dataesr/scientific-paragraphs-categorization huggingface dataset:
Blinding Blinding of participants, health providers, data collectors, and outcome assessors should be possible for this type of eradication study. We considered five double-blind, placebo-controlled studies to be at low risk of bias for blinding of participants and personnel, as well as blinding of outcome assessors (Choi 2020; Cochrane Database of Systematic Reviews of bias for blinding of outcome assessment because pathologists were blinded. One study, in abstract form, had uncertain risk of bias for blinding  (Saito 2005).
Incomplete outcome data We considered one study to be at high risk of bias for incomplete outcome data  (Leung 2004 -Zhou 2014). Data from Zhou 2014 were used for the main analysis due to the longer follow-up period. However, the 10-year follow-up data reported in Zhou 2014 had a smaller sample size, and fewer gastric cancer cases, than those in the earlier full publication  (Leung 2004 ). According to  Leung 2004 , 152 (75 vs 77) were lost to follow-up; these participants were considered as no gastric cancer in the ITT analysis. A er 10 years, 378 subjects had completed the study  (Zhou 2014). Therefore, in total there would be more than 31% participants lost to follow-up. We considered three studies to be at unclear risk of bias  (Correa 2000 -Correa 2001; Saito 2005 ; You 2006 -Li 2019).
E ect of H. pylori eradication therapy, compared with placebo or no therapy, on development of subsequent gastric cancer All seven trials reported a dichotomous outcome for subsequent incidence of gastric cancer. In our primary, modified intentionto-treat (ITT) analysis, we included all arms in the two trials of factorial design that also randomised participants to receive antioxidants or vitamins, as well as the 10-year follow-up data from Zhou 2014. Overall, 68 (1. 6%) of 4206 participants assigned to eradication therapy subsequently developed gastric cancer, compared with 125 (3. 0%) of 4117 participants allocated to placebo or no treatment. There was no statistically significant heterogeneity between individual trial results (heterogeneity test, I 2 = 0%, P = 0. 61). H. pylori eradication therapy reduced the risk of gastric cancer in healthy asymptomatic infected individuals (risk ratio (RR) 0.
Cochrane Database of Systematic Reviews according to presence or absence of preneoplastic lesions at baseline We found no evidence of any benefit of H. pylori eradication therapy in preventing the subsequent occurrence of gastric cancer when we considered only those with preneoplastic lesions at baseline in the analysis. Overall, 42 (2. 4%) of 1734 participants assigned to eradication therapy subsequently developed gastric cancer, compared with 57 (3. 4%) of 1691 participants allocated to placebo or no treatment (RR 0. 86; 95% CI 0. 47 to 1. 59) (Analysis 2. 1). There was no statistically significant heterogeneity between individual trial results (heterogeneity test, I 2 = 23%, P = 0. 27). Nor was there evidence of any benefit of H. pylori eradication therapy in preventing subsequent occurrence of gastric cancer when only those participants without preneoplastic lesions at baseline were considered in the analysis.
Adverse events with H. pylori eradication therapy, compared with placebo or no therapy Only two of the studies we identified reported individual adverse events data with eradication therapy compared with placebo or no treatment (Choi 2020; Gail 1998). Gail 1998 reported that there was no di erence in the incidence of adverse events with eradication therapy, with the exception of skin rash, which occurred in 3. 1% of those receiving eradication therapy compared with 0. 1% of those allocated placebo. Choi 2020 reported that any adverse event was higher in the eradication group (53. 0% vs 19. 1% P <0. 001), and that any adverse event ≥ grade 3 occurred in 0. 8% vs 0. 1% (P = 0. 04). Another study reported that side e ects were monitored closely, and none of any clinical importance were detected, although no.
Library Trusted evidence. Informed decisions. Better health. Cochrane Database of Systematic Reviews this study, although follow-up was limited to four years, which is shorter than all but one of the studies included in our metaanalysis. Finally, the prevalence of erosive oesophagitis at upper gastrointestinal endoscopy increased from 14% at baseline to 27% by 2008, suggesting possible deleterious e ects of population screening and treatment for H. pylori infection, due to a potential for an increased risk of oesophageal adenocarcinoma in the long term. This was something we aimed to assess in our meta-analysis, but incomplete reporting of oesophageal cancers among our included studies prevented us from achieving this.
Implications for research Given that any population-based approach to mass screening for H. pylori, with eradication of the infection in positive individuals, will involve healthy subjects, there needs to be more information on any potential harms of H. pylori eradication before such a strategy can be advocated as a means of preventing gastric cancer. Further trials are therefore needed in di erent populations to extend the evidence base, and these should report on both the benefits and harms of such an approach. Cochrane Database of Systematic Reviews 2. placebo, same number of pills, identical in appearance and taste for 7 days (n=914) Follow-up: median duration of follow-up for gastric cancer development =9. 2 years (IQR, 6. 2 to 10. 6; maximum, 14. 1), and the median duration of follow-up for overall survival was 10.
Incomplete outcome data (attrition bias) All outcomes Unclear risk 976 were randomised but only 852 were eligible and treated after randomisation (7 refused and 117 ineligible). 852 were included in the ITT analyses, and Cochrane Database of Systematic Reviews all randomised participants were included in the sensitivity analyses. 631 participants completed the trial and were included in the complete case analysis. 221 participants withdrew before their 72-month evaluation: 102 quit treatment, 59 were lost to follow-up, 34 dropped out of the study because of pregnancy and other medical conditions, 18 died of causes unrelated to gastric cancer, and eight developed cancer other than gastric cancer. The average rate of loss was 4. 3% per year over the 6-year trial. Withdrew in 72 months = 117 (26.
Incomplete outcome data (attrition bias) All outcomes High risk Data from Zhou 2014 were used for the main analyses due to the longer follow-up period. However, The 10-year follow-up data reported in Zhou 2014 had a smaller sample size and fewer gastric cancer cases than those in the full publication  (Leung 2004 ). According to Leung 2004, 152 (75 vs 77) were lost to follow-up; these participants were considered as no gastric cancer in the ITT analysis. After 10 years, 378 subjects had completed the study  (  Method to confirm H. pylori infection: histological examination and rapid urease testing. 37. 7% participants with preneoplastic lesions at baseline (gastric atrophy, intestinal metaplasia, dysplasia).
Notes This was the first study targeted at a general population (less than 40% with precancerous lesions); a few discrepancies were seen between Wong 2002 abstract and Wong 2004 full publication. Inconsistent sample size between the full publication followed up at 7. 5 years (817 vs 813)  (Wong 2004 ) and the conference abstract followed up at 7 years (819 vs 809)  (Wong 2002). We used data from the full publication.
Study characteristics Methods RCT Participants Country: China. 12 villages in Linqu County, Shandong Province. 1024 participants with H. pylori infection and advanced gastric lesions (severe chronic atrophic gastritis, intestinal metaplasia, indefinite dysplasia, or dysplasia); mean age 53. 0 (range 35 to 64) years, 46. 4% men. Method to confirm H. pylori infection: 13 Carbon-urea breath testing. Histology was also performed. Notes 2x2 factorial design, in the main analysis we did not include data from the two arms that used celecoxib, only data for H. pylori eradication only vs placebo only (n = 513). The celecoxib arms were included in a sensitivity analysis. Eradication rate: 63. 5% Cochrane Database of Systematic Reviews Secondary endpoints: rates of transition from baseline to final histopathologic states and the effects of treatments on these rates of transition; evidence of the effectiveness of amoxicillin and omeprazole in eradicating H.
Cochrane Database of Systematic Reviews Wong BC. Eradication of Helicobacter pylori for prevention of gastric cancer. In: Journal of Gastroenterology and Hepatology. Vol. 27 (Suppl. 5). 2012:5-6. Abstract UA01-05. You 2006 -Li 2019 {published data only} Gail MH, You WC, Chang YS, Zhang L, Blot WJ, Brown LM, et al. Factorial trial of three interventions to reduce the progression of precancerous gastric lesions in Shandong, China: design issues and initial data. Controlled Clinical Trials 1998;19(4):352-69. Li WQ, Ma JL, Zhang L, Brown LM, Li JY, Shen L, et al. E ects of Helicobacter pylori treatment on gastric cancer incidence and mortality in subgroups. Journal of the National Cancer Institute 2014;106(7). [DOI: DOI:10. 1093/jnci/dju116] [PMID: 24925350] * Li WQ, Zhang JY, Ma JL, Li ZX, Zhang L, Zhang Y, et al.
Cochrane Database of Systematic Reviews in the update search (Choi 2020). Therefore, seven studies (Choi 2020; Correa 2000-Correa 2001; Leung 2004-Zhou 2014; Saito 2005; Wong 2004; Wong 2012a;You 2006 -Li 2019) with eleven references contributed data to the analyses concerning incidence of gastric cancer in this systematic review. Please see Characteristics of included studies table. Three of the trials, reported in five separate publications, were of factorial design with some participants randomised to receive vitamins, antioxidants, or celecoxib in addition to H. pylori eradication therapy (Correa 2000-Correa 2001; Wong 2012a; You 2006 -Li 2019). Only one study was conducted in non-Asians, among a population at high risk of gastric cancer in Colombia (Correa 2000-Correa 2001). The shortest duration of follow-up was greater than or equal to 4 years (Saito 2005), and the longest was 22 years (You 2006 -Li 2019).
Data from Zhou 2014 (276 vs 276) rather than Leung 2004 (295 vs 292) were entered in the main analysis, because Zhou 2014 abstract had 10 years of follow-up. Inconsistent data were noted between Zhou 2014 and Leung 2004. Zhou et al. had a series of publications but with smaller sample size and fewer gastric cancers than those reported by Leung 2004. Zhou 2008 that was included in the previous published version was a conference abstract at that time, and was fully published in 2014. No new data analysis was needed after including data from Zhou 2014. Cochrane Database of Systematic Reviews 2. In Zhou 2005a and Zhou 2005b, participants were regrouped as eradicated group and group (included those failing eradication or controls) as 246 vs 306 (276 + 30 vs 276 -30). 3. According toLeung 2004, 152 (75 vs 77) were lost to follow-up; these participants were considered as no gastric cancer in the ITT analysis.
(Ford 2005; Imanzadeh 2004; Lane 2006; Mason 2002). Four studies were RCTs conducted among patients undergoing endoscopic mucosal resection of early gastric cancer (Choi 2014; Choi 2018a; Choi 2018b; Fukase 2008), rather than healthy asymptomatic infected participants, and the final article did not compare the interventions of interest (Fischbach 2009). In the updated search, two articles were protocols from Korea for "HEPTER study" (HELPER study) and one article was protocol from China (Pan 2016)for an ongoing randomised trial. Cochrane Library Trusted evidence. Informed decisions. Better health. Cochrane Database of Systematic Reviews.
Bismuth subsalicylate 262 mg, amoxicillin 500 mg, and metronidazole 375 mg 3 times daily for 2 weeks, including regimens with or without dietary supplements (n = 437). Cochrane Library Trusted evidence. Informed decisions. Better health. Cochrane Database of Systematic Reviews Choi 2020 (Continued) Interventions 1. 6) Outcomes Development of gastric cancer; development of gastric cancer according to H. pylori eradication status during the follow-up period; overall survival, and the development of adenoma Notes H. pylori eradication status was evaluated in 1587 participants during the follow-up period. Eradication rate (70. 1% (551/786) in the treatment group and 7. 1% (57/801) in the placebo group Risk of bias Bias Authors' judgement Support for judgement Random sequence genera- Low risk "computer-generated randomization sequence" tion (selection bias) Allocation concealment Low risk "computer-generated randomization sequence was kept at the trial pharmacy (selection bias) and was not accessible to the investigators who enrolled participants".
Authors' judgement Support for judgement ; prevalence of severe chronic atrophic gastritis, intestinal metaplasia, dysplasia, or gastric cancer; and average severity score, effects of one-time H. pylori treatment and long-term vitamin or garlic supplements in reducing the prevalence of advanced precancerous gastric lesions. Cochrane Library Cochrane Library Trusted evidence. Informed decisions. Better health. Trusted evidence. Informed decisions. Better health. Cochrane Database of Systematic Reviews Wong 2012a (Continued) Blinding of outcome as- Low risk Endoscopists and pathologists were blinded. sessment (detection bias) All outcomes Incomplete outcome data Low risk 234/258 (90. 7%) vs 233/255 (91. 4%) participants had follow-up gastric biop- (attrition bias) sy data and the authors reported outcomes for these, losses to follow-up with All outcomes Wong 2012a reasons were balanced and provided, 89.
Published by John Wiley & Sons, Ltd. Cochrane Library Cochrane Library Trusted evidence. Informed decisions. Better health. Trusted evidence. Informed decisions. Better health. Cochrane Database of Systematic Reviews Cochrane Database of Systematic Reviews You 2006 -Li 2019 (Continued) Study D A T A A N D A N A L Y S E S Reason for exclusion Ogura 2008 Comparison 1. H. pylori eradication vs control -main analyses Cohort study, not RCT Ohkusa 2001 Outcome or subgroup title Not RCT, reported data for glandular atrophy and intestinal metaplasia No. of No. of Statistical method Effect size studies partici- Take 2005 Cohort study, not RCT pants Take 2007 1. 1 Incidence of gastric cancer -modified ITT Cohort study, not RCT 7 8323 Risk Ratio (M-H, Random, 95% CI) 0. 54 [0. 40, 0. 72] analysis Takenaka 2007 Cohort study, not RCT 1.
pylori eradication vs control -main analyses, Outcome 1: Incidence of gastric cancer -modified ITT analysis Study or Subgroup Cochrane Library Trusted evidence. Informed decisions. Better health. Cochrane Database of Systematic Reviews Analysis 1. 2 Hp eradication Control Risk Ratio Risk Ratio Events Total Events Total Weight M-H, Random, 95% CI M-H, Random, 95% CI Correa 2000-Correa 2001 3 437 2 415 2. 7% 1. 42 [0. 24 , 8. 48] Wong 2004 7 817 11 813 9. 7% 0. 63 [0. 25 , 1. 63] Saito 2005 2 379 3 313 2. 7% 0. 55 [0. 09 , 3. 27] Wong 2012a 3 255 1 258 1. 7% 3. 04 [0. 32 , 28. 99] Leung 2004-Zhou 2014 2 276 7 276 3. 5% 0. 29 [0. 06 , 1. 36] You 2006 -Li 2019 41 1130 78 1128 63. 6% 0. 52 [0. 36 , 0. 76] Choi 2020 10 912 23 914 16. 0% 0. 44 [0. 21 , 0. 91] Total (95% CI) 4206 4117 100. 0% 0. 54 [0.
4. Comparison 1: H. pylori eradication vs control -main analyses, Outcome 4: Death from all causes -modified ITT analysis Study or Subgroup Cochrane Library Trusted evidence. Informed decisions. Better health. Cochrane Database of Systematic Reviews Analysis 1. 5 Hp eradication Control Risk Ratio Risk Ratio Events Total Events Total Weight M-H, Random, 95% CI M-H, Random, 95% CI Choi 2020 16 912 18 914 4. 3% 0. 89 [0. 46 , 1. 74] Correa 2000-Correa 2001 12 437 6 415 2. 0% 1. 90 [0. 72 , 5. 01] Wong 2004 22 817 23 813 5. 8% 0. 95 [0. 53 , 1. 69] Wong 2012a 1 255 4 258 0. 4% 0. 25 [0. 03 , 2. 25] You 2006 -Li 2019 264 1130 272 1128 87. 5% 0. 97 [0. 84 , 1. 12] Total (95% CI) 3551 3528 100. 0% 0. 97 [0. 85 , 1. 12] Total events: 315 323 Heterogeneity: Tau² = 0. 00; Chi² = 3. 36, df = 4 (P = 0.
pylori eradication vs control -subgroup analysis according to presence or absence of pre- neoplastic lesions at baseline Outcome or subgroup title No. of studies Cochrane Library Trusted evidence. Informed decisions. Better health. Cochrane Database of Systematic Reviews Analysis 2. 1 No. of Statistical method Effect size partici- pants 2. 1 Incidence of gastric cancer according to presence 7 8307 Risk Ratio (M-H, Random, 95% 0. 64 [0. 43, or absence of pre-neoplastic lesions at baseline CI) 0. 96] 2. 1. 1 Patients with precancerous lesions 4 3425 Risk Ratio (M-H, Random, 95% 0. 86 [0. 47, CI) 1. 59] 2. 1. 2 Patients without precancerous lesions 2 1812 Risk Ratio (M-H, Random, 95% 0. 42 [0. 02, CI) 7. 69] 2. 1. 3 Mixed patients with and without precancerous 3 3070 Risk Ratio (M-H, Random, 95% 0.
3. H. pylori eradication vs control -subgroup analysis according to use of vitamins or antioxidants Outcome or subgroup title No. of studies No. of partici- pants Statistical method Effect size Cochrane Library Trusted evidence. Informed decisions. Better health. Cochrane Database of Systematic Reviews Analysis 3. 1 3. 1 Incidence of gastric cancer according to 7 8323 Risk Ratio (M-H, Random, 95% CI) 0. 61 [0. 43, 0. 87] use of vitamins or anti-oxidants 3. 1. 1 Without antioxidants 7 5986 Risk Ratio (M-H, Random, 95% CI) 0. 69 [0. 41, 1. 14] 3. 1. 2 With antioxidants 2 2337 Risk Ratio (M-H, Random, 95% CI) 0. 52 [0. 31, 0. 87].
H. pylori eradication vs control -sensitivity analyses Outcome or subgroup title No. of studies Incidence of gastric cancer -complete case analysis substituting the 10-year follow-up data from Zhou 2014 with the 5-year follow-up data Assuming incidence of gastric cancer for missing participants in treatment arm same as observed in the trial control arm, but no new gastric cancer cases in the control arm among those with missing data Cochrane Library Trusted evidence. Informed decisions. Better health. Cochrane Database of Systematic Reviews Outcome or subgroup title No. of No. of Statistical Effect studies partici- method size pants 4. 5. 1 Assuming incidence of gastric cancer for missing participants in 7 8323 Risk Ratio (M-H, 0. 55 [0. 41, both arms same as observed in the trial control arm Random, 95% CI) 0.
Comparison 4: H. pylori eradication vs control -sensitivity analyses, Outcome 2: Incidence of gastric cancer -complete case analysis substituting the 10- year follow-up data from Zhou 2014 with the 5-year follow-up data from Leung 2004 Study or Subgroup Cochrane Library Trusted evidence. Informed decisions. Better health. Cochrane Database of Systematic Reviews Analysis 4. 3 Hp eradication Control Risk Ratio Risk Ratio Events Total Events Total Weight M-H, Random, 95% CI M-H, Random, 95% CI Correa 2000-Correa 2001 3 320 2 311 2. 7% 1. 46 [0. 25 , 8. 67] Wong 2004 7 735 11 703 9. 6% 0. 61 [0. 24 , 1. 56] Saito 2005 2 379 3 313 2. 7% 0. 55 [0. 09 , 3. 27] Wong 2012a 3 233 1 234 1. 7% 3. 01 [0. 32 , 28. 75] Leung 2004-Zhou 2014 4 220 6 215 5. 4% 0. 65 [0. 19 , 2. 28] You 2006 -Li 2019 41 1130 78 1128 62.
36 , 0. 76] Choi 2020 10 912 23 914 16. 0% 0. 44 [0. 21 , 0. 91] Total (95% CI) 4272 4202 100. 0% 0. 54 [0. 40 , 0. 72] Total events: 68 125 Heterogeneity: Tau² = 0. 00; Chi² = 4. 57, df = 6 (P = 0. 60); I² = 0% 0. 01 0. 1 1 10 100 Test for overall effect: Z = 4. 11 (P < 0. 0001) Favours Hp eradication Favours Control Test for subgroup differences: Not applicable Cochrane Database of Systematic Reviews.
Ventrodorsal radiographic images of the chickens' whole bodies were produced with a stationary radiographic system (Philips SRM0310 Xray machine, Philips Super CP 80 generator, Philips Optimus M200 gantry, Philips Super CP 50 terminal, Philips XD6028 collimator, Konica Minolta Regius 110HQ digitizer). The working distance was 127 cm. Voltage, load, and exposure time were set to 40 kV, 32 mAs, and 386 ms, respectively. The radiographs were analyzed as digital images (DCM files) using the software PDI viewer V2. 20R03 (Konica Minolta, Inc. ). No enhancements, such as grayscale or contrast adjustments, were applied to the radiographs after production. Before detailed evaluation, each image was rotated by 90 clockwise until the chicken's head pointed to the top of the picture and its feed to the bottom.
If the chickens stayed immobile for at least 10 s after releasing, time monitoring was continued until the bird righted itself or until a maximum TI duration of 5 min was reached. If the chicken returned to an upright position within 10 s, TI was induced again up to a maximum of 5 inductions. The experimenter recorded the number of successful TI inductions, the number of TI induction attempts needed, TI duration, and vocalization (yes/no) during TI. The NO was conducted first, followed by the TI test. Subsequently, all tested chickens were weighed and scored for plumage cleanliness, hock burn, and footpad dermatitis (in accordance with Welfare Quality, 2009). After data collection on day 15, all chickens were killed humanely.
, 2007; Aujoulat et al. , 2014; Burygin et al. , 2019; Gazolla Volpiano et al. , 2019; Krzyżanowska et al. , 2019). More recently, whole genome phylogenetic studies started to emerge but generally focused on a limited number of isolates of few species and could not provide a comprehensive view of the phylogenetic relationships at the family level or even at the Ochrobactrum genus level  (Gazolla Volpiano et al. , 2019; Krzyżanowska et al. , 2019). Finally, the question of the Brucellaceae positioning among the Rhizobiales order have not been thoroughly investigated to date. Depending on the studies, the Brucellaceae family is a sister group of the Bartonellaceae, the Rhizobiaceae, or the Phyllobacteriaceae  (Gupta and Mok, 2007; Scholz et al. , 2008a; Kämpfer et al. , 2015). In the present study, the taxonomic organization of the Brucellaceae genera and their species among the Rhizobiales order was determined at the genomic scale using a representative sample of genome sequences available in GenBank, and the inter-relationship between members of the family Brucellaceae was investigated using a comprehensive phylogenomic analysis including most GenBank genomes and newly sequenced isolates.
Genome Sequences The 101 non-Brucella Brucellaceae genomes available in the GenBank assembly summary file as of 07/14/2019 were downloaded from the NCBI FTP repository 1  in fasta format. Since almost 800 Brucella genomes were available at the time of this study and that the phylogenomic organization of the genus was already thoroughly investigated before  (Wattam et al. , 2014; Al Dahouk et al. , 2017) , only 12 genomes spanning the diversity of the classical and non-classical Brucella species were used in our analyses (Supplementary Table  S1 ). A set of 43 diverse non-Brucellaceae Rhizobiales genomes listed as 'reference' or 'representative' genomes in the NCBI database were also downloaded, as well as the genome of two Caulobacteriales (Caulobacter vibrioides and Parvularcula bermudensis) to serve as outgroups.
GenBank assembly identifiers of all downloaded genomes are given in Supplementary Table  S1. Additionally, the genomes of 32 Ochrobactrum spp. isolates were sequenced and added to the analysis. For the 32 isolates, bacterial DNA was extracted with DNeasy Blood & Tissue kit from QIAGEN. Genome sequencing was performed by Genoscreen (Lille, France) on an Illumina MiSeq apparatus (paired end 250 bp), with an average of 60x coverage per genome, except for the Ochrobactrum sp. strain Kaboul genome which was sequenced on a Pacific Bioscience SMRT device. Resulting reads were quality trimmed with Trimmomatic v. 0. 33  (Bolger et al. , 2014)  and assembled using the Spades v. 3. 11. 1 assembly software  (Bankevich et al. , 2012). Information and accession/assembly number of these newly sequenced genomes are given in Supplementary Table  S2.