such, it does not provide any support or contrast to the claim.


Input: Task: pass the claim using the given text. Claim: Bioinformatics is crucial for analyzing genomic data. [SEP] Text: As data production and research are a constantly moving target, any tools provided to mine the data must be developed as quickly as the data is being produced. As creating entirely new tools is a time and developer intensive process, using rapid application development (RAD) techniques, appropriate visual analytics can be quickly provided. By adapting tools and using appropriate frameworks, rather than creating entirely new ones, it becomes practical to create views that are specific to a particular task or research direction. For the work discussed in this paper we adopted a number of standard software frameworks. A number of web-based frameworks for both data and visual development were used that enable both rapid application development and rapid data delivery. These include: the Source libraries for simple, standard data access using SQL database-like language; ExtJS and GXTJS (JavaScript frameworks) for quickly creating intuitive, web-based user interfaces; and web-based visual libraries such as Protovis [52]. Well-known and understood desktop tools such as Cytoscape are also adopted and integrated where appropriate. The use of existing libraries and visual tools has enabled the development of interactive, usable tools (see Figures 4, 5, and 6) within days or weeks rather than months or more. Nested task specific viewsWhile it is necessary to enable general exploration, researchers often need to explore the data from a particular starting point. Our visualizations are generally dedicated to a limited set of tasks however, so providing multiple levels of linked visualization for the data becomes necessary (e. g. cross-population, whole genome, chromosomal location). Information visualization has advocated common workflows and scopes for the development of visualizations which are useful when accessing massive data sets. The macro and micro view [53] ideas have more recently evolved into the information seeking mantra [54] workflow (overview, filter, data on demand). Such a workflow offers a practical approach to the delivery of visualizations, so that they can be accessed using desktop and web based tools. However, development of initial "overview" or macro visualizations is not straightforward with large research data sets, and depends largely on the task that is going to be undertaken. For this reason we have typically provide a number of macro views which can be used to start filtering or analyzing the data. In the PeptideAtlas project the visual tools provide three different "overview" starting points to explore the underlying data. [SEP] Justify:

Output: The text does not directly address the claim about bioinformatics being crucial for analyzing genomic data. Instead, it discusses the development of tools and frameworks for data visualization and management in a broader context, which may indirectly relate to bioinformatics but does not explicitly corroborate or contrast with the claim.