The sensitivity and specificity of a diagnostic test of sequence-space synesthesia

People with sequence-space synesthesia (SSS) report stable visuo-spatial forms corresponding to numbers, days, and months (amongst others). This type of synesthesia has intrigued scientists for over 130 years but the lack of an agreed upon tool for assessing it has held back research on this phenomenon. The present study builds on previous tests by measuring the consistency of spatial locations that is known to discriminate controls from synesthetes. We document, for the first time, the sensitivity and specificity of such a test and suggest a diagnostic cut-off point for discriminating between the groups based on the area bounded by different placement attempts with the same item.

Next-state comfort in learning a vertical stick transportation sequence

Over the last decade, the end-state comfort effect (e.g., Rosenbaum et al., 2006) has received a considerable amount of attention. However, some of the underlying mechanisms are still to be investigated, amongst others, how sequential planning affects end-state comfort and how this effect develops over learning. In a two-step sequencing task, e.g., postural comfort can be planned on the intermediate position (next state) or on the actual end position (final state). It might be hypothesized that, in initial acquisition, next state’s comfort is crucial for action planning but that, in the course of learning, final state’s comfort is taken more and more into account. To test this hypothesis, a variant of Rosenbaum’s vertical stick transportation task was used. Participants (N = 16, right-handed) received extensive practice on a two-step transportation task (10,000 trials over 12 sessions). From the initial position on the middle stair of a staircase in front of the participant, the stick had to be transported either 20 cm upwards and then 40 cm downwards or 20 cm downwards and then 40 cm upwards (N = 8 per subgroup). Participants were supposed to produce fluid movements without changing grasp. In the pre- and posttest, participants were tested on both two-step sequencing tasks as well as on 20 cm single-step upwards and downwards movements (10 trials per condition). For the test trials, grasp height was calculated kinematographically. In the pretest, large end/next/final-state comfort effects for single-step transportation tasks and large next-state comfort effects for sequenced tasks were found. However, no change in grasp height from pre- to posttest could be revealed. Results show that, in vertical stick transportation sequences, the final state is not taken into account when planning grasp height. Instead, action planning seems to be solely based on aspects of the next action goal that is to be reached.

Beyond statistical learning? Continuous sequence repetition matters in implicit sequence learning

Typically, statistical learning is investigated by testing the acquisition of specific items or forming general rules. As implicit sequence learning also involves the extraction of regularities from the environment, it can also be considered as an instance of statistical learning. In the present study, a Serial Reaction Time Task was used to test whether the continuous versus interleaved repetition of a sequence affects implicit learning despite the equal exposure to the sequences. The results revealed a sequence learning advantage for the continuous repetition condition compared to the interleaved condition. This suggests that by repetition, additional sequence information was extracted although the exposure to the sequences was identical as in the interleaved condition. The results are discussed in terms of similarities and potential differences between typical statistical learning paradigms and sequence learning.

8p23 beta-defensin copy number determination by single-locus pseudogene-based paralog ratio tests risk bias due to low-frequency sequence variations.

BACKGROUND The copy number variation (CNV) in beta-defensin genes (DEFB) on human chromosome 8p23 has been proposed to contribute to the phenotypic differences in inflammatory diseases. However, determination of exact DEFB CN is a major challenge in association studies. Quantitative real-time PCR (qPCR), paralog ratio tests (PRT) and multiplex ligation-dependent probe amplification (MLPA) have been extensively used to determine DEFB CN in different laboratories, but inter-method inconsistencies were observed frequently. In this study we asked which one is superior among the three methods for DEFB CN determination. RESULTS We developed a clustering approach for MLPA and PRT to statistically correlate data from a single experiment. Then we compared qPCR, a newly designed PRT and MLPA for DEFB CN determination in 285 DNA samples. We found MLPA had the best convergence and clustering results of the raw data and the highest call rate. In addition, the concordance rates between MLPA or PRT and qPCR (32.12% and 37.99%, respectively) were unacceptably low with underestimated CN by qPCR. Concordance rate between MLPA and PRT (90.52%) was high but PRT systematically underestimated CN by one in a subset of samples. In these samples a sequence variant which caused complete PCR dropout of the respective DEFB cluster copies was found in one primer binding site of one of the targeted paralogous pseudogenes. CONCLUSION MLPA is superior to PRT and even more to qPCR for DEFB CN determination. Although the applied PRT provides in most cases reliable results, such a test is particularly sensitive to low-frequency sequence variations preferably accumulating in loci like pseudogenes which are most likely not under selective pressure. In the light of the superior performance of multiplex assays, the drawbacks of such single PRTs could be overcome by combining more test markers.

Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants

Background Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. Methods Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. Results We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. Conclusions The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants.

Multimodal sequence learning

While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence.