Effects of response sequence length on motor programming: A chronometric analysis

AbstractEncoding and recognising complex natural sequences provides a challenge for human vision. We found that observers could recognise a previously presented segment of a video of a hearth fire when embedded in a longer sequence. Recognition performance declined when the test video was spatially inverted, but not when it was hue reversed or temporally reversed. Sampled motion degraded forwards/reversed playback discrimination, indicating observers were sensitive to the asymmetric pattern of motion of flames. For brief targets, performance increased with target length. More generally, performance depended on the relative lengths of the target and embedding sequence. Increased errors with embedded sequence length were driven by positive responses to non-target sequences (false alarms) rather than omissions. Taken together these observations favour interpreting performance in terms of an incremental decision-making model based on a sequential statistical analysis in which evidence accrues for one of two alternatives. We also suggest that prediction could provide a means of providing and evaluating evidence in a sequential analysis model.

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Murine Albino-Deletion Complex: High-Resolution Microsatellite Map and Genetically Anchored YAC Framework Map

Genetics ◽

10.1093/genetics/147.2.787 ◽

1997 ◽

Vol 147 (2) ◽

pp. 787-799

Author(s):

Brad A Rikke ◽

Dabney K Johnson ◽

Thomas E Johnson

Keyword(s):

Positional Cloning ◽

Interspecific Backcross ◽

Genetic Distances ◽

Sequence Length ◽

Recombination Rates ◽

Oak Ridge ◽

Artificial Chromosomes ◽

Microsatellite Map ◽

Specific Locus ◽

Yeast Artificial Chromosomes

The murine albino-deletion complex developed as part of the Oak Ridge specific-locus test covers 6–11 cM of chromosome 7. This complex has proven to be a valuable resource for localizing traits to a small target region suitable for positional cloning. In this study, we mapped the endpoints of deletions in this complex using all of the available Mit simple-sequence length polymorphism (SSLP) markers. Concurrently, this mapping has determined the map order of nearly all of the SSLP markers, most of which were previously unresolved. The SSLP-based deletion map was confirmed and genetic distances were determined using the European Collaborative Interspecific Backcross panel of nearly a thousand mice. The average SSLP marker resolution is 0.3–0.4 cM, comparable to the cloning capacity of yeast artificial chromosomes (YACs). The SSLP markers were then used to construct a genetically anchored YAC framework map that further confirms the deletion map. We find that the largest deleted region distal to Tyr is about two to three times larger than the largest proximal deleted region, and the original C3H/101 regions flanking the deletions (moved to an St2A cch/cch background) are smaller than anticipated, which we suggest may result from increased recombination rates immediately flanking the deleted regions.

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In Silico Study Suggesting the Bias of Primers Choice in the Molecular Identification of Fungal Aerosols

Journal of Fungi ◽

10.3390/jof7020099 ◽

2021 ◽

Vol 7 (2) ◽

pp. 99

Author(s):

Hamza Mbareche ◽

Marc Veillette ◽

Guillaume J. Bilodeau

Keyword(s):

In Silico ◽

Fungal Diversity ◽

High Throughput Sequencing ◽

In Silico Analysis ◽

Its Region ◽

Internal Transcribed Spacers ◽

Sequence Length ◽

Universal Method ◽

Continuous Work ◽

Its1 And Its2

This paper presents an in silico analysis to assess the current state of the fungal UNITE database in terms of the two eukaryote nuclear ribosomal regions, Internal Transcribed Spacers 1 and 2 (ITS1 and ITS2), used in describing fungal diversity. Microbial diversity is often evaluated with amplicon-based high-throughput sequencing approaches, which is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing. Thus, the results are highly dependent on the quality of the primers used for amplification. The goal of this study is to validate if the mismatches of the primers on the binding sites of the targeted taxa could explain the differences observed when using either ITS1 or ITS2 in describing airborne fungal diversity. Hence, the choice of the pairs of primers for each barcode concur with a study comparing the performance of ITS1 and ITS2 in three occupational environments. The sequence length varied between the amplicons retrieved from the UNITE database using the pair of primers targeting ITS1 and ITS2. However, the database contains an equal number of unidentified taxa from ITS1 and ITS2 regions in the six taxonomic levels employed (phylum, class, order, family, genus, species). The chosen ITS primers showed differences in their ability to amplify fungal sequences from the UNITE database. Eleven taxa consisting of Trichocomaceae, Dothioraceae, Botryosphaeriaceae, Mucorales, Saccharomycetes, Pucciniomycetes, Ophiocordyceps, Microsporidia, Archaeorhizomycetes, Mycenaceae, and Tulasnellaceae showed large variations between the two regions. Note that members of the latter taxa are not all typical fungi found in the air. As no universal method is currently available to cover all the fungal kingdom, continuous work in designing primers, and particularly combining multiple primers targeting the ITS region is the best way to compensate for the biases of each one to get a larger view of the fungal diversity.

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The new Internal Transcribed Spacer 2 diagnostic tool clarifies the taxonomic position and geographic distribution of the North American malaria vector Anopheles punctipennis

Malaria Journal ◽

10.1186/s12936-021-03676-4 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

James M. Hodge ◽

Andrey A. Yurchenko ◽

Dmitriy A. Karagodin ◽

Reem A. Masri ◽

Ryan C. Smith ◽

...

Keyword(s):

Malaria Vector ◽

Internal Transcribed Spacer ◽

Single Species ◽

Its2 Sequence ◽

Pathogen Transmission ◽

Molecular Diagnostic ◽

Diagnostic Tools ◽

Sequence Length ◽

Phylogenetic Position ◽

Internal Transcribed Spacer 2

Abstract Background The malaria mosquito Anopheles punctipennis, a widely distributed species in North America, is capable of transmitting human malaria and is actively involved in the transmission of the ungulate malaria parasite Plasmodium odocoilei. However, molecular diagnostic tools based on Internal Transcribed Spacer 2 (ITS2) of ribosomal DNA are lacking for this species. Anopheles punctipennis is a former member of the Anopheles maculipennis complex but its systematic position remains unclear. Methods In this study, ITS2 sequences were obtained from 276 An. punctipennis specimens collected in the eastern and midwestern United States and a simple and robust Restriction Fragment Length Polymorphism approach for species identification was developed. The maximum-likelihood phylogenetic tree was constructed based on ITS2 sequences available through this study and from GenBank for 20 species of Anopheles. Results The analysis demonstrated a consistent ITS2 sequence length and showed no indications of intragenomic variation among the samples based on ITS2, suggesting that An. punctipennis represents a single species in the studied geographic locations. In this study, An. punctipennis was found in urban, rural, and forest settings, suggesting its potential broad role in pathogen transmission. Phylogeny based on ITS2 sequence comparison demonstrated the close relationship of this species with other members of the Maculipennis group. Conclusions This study developed molecular tools based on ITS2 sequences for the malaria vector An. punctipennis and clarified the phylogenetic position of the species within the Maculipennis group.

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Chronotype-specific Sleep in Two Versus Four Consecutive Shifts

Journal of Biological Rhythms ◽

10.1177/07487304211006073 ◽

2021 ◽

pp. 074873042110060

Author(s):

Dorothee Fischer ◽

Till Roenneberg ◽

Céline Vetter

Keyword(s):

Night Shift ◽

Sleep Diary ◽

Sequence Length ◽

Consecutive Night ◽

Shift Workers ◽

Subject Field ◽

Sleep Diaries ◽

Social Jetlag ◽

Sleep Debt ◽

Night Shifts

The study aimed to explore chronotype-specific effects of two versus four consecutive morning or night shifts on sleep-wake behavior. Sleep debt and social jetlag (a behavioral proxy of circadian misalignment) were estimated from sleep diary data collected for 5 weeks in a within-subject field study of 30 rotating night shift workers (29.9 ± 7.3 years, 60% female). Mixed models were used to examine whether effects of shift sequence length on sleep are dependent on chronotype, testing the interaction between sequence length (two vs. four) and chronotype (determined from sleep diaries). Analyses of two versus four morning shifts showed no significant interaction effects with chronotype. In contrast, increasing the number of night shifts from two to four increased sleep debt in early chronotypes, but decreased sleep debt in late types, with no change in intermediate ones. In early types, the higher sleep debt was due to accumulated sleep loss over four night shifts. In late types, sleep duration did not increase over the course of four night shifts, so that adaptation is unlikely to explain the observed lower sleep debt. Late types instead had increased sleep debt after two night shifts, which was carried over from two preceding morning shifts in this schedule. Including naps did not change the findings. Social jetlag was unaffected by the number of consecutive night shifts. Our results suggest that consecutive night shifts should be limited in early types. For other chronotypes, working four night shifts might be a beneficial alternative to working two morning and two night shifts. Studies should record shift sequences in rotating schedules.

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The Ancestry of a Sample of Sequences Subject to Recombination

Genetics ◽

10.1093/genetics/151.3.1217 ◽

1999 ◽

Vol 151 (3) ◽

pp. 1217-1228 ◽

Cited By ~ 1

Author(s):

Carsten Wiuf ◽

Jotun Hein

Keyword(s):

Genetic Distance ◽

Population Size ◽

Upper Bound ◽

Recombination Rate ◽

Common Ancestor ◽

Recent Common Ancestor ◽

Sequence Length ◽

Most Recent Common Ancestor ◽

The Mean ◽

Mean Time

Abstract In this article we discuss the ancestry of sequences sampled from the coalescent with recombination with constant population size 2N. We have studied a number of variables based on simulations of sample histories, and some analytical results are derived. Consider the leftmost nucleotide in the sequences. We show that the number of nucleotides sharing a most recent common ancestor (MRCA) with the leftmost nucleotide is ≈log(1 + 4N Lr)/4Nr when two sequences are compared, where L denotes sequence length in nucleotides, and r the recombination rate between any two neighboring nucleotides per generation. For larger samples, the number of nucleotides sharing MRCA with the leftmost nucleotide decreases and becomes almost independent of 4N Lr. Further, we show that a segment of the sequences sharing a MRCA consists in mean of 3/8Nr nucleotides, when two sequences are compared, and that this decreases toward 1/4Nr nucleotides when the whole population is sampled. A measure of the correlation between the genealogies of two nucleotides on two sequences is introduced. We show analytically that even when the nucleotides are separated by a large genetic distance, but share MRCA, the genealogies will show only little correlation. This is surprising, because the time until the two nucleotides shared MRCA is reciprocal to the genetic distance. Using simulations, the mean time until all positions in the sample have found a MRCA increases logarithmically with increasing sequence length and is considerably lower than a theoretically predicted upper bound. On the basis of simulations, it turns out that important properties of the coalescent with recombinations of the whole population are reflected in the properties of a sample of low size.

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Stochastic modelling of gradient copolymer chemical composition distribution and sequence length distribution

Molecular Simulation ◽

10.1080/08927020903513035 ◽

2010 ◽

Vol 36 (15) ◽

pp. 1219-1236 ◽

Cited By ~ 11

Author(s):

Andrew S. Cho ◽

Linda J. Broadbelt

Keyword(s):

Chemical Composition ◽

Length Distribution ◽

Stochastic Modelling ◽

Sequence Length ◽

Composition Distribution ◽

Gradient Copolymer ◽

Chemical Composition Distribution

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Endangered Uyghur Medicinal PlantFerulaIdentification through the Second Internal Transcribed Spacer

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2015/479879 ◽

2015 ◽

Vol 2015 ◽

pp. 1-6 ◽

Cited By ~ 2

Author(s):

Congzhao Fan ◽

Xiaojin Li ◽

Jun Zhu ◽

Jingyuan Song ◽

Hui Yao

Keyword(s):

Medicinal Plant ◽

Related Species ◽

Internal Transcribed Spacer ◽

Morphological Characteristics ◽

Its2 Sequence ◽

Sequence Length ◽

Local Alignment ◽

Accurate Identification ◽

Distance Method ◽

Closely Related Species

The medicinal plantFerulahas been widely used in Asian medicine, especially in Uyghur medicine in Xinjiang, China. Given that various substitutes and closely related species have similar morphological characteristics,Ferulais difficult to distinguish based on morphology alone, thereby causing confusion and threatening the safe use ofFerula. In this study, internal transcribed spacer 2 (ITS2) sequences were analyzed and assessed for the accurate identification of two salableFerulaspecies (Ferula sinkiangensisandFerula fukangensis) and eight substitutes or closely related species. Results showed that the sequence length of ITS2 ranged from 451 bp to 45 bp, whereas guanine and cytosine contents (GC) were from 53.6% to 56.2%. A total of 77 variation sites were detected, including 63 base mutations and 14 insertion/deletion mutations. The ITS2 sequence correctly identified 100% of the samples at the species level using the basic local alignment search tool 1 and nearest-distance method. Furthermore, neighbor-joining tree successfully identified the genuine plantsF. sinkiangensisandF. fukangensisfrom their succedaneum and closely related species. These results indicated that ITS2 sequence could be used as a valuable barcode to distinguish Uyghur medicineFerulafrom counterfeits and closely related species. This study may broaden DNA barcoding application in the Uyghur medicinal plant field.

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