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The phrase "although there were significant differences in" is correct and usable in written English.
It can be used to introduce a contrast or exception in a discussion, typically when comparing two or more subjects or variables.
Example: "Although there were significant differences in the results, the overall trend remained consistent across all experiments."
Alternatives: "despite the notable differences in" or "even though there were considerable variations in".
Exact(25)
The results indicated that although there were significant differences in fluoride concentrations among different brands and between different batches from the same brand, all products had fluoride concentrations lower than the ADA-accepted standard for optimally fluoridated water (i.e., 0.7 1.2 mg/L dependent on the average maximum daily air temperature of an area).
Although there were significant differences in the ways in which the two prosecutors were killed, another law enforcement official said the killer seemed to be familiar with the area and the routines of the victims.
For example, although there were significant differences in ratios between the undamaged and optimized blend (Table 1), we did not observe differences in orientation behavior (Fig. 4).
Although there were significant differences in the IL-17A concentrations, there was no significant difference in the Th17 ratios.
Although there were significant differences in the types of initial immunosuppression between cohorts this did not explain the differences detected.
Although there were significant differences in ICC values, there was nevertheless substantial overlap between groups, suggesting that only a subset of children with SLI have atypical ERPs.
Similar(35)
Results indicated that although there were significant differences when comparing operations in dilute conditions, there were no significant differences between the two methods in the fast fluidized and dense transport regimes.
Although all DNA molecules underwent resection, there were significant differences in their stability.
Conclusions: Although there was no difference in patients' perceptions of the physician's professionalism or competence, there were significant differences in attributes required for a desired working relationship.
So there were significant differences in the approach.
Although there were no significant differences between the three groups in terms of their overall scores on the TCDS and TABS, there were significant differences in specific areas on the tests.
More suggestions(19)
although there were substantial differences in
although there were considerable differences in
although there were notable differences in
although there were major differences in
although there were slight differences in
although there were significant limitations in
although there were subtle differences in
although there were minor differences in
although there were significant shortcomings in
although there were significant changes in
although there were quantitative differences in
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although there were significant variations in
although there were significant increases in
although there were significant responses in
although there were reproducible differences in
although there were ethnic differences in
although there were significant improvements in
although there were significant disparities in
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com