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For articles published in , an evaluation of impact factors between and showed little variation across these years appendix 1 p 16 ; therefore, the values were used. One paper in did not have an impact factor and was excluded from the analysis. Moreover, due to low individual country counts, we analysed author affiliation by continent. There was only one study in South America, which was subsequently combined with North America to form the category Americas appendix 1 p Univariate and multivariate analyses for quasi-Poisson regression and tobit regression models are presented in table 3 and appendix 1 p 20 , respectively.

There was no association between sample size of isolates, impact factor, or geographic region of the senior author, and the number of STROME-ID criteria fulfilled. Given that genomic epidemiology studies aim to inform public health, we investigated whether any articles reported clinical or public health actions as a result of their findings.

STROME-ID was developed by an interdisciplinary team with expertise in infection control and infectious diseases, 9 to facilitate the reporting of a minimal set of study variables that were considered critical for assessment of bias and study quality.

Herein, we have used STROME-ID as the framework to evaluate the reporting and transparency of genomic epidemiology studies of tuberculosis and have explored the association between specific journal or study characteristics and reporting practices. Publication of guidelines has previously been shown to improve reporting practices. However, this difference could simply be due to temporal changes, such as an increased demand for reproducibility, and could be unrelated to STROME-ID.

Given that only one included article specifically cited the guidelines, lack of awareness could be an issue. Other practical limitations, such as article word count and absence of online supplements, could have also influenced reporting practices. We also did not find any articles that completed all STROME-ID criteria, which could suggest that some of the criteria in the guidelines are too vague or difficult to complete in practice. In terms of which criteria were less likely to be reported, we found STROME-ID criteria that concerned key definitions, methods, and potential limitations to be more poorly reported.

Although it might seem trivial that the least completed STROME-ID criteria related to the defining of molecular terminology, we would argue that standardisation of basic microbiological terminology is essential to allow for clear comparisons between studies and correct interpretation of results for public health. Despite this, even in the same academic field, terms such as strain, isolate, and clone are sometimes used differently by researchers.

Although this criterion was investigated by some of the included papers, methods for discriminating within-host diversity using WGS data are an area of active research, 85 , which could explain why these were less frequently discussed. Journal impact factor has often been used as an indicator of quality, by funding organisations, , and even for academic promotion.

Similarly, we found no association between h-index and reporting quality. These findings highlight the limitations of such indicators as correlates of the quality of scientific publications, supporting previous studies. Therefore, although this result is statistically significant, we suspect that it is not an epidemiologically meaningful difference.

In addition to STROME-ID criteria, we also investigated whether bioinformatics tools at a minimum were well documented in tuberculosis genomic epidemiology papers, because reproducibility is a critical concern in genomic studies. Even more surprisingly, we found that nearly a quarter of studies did not provide a Sequence Read Archive or Genbank accession number for their sequencing data, with no improvement across the study period.

This is problematic because it not only prevents researchers from reproducing analyses and verifying results, but in the context of infectious diseases, it can hinder public health investigations that rely on global strain depositions for genomic context or for evaluation of cross-jurisdictional transmission.

We therefore suggest that data deposition should be a requirement for publication, rather than just a social norm in genomic epidemiology. However, such a change will be unlikely without collaboration and enforcement by funders, publishers, or both.

Overall, this study has several strengths. First, it represents a comprehensive review of reporting practices in tuberculosis genomic epidemiology studies, starting with the first publication in tuberculosis genomic epidemiology in , and including a search of unpublished literature. Using STROME-ID guidelines, we have identified key gaps in current reporting practices that could affect interpretation of results, adding to previous work that highlighted the implications of differences in analytic pipelines.

In terms of analysis, we used a rigorous analytical approach and did numerous sensitivity analyses to assess the robustness of our results, lending further support to our inferences. Finally, in addition to STROME-ID criteria, we also examined variables related to reproducibility, highlighting that even in a field that has arguably embraced open science, a large proportion of studies continue to not share their underlying genomic data. The study has also several limitations. First, we note that, given that the STROME-ID guidelines were only published in , there may have not been enough time for widespread uptake of these reporting guidelines at the time this study was done.

However, because we did not observe increased reporting practices even in , 5 years after publication, we consider this to be unlikely. However, because we did not see evidence of any such trends on visual assessment by year, this is unlikely to affect our comparison of reporting before and after guideline publication. We also note that, as bioinformatics pipelines are not yet standardised, 4 our review of the reporting of bioinformatics tools was qualitative and did not require adherence to a specific pipeline or set of steps.

Had we required a minimum set of tools or analytic steps be reported, we expect the reproducibility would have been assessed as being even lower. Similarly, for bioinformatics version numbers, we considered reporting to be complete only if steps were reported with versions for all included tools; there could be differences in the reporting of version numbers across different steps in the analysis.

Although good reporting practices themselves do not guarantee a study is of high quality, transparency of design, methods, and results are critical for such an assessment. The scope of the current study is limited to tuberculosis, but we expect that many of these reporting and transparency issues also apply to genomic epidemiology studies of other pathogens as well.

The reasons underlying the low level of reporting are unclear, although similar reporting practices have been found with other guidelines for other types of studies. Alternatively, these guidelines may be too difficult to implement in practice. Further study is warranted to investigate these hypotheses. To improve data sharing, we suggest that data deposition should be a requirement for publication of genomic epidemiology studies. This stance will require active support from journals, with real consequences for failing to meet this obligation.

Pathogen genomics are playing an increasingly important role in infectious disease epidemiology and public health. However, the ability of genome sequencing to inform interventions depends on the quality of the studies that use this technology. In , guidelines called the Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases STROME-ID were published by a team of experts in the field, to provide authors with a minimum set of criteria for reporting and to help readers assess the validity of study methodology and results.

Evidence of the impact of reporting guidelines on reporting practices in other fields is mixed. There was no significant difference in reporting before versus after STROME-ID publication, nor did reporting appear to be associated with impact factor, h-index, geographical region of the senior author, or with the number of isolates included in the study.

We also examined several important considerations for reproducibility of these studies. Detailed reporting of study methodology is critical to properly evaluate quality and determine how and whether results can inform public health interventions. Similarly, open sharing of pathogen genomic data is crucial for reproducibility of results, and as a resource for the greater scientific community.

Our study suggests reporting practices in genomic epidemiology studies of tuberculosis require considerable improvement to meet guidelines. We would anticipate that many of the reporting and transparency issues identified here also apply to genomic epidemiology studies of other pathogens. We suggest that active support from scientific journals might be essential in addressing these crucial issues.

The data supporting the findings of this study are available within the appendices. Editorial note: the Lancet Group takes a neutral position with respect to territorial claims in published tables. Lancet Microbe. Author manuscript; available in PMC Apr 9. Author information Copyright and License information Disclaimer. Contributors BC was responsible for screening abstracts and titles for inclusion, data extraction, statistical analysis, making the tables and figures, interpreting the data, and writing the first draft of the manuscript.

MAB assisted with interpreting the data, reviewed drafts of the manuscript, and co-supervised BC. BPH and TC contributed to the protocol development and reviewed the final draft of the manuscript. TC also served as arbitrator for disagreement in study inclusion. RSL conceived and led the study, designed the protocol and ran the searches, screened abstracts and titles for inclusion, guided statistical analyses and interpretation of the data, wrote the first draft of the manuscript with BC and co-supervised BC.

BC and RSL accessed and verified the data. Copyright notice. The publisher's final edited version of this article is available at Lancet Microbe. Associated Data Supplementary Materials 1. Summary Background Pathogen genomics have become increasingly important in infectious disease epidemiology and public health.

Findings titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. Interpretation The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between and was low, with implications for assessment of study quality. Introduction Whole genome sequencing WGS has been increasingly used in genomic epidemiology studies. Methods Search strategy and selection criteria This systematic review was done according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.

Role of the funding source The funder of this study had no role in study design, data collection, data analysis, data interpretation, or writing of the report. Results Our initial search identified studies, of which were duplicates and were excluded. Open in a separate window.

Figure Table 1: Summary of included studies. Table 3: Quasi-Poisson univariate and multivariate analyses of study characteristics. Discussion STROME-ID was developed by an interdisciplinary team with expertise in infection control and infectious diseases, 9 to facilitate the reporting of a minimal set of study variables that were considered critical for assessment of bias and study quality. Evidence before this study Pathogen genomics are playing an increasingly important role in infectious disease epidemiology and public health.

Added value of this study In this study, we evaluated reporting practices of genomic epidemiology studies of tuberculosis using the STROME-ID guidelines as our benchmark. Implications of all the available evidence Detailed reporting of study methodology is critical to properly evaluate quality and determine how and whether results can inform public health interventions.

Supplementary Material 1 Click here to view. Footnotes Declaration of interests We declare no competing interests. Data sharing The data supporting the findings of this study are available within the appendices. References 1. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.

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Engine differences The engine is an obvious place to start this head-to-head look at these two popular models and, although both were four-cylinder motors, their features made them noticeably different in operation. It shares the same bore and stroke dimensions as the , , and , which minimised the number of parts used and resulted in better availability.

Despite some owners retrofitting turbochargers to the D and later models — like the Turbo Special, and , using a turbocharged version of the engine — it seems to suit natural aspiration. Although seen here with a three-furrow reversible, the is perfectly capable of handling a four-furrow plough….

The two-wheel-drive variants have a turning radius of cm and cm respectively without brakes , while the four-wheel-drive tractors require a larger radius of cm and cm respectively without brakes , so the XL is definitely more agile. When teamed with front axle beam extensions, the tractor was ideal for row-crop work or specialist applications. The gearbox perhaps provides a most noticeable difference between the two tractors. Synchromesh was standard on both, but the is by far the more versatile in terms of the options offered.

This system, providing four speeds with clutch-less changes and engine braking, had been around for a number of years, but was well liked and proved its worth in many applications. Power take-off Both tractors feature a two-speed power take-off as standard, but their output is quite different. The , on the other hand, features a reversible shaft to switch between six and 21 splines, and an in-cab selector lever to change the speed.

The PTO system is also one of the most noticeable differences between these two tractors, because of the power output at the shaft. Considering the difference in engine power is just 0. PTO power at rpm is With the power take-off set to rpm, output at the shaft is Hydraulic systems David Brown gained a good reputation for its Selectamatic hydraulic system and, although the look of its tractors had changed somewhat since its introduction, the 94 Series was praised by many for its ability in the field.

The is fitted with a tandem hydraulic pump arrangement as standard, but four-wheel-drive versions of the other models in the range also enjoy this luxury. Hydraulic power is Fitted with a single, large-capacity pump, the XL can muster a flow rate 11gpm 49lpm and hydraulic power of Another point to the !

Draft and position control were standard on both machines, while the XL features raise response and drop response controls for the draft system. The utilises lowering control and a useful dump valve for fast lowering, with little or no load to speed up cycle times. Up to three spool valves can be fitted to both models. Noise levels are very similar and long-term users of each tractor will argue for and against their respective steeds, but it really is a close-run contest in this department.

Keep each shift rail assembly together as they are removed. Use a wooden wedge to lock differential assembly, then remove pinion shaft nut Pinion shaft nut has left-hand threads. Remove four nuts from housing spacer rods, then withdraw front end housing Remove idler shaft retainer plate 50 , then remove idler shaft 61 and idler gear Remove remaining bearing cups from end housing as necessary. Case , Tractor transmission components - End plates, shift rods and shift 1.

Front end plate, 2. Top spacer bar, 3. Rear end plate, 4. Shim, 5. Bushing, 6. Mounting bolts, 7. Tab washer, 8. Differential cap bolt, 9. Bottom spacer bar, Gear lock, Selector, Roll pin, Detent ball, Detent spring, Range shift rod, Shifter fork, Hi-Lo, Sleeve, Steel ball, Plunger, Safety start switch Remove neutral start plungers 27 and 28 and detent balls 26 from rear housing.

Remove first and reverse shift rod assembly and second and third shift rod assembly. Remove countershaft assembly 69 and rear input shaft 17 assembly. Press front bearing 12 off rear input shaft Remove spacer 13 , snap ring 14 and range pinion gear Press reverse idler gear carrier 18 , idler gear 20 and bearing 23 together off rear input shaft.

Use care not to lose dowel pin Remove bushings 10 and 19 from input shaft and reverse idler gear if necessary. Remove first and reverse gear shift fork from pinion shaft assembly. Remove spacer 35 , shims 36 , spacer 37 , washer 51 and third gear 52 from pinion shaft 59 , Remove the six bearing pads 38 , then lift synchronizer 40 with shift fork off shaft. Remove front and rear synchronizer gears, second gear 41 and the six bearing pads Remove splined washer 42 and split retainer ring Remove first and reverse gear Remove pinion shaft retainer plate 57 and shims Remove pinion shaft 59 and press bearing 58 off shaft.

Examine bearings and bushings for wear or damage. If renewing a bearing, renew its respective mating cup. Gear teeth should be evenly marked along length of teeth. If gear teeth have been shaved or show irregular wear pattern, gear should be renewed along with its mating gear. If shifting into second or third has been difficult, examine synchronizer friction surfaces and the synchronizer pads 38 and Slight radial clearance looseness in synchronizer is normal and the pads should slide easily into their grooves without binding.

No attempt should be made to disassemble synchronizer assembly as individual service parts are not available. Shift rail grooves should have straight 60 degree sides and balls must be smooth with no pits, rust or flat spots. If necessary, grind bottom of groove, taking care not to damage sides, until detent ball has sufficient clearance at bottom of groove.

Check detent spring length which should be Examine all thrust washers and spacers for excessive wear or damage and renew as necessary. If pinion shaft, end housings, center housing, or pinion shaft bearings are renewed, pinion shaft protrusion must be set before Case IH , Tractor transmission reassembly. Pinion shaft assembly With pinion shaft 59 , bearing 58 and correct thickness of shims 44 in position, install retainer plate 57 and tighten retaining bolts to 40 N-m 30 ft.

Install split rings 43 and spacer Apply grease to the six bearing pads 55 and install pads in splines of pinion shaft Install: - second gear 41 on pinion shaft and bearing pads with gear side toward retainer plate Make certain front and rear synchronizer splines teeth are aligned. Place shift fork in groove on synchronizer, then install synchronizer and shift fork together making certain shift fork slides easily on spacer bar. Apply grease to the six bearing pads 38 and install in splines of pinion shaft Do Not install shims 36 or spacer 35 at this time.

Rear input shaft assembly Press bushing 10 into rear input shaft Press bushing 19 into reverse idler gear Install: - snap ring 16 in groove of rear input shaft at bushing carrier 18 end. Lubricate and install reverse idler gear Mount dial indicator on front housing so probe touches end of rear input shaft. Move shaft up and down and measure end play.

Correct end play is 0. Remove front housing and the rear input shaft assembly. Assemble and install shims 24 as necessary in rear housing bearing bore to obtain correct end play. Reinstall rear input shaft assembly. Install: - bearing cup in rear housing without shims Position countershaft in rear end housing. Mount a dial indicator on rear housing so probe contacts face of rear gear of countershaft.

Specified end play is 0. Remove front end housing, countershaft and rear bearing cup. Front housing assembly Install: - bearings 63 and 66 and spacer 64 into range idler gear Bearing cages should be slightly below end surface of range idler gear when installed.

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CASE IH - Steiger - Transmissão full powershift - PT-BR

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