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Purpose The Computerized Language ANalysis–Index of Productive Syntax (CLAN-IPSyn) system is designed to facilitate automatic computation of the IPSyn measure of productive child syntax. Roberts et al. (2020) conducted a thorough comparison of hand-generated and automatic scores on the Index of Productive Syntax (IPSyn) measure (Scarborough, 1990) and found a high level of error for CLAN-IPSyn. We report on the use of the Roberts et al. analysis to reduce and eliminate errors in CLAN-IPSyn, to improve its accuracy. Method Scores provided by manual and machine scoring of the 20 transcripts used in Roberts et al. (2020) were compared. Divergences in point assignment were examined and significant modifications made to the CLAN-IPSyn program to increase its accuracy. Conclusion The currently available, free version of CLAN at https://talkbank.org is now significantly more correct in terms of exemplars produced, and should assist clinicians and researchers in using the revised IPSyn (Altenberg et al. 2018).

Purpose The results of automatic machine scoring of the Index of Productive Syntax from the Computerized Language ANalysis (CLAN) tools of the Child Language Data Exchange System of TalkBank (MacWhinney, 2000) were compared to manual scoring to determine the accuracy of the machine-scored method. Method Twenty transcripts of 10 children from archival data of the Weismer Corpus from the Child Language Data Exchange System at 30 and 42 months were examined. Measures of absolute point difference and point-to-point accuracy were compared, as well as points erroneously given and missed. Two new measures for evaluating automatic scoring of the Index of Productive Syntax were introduced: Machine Item Accuracy (MIA) and Cascade Failure Rate— these measures further analyze points erroneously given and missed. Differences in total scores, subscale scores, and individual structures were also reported. Results Mean absolute point difference between machine and hand scoring was 3.65, point-to-point agreement was 72.6%, and MIA was 74.9%. There were large differences in subscales, with Noun Phrase and Verb Phrase subscales generally providing greater accuracy and agreement than Question/Negation and Sentence Structures subscales. There were significantly more erroneous than missed items in machine scoring, attributed to problems of mistagging of elements, imprecise search patterns, and other errors. Cascade failure resulted in an average of 4.65 points lost per transcript. Conclusions The CLAN program showed relatively inaccurate outcomes in comparison to manual scoring on both traditional and new measures of accuracy. Recommendations for improvement of the program include accounting for second exemplar violations and applying cascaded credit, among other suggestions. It was proposed that research on machine-scored syntax routinely report accuracy measures detailing erroneous and missed scores, including MIA, so that researchers and clinicians are aware of the limitations of a machine-scoring program. Supplemental Material https://doi.org/10.23641/asha.11984364

ObjectiveThe purpose of this project was to use an in vivo method to discover riboswitches that are activated by new ligands. We employed phage-assisted continuous evolution (PACE) to evolve new riboswitches in vivo. We started with one translational riboswitch and one transcriptional riboswitch, both of which were activated by theophylline. We used xanthine as the new target ligand during positive selection followed by negative selection using theophylline. The goal was to generate very large M13 phage populations that contained unknown mutations, some of which would result in new aptamer specificity. We discovered side products of three new theophylline translational riboswitches with different levels of protein production.ResultsWe used next generation sequencing to identify M13 phage that carried riboswitch mutations. We cloned and characterized the most abundant riboswitch mutants and discovered three variants that produce different levels of translational output while retaining their theophylline specificity. Although we were unable to demonstrate evolution of new riboswitch ligand specificity using PACE, we recommend careful design of recombinant M13 phage to avoid evolution of “cheaters” that short circuit the intended selection pressure.Electronic supplementary materialThe online version of this article (10.1186/s13104-018-3965-6) contains supplementary material, which is available to authorized users.

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